Index
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form
A
- A - Variable in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.LTMatrix
- A - Variable in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.LTMatrixF
- A - Variable in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.Matrix
- A - Variable in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.MatrixF
- aa - Enum constant in enum class edu.cmu.tetrad.graph.EdgeTypeProbability.EdgeType
- absoluteValue - Enum constant in enum class edu.cmu.tetrad.search.Lofs.Score
- AbstractAnnotations<T extends Annotation> - Class in edu.cmu.tetrad.annotation
-
Abstract class for annotations.
- AbstractAnnotations(String, Class<T>) - Constructor for class edu.cmu.tetrad.annotation.AbstractAnnotations
-
Constructor.
- AbstractNbComponent - Class in edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin
-
Abstract NB component.
- AbstractNbComponent(double, double, NbComponent[], int[], String) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.AbstractNbComponent
-
Constructs a new component with the given factor, power, parents, and
- AbstractVariable - Class in edu.cmu.tetrad.data
-
Base class for variable specifications for DataSet.
- ac - Enum constant in enum class edu.cmu.tetrad.graph.EdgeTypeProbability.EdgeType
- ActiveLagGraph - Class in edu.cmu.tetrad.study.gene.tetrad.gene.graph
-
Adds Javabean property change events so that it can be used in a MVC type architecture.
- ActiveLagGraph() - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ActiveLagGraph
-
Creates new ActiveLagGraph
- add(int, DataModel) - Method in class edu.cmu.tetrad.data.DataModelList
-
Adds the given DataModel to the list at the given index.
- add(Algorithm) - Method in class edu.cmu.tetrad.algcomparison.algorithm.Algorithms
-
Adds an algorithm.
- add(Simulation) - Method in class edu.cmu.tetrad.algcomparison.simulation.Simulations
-
Adds an simulation.
- add(Statistic) - Method in class edu.cmu.tetrad.algcomparison.statistic.Statistics
-
Adds a statistic.
- add(IndependenceFact) - Method in class edu.cmu.tetrad.data.IndependenceFacts
- add(OutputStream, Level) - Method in class edu.cmu.tetrad.util.LogUtils
-
Adds the given stream to logging.
- ADD - Enum constant in enum class edu.cmu.tetrad.search.work_in_progress.HbsmsBeam.Move.Type
- ADD_COLLIDER - Enum constant in enum class edu.cmu.tetrad.search.work_in_progress.HbsmsBeam.Move.Type
- ADD_ORIGINAL_DATASET - Static variable in class edu.cmu.tetrad.util.Params
- addAll(SepsetMap) - Method in class edu.cmu.tetrad.search.utils.SepsetMap
-
Adds all entries in the given sepset map to the current one.
- addAmbiguousTriple(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.Dag
- addAmbiguousTriple(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
- addAmbiguousTriple(Node, Node, Node) - Method in interface edu.cmu.tetrad.graph.Graph
- addAmbiguousTriple(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.LagGraph
- addAmbiguousTriple(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.SemGraph
- addAmbiguousTriple(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- addAmbiguousTriple(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.Underlines
- addAttribute(String, Object) - Method in class edu.cmu.tetrad.data.ContinuousVariable
- addAttribute(String, Object) - Method in class edu.cmu.tetrad.data.DiscreteVariable
- addAttribute(String, Object) - Method in class edu.cmu.tetrad.graph.Dag
- addAttribute(String, Object) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
- addAttribute(String, Object) - Method in interface edu.cmu.tetrad.graph.Graph
- addAttribute(String, Object) - Method in class edu.cmu.tetrad.graph.GraphNode
- addAttribute(String, Object) - Method in class edu.cmu.tetrad.graph.LagGraph
- addAttribute(String, Object) - Method in interface edu.cmu.tetrad.graph.Node
- addAttribute(String, Object) - Method in class edu.cmu.tetrad.graph.SemGraph
- addAttribute(String, Object) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- addAttribute(String, Object) - Method in class edu.cmu.tetrad.session.SessionNode
- addBidirectedEdge(Node, Node) - Method in class edu.cmu.tetrad.graph.Dag
- addBidirectedEdge(Node, Node) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
-
Adds a bidirected edge to the graph from node A to node B.
- addBidirectedEdge(Node, Node) - Method in interface edu.cmu.tetrad.graph.Graph
-
Adds a bidirected edges <-> to the graph.
- addBidirectedEdge(Node, Node) - Method in class edu.cmu.tetrad.graph.LagGraph
- addBidirectedEdge(Node, Node) - Method in class edu.cmu.tetrad.graph.SemGraph
- addBidirectedEdge(Node, Node) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- addCategory(int, int) - Method in class edu.cmu.tetrad.bayes.Proposition
- addChild(SessionNode) - Method in class edu.cmu.tetrad.session.SessionNode
-
Adds a child to the node, provided this node can be added as a parent to the child node.
- addCollider(Triple) - Method in class edu.cmu.tetrad.search.work_in_progress.GraphChange
-
Add another collider operation to the GraphChange.
- addConditioningVariable(String, double, double) - Method in class edu.cmu.tetrad.data.Histogram
-
Adds a continuous conditioning variables, conditioning on a range of values.
- addConditioningVariable(String, int) - Method in class edu.cmu.tetrad.data.Histogram
-
Adds a discrete conditioning variable, conditioning on a particular value.
- addDirectedEdge(Node, Node) - Method in class edu.cmu.tetrad.graph.Dag
- addDirectedEdge(Node, Node) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
-
Adds a directed edge to the graph from node A to node B.
- addDirectedEdge(Node, Node) - Method in interface edu.cmu.tetrad.graph.Graph
-
Adds a directed edge --> to the graph.
- addDirectedEdge(Node, Node) - Method in class edu.cmu.tetrad.graph.LagGraph
- addDirectedEdge(Node, Node) - Method in class edu.cmu.tetrad.graph.SemGraph
- addDirectedEdge(Node, Node) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- addDottedUnderlineTriple(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.Dag
- addDottedUnderlineTriple(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
- addDottedUnderlineTriple(Node, Node, Node) - Method in interface edu.cmu.tetrad.graph.Graph
- addDottedUnderlineTriple(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.LagGraph
- addDottedUnderlineTriple(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.SemGraph
- addDottedUnderlineTriple(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- addDottedUnderlineTriple(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.Underlines
- addEdge(Edge) - Method in class edu.cmu.tetrad.graph.Dag
- addEdge(Edge) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
-
Adds an edge to the graph.
- addEdge(Edge) - Method in interface edu.cmu.tetrad.graph.Graph
-
Adds the specified edge to the graph, provided it is not already in the graph.
- addEdge(Edge) - Method in class edu.cmu.tetrad.graph.LagGraph
- addEdge(Edge) - Method in class edu.cmu.tetrad.graph.SemGraph
- addEdge(Edge) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- addEdge(String, LaggedFactor) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ActiveLagGraph
-
Attempts to add an edge to the graph.
- addEdge(String, LaggedFactor) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ManualLagGraph
- addEdge(String, LaggedFactor) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.BasicLagGraph
-
Adds an edge to the given factor at lag 0 from the specified lagged factor.
- addEdge(String, LaggedFactor) - Method in interface edu.cmu.tetrad.study.gene.tetrad.gene.history.LagGraph
-
Adds an edge to the given factor at lag 0 from the specified lagged factor.
- addEdgeTypeProbability(EdgeTypeProbability) - Method in class edu.cmu.tetrad.graph.Edge
- addFactor(String) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ActiveLagGraph
-
Attempts to add a factor to the graph.
- addFactor(String) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ManualLagGraph
- addFactor(String) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.BasicLagGraph
-
Adds a factor to the graph.
- addFactor(String) - Method in interface edu.cmu.tetrad.study.gene.tetrad.gene.history.LagGraph
-
Adds a factor to the graph.
- addFactors(String, int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ActiveLagGraph
- addFactors(String, int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ManualLagGraph
- addFactors(String, int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.BasicLagGraph
- addFactors(String, int) - Method in interface edu.cmu.tetrad.study.gene.tetrad.gene.history.LagGraph
-
Returns a string representation of the graph, indicating for each factor which lagged factors map into it.
- addForbiddenReverseEdgesForDirectedEdges(Graph, Knowledge) - Static method in class edu.cmu.tetrad.graph.GraphUtils
- addIndex(DataSet) - Static method in class edu.cmu.tetrad.search.utils.TsUtils
-
Creates new time series dataset from the given one with index variable (e.g., time)
- ADDING_EDGE - Static variable in class edu.cmu.tetrad.session.SessionEvent
- addingEdge(SessionEvent) - Method in class edu.cmu.tetrad.session.SessionAdapter
-
Indicates that the model is contemplating adding an edge (but hasn't yet).
- addingEdge(SessionEvent) - Method in interface edu.cmu.tetrad.session.SessionListener
-
Indicates that the model is contemplating adding an edge (but hasn't yet).
- addKnowledgeGroup(KnowledgeGroup) - Method in class edu.cmu.tetrad.data.Knowledge
-
Adds a knowledge group.
- addMissingData(DataSet, double[]) - Static method in class edu.cmu.tetrad.data.DataTransforms
-
Adds missing data values to cases in accordance with probabilities specified in a double array which has as many elements as there are columns in the input dataset.
- addNode(Node) - Method in class edu.cmu.tetrad.graph.Dag
- addNode(Node) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
-
Adds a node to the graph.
- addNode(Node) - Method in interface edu.cmu.tetrad.graph.Graph
-
Adds a node to the graph.
- addNode(Node) - Method in class edu.cmu.tetrad.graph.LagGraph
- addNode(Node) - Method in class edu.cmu.tetrad.graph.SemGraph
- addNode(Node) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
-
Nodes may be added into the getModel time step only.
- addNode(SessionNode) - Method in class edu.cmu.tetrad.session.Session
-
Adds the given node to the session, provided the node is in a freshly created state.> 0
- addNodeList(List<SessionNode>) - Method in class edu.cmu.tetrad.session.Session
-
Adds a list of nodes to the session.
- addNonCollider(Triple) - Method in class edu.cmu.tetrad.search.work_in_progress.GraphChange
-
Add another non-collider operation to the GraphChange.
- addNondirectedEdge(Node, Node) - Method in class edu.cmu.tetrad.graph.Dag
- addNondirectedEdge(Node, Node) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
-
Adds a nondirected edge to the graph from node A to node B.
- addNondirectedEdge(Node, Node) - Method in interface edu.cmu.tetrad.graph.Graph
-
Adds a nondirected edges o-o to the graph.
- addNondirectedEdge(Node, Node) - Method in class edu.cmu.tetrad.graph.LagGraph
- addNondirectedEdge(Node, Node) - Method in class edu.cmu.tetrad.graph.SemGraph
- addNondirectedEdge(Node, Node) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- addOrient(Node, Node) - Method in class edu.cmu.tetrad.search.work_in_progress.GraphChange
-
Add another orient operation to the GraphChange.
- addOutputStream(OutputStream) - Method in class edu.cmu.tetrad.util.TetradLogger
-
Sets the
OutputStreamthat is used to log matters out to. - addPagColoring(Graph) - Static method in class edu.cmu.tetrad.graph.GraphUtils
- addParent(SessionNode) - Method in class edu.cmu.tetrad.session.SessionNode
-
Adds a parent to this node provided the resulting set of parents taken together provides some combination of possible model classes that can be used as a constructor to some one of the model classes for this node.
- addParent(NbComponent, int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.AbstractNbComponent
- addParent(NbComponent, int) - Method in interface edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.NbComponent
-
Returns the parents of this component.
- addParent2(SessionNode) - Method in class edu.cmu.tetrad.session.SessionNode
-
Same as addParent except tests if this has already been created.
- addPartiallyOrientedEdge(Node, Node) - Method in class edu.cmu.tetrad.graph.Dag
- addPartiallyOrientedEdge(Node, Node) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
-
Adds a partially oriented edge to the graph from node A to node B.
- addPartiallyOrientedEdge(Node, Node) - Method in interface edu.cmu.tetrad.graph.Graph
-
Adds a partially oriented edge o-> to the graph.
- addPartiallyOrientedEdge(Node, Node) - Method in class edu.cmu.tetrad.graph.LagGraph
- addPartiallyOrientedEdge(Node, Node) - Method in class edu.cmu.tetrad.graph.SemGraph
- addPartiallyOrientedEdge(Node, Node) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- addProperty(Edge.Property) - Method in class edu.cmu.tetrad.graph.Edge
- addProperty(Edge.Property) - Method in class edu.cmu.tetrad.graph.EdgeTypeProbability
- addPropertyChangeListener(PropertyChangeListener) - Method in class edu.cmu.tetrad.data.ContinuousVariable
-
Adds a property change listener.
- addPropertyChangeListener(PropertyChangeListener) - Method in class edu.cmu.tetrad.data.DiscreteVariable
-
Adds a property change listener.
- addPropertyChangeListener(PropertyChangeListener) - Method in class edu.cmu.tetrad.graph.Dag
- addPropertyChangeListener(PropertyChangeListener) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
- addPropertyChangeListener(PropertyChangeListener) - Method in interface edu.cmu.tetrad.graph.Graph
-
Adds a PropertyChangeListener to the graph.
- addPropertyChangeListener(PropertyChangeListener) - Method in class edu.cmu.tetrad.graph.GraphNode
-
Adds a property change listener.
- addPropertyChangeListener(PropertyChangeListener) - Method in class edu.cmu.tetrad.graph.LagGraph
- addPropertyChangeListener(PropertyChangeListener) - Method in interface edu.cmu.tetrad.graph.Node
-
Adds a property change listener.
- addPropertyChangeListener(PropertyChangeListener) - Method in class edu.cmu.tetrad.graph.SemGraph
- addPropertyChangeListener(PropertyChangeListener) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- addPropertyChangeListener(PropertyChangeListener) - Method in class edu.cmu.tetrad.session.SessionNode
- addPropertyChangeListener(PropertyChangeListener) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ActiveLagGraph
-
Registers a listener to events concerning the lag graph.
- addRecord(Node, SortedSet<Node>, SortedSet<Node>, SortedSet<Node>) - Method in class edu.cmu.tetrad.search.work_in_progress.DMSearch.LatentStructure
- addRemove(Edge) - Method in class edu.cmu.tetrad.search.work_in_progress.GraphChange
-
Add another remove operation to the GraphChange.
- addRow(List<? extends V>) - Method in interface edu.pitt.isp.sverchkov.data.DataTable
- addRow(List<? extends V>) - Method in class edu.pitt.isp.sverchkov.data.DataTableImpl
- addSessionListener(SessionListener) - Method in class edu.cmu.tetrad.session.Session
-
Adds a session listener.
- addSessionListener(SessionListener) - Method in class edu.cmu.tetrad.session.SessionNode
-
Adds a session listener.
- addSessionListener(SessionListener) - Method in class edu.cmu.tetrad.session.SessionSupport
-
Adds a listener for SessionEvents.
- addSessionListener(SessionListener) - Method in class edu.cmu.tetrad.session.SimulationStudy
-
Adds a session listener.
- addSimilarEdges(Node, Node) - Method in class edu.cmu.tetrad.search.SvarFges
- addStatistic(Statistic) - Method in class edu.cmu.tetrad.algcomparison.comparegraphs.CompareTwoGraphs
- addTetradLoggerConfig(Class, TetradLoggerConfig) - Method in class edu.cmu.tetrad.util.TetradLogger
-
Adds the given
TetradLoggerConfigto the logger, so that it can be used throughout the life of the application. - addTetradLoggerListener(TetradLoggerListener) - Method in class edu.cmu.tetrad.util.TetradLogger
-
Adds the given listener to the logger.
- addToCluster(int, String) - Method in class edu.cmu.tetrad.data.Clusters
-
Adds the given variable to the given index.
- addToTable(DataSet, int[]) - Method in class edu.cmu.tetrad.data.CellTable
- addToTier(int, String) - Method in class edu.cmu.tetrad.data.Knowledge
-
Adds the given variable or wildcard cpdag to the given tier.
- addToTiersByVarNames(List<String>) - Method in class edu.cmu.tetrad.data.Knowledge
-
Puts a variable into tier i if its name is xxx:ti for some xxx and some i.
- addTwoCycles(Graph, int) - Static method in class edu.cmu.tetrad.graph.RandomGraph
- addUnderlineTriple(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.Dag
- addUnderlineTriple(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
- addUnderlineTriple(Node, Node, Node) - Method in interface edu.cmu.tetrad.graph.Graph
- addUnderlineTriple(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.LagGraph
- addUnderlineTriple(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.SemGraph
- addUnderlineTriple(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- addUnderlineTriple(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.Underlines
- addUndirectedEdge(Node, Node) - Method in class edu.cmu.tetrad.graph.Dag
- addUndirectedEdge(Node, Node) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
-
Adds an undirected edge to the graph from node A to node B.
- addUndirectedEdge(Node, Node) - Method in interface edu.cmu.tetrad.graph.Graph
-
Adds an undirected edge --- to the graph.
- addUndirectedEdge(Node, Node) - Method in class edu.cmu.tetrad.graph.LagGraph
- addUndirectedEdge(Node, Node) - Method in class edu.cmu.tetrad.graph.SemGraph
- addUndirectedEdge(Node, Node) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- addValue(Matrix, double) - Static method in class jgpml.covariancefunctions.MatrixOperations
-
Adds a value to each elemnts of the
Matrix - addVariable(int, Node) - Method in class edu.cmu.tetrad.data.BoxDataSet
-
Adds the given variable to the dataset, increasing the number of columns by one, moving columns i >=
indexto column i + 1, and inserting a column of missing values at column i. - addVariable(int, Node) - Method in interface edu.cmu.tetrad.data.DataSet
-
Adds the given variable at the given index.
- addVariable(int, Node) - Method in class edu.cmu.tetrad.data.NumberObjectDataSet
-
Adds the given variable to the dataset, increasing the number of columns by one, moving columns i >=
indexto column i + 1, and inserting a column of missing values at column i. - addVariable(Node) - Method in class edu.cmu.tetrad.data.BoxDataSet
-
Adds the given variable to the data set, increasing the number of columns by one, moving columns i >=
indexto column i + 1, and inserting a column of missing values at column i. - addVariable(Node) - Method in interface edu.cmu.tetrad.data.DataSet
-
Adds the given variable to the data set.
- addVariable(Node) - Method in class edu.cmu.tetrad.data.MixedDataBox
- addVariable(Node) - Method in class edu.cmu.tetrad.data.NumberObjectDataSet
-
Adds the given variable to the data set, increasing the number of columns by one, moving columns i >=
indexto column i + 1, and inserting a column of missing values at column i. - addVariable(String) - Method in class edu.cmu.tetrad.data.Knowledge
- addVariable(String) - Method in class edu.cmu.tetrad.graph.LagGraph
- AdjacencyConfusion - Class in edu.cmu.tetrad.algcomparison.statistic.utils
-
A confusion matrix for adjacencies--i.e.
- AdjacencyConfusion(Graph, Graph) - Constructor for class edu.cmu.tetrad.algcomparison.statistic.utils.AdjacencyConfusion
-
Constructs a new AdjacencyConfusion object from the given graphs.
- AdjacencyFn - Class in edu.cmu.tetrad.algcomparison.statistic
-
The adjacency precision.
- AdjacencyFn() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.AdjacencyFn
-
Constructs the statistic.
- AdjacencyFp - Class in edu.cmu.tetrad.algcomparison.statistic
-
The adjacency precision.
- AdjacencyFp() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.AdjacencyFp
-
Constructs the statistic.
- AdjacencyFpr - Class in edu.cmu.tetrad.algcomparison.statistic
-
The adjacency true positive rate.
- AdjacencyFpr() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.AdjacencyFpr
-
Constructs the statistic.
- AdjacencyPrecision - Class in edu.cmu.tetrad.algcomparison.statistic
-
The adjacency precision.
- AdjacencyPrecision() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.AdjacencyPrecision
-
Constructs the statistic.
- AdjacencyRecall - Class in edu.cmu.tetrad.algcomparison.statistic
-
The adjacency recall.
- AdjacencyRecall() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.AdjacencyRecall
-
Constructs the statistic.
- AdjacencyTn - Class in edu.cmu.tetrad.algcomparison.statistic
-
The adjacency precision.
- AdjacencyTn() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.AdjacencyTn
-
Constructs the statistic.
- AdjacencyTp - Class in edu.cmu.tetrad.algcomparison.statistic
-
The adjacency precision.
- AdjacencyTp() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.AdjacencyTp
-
Constructs the statistic.
- AdjacencyTpr - Class in edu.cmu.tetrad.algcomparison.statistic
-
The adjacency true positive rate.
- AdjacencyTpr() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.AdjacencyTpr
-
Constructs the statistic.
- adjacent(Node, Node) - Method in class edu.cmu.tetrad.search.utils.TeyssierScorer
-
Returns True iff a is adjacent to b in the current graph.
- ADJACENT_TO_TARGETS - Enum constant in enum class edu.cmu.tetrad.search.FgesMb.TrimmingStyle
- AdjCor - Enum constant in enum class edu.cmu.tetrad.study.performance.Comparison.TableColumn
- AdjCor - Enum constant in enum class edu.cmu.tetrad.study.performance.Comparison2.TableColumn
- AdjFn - Enum constant in enum class edu.cmu.tetrad.study.performance.Comparison.TableColumn
- AdjFn - Enum constant in enum class edu.cmu.tetrad.study.performance.Comparison2.TableColumn
- AdjFp - Enum constant in enum class edu.cmu.tetrad.study.performance.Comparison.TableColumn
- AdjFp - Enum constant in enum class edu.cmu.tetrad.study.performance.Comparison2.TableColumn
- adjMatFromMGM() - Method in class edu.pitt.csb.mgm.Mgm
-
Converts MGM to matrix of doubles.
- AdjPrec - Enum constant in enum class edu.cmu.tetrad.study.performance.Comparison.TableColumn
- AdjPrec - Enum constant in enum class edu.cmu.tetrad.study.performance.Comparison2.TableColumn
- AdjRec - Enum constant in enum class edu.cmu.tetrad.study.performance.Comparison.TableColumn
- AdjRec - Enum constant in enum class edu.cmu.tetrad.study.performance.Comparison2.TableColumn
- AdLeafTree - Class in edu.cmu.tetrad.search.utils
-
Constructs and AD leaf tree on the fly.
- AdLeafTree(DataSet) - Constructor for class edu.cmu.tetrad.search.utils.AdLeafTree
-
Constructs an AD Leaf Tree for the given dataset.
- AdTree<A,
V> - Class in edu.pitt.isp.sverchkov.data -
An implementation of a static AD tree based on Moore and Lee 1998 (mostly)
- AdTree(DataTable<A, V>) - Constructor for class edu.pitt.isp.sverchkov.data.AdTree
-
Constructs an AD tree for the given data set.
- AdTreeTest - Class in edu.pitt.isp.sverchkov.data
-
A test of the AD tree implementation.
- AdTreeTest() - Constructor for class edu.pitt.isp.sverchkov.data.AdTreeTest
-
Creates a new AdTreeTest object.
- AhdCor - Enum constant in enum class edu.cmu.tetrad.study.performance.Comparison.TableColumn
- AhdCor - Enum constant in enum class edu.cmu.tetrad.study.performance.Comparison2.TableColumn
- AhdFn - Enum constant in enum class edu.cmu.tetrad.study.performance.Comparison.TableColumn
- AhdFn - Enum constant in enum class edu.cmu.tetrad.study.performance.Comparison2.TableColumn
- AhdFp - Enum constant in enum class edu.cmu.tetrad.study.performance.Comparison.TableColumn
- AhdFp - Enum constant in enum class edu.cmu.tetrad.study.performance.Comparison2.TableColumn
- AhdPrec - Enum constant in enum class edu.cmu.tetrad.study.performance.Comparison.TableColumn
- AhdPrec - Enum constant in enum class edu.cmu.tetrad.study.performance.Comparison2.TableColumn
- AhdRec - Enum constant in enum class edu.cmu.tetrad.study.performance.Comparison.TableColumn
- AhdRec - Enum constant in enum class edu.cmu.tetrad.study.performance.Comparison2.TableColumn
- airities - Variable in class edu.pitt.isp.sverchkov.data.AdTree
-
The airities of the attributes.
- Algorithm - Interface in edu.cmu.tetrad.algcomparison.algorithm
-
Interface that algorithm must implement.
- Algorithm - Annotation Interface in edu.cmu.tetrad.annotation
-
Sep 5, 2017 10:47:30 AM
- AlgorithmAnnotations - Class in edu.cmu.tetrad.annotation
-
Annotations for algorithms.
- AlgorithmDescriptions - Class in edu.cmu.tetrad.util
-
Algorithm descriptions.
- AlgorithmFactory - Class in edu.cmu.tetrad.algcomparison.algorithm
-
Aug 30, 2017 3:14:40 PM
- Algorithms - Class in edu.cmu.tetrad.algcomparison.algorithm
-
A list of algorithm to be compared.
- Algorithms() - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.Algorithms
-
Constructs an empty list of algorithms.
- algoType() - Element in annotation interface edu.cmu.tetrad.annotation.Algorithm
-
Description of the algorithm.
- AlgType - Enum Class in edu.cmu.tetrad.annotation
-
Author : Jeremy Espino MD Created 6/30/17 10:36 AM
- All - Enum constant in enum class edu.cmu.tetrad.data.DataType
- ALL_SUBSETS - Enum constant in enum class edu.cmu.tetrad.search.MarkovCheck.ConditioningSetType
- AllCliquesAlgorithm() - Constructor for class edu.cmu.tetrad.graph.Paths.AllCliquesAlgorithm
- allDirectedPathsFromTo(Node, Node, int) - Method in class edu.cmu.tetrad.graph.Paths
- allEdgeStats(Graph, Graph) - Static method in class edu.pitt.csb.mgm.MixedUtils
- allEdgeStats(Graph, Graph, HashMap<String, String>) - Static method in class edu.pitt.csb.mgm.MixedUtils
- allEigenvaluesAreSmallerThanOneInModulus(Matrix) - Static method in class edu.cmu.tetrad.search.utils.TsUtils
- allNodePairs(List<Node>) - Static method in class edu.cmu.tetrad.search.work_in_progress.ResolveSepsetsDci
-
Generates NodePairs of all possible pairs of nodes from given list of nodes.
- ALLOW_INTERNAL_RANDOMNESS - Static variable in class edu.cmu.tetrad.util.Params
- allow_latent_common_causes - Enum constant in enum class edu.cmu.tetrad.annotation.AlgType
-
If an algorithm allows latent common causes.
- allPathsFromTo(Node, Node, int) - Method in class edu.cmu.tetrad.graph.Paths
- AllSubsetsIndependenceFacts(List<IndependenceFact>, List<IndependenceFact>) - Constructor for class edu.cmu.tetrad.search.MarkovCheck.AllSubsetsIndependenceFacts
- allToString() - Method in class edu.cmu.tetrad.simulation.PRAOerrors
- alongPathIn(Graph) - Method in class edu.cmu.tetrad.graph.Triple
- alpha - Variable in class jgpml.GaussianProcess
-
partial factor
- ALPHA - Static variable in interface edu.cmu.tetrad.graph.Node
- ALPHA - Static variable in class edu.cmu.tetrad.util.Params
- ALPHA_NUM - Static variable in interface edu.cmu.tetrad.graph.Node
- AMBIGUOUS - Enum constant in enum class edu.cmu.tetrad.search.utils.GraphSearchUtils.CpcTripleType
- AMBIGUOUS - Enum constant in enum class edu.cmu.tetrad.search.work_in_progress.VcPc.CpcTripleType
- AMBIGUOUS - Enum constant in enum class edu.cmu.tetrad.search.work_in_progress.VcPcFast.CpcTripleType
- AncestorF1 - Class in edu.cmu.tetrad.algcomparison.statistic
-
Calculates the F1 statistic for adjacencies.
- AncestorF1() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.AncestorF1
-
Constructs the statistic.
- AncestorPrecision - Class in edu.cmu.tetrad.algcomparison.statistic
-
Ancestor precision.
- AncestorPrecision() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.AncestorPrecision
-
Constructs the statistic.
- AncestorRecall - Class in edu.cmu.tetrad.algcomparison.statistic
-
Ancestor recall.
- AncestorRecall() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.AncestorRecall
-
Constructs the statistic.
- AncestralPrecision - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- AncestralPrecision() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.AncestralPrecision
-
Constructs the statistic.
- AncestralRecall - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- AncestralRecall() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.AncestralRecall
-
Constructs the statistic.
- andersonDarling - Enum constant in enum class edu.cmu.tetrad.search.Lofs.Score
- AndersonDarlingTest - Class in edu.cmu.tetrad.data
-
Implements the Anderson-Darling test for normality, with P values calculated as in R's ad.test method (in package nortest).
- AndersonDarlingTest(double[]) - Constructor for class edu.cmu.tetrad.data.AndersonDarlingTest
-
Constructs an Anderson-Darling test for the given column of data.
- AnnotatedClass<T extends Annotation> - Class in edu.cmu.tetrad.annotation
-
Sep 5, 2017 11:02:14 AM
- AnnotatedClass(Class, T) - Constructor for class edu.cmu.tetrad.annotation.AnnotatedClass
-
Creates an annotated class.
- annotatedClasses - Variable in class edu.cmu.tetrad.annotation.AbstractAnnotations
-
Annotated classes.
- AnnotatedClassUtils - Class in edu.cmu.tetrad.annotation
-
Sep 6, 2017 11:11:38 AM
- ANY_DAG - Static variable in class edu.cmu.tetrad.graph.RandomGraph.UniformGraphGenerator
- append(int[], int) - Method in interface edu.cmu.tetrad.search.score.Score
-
Appends an extra int to a list of ints.
- APPLY_R1 - Static variable in class edu.cmu.tetrad.util.Params
- applyDmSearch(Graph, Set<String>, double) - Method in class edu.cmu.tetrad.search.work_in_progress.DMSearch
- applyTo(Graph) - Method in class edu.cmu.tetrad.search.work_in_progress.GraphChange
-
Outputs a new PAG, a copy of the input excepting the applied changes of this object.
- ApproximateUpdater - Class in edu.cmu.tetrad.bayes
-
Calculates updated marginals for a Bayes net by simulating data and calculating likelihood ratios.
- ApproximateUpdater(BayesIm) - Constructor for class edu.cmu.tetrad.bayes.ApproximateUpdater
-
Constructs a new updater for the given Bayes net.
- ApproximateUpdater(BayesIm, Evidence) - Constructor for class edu.cmu.tetrad.bayes.ApproximateUpdater
-
Constructs a new updater for the given Bayes net.
- ar(DataSet, int) - Static method in class edu.cmu.tetrad.search.utils.TsUtils
- ar2(DataSet, int) - Static method in class edu.cmu.tetrad.search.utils.TsUtils
- archiveCurrentDirectory() - Method in class edu.cmu.tetrad.util.TetradSerializableUtils
-
Creates a zip archive of the currently serialized files in getCurrentDirectory(), placing the archive in getArchiveDirectory().
- arrangeByKnowledgeTiers(Graph) - Static method in class edu.cmu.tetrad.search.utils.GraphSearchUtils
- arrangeByKnowledgeTiers(Graph, Knowledge) - Static method in class edu.cmu.tetrad.search.utils.GraphSearchUtils
- arrangeByLayout(Graph, HashMap<String, PointXy>) - Static method in class edu.cmu.tetrad.graph.LayoutUtil
- arrangeBySourceGraph(Graph, Graph) - Static method in class edu.cmu.tetrad.graph.LayoutUtil
-
Arranges the nodes in the result graph according to their positions in the source graph.
- arrayPermute(double[]) - Static method in class edu.pitt.csb.mgm.MixedUtils
- arrayPermute(int[]) - Static method in class edu.pitt.csb.mgm.MixedUtils
- ARROW - Enum constant in enum class edu.cmu.tetrad.graph.Endpoint
- ArrowConfusion - Class in edu.cmu.tetrad.algcomparison.statistic.utils
-
A confusion matrix for arrows--i.e.
- ArrowConfusion(Graph, Graph) - Constructor for class edu.cmu.tetrad.algcomparison.statistic.utils.ArrowConfusion
-
Constructs a new ArrowConfusion object.
- ArrowConfusion(Graph, Graph, boolean) - Constructor for class edu.cmu.tetrad.algcomparison.statistic.utils.ArrowConfusion
-
Constructs a new ArrowConfusion object.
- ArrowheadFn - Class in edu.cmu.tetrad.algcomparison.statistic
-
The arrow precision.
- ArrowheadFn() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.ArrowheadFn
-
Constructs the statistic.
- ArrowheadFp - Class in edu.cmu.tetrad.algcomparison.statistic
-
The arrow precision.
- ArrowheadFp() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.ArrowheadFp
-
Constructs the statistic.
- ArrowheadFpr - Class in edu.cmu.tetrad.algcomparison.statistic
-
The adjacency true positive rate.
- ArrowheadFpr() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.ArrowheadFpr
-
Constructs the statistic.
- ArrowheadPrecision - Class in edu.cmu.tetrad.algcomparison.statistic
-
The arrow precision.
- ArrowheadPrecision() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.ArrowheadPrecision
-
Constructs the statistic.
- ArrowheadPrecisionCommonEdges - Class in edu.cmu.tetrad.algcomparison.statistic
-
The arrow precision.
- ArrowheadPrecisionCommonEdges() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.ArrowheadPrecisionCommonEdges
-
Constructs the statistic.
- ArrowheadRecall - Class in edu.cmu.tetrad.algcomparison.statistic
-
The arrow recall.
- ArrowheadRecall() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.ArrowheadRecall
-
Constructs the statistic.
- ArrowheadRecallCommonEdges - Class in edu.cmu.tetrad.algcomparison.statistic
-
The arrow recall.
- ArrowheadRecallCommonEdges() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.ArrowheadRecallCommonEdges
-
Constructs the statistic.
- ArrowheadTn - Class in edu.cmu.tetrad.algcomparison.statistic
-
The arrow precision.
- ArrowheadTn() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.ArrowheadTn
-
Constructs the statistic.
- ArrowheadTp - Class in edu.cmu.tetrad.algcomparison.statistic
-
The arrow precision.
- ArrowheadTp() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.ArrowheadTp
-
Constructs the statistic.
- ASCENDING - Static variable in class edu.cmu.tetrad.util.RocCalculator
- asin(Matrix) - Static method in class jgpml.covariancefunctions.MatrixOperations
-
Computes the arcsin of the input
Matrix(element by element) - asList(int[], List<Node>) - Static method in class edu.cmu.tetrad.graph.GraphUtils
-
Constructs a list of nodes from the given
nodeslist at the given indices in that list. - asRow(double[]) - Static method in class edu.cmu.tetrad.util.MatrixUtils
- asSet(int[], List<Node>) - Static method in class edu.cmu.tetrad.graph.GraphUtils
- asSet(Node...) - Static method in class edu.cmu.tetrad.graph.GraphUtils
- assign(double) - Method in class edu.cmu.tetrad.util.Vector
- assign(Matrix) - Method in class edu.cmu.tetrad.util.Matrix
- assign(Matrix2) - Method in class edu.cmu.tetrad.util.Matrix2
- assign(Vector) - Method in class edu.cmu.tetrad.util.Vector
- assignClasses(Class[], Class[], boolean, List<SessionNode>) - Method in class edu.cmu.tetrad.session.SessionNode
- assignColumn(int, Vector) - Method in class edu.cmu.tetrad.util.Matrix
- assignColumn(int, Vector) - Method in class edu.cmu.tetrad.util.Matrix2
- assignParameters(Class[], List) - Method in class edu.cmu.tetrad.session.SessionNode
-
Returns the objects in the List as an array in the same order as the parameter types.
- assignRow(int, Vector) - Method in class edu.cmu.tetrad.util.Matrix
- assignRow(int, Vector) - Method in class edu.cmu.tetrad.util.Matrix2
- at - Enum constant in enum class edu.cmu.tetrad.graph.EdgeTypeProbability.EdgeType
- average - Enum constant in enum class edu.cmu.tetrad.search.utils.ResolveSepsets.Method
- average - Enum constant in enum class edu.cmu.tetrad.search.work_in_progress.ResolveSepsetsDci.Method
- AverageDegreeEst - Class in edu.cmu.tetrad.algcomparison.statistic
-
The adjacency precision.
- AverageDegreeEst() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.AverageDegreeEst
-
Constructs the statistic.
- AverageDegreeTrue - Class in edu.cmu.tetrad.algcomparison.statistic
-
The adjacency precision.
- AverageDegreeTrue() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.AverageDegreeTrue
-
Constructs the statistic.
- averageDeviation(double[]) - Static method in class edu.cmu.tetrad.util.StatUtils
- averageDeviation(double[], int) - Static method in class edu.cmu.tetrad.util.StatUtils
- averageDeviation(long[]) - Static method in class edu.cmu.tetrad.util.StatUtils
- averageDeviation(long[], int) - Static method in class edu.cmu.tetrad.util.StatUtils
- averagetest - Enum constant in enum class edu.cmu.tetrad.search.utils.ResolveSepsets.Method
- averagetest - Enum constant in enum class edu.cmu.tetrad.search.work_in_progress.ResolveSepsetsDci.Method
- AVG_DEGREE - Static variable in class edu.cmu.tetrad.util.Params
B
- badIndexXcp(int, int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.BasicMatrix
-
Throws a bad index exception.
- badNodeIndex(int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.BasicGraph
-
Returns a specially formatted string with all the contents of the set of edges in this Graph.
- BasalInitializer - Class in edu.cmu.tetrad.study.gene.tetrad.gene.history
-
Initializes a history array by setting the value of each variable to basal if it is unregulated (has no parents other than itself one time step back) and to a random value chosen from a N(basal, initStDev) distribution otherwise.
- BasalInitializer(UpdateFunction, double, double) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.history.BasalInitializer
-
Constructs a new history that will initialize genes using the given basal expression and initial standard deviation.
- basicCpdag(Graph) - Static method in class edu.cmu.tetrad.search.utils.GraphSearchUtils
-
Get a graph and direct only the unshielded colliders.
- basicCpdagRestricted2(Graph, Node) - Static method in class edu.cmu.tetrad.search.utils.GraphSearchUtils
- BasicGraph - Class in edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util
-
Basic functionality that all graph-derived classes should provide.
- BasicGraph() - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.BasicGraph
-
Default constructor
- BasicGraph(String) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.BasicGraph
-
Creates a Graph reading it from file
fname. - BasicGraph(String, int) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.BasicGraph
-
Creates a graph with
gNamename, andnnodes. - BasicLagGraph - Class in edu.cmu.tetrad.study.gene.tetrad.gene.history
-
Stores a time series in the "update" (rather than, say, the "repeated") form--that is, for a given set of factors (the word "factor" is being used here to avoid ambiguity), only lags behind the getModel time step are recorded temporally, with causal edges extending from lagged factors with lags >= 1 to factors in the getModel time step (lag = 0) only.
- BasicLagGraph() - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.history.BasicLagGraph
-
Constructs an empty update graph--that is, a graph with no factors (and therefore no edges).
- BasicLagGraph(LagGraph) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.history.BasicLagGraph
-
Constructs a copy of the given lag graph.
- BasicLTMatrix - Class in edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util
-
Implements a space-efficient Lower Triangular Matrix of elements of type
short - BasicLTMatrix(String) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.BasicLTMatrix
-
Creates a lower triangular matrix reading it from file
fname. - BasicLTMatrix(String, int) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.BasicLTMatrix
-
Creates a lower triangular matrix with
nrowsrows. - BasicMatrix - Class in edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util
-
Basic functionality of a Matrix
- BasicMatrix() - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.BasicMatrix
-
No parameters constructor, only used within the package
- BasicMatrix(String) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.BasicMatrix
-
Creates a matrix reading it from a file
fname. - BasicMatrix(String, int) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.BasicMatrix
-
Creates a matrix with
nrowsrows, and with namemname. - BASIS_TYPE - Static variable in class edu.cmu.tetrad.util.Params
- BayesianConstraintInference - Class in edu.pitt.dbmi.algo.bayesian.constraint.inference
-
Feb 22, 2014 3:26:17 PM
- BayesianConstraintInference() - Constructor for class edu.pitt.dbmi.algo.bayesian.constraint.inference.BayesianConstraintInference
-
Constructor.
- BayesianConstraintInferenceTest - Class in edu.pitt.dbmi.algo.bayesian.constraint.inference
-
Feb 22, 2014 3:35:38 PM
- BayesianConstraintInferenceTest() - Constructor for class edu.pitt.dbmi.algo.bayesian.constraint.inference.BayesianConstraintInferenceTest
-
Constructor.
- BayesIm - Interface in edu.cmu.tetrad.bayes
-
Interface implemented by Bayes instantiated models.
- BayesImParser - Class in edu.cmu.tetrad.search.utils
-
Takes an xml element representing a bayes im and converts it to a BayesIM
- BayesImParser() - Constructor for class edu.cmu.tetrad.search.utils.BayesImParser
-
Creates a new BayesImParser.
- BayesImProbs - Class in edu.cmu.tetrad.bayes
-
Calculates cell probabilities from conditional BayesIm probabilities on the fly without constructing the entire table.
- BayesImProbs(BayesIm) - Constructor for class edu.cmu.tetrad.bayes.BayesImProbs
-
Constructs a BayesImProbs object from the given BayesIm.
- BayesNetSimulation - Class in edu.cmu.tetrad.algcomparison.simulation
-
Bayes net simulation.
- BayesNetSimulation(RandomGraph) - Constructor for class edu.cmu.tetrad.algcomparison.simulation.BayesNetSimulation
-
Constructs a new BayesNetSimulation.
- BayesNetSimulation(BayesIm) - Constructor for class edu.cmu.tetrad.algcomparison.simulation.BayesNetSimulation
-
Constructs a new BayesNetSimulation.
- BayesNetSimulation(BayesPm) - Constructor for class edu.cmu.tetrad.algcomparison.simulation.BayesNetSimulation
-
Constructs a new BayesNetSimulation.
- BayesPm - Class in edu.cmu.tetrad.bayes
-
Implements a discrete Bayes parametric model--that is, a DAG together with a map from the nodes in the graph to a set of discrete variables, specifying the number of categories for each variable and the name of each category for each variable.
- BayesPm(BayesPm) - Constructor for class edu.cmu.tetrad.bayes.BayesPm
-
Copy constructor.
- BayesPm(Graph) - Constructor for class edu.cmu.tetrad.bayes.BayesPm
-
Construct a new BayesPm using the given DAG, assigning each variable two values named "value1" and "value2" unless nodes are discrete variables with categories already defined.
- BayesPm(Graph, int, int) - Constructor for class edu.cmu.tetrad.bayes.BayesPm
-
Constructs a new BayesPm from the given DAG, assigning each variable a random number of values between
lowerBoundandupperBound. - BayesPm(Graph, BayesPm) - Constructor for class edu.cmu.tetrad.bayes.BayesPm
-
Constructs a new BayesPm using a given DAG, using as much information from the old BayesPm as possible.
- BayesPm(Graph, BayesPm, int, int) - Constructor for class edu.cmu.tetrad.bayes.BayesPm
-
Constructs a new BayesPm from the given DAG, using as much information from the old BayesPm as possible.
- BayesProperties - Class in edu.cmu.tetrad.bayes
-
Calculates some scores for Bayes nets as a whole.
- BayesProperties(DataSet) - Constructor for class edu.cmu.tetrad.bayes.BayesProperties
- BayesProperties.LikelihoodRet - Class in edu.cmu.tetrad.bayes
- BayesUpdater - Interface in edu.cmu.tetrad.bayes
-
Interface for a discrete Bayes updating algorithm.
- BayesXmlParser - Class in edu.cmu.tetrad.bayes
-
Parses Bayes elements back to objects.
- BayesXmlParser() - Constructor for class edu.cmu.tetrad.bayes.BayesXmlParser
- BayesXmlRenderer - Class in edu.cmu.tetrad.bayes
-
Renders Bayes nets and related models in XML.
- BayesXmlRenderer() - Constructor for class edu.cmu.tetrad.bayes.BayesXmlRenderer
- BAYS_NET - Static variable in class edu.cmu.tetrad.algcomparison.simulation.SimulationTypes
- BCCausalInference - Class in edu.pitt.dbmi.algo.bayesian.constraint.inference
-
This is a thread-safe version of BCInference.
- BCCausalInference(int[], int[][]) - Constructor for class edu.pitt.dbmi.algo.bayesian.constraint.inference.BCCausalInference
- BCCausalInference.OP - Enum Class in edu.pitt.dbmi.algo.bayesian.constraint.inference
- BCInference - Class in edu.pitt.dbmi.algo.bayesian.constraint.inference
-
Feb 26, 2014 8:07:20 PM
- BCInference(int[][], int[]) - Constructor for class edu.pitt.dbmi.algo.bayesian.constraint.inference.BCInference
-
Cases is a two-dimensional array dataset.
- BCInference.OP - Enum Class in edu.pitt.dbmi.algo.bayesian.constraint.inference
- BdeMetricCache - Class in edu.cmu.tetrad.bayes
-
Provides a method for computing the score of a model, called the BDe metric (Bayesian Dirchlet likelihood equivalence), given a dataset (assumes no missing values) and a Bayes parameterized network (assumes no latent variables).> 0
- BdeMetricCache(DataSet, BayesPm) - Constructor for class edu.cmu.tetrad.bayes.BdeMetricCache
- BdeScore - Class in edu.cmu.tetrad.search.score
-
Calculates the BDe score (Bayes Dirichlet Equivalent) score for analyzing discrete multinomial data.
- BdeScore(DataSet) - Constructor for class edu.cmu.tetrad.search.score.BdeScore
-
Constructs a BDe score for the given dataset.
- BDeu - Enum constant in enum class edu.cmu.tetrad.sem.ScoreType
- BdeuScore - Class in edu.cmu.tetrad.algcomparison.score
-
Wrapper for Fisher Z test.
- BdeuScore - Class in edu.cmu.tetrad.search.score
-
Calculates the BDeu score, which the BDe (Bayes Dirichlet Equivalent) score with uniform priors.
- BdeuScore() - Constructor for class edu.cmu.tetrad.algcomparison.score.BdeuScore
- BdeuScore(DataSet) - Constructor for class edu.cmu.tetrad.search.score.BdeuScore
-
Constructs a BDe score for the given dataset.
- BdeuTest - Class in edu.cmu.tetrad.algcomparison.independence
-
Wrapper for Fisher Z test.
- BdeuTest() - Constructor for class edu.cmu.tetrad.algcomparison.independence.BdeuTest
- bernoulliRand(double) - Static method in class edu.cmu.tetrad.util.ProbUtils
- bes(Graph, List<Node>) - Method in class edu.cmu.tetrad.search.utils.Bes
-
Runs BES for a graph over the given list of variables
- bes(Graph, List<Node>, List<Node>) - Method in class edu.cmu.tetrad.search.utils.BesPermutation
-
Runs BES.
- Bes - Class in edu.cmu.tetrad.search.utils
-
Extracts the backward step of GES for use GES but also in other algorithms.
- Bes(Score) - Constructor for class edu.cmu.tetrad.search.utils.Bes
- BesPermutation - Class in edu.cmu.tetrad.search.utils
-
Implements a version of the BES (Best Equivalent Search) algorithm that takes a permutation as input and yields a permtuation as output, where the related DAG or CPDAG models are implied by the ordering or variables in these permutations.
- BesPermutation(Score) - Constructor for class edu.cmu.tetrad.search.utils.BesPermutation
-
Constructor.
- bestOrder(List<Node>) - Method in class edu.cmu.tetrad.search.Grasp
-
Given an initial permutation, 'order,' of the variables, searches for a best permutation of the variables by rearranging the variables in 'order.'
- bestOrder(List<Node>) - Method in class edu.cmu.tetrad.search.work_in_progress.GraspTol
- bestOrder(List<Node>) - Method in class edu.cmu.tetrad.search.work_in_progress.OtherPermAlgs
- beta(double, double) - Static method in class edu.cmu.tetrad.util.StatUtils
-
Calculates the value of beta for doubles
- Beta - Class in edu.cmu.tetrad.util.dist
-
Implements a Beta distribution for purposes of drawing random numbers.
- betaCdf(double, double, double) - Static method in class edu.cmu.tetrad.util.ProbUtils
-
Incomplete Beta function.
- betaPdf(double, double, double) - Static method in class edu.cmu.tetrad.util.ProbUtils
- betaQuantile(double, double, double) - Static method in class edu.cmu.tetrad.util.ProbUtils
- betaRand(double, double) - Static method in class edu.cmu.tetrad.util.ProbUtils
-
Beta distribution random generator.
- betterMutation(TeyssierScorer) - Method in class edu.cmu.tetrad.search.work_in_progress.GraspTol
- Bfci - Class in edu.cmu.tetrad.algcomparison.algorithm.oracle.pag
-
Adjusts GFCI to use a permutation algorithm (such as BOSS-Tuck) to do the initial steps of finding adjacencies and unshielded colliders.
- Bfci() - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Bfci
-
No-arg constructor.
- Bfci(IndependenceWrapper, ScoreWrapper) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Bfci
- BFci - Class in edu.cmu.tetrad.search
-
Uses BOSS in place of FGES for the initial step in the GFCI algorithm.
- BFci(IndependenceTest, Score) - Constructor for class edu.cmu.tetrad.search.BFci
-
Constructor.
- bic - Variable in class edu.cmu.tetrad.bayes.BayesProperties.LikelihoodRet
- BIC - Enum constant in enum class edu.cmu.tetrad.search.score.GicScores.RuleType
- BicDiff - Class in edu.cmu.tetrad.algcomparison.statistic
-
Difference between the true and estiamted BIC scores.
- BicDiff() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.BicDiff
- BicDiffPerRecord - Class in edu.cmu.tetrad.algcomparison.statistic
-
Difference between the true and estiamted BIC scores.
- BicDiffPerRecord() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.BicDiffPerRecord
- BicEst - Class in edu.cmu.tetrad.algcomparison.statistic
-
Estimated BIC score.
- BicEst() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.BicEst
- BicEst(double) - Constructor for class edu.cmu.tetrad.algcomparison.statistic.BicEst
- BicTrue - Class in edu.cmu.tetrad.algcomparison.statistic
-
True BIC score.
- BicTrue() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.BicTrue
- BidirectedConfusion - Class in edu.cmu.tetrad.algcomparison.statistic.utils
-
A confusion matrix for bidireced edges--i.e.
- BidirectedConfusion(Graph, Graph) - Constructor for class edu.cmu.tetrad.algcomparison.statistic.utils.BidirectedConfusion
- bidirectedEdge(Node, Node) - Static method in class edu.cmu.tetrad.graph.Edges
-
Constructs a new bidirected edge from nodeA to nodeB (<->).
- BidirectedEst - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- BidirectedEst() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.BidirectedEst
- BidirectedFP - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected false negatives.
- BidirectedFP() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.BidirectedFP
- BidirectedLatentPrecision - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- BidirectedLatentPrecision() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.BidirectedLatentPrecision
- BidirectedPrecision - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected edge precision.
- BidirectedPrecision() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.BidirectedPrecision
- BidirectedRecall - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected edge precision.
- BidirectedRecall() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.BidirectedRecall
- bidirectedToUndirected(Graph) - Static method in class edu.cmu.tetrad.graph.GraphUtils
- BidirectedTP - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- BidirectedTP() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.BidirectedTP
- BidirectedTrue - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- BidirectedTrue() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.BidirectedTrue
- binomialCdf(int, int, double) - Static method in class edu.cmu.tetrad.util.ProbUtils
-
Binomial cumulative distribution function.
- binomialPmf(int, int, double) - Static method in class edu.cmu.tetrad.util.ProbUtils
- binomialQuantile(double, int, double) - Static method in class edu.cmu.tetrad.util.ProbUtils
- binomialRand(int, double) - Static method in class edu.cmu.tetrad.util.ProbUtils
-
Binomial random generator from Numerical Recipes
- biNormalCdf(double, double, double) - Static method in class edu.cmu.tetrad.util.ProbUtils
-
Bivariate normal CDF.
- Biolingua - Class in edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.biolingua
-
Implements an algorithm for revising regulatory models with expression data.
- BiolinguaAlgorithm(SymMatrixF, BiolinguaDigraph) - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.biolingua.Biolingua
-
Runs the biolingua algorithm using the given correlation matrix (all values are assumed significant) and the initial graph, and uses some default values for the coefficients in the evaluation metric for annotations, errors, links, and predictions.
- BiolinguaAlgorithm(SymMatrixF, BiolinguaDigraph, float, float, float, float) - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.biolingua.Biolingua
-
Runs the biolingua algorithm using the given correlation matrix (all values are assumed significant), an initial graph, and the coefficients in the evaluation metric for annotations, errors, links, and predictions.
- BiolinguaAlgorithm(SymMatrixF, SymMatrixF, BiolinguaDigraph, float, float, float, float) - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.biolingua.Biolingua
-
Runs the biolingua algorithm using the given correlation matrix, significance matrix, the initial graph, and the coefficients in the evaluation metric for annotations, errors, links, and predictions.
- BiolinguaDigraph - Class in edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.biolingua
-
Implements a digraph to be used by the Biolingua algorithm.
- BiolinguaDigraph(BiolinguaDigraph) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.biolingua.BiolinguaDigraph
-
Copy constructor.
- BiolinguaDigraph(String) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.biolingua.BiolinguaDigraph
-
Creates a BiolinguaDigraph reading it from file
fname. - BiolinguaDigraph(String, int) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.biolingua.BiolinguaDigraph
-
Creates a BiolinguaDigraph with name
gNameandnnodes - BiolinguaRunner - Class in edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.biolingua
-
Client of the Biolingua class, can be used to easily run the algorithm with different inputs.
- BiolinguaRunner() - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.biolingua.BiolinguaRunner
- blankDirichletIm(BayesPm) - Static method in class edu.cmu.tetrad.bayes.DirichletBayesIm
- bookmark() - Method in class edu.cmu.tetrad.search.utils.TeyssierScorer
-
Bookmarks the current pi with index Integer.MIN_VALUE.
- bookmark(int) - Method in class edu.cmu.tetrad.search.utils.TeyssierScorer
-
Bookmarks the current pi as index key.
- bool2(int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.akutsu.BoolSearch
-
Implements the BOOL-2 algorithm of Akutsu, et al, found in section 2.2 of their paper "Algorithms for Inferring Qualitative Models of Biological Networks".
- bool2(int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.BoolSearch
-
Implements the BOOL-2 algorithm of Akutsu, et al, found in section 2.2 of their paper "Algorithms for Inferring Qualitative Models of Biological Networks".
- BOOLEAN_GLASS_SIMULATION - Static variable in class edu.cmu.tetrad.algcomparison.simulation.SimulationTypes
- BooleanFunction - Class in edu.cmu.tetrad.study.gene.tetrad.gene.history
-
Stores a boolean function from a set of boolean-valued parents to a single boolean-valued column.
- BooleanFunction(IndexedParent[]) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.history.BooleanFunction
-
Constructs a new boolean function for the given array of parents.
- BooleanGlassFunction - Class in edu.cmu.tetrad.study.gene.tetrad.gene.history
-
Updates a gene given a history using the formula Gi.0 = max(Gi.1 - decayRate * -Gi.1 + booleanInfluenceRate * F(Parents(Gi) in the graph \ Gi.1), lowerBound), as described in Edwards and Glass, (2000), "Combinatorial explosion in model gene networks", American Institute of Physics.
- BooleanGlassFunction(LagGraph) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.history.BooleanGlassFunction
-
Constructs a new random boolean Glass function using the given lag graph, with a basalExpression of 0.0, a true value of +1.0 and a false value of -1.0.
- BooleanGlassFunction(LagGraph, double, double) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.history.BooleanGlassFunction
-
Constructs a new random boolean Glass function using the given lag graph, lower bound, and basalExpression.
- BooleanGlassGeneIm - Class in edu.cmu.tetrad.study.gene.tetradapp.model
-
Wraps the MeasurementSimulator class as an instantiated model.
- BooleanGlassGeneIm(BooleanGlassGenePm, Parameters) - Constructor for class edu.cmu.tetrad.study.gene.tetradapp.model.BooleanGlassGeneIm
-
Obtains a boolean Glass function from the boolean Glass gene PM provided and uses it to create a Glass history and a measurement simulator.
- BooleanGlassGenePm - Class in edu.cmu.tetrad.study.gene.tetradapp.model
-
Implements a parametric model for Boolean Glass gene PM's, which in this case just presents the underlying workbench.
- BooleanGlassGenePm(ManualActiveLagGraph) - Constructor for class edu.cmu.tetrad.study.gene.tetradapp.model.BooleanGlassGenePm
- BooleanGlassGenePm(RandomActiveLagGraph) - Constructor for class edu.cmu.tetrad.study.gene.tetradapp.model.BooleanGlassGenePm
- BooleanGlassSimulation - Class in edu.cmu.tetrad.algcomparison.simulation
-
A version of the Lee and Hastic simulation which is guaranteed to generate a discrete data set.
- BooleanGlassSimulation(RandomGraph) - Constructor for class edu.cmu.tetrad.algcomparison.simulation.BooleanGlassSimulation
- booleanRepresentation(int, int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.akutsu.BoolSearch
-
Computes a byte vector which corresponds to the argument ind.
- booleanRepresentation(int, int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.ideker.ItkPredictorSearch
-
Computes a byte vector which corresponds to the argument ind.
- booleanRepresentation(int, int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.reveal.RevealEvaluator
-
Computes a byte vector which corresponds to the argument ind.
- booleanRepresentation(int, int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.BoolSearch
-
Computes a byte vector which corresponds to the argument ind.
- booleanRepresentation(int, int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.LTestReveal
-
Computes a byte vector which corresponds to the argument ind.
- booleanRepresentation(int, int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.RevealEvaluator
-
Computes a byte vector which corresponds to the argument ind.
- BoolSearch - Class in edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.akutsu
-
This class contains as a member variable (cases) the time series data stored in an int array of microarray measurements.
- BoolSearch - Class in edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin
-
This class contains as a member variable (cases) the time series data stored in an int array of microarray measurements.
- BoolSearch(int[][], String[]) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.akutsu.BoolSearch
- BoolSearch(int[][], String[]) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.BoolSearch
- BOOTSTRAP - Enum constant in enum class edu.cmu.tetrad.search.Cstar.SampleStyle
- Bootstrapping - Annotation Interface in edu.cmu.tetrad.annotation
-
Indicate algorithm can do bootstrapping.
- BootstrapSampler - Class in edu.cmu.tetrad.data
-
Provides a static method for sampling with replacement from a dataset to create a new dataset with a sample size supplied by the user.
- BootstrapSampler() - Constructor for class edu.cmu.tetrad.data.BootstrapSampler
-
Constructs a sample that does not do any logging.
- bootStrapSampling(DataSet, int) - Method in class edu.cmu.tetrad.calibration.DataForCalibrationRfci
- Boss - Class in edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag
-
BOSS-DC (Best Order Score Search Divide and Conquer)
- Boss - Class in edu.cmu.tetrad.search
-
Implements Best Order Score Search (BOSS).
- Boss() - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Boss
- Boss(ScoreWrapper) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Boss
- Boss(Score) - Constructor for class edu.cmu.tetrad.search.Boss
-
This algorithm will work with an arbitrary BIC score.
- BOSS - Enum constant in enum class edu.cmu.tetrad.search.Cstar.CpdagAlgorithm
- BOSS - Enum constant in enum class edu.cmu.tetrad.search.Fask.AdjacencyMethod
- BOSS_ALG - Static variable in class edu.cmu.tetrad.util.Params
- BOTH - Enum constant in enum class edu.cmu.tetrad.calculator.expression.ExpressionDescriptor.Position
- BoxDataSet - Class in edu.cmu.tetrad.data
-
Wraps a DataBox in such a way that mixed data sets can be stored.
- BoxDataSet(BoxDataSet) - Constructor for class edu.cmu.tetrad.data.BoxDataSet
-
Makes of copy of the given data set.
- BoxDataSet(DataBox, List<Node>) - Constructor for class edu.cmu.tetrad.data.BoxDataSet
- Bpc - Class in edu.cmu.tetrad.algcomparison.algorithm.cluster
-
Build Pure Clusters.
- Bpc - Class in edu.cmu.tetrad.search
-
Implements the Build Pure Clusters (BPC) algorithm, which allows one to identify clusters of measured variables in a dataset that are explained by a single latent.
- Bpc() - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.cluster.Bpc
- Bpc(DataSet, double, BpcTestType) - Constructor for class edu.cmu.tetrad.search.Bpc
-
Constructor.
- Bpc(ICovarianceMatrix, double, BpcTestType) - Constructor for class edu.cmu.tetrad.search.Bpc
-
Constructor.
- BpcAlgorithmType - Enum Class in edu.cmu.tetrad.search.utils
-
Enumerates the algorithm types for BuildPureClusters, and Purify.
- BpcTestType - Enum Class in edu.cmu.tetrad.search.utils
-
Enumerates the test types for BuildPureClusters, and Purify.
- BpcTetradPurifyWashdown - Class in edu.cmu.tetrad.search.work_in_progress
-
Implements a really simple idea for building pure clusters, just using the Purify algorithm.
- BpcTetradPurifyWashdown(DataSet, BpcTestType, double) - Constructor for class edu.cmu.tetrad.search.work_in_progress.BpcTetradPurifyWashdown
-
Construct the algorithm using a data set.
- BpcTetradPurifyWashdown(ICovarianceMatrix, BpcTestType, double) - Constructor for class edu.cmu.tetrad.search.work_in_progress.BpcTetradPurifyWashdown
-
Construct the algorithm using a covariance matrix.
- BREAK_TIES - Static variable in class edu.cmu.tetrad.util.Params
- BryanSensitivityStudy - Class in edu.cmu.tetrad.study.examples.conditions
-
An example script to simulate data and run a comparison analysis on it.
- BryanSensitivityStudy() - Constructor for class edu.cmu.tetrad.study.examples.conditions.BryanSensitivityStudy
- bStar(Matrix) - Static method in class edu.cmu.tetrad.search.score.SemBicScore
- BUILD_PURE_CLUSTERS - Enum constant in enum class edu.cmu.tetrad.search.utils.BpcAlgorithmType
- bumpInitialization(double) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.DishModel
-
Bumps the given expression value in the manner prescribed for the getModel dish.
- ByteDataBox - Class in edu.cmu.tetrad.data
-
Stores a 2D array of byte data.
- ByteDataBox(byte[][]) - Constructor for class edu.cmu.tetrad.data.ByteDataBox
-
Constructs a new data box using the given 2D byte data array as data.
- ByteDataBox(int, int) - Constructor for class edu.cmu.tetrad.data.ByteDataBox
-
Constructs an 2D byte array consisting entirely of missing values (-99).
C
- ca - Enum constant in enum class edu.cmu.tetrad.graph.EdgeTypeProbability.EdgeType
- CACHE_SCORES - Static variable in class edu.cmu.tetrad.util.Params
- calcChiSquare(int[]) - Method in class edu.cmu.tetrad.search.test.ChiSquareTest
-
Calculates chi square for a conditional cross-tabulation table for independence question 0 _||_ 1 | 2, 3, ...max by summing up chi square and degrees of freedom for each conditional table in turn, where rows or columns that consist entirely of zeros have been removed.
- calcChiSquare(Sextad[]) - Method in class edu.cmu.tetrad.search.utils.DeltaSextadTest
-
Takes a list of tetrads for the given data set and returns the chi square value for the test.
- calcChiSquare(Tetrad...) - Method in class edu.cmu.tetrad.search.utils.DeltaTetradTest
-
Takes a list of tetrads for the given data set and returns the chi square value for the test.
- calcGSquare(int[]) - Method in class edu.cmu.tetrad.search.test.GSquareTest
-
Calculates g square for a conditional crosstabulation table for independence question 0 _||_ 1 | 2, 3, ...max by summing up g square and degrees of freedom for each conditional table in turn, where rows or columns that consist entirely of zeros have been removed.
- calcMargin(int[]) - Method in class edu.cmu.tetrad.data.CellTable
-
Calculates a marginal sum for the cell table.
- calcMargin(int[], int[]) - Method in class edu.cmu.tetrad.data.CellTable
-
An alternative way to specify a marginal calculation.
- CALCULATE_FROM_SEM - Enum constant in enum class edu.cmu.tetrad.sem.StandardizedSemIm.Initialization
- calculateMinimumEffectsOnY(Node) - Method in class edu.cmu.tetrad.search.Ida
-
Returns a map from nodes in V \ {Y} to their minimum effects.
- calculatePriorMarginals(int) - Method in class edu.cmu.tetrad.bayes.ApproximateUpdater
- calculatePriorMarginals(int) - Method in interface edu.cmu.tetrad.bayes.BayesUpdater
-
Calculates the prior marginal probabilities of the given node.
- calculatePriorMarginals(int) - Method in class edu.cmu.tetrad.bayes.CptInvariantUpdater
- calculatePriorMarginals(int) - Method in class edu.cmu.tetrad.bayes.Identifiability
- calculatePriorMarginals(int) - Method in class edu.cmu.tetrad.bayes.JunctionTreeUpdater
- calculatePriorMarginals(int) - Method in class edu.cmu.tetrad.bayes.RowSummingExactUpdater
- calculateUpdatedMarginals(int) - Method in class edu.cmu.tetrad.bayes.ApproximateUpdater
- calculateUpdatedMarginals(int) - Method in interface edu.cmu.tetrad.bayes.BayesUpdater
-
Calculates the updated marginal probabilities of the given node, given the evidence.
- calculateUpdatedMarginals(int) - Method in class edu.cmu.tetrad.bayes.CptInvariantUpdater
- calculateUpdatedMarginals(int) - Method in class edu.cmu.tetrad.bayes.Identifiability
- calculateUpdatedMarginals(int) - Method in class edu.cmu.tetrad.bayes.JunctionTreeUpdater
- calculateUpdatedMarginals(int) - Method in class edu.cmu.tetrad.bayes.RowSummingExactUpdater
- call() - Method in class edu.pitt.dbmi.algo.resampling.task.GeneralResamplingSearchRunnable
- CanCor(double[][], double[][]) - Static method in class edu.cmu.tetrad.search.utils.EstimateRank
-
Compute canonical correlations from data.
- CanCor(int[], int[], double[][]) - Static method in class edu.cmu.tetrad.search.utils.EstimateRank
-
Compute canonical correlations from covariance matrix.
- CaseExpander - Class in edu.cmu.tetrad.data
-
Makes a new data set in which cases in the given data set that have been assigned multiplicies other than n = 1 are copied out n times.
- CaseExpander() - Constructor for class edu.cmu.tetrad.data.CaseExpander
- cauchyCdf(double) - Static method in class edu.cmu.tetrad.util.ProbUtils
-
Cauchy CDF
- cauchyPdf(double) - Static method in class edu.cmu.tetrad.util.ProbUtils
- cauchyQuantile(double) - Static method in class edu.cmu.tetrad.util.ProbUtils
- cauchyRand() - Static method in class edu.cmu.tetrad.util.ProbUtils
-
Cauchy random generator.
- cc - Enum constant in enum class edu.cmu.tetrad.graph.EdgeTypeProbability.EdgeType
- Ccd - Class in edu.cmu.tetrad.algcomparison.algorithm.oracle.pag
-
CCD (Cyclic Causal Discovery)
- Ccd - Class in edu.cmu.tetrad.search
-
Implemented the Cyclic Causal Discovery (CCD) algorithm by Thomas Richardson.
- Ccd() - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Ccd
- Ccd(IndependenceWrapper) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Ccd
- Ccd(IndependenceTest) - Constructor for class edu.cmu.tetrad.search.Ccd
-
Construct a CCD algorithm with the given independence test.
- CCI_SCORE_ALPHA - Static variable in class edu.cmu.tetrad.util.Params
- CciScore - Class in edu.cmu.tetrad.algcomparison.score
- CciScore() - Constructor for class edu.cmu.tetrad.algcomparison.score.CciScore
- CciTest - Class in edu.cmu.tetrad.algcomparison.independence
-
Wrapper for Daudin Conditional Independence test.
- CciTest() - Constructor for class edu.cmu.tetrad.algcomparison.independence.CciTest
- CellTable - Class in edu.cmu.tetrad.data
-
Stores a cell count table of arbitrary dimension.
- CellTable(int[]) - Constructor for class edu.cmu.tetrad.data.CellTable
-
Constructs a new cell table using the given array for dimensions, initializing all cells in the table to zero.
- CellTableProbs - Class in edu.cmu.tetrad.bayes
-
Estimates probabilities from data by constructing the entire cell count table for the data.
- CellTableProbs(DataSet) - Constructor for class edu.cmu.tetrad.bayes.CellTableProbs
-
Creates a cell count table for the given data set.
- center(double[]) - Static method in class edu.cmu.tetrad.data.DataTransforms
- center(DataSet) - Static method in class edu.cmu.tetrad.data.DataTransforms
-
Subtracts the mean of each column from each datum that column.
- center(List<DataSet>) - Static method in class edu.cmu.tetrad.data.DataTransforms
- centerData(Matrix) - Static method in class edu.cmu.tetrad.data.DataTransforms
- centeringComp() - Static method in class edu.cmu.tetrad.util.JOptionUtils
- Cfci - Class in edu.cmu.tetrad.algcomparison.algorithm.oracle.pag
-
FCI.
- Cfci - Class in edu.cmu.tetrad.search
-
Adjusts FCI (see) to use conservative orientation as in CPC (see).
- Cfci() - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Cfci
- Cfci(IndependenceWrapper) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Cfci
- Cfci(IndependenceTest) - Constructor for class edu.cmu.tetrad.search.Cfci
-
Constructs a new FCI search for the given independence test and background knowledge.
- CG_EXACT - Static variable in class edu.cmu.tetrad.util.Params
- changeName(String, String) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
- changeVariable(Node, Node) - Method in class edu.cmu.tetrad.data.BoxDataSet
-
Changes the variable for the given column from
fromtoto. - changeVariable(Node, Node) - Method in interface edu.cmu.tetrad.data.DataSet
-
Changes the variable for the given column from
fromtoto. - changeVariable(Node, Node) - Method in class edu.cmu.tetrad.data.NumberObjectDataSet
-
Changes the variable for the given column from
fromtoto. - CHECK_TYPE - Static variable in class edu.cmu.tetrad.util.Params
- checkIndependence(Node, Node, Node...) - Method in interface edu.cmu.tetrad.search.IndependenceTest
-
Checks the independence fact in question and returns and independence result.
- checkIndependence(Node, Node, Node...) - Method in class edu.cmu.tetrad.search.test.IndTestProbabilistic
- checkIndependence(Node, Node, Node...) - Method in class edu.cmu.tetrad.search.work_in_progress.ProbabilisticMapIndependence
- checkIndependence(Node, Node, Set<Node>) - Method in interface edu.cmu.tetrad.search.IndependenceTest
- checkIndependence(Node, Node, Set<Node>) - Method in class edu.cmu.tetrad.search.IndTestIod
-
Checks the indicated independence fact by pooling available tests for the given variables.
- checkIndependence(Node, Node, Set<Node>) - Method in class edu.cmu.tetrad.search.test.IndTestChiSquare
-
Determines whether variable x is independent of variable y given a list of conditioning varNames z.
- checkIndependence(Node, Node, Set<Node>) - Method in class edu.cmu.tetrad.search.test.IndTestConditionalCorrelation
-
Checks the independence of x _||_ y | z
- checkIndependence(Node, Node, Set<Node>) - Method in class edu.cmu.tetrad.search.test.IndTestConditionalGaussianLrt
-
Returns and independence result that states whether x _||_y | z and what the p-value of the test is.
- checkIndependence(Node, Node, Set<Node>) - Method in class edu.cmu.tetrad.search.test.IndTestDegenerateGaussianLrt
-
Returns an independence result specifying whether x _||_ y | Z and what its p-values are.
- checkIndependence(Node, Node, Set<Node>) - Method in class edu.cmu.tetrad.search.test.IndTestFisherZ
-
Determines whether variable x _||_ y | z given a list of conditioning variables z.
- checkIndependence(Node, Node, Set<Node>) - Method in class edu.cmu.tetrad.search.test.IndTestFisherZConcatenateResiduals
-
Determines whether x _||_ y | z.
- checkIndependence(Node, Node, Set<Node>) - Method in class edu.cmu.tetrad.search.test.IndTestFisherZFisherPValue
-
Determines whether variable x is independent of variable y given a list of conditioning variables z.
- checkIndependence(Node, Node, Set<Node>) - Method in class edu.cmu.tetrad.search.test.IndTestGSquare
-
Determines whether variable x is independent of variable y given a list of conditioning varNames z.
- checkIndependence(Node, Node, Set<Node>) - Method in class edu.cmu.tetrad.search.test.IndTestHsic
-
Determines whether variable x is independent of variable y given a list of conditioning variables z.
- checkIndependence(Node, Node, Set<Node>) - Method in class edu.cmu.tetrad.search.test.IndTestIndependenceFacts
-
Checks independence by looking up facts in the list of facts supplied in the constructor.
- checkIndependence(Node, Node, Set<Node>) - Method in class edu.cmu.tetrad.search.test.IndTestMulti
-
Determines whether variable x is independent of variable y given a list of conditioning variables z.
- checkIndependence(Node, Node, Set<Node>) - Method in class edu.cmu.tetrad.search.test.IndTestMvpLrt
-
Returns an independence result for x _||_ y | z.
- checkIndependence(Node, Node, Set<Node>) - Method in class edu.cmu.tetrad.search.test.IndTestProbabilistic
- checkIndependence(Node, Node, Set<Node>) - Method in class edu.cmu.tetrad.search.test.IndTestRegression
-
Determines whether variable x is independent of variable y given a list of conditioning variables z.
- checkIndependence(Node, Node, Set<Node>) - Method in class edu.cmu.tetrad.search.test.IndTestTrekSep
-
Determines whether variable x is independent of variable y given a list of conditioning variables z.
- checkIndependence(Node, Node, Set<Node>) - Method in class edu.cmu.tetrad.search.test.Kci
-
Returns True if the given independence question is judged true, false if not.
- checkIndependence(Node, Node, Set<Node>) - Method in class edu.cmu.tetrad.search.test.MsepTest
-
Checks the indicated m-separation fact, msep(x , y | z).
- checkIndependence(Node, Node, Set<Node>) - Method in class edu.cmu.tetrad.search.test.ScoreIndTest
-
Determines whether x _||_ y | z
- checkIndependence(Node, Node, Set<Node>) - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestCramerT
-
Determines whether variable x is independent of variable y given a list of conditioning variables z.
- checkIndependence(Node, Node, Set<Node>) - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestFisherZGeneralizedInverse
-
Determines whether variable x is independent of variable y given a list of conditioning variables z.
- checkIndependence(Node, Node, Set<Node>) - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestFisherZPercentIndependent
- checkIndependence(Node, Node, Set<Node>) - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestFisherZRecursive
-
Determines whether variable x is independent of variable y given a list of conditioning variables z.
- checkIndependence(Node, Node, Set<Node>) - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestMixedMultipleTTest
- checkIndependence(Node, Node, Set<Node>) - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestMnlrLr
- checkIndependence(Node, Node, Set<Node>) - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestMultinomialLogisticRegression
- checkIndependence(Node, Node, Set<Node>) - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestPositiveCorr
-
Determines whether variable x is independent of variable y given a list of conditioning variables z.
- checkIndependence(Node, Node, Set<Node>) - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestSepsetDci
-
Checks the indicated independence fact.
- checkIndependence(Node, Node, Set<Node>) - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestUniformScatter
- checkIndependence(Node, Node, Set<Node>) - Method in class edu.cmu.tetrad.search.work_in_progress.ProbabilisticMapIndependence
- checkIndependence(Node, Node, Set<Node>) - Method in class edu.pitt.csb.mgm.IndTestMultinomialLogisticRegressionWald
- checkNestingOfFields() - Method in class edu.cmu.tetrad.util.TetradSerializableUtils
-
Checks all of the classes in the serialization scope that implement TetradSerializable to make sure all of their fields are either themselves (a) primitive, (b) TetradSerializable, or (c) assignable from types designated as safely serializable by virtue of being included in the safelySerializableTypes array (see), or are arrays whose lowest order component types satisfy either (a), (b), or (c).
- checkProbFileExists(String, int, int, int, int, String, int, double, double, String) - Method in class edu.cmu.tetrad.calibration.DataForCalibrationRfci
- checkValue(int) - Method in class edu.cmu.tetrad.data.DiscreteVariable
- checkValue(Object) - Method in class edu.cmu.tetrad.data.AbstractVariable
-
Checks to see whether the passed value is an acceptable value for this variable.
- checkValue(Object) - Method in class edu.cmu.tetrad.data.ContinuousVariable
-
Checks the value to make sure it's a legitimate value for this column.
- checkValue(Object) - Method in interface edu.cmu.tetrad.data.Variable
-
Checks to see whether the passed value can be converted into a value for this variable.
- CHICKERING - Enum constant in enum class edu.cmu.tetrad.search.score.SemBicScore.RuleType
- chidist(double, int) - Static method in class edu.cmu.tetrad.util.StatUtils
-
Calculates the one-tail probability of the Chi-squared distribution for doubles
- chiSq - Variable in class edu.cmu.tetrad.bayes.BayesProperties.LikelihoodRet
- chisqCdf(double, double) - Static method in class edu.cmu.tetrad.util.ProbUtils
- chisqPdf(double, double) - Static method in class edu.cmu.tetrad.util.ProbUtils
- chisqQuantile(double, double) - Static method in class edu.cmu.tetrad.util.ProbUtils
- chisqRand(double) - Static method in class edu.cmu.tetrad.util.ProbUtils
-
Chi square random generator.
- ChiSquare - Class in edu.cmu.tetrad.algcomparison.independence
-
Wrapper for Fisher Z test.
- ChiSquare - Class in edu.cmu.tetrad.util.dist
-
Wraps a chi square distribution for purposes of drawing random samples.
- ChiSquare - Enum constant in enum class edu.cmu.tetrad.study.performance.ComparisonParameters.IndependenceTestType
- ChiSquare() - Constructor for class edu.cmu.tetrad.algcomparison.independence.ChiSquare
- ChiSquareTest - Class in edu.cmu.tetrad.search.test
-
Calculates marginal chi square test results for a discrete dataset.
- ChiSquareTest(DataSet, double) - Constructor for class edu.cmu.tetrad.search.test.ChiSquareTest
-
Constructs a test using the given data set and significance level.
- ChiSquareTest.Result - Class in edu.cmu.tetrad.search.test
-
Simple class to store the parameters of the result returned by the G Square test.
- ChoiceGenerator - Class in edu.cmu.tetrad.util
-
Generates (nonrecursively) all of the combinations of a choose b, where a, b are nonnegative integers and a >= b.
- ChoiceGenerator(int, int) - Constructor for class edu.cmu.tetrad.util.ChoiceGenerator
-
Constructs a new choice generator for a choose b.
- cholesky(Matrix) - Static method in class edu.cmu.tetrad.util.MatrixUtils
- choleskySimulation(CovarianceMatrix) - Static method in class edu.cmu.tetrad.data.DataUtils
- choose(int, int) - Static method in class edu.cmu.tetrad.util.MathUtils
- CIRCLE - Enum constant in enum class edu.cmu.tetrad.graph.Endpoint
- ClassifierBayesUpdaterDiscrete - Class in edu.cmu.tetrad.classify
-
This class contains a method classify which uses an instantiated Bayes net (BayesIm) provided in the constructor.
- ClassifierBayesUpdaterDiscrete(BayesIm, DataSet) - Constructor for class edu.cmu.tetrad.classify.ClassifierBayesUpdaterDiscrete
- ClassifierDiscrete - Interface in edu.cmu.tetrad.classify
-
Interface implemented by classes that do discrete classification.
- ClassifierMbDiscrete - Class in edu.cmu.tetrad.classify
-
Performs a Bayesian classification of a test set based on a given training set.
- ClassifierMbDiscrete(String, String, String, String, String, String, String) - Constructor for class edu.cmu.tetrad.classify.ClassifierMbDiscrete
- classify() - Method in class edu.cmu.tetrad.classify.ClassifierBayesUpdaterDiscrete
-
Computes and returns the cross-tabulation of observed versus estimated values of the target variable as described above.
- classify() - Method in interface edu.cmu.tetrad.classify.ClassifierDiscrete
- classify() - Method in class edu.cmu.tetrad.classify.ClassifierMbDiscrete
-
Classifies the test data by Bayesian updating.
- clear() - Method in class edu.cmu.tetrad.data.Knowledge
-
Removes explicit knowledge and tier information.
- clear() - Method in class edu.cmu.tetrad.graph.Dag
- clear() - Method in class edu.cmu.tetrad.graph.EdgeListGraph
-
Removes all nodes (and therefore all edges) from the graph.
- clear() - Method in interface edu.cmu.tetrad.graph.Graph
-
Removes all nodes (and therefore all edges) from the graph.
- clear() - Method in class edu.cmu.tetrad.graph.LagGraph
- clear() - Method in class edu.cmu.tetrad.graph.SemGraph
- clear() - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- clear() - Method in class edu.cmu.tetrad.util.LogUtils
-
Removes all streams from logging.
- clear() - Method in class edu.cmu.tetrad.util.TetradLogger
-
Removes all streams from the logger.
- clearArchiveDirectory() - Method in class edu.cmu.tetrad.util.TetradSerializableUtils
-
Clears the archive directory.
- clearBookmarks() - Method in class edu.cmu.tetrad.search.utils.TeyssierScorer
-
Clears all bookmarks.
- clearCellTable() - Method in class edu.cmu.tetrad.bayes.StoredCellProbsObs
- clearEdges() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ActiveLagGraph
- clearEdges() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ManualLagGraph
- clearEdges() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.BasicLagGraph
-
Removes all edges from the graph.
- clearEdges() - Method in interface edu.cmu.tetrad.study.gene.tetrad.gene.history.LagGraph
-
Removes all edges from the graph.
- clearNodes() - Method in class edu.cmu.tetrad.session.Session
-
Removes all nodes.
- clearRow(int, int) - Method in interface edu.cmu.tetrad.bayes.BayesIm
-
Assigns random probability values to the child values of this row that add to 1.
- clearRow(int, int) - Method in class edu.cmu.tetrad.bayes.DirichletBayesIm
-
Assigns random probability values to the child values of this row that add to 1.
- clearRow(int, int) - Method in class edu.cmu.tetrad.bayes.MlBayesIm
-
Assigns random probability values to the child values of this row that add to 1.
- clearRow(int, int) - Method in class edu.cmu.tetrad.bayes.MlBayesImObs
-
Assigns random probability values to the child values of this row that add to 1.
- clearRow(int, int) - Method in class edu.cmu.tetrad.bayes.UpdatedBayesIm
- clearSelection() - Method in class edu.cmu.tetrad.data.BoxDataSet
-
Marks all variables as deselected.
- clearSelection() - Method in class edu.cmu.tetrad.data.CorrelationMatrixOnTheFly
- clearSelection() - Method in class edu.cmu.tetrad.data.CovarianceMatrix
- clearSelection() - Method in class edu.cmu.tetrad.data.CovarianceMatrixOnTheFly
- clearSelection() - Method in interface edu.cmu.tetrad.data.DataSet
-
Marks all variables as deselected.
- clearSelection() - Method in interface edu.cmu.tetrad.data.ICovarianceMatrix
- clearSelection() - Method in class edu.cmu.tetrad.data.NumberObjectDataSet
-
Marks all variables as deselected.
- clearTable(int) - Method in interface edu.cmu.tetrad.bayes.BayesIm
-
Randomizes every row in the table for the given node index.
- clearTable(int) - Method in class edu.cmu.tetrad.bayes.DirichletBayesIm
-
Randomizes every row in the table for the given node index.
- clearTable(int) - Method in class edu.cmu.tetrad.bayes.MlBayesIm
-
Randomizes every row in the table for the given node index.
- clearTable(int) - Method in class edu.cmu.tetrad.bayes.MlBayesImObs
-
Randomizes every row in the table for the given node index.
- clearTable(int) - Method in class edu.cmu.tetrad.bayes.UpdatedBayesIm
- clique(List<Node>) - Method in class edu.cmu.tetrad.search.utils.TeyssierScorer
-
True iff the nodes in W form a clique in the current DAG.
- Clique - Enum constant in enum class edu.cmu.tetrad.search.utils.ClusterSignificance.CheckType
- cliques(Graph) - Method in class edu.cmu.tetrad.sem.Ricf
- clone() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.biolingua.BiolinguaDigraph
-
Returns a clone of this graph
- clone() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.biolingua.Digraph
-
Returns a clone of this graph
- clone() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.BasicGraph
-
Returns a clone of this graph
- cluster(Matrix) - Method in interface edu.cmu.tetrad.cluster.ClusteringAlgorithm
-
Clusters the given data set.
- cluster(Matrix) - Method in class edu.cmu.tetrad.cluster.KMeans
-
Runs the batch K-means clustering algorithm on the data, returning a result.
- ClusterAlgorithm - Interface in edu.cmu.tetrad.algcomparison.algorithm.cluster
-
Tags an algorithm that generates clusters.
- ClusteringAlgorithm - Interface in edu.cmu.tetrad.cluster
-
Represents a clustering algorithm to cluster some data.
- Clusters - Class in edu.cmu.tetrad.data
-
Stores clusters of variables for MimBuild, Purify, etc.
- Clusters() - Constructor for class edu.cmu.tetrad.data.Clusters
-
Constructs a blank knowledge object.
- Clusters(Clusters) - Constructor for class edu.cmu.tetrad.data.Clusters
-
Copy constructor.
- ClusterSignificance - Class in edu.cmu.tetrad.search.utils
-
Provides some methods to check significance of clusters for clustering algroithms.
- ClusterSignificance(List<Node>, DataModel) - Constructor for class edu.cmu.tetrad.search.utils.ClusterSignificance
- ClusterSignificance.CheckType - Enum Class in edu.cmu.tetrad.search.utils
-
Gives the options for checking significance of clusters--could check the significance using a regression model, or could check to see if the cluster is a clique, or could not do the check.
- clustersToPartition(Clusters, List<Node>) - Static method in class edu.cmu.tetrad.search.utils.ClusterUtils
- ClusterUtils - Class in edu.cmu.tetrad.search.utils
-
Provides some general utilities for dealing with clustering input and output.
- ClusterUtils() - Constructor for class edu.cmu.tetrad.search.utils.ClusterUtils
- COEF - Static variable in class edu.cmu.tetrad.sem.ParamType
-
A coefficient parameter.
- COEF_HIGH - Static variable in class edu.cmu.tetrad.util.Params
- COEF_LOW - Static variable in class edu.cmu.tetrad.util.Params
- COEF_SYMMETRIC - Static variable in class edu.cmu.tetrad.util.Params
- collider(Node, Node, Node) - Method in class edu.cmu.tetrad.search.utils.TeyssierScorer
-
Returns true iff [a, b, c] is a collider.
- COLLIDER - Enum constant in enum class edu.cmu.tetrad.search.utils.GraphSearchUtils.CpcTripleType
- COLLIDER - Enum constant in enum class edu.cmu.tetrad.search.work_in_progress.VcPc.CpcTripleType
- COLLIDER - Enum constant in enum class edu.cmu.tetrad.search.work_in_progress.VcPcFast.CpcTripleType
- COLLIDER_DISCOVERY_RULE - Static variable in class edu.cmu.tetrad.util.Params
- colliderOrientedMsg(Node, Node, Node) - Static method in class edu.cmu.tetrad.search.utils.LogUtilsSearch
- colliderOrientedMsg(Node, Node, Node, Set<Node>) - Static method in class edu.cmu.tetrad.search.utils.LogUtilsSearch
- colliderOrientedMsg(String, Node, Node, Node) - Static method in class edu.cmu.tetrad.search.utils.LogUtilsSearch
- colMax(DoubleMatrix2D) - Static method in class edu.pitt.csb.mgm.MixedUtils
-
return vector of the maximum of each column in m (as ints, i.e.
- COLON - Static variable in class edu.cmu.tetrad.data.DelimiterType
- columnCount() - Method in interface edu.pitt.isp.sverchkov.data.DataTable
- columnCount() - Method in class edu.pitt.isp.sverchkov.data.DataTableImpl
- CombinationGenerator - Class in edu.cmu.tetrad.util
-
Generates (nonrecursively) all of the combinations of objects, where the number of objects in each dimension is specified.
- CombinationGenerator(int[]) - Constructor for class edu.cmu.tetrad.util.CombinationGenerator
-
Constructs a new combination of objects, choosing one object from each dimension.
- CombinationIterator - Class in edu.cmu.tetrad.util
-
Iterates through all the posible combinations for a set of variables (each with a different number of possible values).
- CombinationIterator(int[]) - Constructor for class edu.cmu.tetrad.util.CombinationIterator
-
Creates a combination set for a set of variables with the given number of maxValues
- combineContinuousData(List<DataModel>, double[][]) - Static method in class edu.cmu.tetrad.util.MultidataUtils
- combineDataset(List<DataModel>) - Static method in class edu.cmu.tetrad.util.MultidataUtils
- combineDiscreteDataToDiscreteVerticalData(List<DataModel>, List<Node>, int[][], int, int) - Static method in class edu.cmu.tetrad.util.MultidataUtils
- combineMixedContinuousData(List<DataModel>, List<Node>, double[][], int, int) - Static method in class edu.cmu.tetrad.util.MultidataUtils
- combineMixedDiscreteData(List<DataModel>, List<Node>, int[][], int, int) - Static method in class edu.cmu.tetrad.util.MultidataUtils
- combineVariables(List<DataModel>, List<Node>) - Static method in class edu.cmu.tetrad.util.MultidataUtils
-
Combine the list of variables from each of data model in the list into one variable list.
- COMMA - Enum constant in enum class edu.cmu.tetrad.calculator.parser.Token
- COMMA - Enum constant in enum class edu.cmu.tetrad.util.TextTable.Delimiter
- COMMA - Static variable in class edu.cmu.tetrad.data.DelimiterType
- command() - Element in annotation interface edu.cmu.tetrad.annotation.Algorithm
-
Command of the algorithm.
- command() - Element in annotation interface edu.cmu.tetrad.annotation.Score
- command() - Element in annotation interface edu.cmu.tetrad.annotation.TestOfIndependence
- CommonAncestorFalseNegativeBidirected - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- CommonAncestorFalseNegativeBidirected() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.CommonAncestorFalseNegativeBidirected
- CommonAncestorFalsePositiveBidirected - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- CommonAncestorFalsePositiveBidirected() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.CommonAncestorFalsePositiveBidirected
- CommonAncestorTruePositiveBidirected - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- CommonAncestorTruePositiveBidirected() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.CommonAncestorTruePositiveBidirected
- CommonMeasuredAncestorRecallBidirected - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- CommonMeasuredAncestorRecallBidirected() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.CommonMeasuredAncestorRecallBidirected
- compare(ComparisonParameters) - Static method in class edu.cmu.tetrad.study.performance.Comparison
-
Simulates data from model paramerizing the given DAG, and runs the algorithm on that data, printing out error statistics.
- compare(ComparisonParameters) - Static method in class edu.cmu.tetrad.study.performance.Comparison2
-
Simulates data from model parameterizing the given DAG, and runs the algorithm on that data, printing out error statistics.
- CompareExternalAlgorithms - Class in edu.cmu.tetrad.algcomparison.examples
-
An example script to load in data sets and graphs from files and analyze them.
- CompareExternalAlgorithms() - Constructor for class edu.cmu.tetrad.algcomparison.examples.CompareExternalAlgorithms
- compareFromFiles(String, Algorithms, Statistics, Parameters) - Method in class edu.cmu.tetrad.algcomparison.Comparison
- compareFromFiles(String, Algorithms, Statistics, Parameters, long, TimeUnit) - Method in class edu.cmu.tetrad.algcomparison.TimeoutComparison
- compareFromFiles(String, String, Algorithms, Statistics, Parameters) - Method in class edu.cmu.tetrad.algcomparison.Comparison
-
Compares algorithms.
- compareFromFiles(String, String, Algorithms, Statistics, Parameters, long, TimeUnit) - Method in class edu.cmu.tetrad.algcomparison.TimeoutComparison
-
Compares algorithms.
- compareFromSimulations(String, Simulations, Algorithms, Statistics, Parameters) - Method in class edu.cmu.tetrad.algcomparison.Comparison
- compareFromSimulations(String, Simulations, Algorithms, Statistics, Parameters, long, TimeUnit) - Method in class edu.cmu.tetrad.algcomparison.TimeoutComparison
- compareFromSimulations(String, Simulations, String, Algorithms, Statistics, Parameters) - Method in class edu.cmu.tetrad.algcomparison.Comparison
-
Compares algorithms.
- compareFromSimulations(String, Simulations, String, Algorithms, Statistics, Parameters, long, TimeUnit) - Method in class edu.cmu.tetrad.algcomparison.TimeoutComparison
-
Compares algorithms.
- compareTo(ScoredGraph) - Method in class edu.cmu.tetrad.search.score.ScoredGraph
- compareTo(Point) - Method in class edu.cmu.tetrad.util.Point
-
True iff the given object is a point with the same coordinates as this one.
- compareTo(Edge) - Method in class edu.cmu.tetrad.graph.Edge
- compareTo(IndependenceFact) - Method in class edu.cmu.tetrad.graph.IndependenceFact
-
Note that this compareTo method gives a lexical ordering for independence facts and doesn't reflect independence fact equality.
- compareTo(Node) - Method in interface edu.cmu.tetrad.graph.Node
-
Returns the hashcode for this node.
- compareTo(Node) - Method in class edu.cmu.tetrad.session.SessionNode
- compareTo(Object) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.ideker.ItkPredictorSearch.Gene
- compareTo(Object) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.LaggedFactor
-
Determines whether the given lagged factor is temporally prior to this lagged factor.
- CompareTwoGraphs - Class in edu.cmu.tetrad.algcomparison.comparegraphs
- CompareTwoGraphs - Class in edu.cmu.tetrad.algcomparison
-
Gives the comparison of a target graph to a reference graph that is implemented in the interface.
- CompareTwoGraphs() - Constructor for class edu.cmu.tetrad.algcomparison.CompareTwoGraphs
- CompareTwoGraphs(Graph, Graph) - Constructor for class edu.cmu.tetrad.algcomparison.comparegraphs.CompareTwoGraphs
- CompareTwoGraphs.CompareToType - Enum Class in edu.cmu.tetrad.algcomparison.comparegraphs
- CompareTwoGraphs.ComparisonType - Enum Class in edu.cmu.tetrad.algcomparison.comparegraphs
- Comparison - Class in edu.cmu.tetrad.algcomparison
-
Script to do a comparison of a list of algorithms using a list of statistics and a list of parameters and their values.
- Comparison - Class in edu.cmu.tetrad.study.performance
-
Does a comparison of algorithm results across algorithm type, sample sizes, etc.
- Comparison() - Constructor for class edu.cmu.tetrad.algcomparison.Comparison
- Comparison() - Constructor for class edu.cmu.tetrad.study.performance.Comparison
- Comparison.ComparisonGraph - Enum Class in edu.cmu.tetrad.algcomparison
- Comparison.TableColumn - Enum Class in edu.cmu.tetrad.study.performance
- Comparison2 - Class in edu.cmu.tetrad.study.performance
-
Does a comparison of algorithm results across algorithm type, sample sizes, etc.
- Comparison2() - Constructor for class edu.cmu.tetrad.study.performance.Comparison2
- Comparison2.TableColumn - Enum Class in edu.cmu.tetrad.study.performance
- ComparisonParameters - Class in edu.cmu.tetrad.study.performance
-
Created by jdramsey on 3/24/16.
- ComparisonParameters() - Constructor for class edu.cmu.tetrad.study.performance.ComparisonParameters
- ComparisonParameters(ComparisonParameters) - Constructor for class edu.cmu.tetrad.study.performance.ComparisonParameters
- ComparisonParameters.Algorithm - Enum Class in edu.cmu.tetrad.study.performance
- ComparisonParameters.DataType - Enum Class in edu.cmu.tetrad.study.performance
- ComparisonParameters.IndependenceTestType - Enum Class in edu.cmu.tetrad.study.performance
- ComparisonParameters.ResultType - Enum Class in edu.cmu.tetrad.study.performance
- ComparisonResult - Class in edu.cmu.tetrad.study.performance
-
.
- ComparisonResult(ComparisonParameters) - Constructor for class edu.cmu.tetrad.study.performance.ComparisonResult
- ComparisonScript - Class in edu.cmu.tetrad.study.performance
-
Runs algorithm on data set (simulation is OK), printing out error statistics.
- ComparisonScript() - Constructor for class edu.cmu.tetrad.study.performance.ComparisonScript
- compatible(Edge, Edge) - Static method in class edu.cmu.tetrad.graph.GraphUtils
- compileTable() - Method in class edu.cmu.tetrad.study.examples.conditions.Condition1
- compileTable() - Method in class edu.cmu.tetrad.study.examples.conditions.Condition2
- COMPLETE_RULE_SET_USED - Static variable in class edu.cmu.tetrad.util.Params
- completeGraph(Graph) - Static method in class edu.cmu.tetrad.graph.GraphUtils
- composition() - Method in class edu.cmu.tetrad.search.utils.GraphoidAxioms
-
Checks if composition holds--e.g., (X ⊥⊥ Y | Z) ∧ (X ⊥⊥ W |Z) ==> X ⊥⊥ (Y ∪ W) |Z
- compositionalGraphoid() - Method in class edu.cmu.tetrad.search.utils.GraphoidAxioms
-
Checks whether the IM is a compositional graphoid.
- compressedCorrelation(Vector, Vector) - Static method in class edu.cmu.tetrad.util.StatUtils
- compute(boolean) - Method in interface edu.cmu.tetrad.stat.correlation.Covariance
- compute(boolean) - Method in class edu.cmu.tetrad.stat.correlation.CovarianceMatrix
- compute(boolean) - Method in interface edu.cmu.tetrad.stat.correlation.RealCovariance
- compute(boolean) - Method in class edu.cmu.tetrad.stat.correlation.RealCovarianceMatrix
- compute(boolean) - Method in class edu.cmu.tetrad.stat.correlation.RealCovarianceMatrixForkJoin
- compute(boolean) - Method in interface edu.cmu.tetrad.stat.RealVariance
- compute(boolean) - Method in class edu.cmu.tetrad.stat.RealVarianceVector
- compute(boolean) - Method in class edu.cmu.tetrad.stat.RealVarianceVectorForkJoin
- compute(boolean) - Method in interface edu.cmu.tetrad.stat.Variance
- compute(boolean) - Method in class edu.cmu.tetrad.stat.VarianceVector
- compute(boolean) - Method in class edu.cmu.tetrad.stat.VarianceVectorForkJoin
- compute(Matrix, Matrix) - Method in interface jgpml.covariancefunctions.CovarianceFunction
-
Compute covariance matrix of a dataset X
- compute(Matrix, Matrix) - Method in class jgpml.covariancefunctions.CovLINard
-
Compute covariance matrix of a dataset X
- compute(Matrix, Matrix) - Method in class jgpml.covariancefunctions.CovLINone
-
Compute covariance matrix of a dataset X
- compute(Matrix, Matrix) - Method in class jgpml.covariancefunctions.CovNNone
-
Compute covariance matrix of a dataset X
- compute(Matrix, Matrix) - Method in class jgpml.covariancefunctions.CovNNoneNoise
-
Compute covariance matrix of a dataset X
- compute(Matrix, Matrix) - Method in class jgpml.covariancefunctions.CovNoise
-
Compute covariance matrix of a dataset X
- compute(Matrix, Matrix) - Method in class jgpml.covariancefunctions.CovSEard
-
Compute covariance matrix of a dataset X
- compute(Matrix, Matrix) - Method in class jgpml.covariancefunctions.CovSEiso
-
Compute covariance matrix of a dataset X
- compute(Matrix, Matrix) - Method in class jgpml.covariancefunctions.CovSum
-
Compute covariance matrix of a dataset X
- compute(Matrix, Matrix, Matrix) - Method in interface jgpml.covariancefunctions.CovarianceFunction
-
Compute compute test set covariances
- compute(Matrix, Matrix, Matrix) - Method in class jgpml.covariancefunctions.CovLINard
-
Compute compute test set covariances
- compute(Matrix, Matrix, Matrix) - Method in class jgpml.covariancefunctions.CovLINone
-
Compute compute test set covariances
- compute(Matrix, Matrix, Matrix) - Method in class jgpml.covariancefunctions.CovNNone
-
Compute compute test set covariances
- compute(Matrix, Matrix, Matrix) - Method in class jgpml.covariancefunctions.CovNNoneNoise
-
Compute compute test set covariances
- compute(Matrix, Matrix, Matrix) - Method in class jgpml.covariancefunctions.CovNoise
-
Compute compute test set covariances
- compute(Matrix, Matrix, Matrix) - Method in class jgpml.covariancefunctions.CovSEard
-
Compute compute test set covariances
- compute(Matrix, Matrix, Matrix) - Method in class jgpml.covariancefunctions.CovSEiso
-
Compute compute test set covariances
- compute(Matrix, Matrix, Matrix) - Method in class jgpml.covariancefunctions.CovSum
-
Compute compute test set covariances
- computeDerivatives(Matrix, Matrix, int) - Method in interface jgpml.covariancefunctions.CovarianceFunction
-
Coompute the derivatives of this
CovarianceFunctionwith respect to the hyperparameter with indexidx - computeDerivatives(Matrix, Matrix, int) - Method in class jgpml.covariancefunctions.CovLINard
-
Coompute the derivatives of this
CovarianceFunctionwith respect to the hyperparameter with indexidx - computeDerivatives(Matrix, Matrix, int) - Method in class jgpml.covariancefunctions.CovLINone
-
Coompute the derivatives of this
CovarianceFunctionwith respect to the hyperparameter with indexidx - computeDerivatives(Matrix, Matrix, int) - Method in class jgpml.covariancefunctions.CovNNone
-
Coompute the derivatives of this
CovarianceFunctionwith respect to the hyperparameter with indexidx - computeDerivatives(Matrix, Matrix, int) - Method in class jgpml.covariancefunctions.CovNNoneNoise
-
Coompute the derivatives of this
CovarianceFunctionwith respect to the hyperparameter with indexidx - computeDerivatives(Matrix, Matrix, int) - Method in class jgpml.covariancefunctions.CovNoise
-
Coompute the derivatives of this
CovarianceFunctionwith respect to the hyperparameter with indexidx - computeDerivatives(Matrix, Matrix, int) - Method in class jgpml.covariancefunctions.CovSEard
-
Coompute the derivatives of this
CovarianceFunctionwith respect to the hyperparameter with indexidx - computeDerivatives(Matrix, Matrix, int) - Method in class jgpml.covariancefunctions.CovSEiso
-
Coompute the derivatives of this
CovarianceFunctionwith respect to the hyperparameter with indexidx - computeDerivatives(Matrix, Matrix, int) - Method in class jgpml.covariancefunctions.CovSum
-
Coompute the derivatives of this
CovarianceFunctionwith respect to the hyperparameter with indexidx - computeLowerTriangle(boolean) - Method in interface edu.cmu.tetrad.stat.correlation.Covariance
- computeLowerTriangle(boolean) - Method in class edu.cmu.tetrad.stat.correlation.CovarianceMatrix
- computeLowerTriangle(boolean) - Method in interface edu.cmu.tetrad.stat.correlation.RealCovariance
- computeLowerTriangle(boolean) - Method in class edu.cmu.tetrad.stat.correlation.RealCovarianceMatrix
- computeLowerTriangle(boolean) - Method in class edu.cmu.tetrad.stat.correlation.RealCovarianceMatrixForkJoin
- computeStdErrors(ISemIm) - Method in class edu.cmu.tetrad.sem.SemStdErrorEstimator
-
This method computes the information matrix or Hessian matrix of second order partial derivatives of the fitting function (4B_2 on page 135 of Bollen) with respect to the free freeParameters of the estimated SEM.
- concatenate(double[][]) - Static method in class edu.cmu.tetrad.util.MatrixUtils
-
Concatenates the vectors rows[i], i = 0...rows.length, into a single vector.
- concatenate(DataSet...) - Static method in class edu.cmu.tetrad.data.DataTransforms
- concatenate(DataSet, DataSet) - Static method in class edu.cmu.tetrad.data.DataTransforms
- concatenate(Matrix...) - Static method in class edu.cmu.tetrad.data.DataTransforms
- concatenate(List<DataSet>) - Static method in class edu.cmu.tetrad.data.DataTransforms
- ConcurrencyUtils - Class in edu.cmu.tetrad.util
- ConcurrencyUtils() - Constructor for class edu.cmu.tetrad.util.ConcurrencyUtils
- CONCURRENT_FAS - Static variable in class edu.cmu.tetrad.util.Params
- Condition1 - Class in edu.cmu.tetrad.study.examples.conditions
-
An example script to load in data sets and graphs from files and analyze them.
- Condition1() - Constructor for class edu.cmu.tetrad.study.examples.conditions.Condition1
- Condition2 - Class in edu.cmu.tetrad.study.examples.conditions
-
An example script to load in data sets and graphs from files and analyze them.
- Condition2() - Constructor for class edu.cmu.tetrad.study.examples.conditions.Condition2
- CONDITIONAL_GAUSSIAN - Static variable in class edu.cmu.tetrad.algcomparison.simulation.SimulationTypes
- ConditionalCorrelationIndependence - Class in edu.cmu.tetrad.search.test
-
Checks conditional independence of variable in a continuous data set using Daudin's method.
- ConditionalCorrelationIndependence(DataSet) - Constructor for class edu.cmu.tetrad.search.test.ConditionalCorrelationIndependence
-
Constructs a new Independence test which checks independence facts based on the correlation data implied by the given data set (must be continuous).
- ConditionalCorrelationIndependence.Basis - Enum Class in edu.cmu.tetrad.search.test
-
Gives a choice of basis functions to use for judgments of independence for conditional correlation independence.
- ConditionalCorrelationIndependence.Kernel - Enum Class in edu.cmu.tetrad.search.test
-
Gives a choice of kernels to use for the independence judgments for conditional correlation independence.
- ConditionalGaussianBicScore - Class in edu.cmu.tetrad.algcomparison.score
-
Wrapper for Fisher Z test.
- ConditionalGaussianBicScore() - Constructor for class edu.cmu.tetrad.algcomparison.score.ConditionalGaussianBicScore
- ConditionalGaussianLikelihood - Class in edu.cmu.tetrad.search.score
-
Implements a conditional Gaussian likelihood.
- ConditionalGaussianLikelihood(DataSet) - Constructor for class edu.cmu.tetrad.search.score.ConditionalGaussianLikelihood
-
Constructs the score using a covariance matrix.
- ConditionalGaussianLikelihood.Ret - Class in edu.cmu.tetrad.search.score
-
Gives return value for a conditional Gaussain likelihood, returning a likelihood value and the degrees of freedom for it.
- ConditionalGaussianLRT - Class in edu.cmu.tetrad.algcomparison.independence
-
Wrapper for Fisher Z test.
- ConditionalGaussianLRT() - Constructor for class edu.cmu.tetrad.algcomparison.independence.ConditionalGaussianLRT
- ConditionalGaussianScore - Class in edu.cmu.tetrad.search.score
-
Implements a conditional Gaussian BIC score for FGS, which calculates a BIC score for mixed discrete/Gaussian data using the conditional Gaussian likelihood function (see).
- ConditionalGaussianScore(DataSet, double, boolean) - Constructor for class edu.cmu.tetrad.search.score.ConditionalGaussianScore
-
Constructs the score using a covariance matrix.
- ConditionalGaussianSimulation - Class in edu.cmu.tetrad.algcomparison.simulation
-
A simulation method based on the conditional Gaussian assumption.
- ConditionalGaussianSimulation(RandomGraph) - Constructor for class edu.cmu.tetrad.algcomparison.simulation.ConditionalGaussianSimulation
- config(String) - Method in class edu.cmu.tetrad.util.LogUtils
- configuration(String) - Method in class edu.cmu.tetrad.algcomparison.Comparison
- configuration(String) - Method in class edu.cmu.tetrad.algcomparison.TimeoutComparison
- configurationActived(TetradLoggerEvent) - Method in interface edu.cmu.tetrad.util.TetradLoggerListener
-
Invoked whenever a logger configuration is set on the
TetradLoggerand the logger is active (i.e., logging isn't turned off etc). - configurationDeactived(TetradLoggerEvent) - Method in interface edu.cmu.tetrad.util.TetradLoggerListener
-
Invoked whenever a previously set logger config is resert or set to null and the logger is active (i.e., logging isn't turned off etc).
- CONFLICT_RULE - Static variable in class edu.cmu.tetrad.util.Params
- CONNECTED - Static variable in class edu.cmu.tetrad.util.Params
- CONNECTED_DAG - Static variable in class edu.cmu.tetrad.graph.RandomGraph.UniformGraphGenerator
- connectedComponents() - Method in class edu.cmu.tetrad.graph.Paths
- ConnectionFunction - Interface in edu.cmu.tetrad.sem
-
Created by IntelliJ IDEA.
- CONSERVATIVE - Enum constant in enum class edu.cmu.tetrad.search.utils.PcCommon.ColliderDiscovery
- CONSTANT - Static variable in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.LagGraphParams
- CONSTANT - Static variable in class edu.cmu.tetrad.study.gene.tetrad.gene.history.SimpleRandomizer
-
Indicates constant indegree.
- ConstantExpression - Class in edu.cmu.tetrad.calculator.expression
-
Represents a constant expression, that is an expression that always evaluates to the same value.
- ConstantExpression(double) - Constructor for class edu.cmu.tetrad.calculator.expression.ConstantExpression
-
Constructs the constant expression given the value to use.
- constructCentralizedGramMatrix(List<Kernel>, DataSet, List<Node>) - Static method in class edu.cmu.tetrad.search.utils.KernelUtils
-
Constructs the centralized Gram matrix for a given vector valued sample.
- constructGramMatrix(List<Kernel>, DataSet, List<Node>) - Static method in class edu.cmu.tetrad.search.utils.KernelUtils
-
Constructs Gram matrix for a given vector valued sample.
- constructH(int) - Static method in class edu.cmu.tetrad.search.utils.KernelUtils
-
Constructs the projection matrix on 1/m
- contains(GraphChange) - Method in class edu.cmu.tetrad.search.work_in_progress.GraphChange
-
Contains is defined such that if the internal strucs of this GraphChange all individually contain the elements in the corresponding strucs of GraphChange gc, then this "contains" gc.
- contains(SessionNode) - Method in class edu.cmu.tetrad.session.Session
- containsBidirectedEdge(Graph) - Static method in class edu.cmu.tetrad.graph.GraphUtils
- containsChild(SessionNode) - Method in class edu.cmu.tetrad.session.SessionNode
- containsEdge(KnowledgeEdge) - Method in class edu.cmu.tetrad.data.KnowledgeGroup
- containsEdge(Edge) - Method in class edu.cmu.tetrad.graph.Dag
- containsEdge(Edge) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
-
Determines if the graph contains a particular edge.
- containsEdge(Edge) - Method in interface edu.cmu.tetrad.graph.Graph
-
Determines whether this graph contains the given edge.
- containsEdge(Edge) - Method in class edu.cmu.tetrad.graph.LagGraph
- containsEdge(Edge) - Method in class edu.cmu.tetrad.graph.SemGraph
- containsEdge(Edge) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- containsEmptyData() - Method in class edu.cmu.tetrad.data.DataModelList
-
Use this to check if the dataModelList only contains the default empty dataset that is being used to populat the empty spreadsheet - Added by Kevin
- containsLatent(Node) - Method in class edu.cmu.tetrad.search.work_in_progress.DMSearch.LatentStructure
- containsMissingValue(DataSet) - Static method in class edu.cmu.tetrad.data.DataUtils
- containsMissingValue(Matrix) - Static method in class edu.cmu.tetrad.data.DataUtils
- containsNode(Node) - Method in class edu.cmu.tetrad.graph.Dag
- containsNode(Node) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
-
Determines whether the graph contains a particular node.
- containsNode(Node) - Method in interface edu.cmu.tetrad.graph.Graph
-
Determines whether this graph contains the given node.
- containsNode(Node) - Method in class edu.cmu.tetrad.graph.LagGraph
- containsNode(Node) - Method in class edu.cmu.tetrad.graph.SemGraph
- containsNode(Node) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- containsParameter(Edge) - Method in class edu.cmu.tetrad.sem.StandardizedSemIm
- Context - Interface in edu.cmu.tetrad.calculator.expression
-
Looks up the value of a variable.
- Continuous - Enum constant in enum class edu.cmu.tetrad.data.DataType
- Continuous - Enum constant in enum class edu.cmu.tetrad.study.performance.ComparisonParameters.DataType
- ContinuousDiscretizationSpec - Class in edu.cmu.tetrad.data
-
Specifies how a column (continuous or discrete) should be discretized.
- ContinuousDiscretizationSpec(double[], List<String>) - Constructor for class edu.cmu.tetrad.data.ContinuousDiscretizationSpec
- ContinuousDiscretizationSpec(double[], List<String>, int) - Constructor for class edu.cmu.tetrad.data.ContinuousDiscretizationSpec
- ContinuousVariable - Class in edu.cmu.tetrad.data
-
Represents a real-valued variable.
- ContinuousVariable(ContinuousVariable) - Constructor for class edu.cmu.tetrad.data.ContinuousVariable
-
Copy constructor.
- ContinuousVariable(String) - Constructor for class edu.cmu.tetrad.data.ContinuousVariable
-
Constructs a new continuous variable with the given name.
- contraction() - Method in class edu.cmu.tetrad.search.utils.GraphoidAxioms
-
Checks if contraction holds--e.g., (X ⊥⊥ Y |Z) ∧ (X ⊥⊥ W |Z ∪ Y) ==> X ⊥⊥ (Y ∪ W) |Z
- convert() - Method in class edu.cmu.tetrad.search.utils.DagToPag
-
This method does the convertion of DAG to PAG.
- convert() - Method in class edu.cmu.tetrad.search.utils.TsDagToPag
- convert(String) - Static method in class edu.cmu.tetrad.graph.GraphUtils
-
Converts a string spec of a graph--for example, "X1-->X2, X1---X3, X2o->X4, X3<->X4" to a Graph.
- convertCovToCorr(Matrix) - Static method in class edu.cmu.tetrad.util.MatrixUtils
-
Converts a covariance matrix to a correlation matrix in place; the same matrix is returned for convenience, but m is modified in the process.
- convertListToInt(List<List<Node>>, List<Node>) - Static method in class edu.cmu.tetrad.search.utils.ClusterUtils
- convertLowerTriangleToSymmetric(double[][]) - Static method in class edu.cmu.tetrad.util.MatrixUtils
-
Converts a matrix in lower triangular form to a symmetric matrix in square form.
- convertNodes(Set<Edge>, List<Node>) - Static method in class edu.cmu.tetrad.graph.MisclassificationUtils
- convertNumericalDiscreteToContinuous(DataSet) - Static method in class edu.cmu.tetrad.data.DataTransforms
- convertSearchGraph(SemGraph) - Static method in class edu.cmu.tetrad.search.utils.Purify
- convertSearchGraph(List<int[]>, String[]) - Static method in class edu.cmu.tetrad.search.utils.ClusterUtils
- convertToClusters(Graph) - Static method in class edu.cmu.tetrad.search.utils.MimUtils
- convertToClusters(Graph, List<Node>) - Static method in class edu.cmu.tetrad.search.utils.MimUtils
-
Converts a disconnected multiple indicator model into a set of clusters.
- convertToClusters2(Graph) - Static method in class edu.cmu.tetrad.search.utils.MimUtils
- convertToXml(Graph) - Static method in class edu.cmu.tetrad.graph.GraphSaveLoadUtils
- ConvexProximal - Class in edu.pitt.csb.mgm
-
This interface should be used for non-differentiable convex functions that are decomposable such that f(x) = g(x) + h(x) where g(x) is a differentiable convex function (i.e.
- ConvexProximal() - Constructor for class edu.pitt.csb.mgm.ConvexProximal
- copy() - Method in class edu.cmu.tetrad.data.BoxDataSet
- copy() - Method in class edu.cmu.tetrad.data.ByteDataBox
- copy() - Method in class edu.cmu.tetrad.data.CorrelationMatrixOnTheFly
- copy() - Method in class edu.cmu.tetrad.data.CovarianceMatrix
- copy() - Method in class edu.cmu.tetrad.data.CovarianceMatrixOnTheFly
- copy() - Method in interface edu.cmu.tetrad.data.DataBox
- copy() - Method in interface edu.cmu.tetrad.data.DataModel
- copy() - Method in class edu.cmu.tetrad.data.DataModelList
- copy() - Method in interface edu.cmu.tetrad.data.DataSet
- copy() - Method in class edu.cmu.tetrad.data.DoubleDataBox
- copy() - Method in class edu.cmu.tetrad.data.FloatDataBox
- copy() - Method in class edu.cmu.tetrad.data.IndependenceFacts
- copy() - Method in class edu.cmu.tetrad.data.IntDataBox
- copy() - Method in class edu.cmu.tetrad.data.Knowledge
-
Makes a shallow copy.
- copy() - Method in class edu.cmu.tetrad.data.LongDataBox
- copy() - Method in class edu.cmu.tetrad.data.MixedDataBox
- copy() - Method in class edu.cmu.tetrad.data.NumberObjectDataSet
- copy() - Method in class edu.cmu.tetrad.data.ShortDataBox
- copy() - Method in class edu.cmu.tetrad.data.TimeSeriesData
- copy() - Method in class edu.cmu.tetrad.data.VerticalDoubleDataBox
- copy() - Method in class edu.cmu.tetrad.data.VerticalIntDataBox
- copy() - Method in class edu.cmu.tetrad.util.DefaultTetradLoggerConfig
- copy() - Method in class edu.cmu.tetrad.util.Matrix
- copy() - Method in class edu.cmu.tetrad.util.Matrix2
- copy() - Method in class edu.cmu.tetrad.util.TetradLogger.EmptyConfig
- copy() - Method in interface edu.cmu.tetrad.util.TetradLoggerConfig
- copy() - Method in class edu.cmu.tetrad.util.Vector
- copy() - Method in class edu.pitt.csb.stability.DataGraphSearch
- copy() - Method in class edu.pitt.csb.stability.SearchWrappers.FgesWrapper
- copy() - Method in class edu.pitt.csb.stability.SearchWrappers.MGMWrapper
- copy() - Method in class edu.pitt.csb.stability.SearchWrappers.PcStableWrapper
- copyColumn(Node, DataSet, DataSet) - Static method in class edu.cmu.tetrad.data.DataTransforms
- copyOf(double[][]) - Static method in class edu.cmu.tetrad.util.MatrixUtils
- copyOf(int[], int) - Static method in class edu.cmu.tetrad.util.MatrixUtils
- corr(Node, Node, List<Node>) - Method in class edu.cmu.tetrad.search.utils.PartialCorrelation
-
Calculates the partial correlation of x and y conditional on the nodes in z recursively.
- correctnessRatio(int[][]) - Static method in class edu.cmu.tetrad.simulation.HsimUtils
- CorrectSkeleton - Class in edu.cmu.tetrad.algcomparison.statistic
-
Outputs 1 if the skeleton is correct, 0 if not..
- CorrectSkeleton() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.CorrectSkeleton
- correctSkewness(double[], double) - Static method in class edu.cmu.tetrad.search.Fask
- correlation(double[], double[]) - Static method in class edu.cmu.tetrad.util.StatUtils
- correlation(double[], double[], int) - Static method in class edu.cmu.tetrad.util.StatUtils
- correlation(long[], long[]) - Static method in class edu.cmu.tetrad.util.StatUtils
- correlation(long[], long[], int) - Static method in class edu.cmu.tetrad.util.StatUtils
- correlation(Vector, Vector) - Static method in class edu.cmu.tetrad.util.StatUtils
- CorrelationMatrix - Class in edu.cmu.tetrad.data
-
Stores a correlation matrix together with variable names and sample size; intended as a representation of a data set.
- CorrelationMatrix(DataSet) - Constructor for class edu.cmu.tetrad.data.CorrelationMatrix
-
Constructs a new correlation matrix from the the given DataSet.
- CorrelationMatrix(ICovarianceMatrix) - Constructor for class edu.cmu.tetrad.data.CorrelationMatrix
-
Constructs a new correlation matrix using the covariances in the given covariance matrix.
- CorrelationMatrix(List<Node>, Matrix, int) - Constructor for class edu.cmu.tetrad.data.CorrelationMatrix
-
Constructs a correlation matrix data set using the given information.
- CorrelationMatrixOnTheFly - Class in edu.cmu.tetrad.data
-
Stores a covariance matrix together with variable names and sample size, intended as a representation of a data set.
- CorrelationMatrixOnTheFly(ICovarianceMatrix) - Constructor for class edu.cmu.tetrad.data.CorrelationMatrixOnTheFly
-
Constructs a new covariance matrix from the given data set.
- Cosine - Enum constant in enum class edu.cmu.tetrad.search.test.ConditionalCorrelationIndependence.Basis
- CouldNotCreateModelException - Exception in edu.cmu.tetrad.session
-
Indicates that a model could not be created.
- CouldNotCreateModelException(Class) - Constructor for exception edu.cmu.tetrad.session.CouldNotCreateModelException
- count(int[], AdTreeHelper.CountNode) - Method in class edu.pitt.isp.sverchkov.data.AdTree
-
Constructs an AD tree helper for the given data set.
- count(Map<A, V>) - Method in class edu.pitt.isp.sverchkov.data.AdTree
-
Returns the number of rows in the data set.
- countAdjErrors(Graph, Graph) - Static method in class edu.cmu.tetrad.graph.GraphUtils
-
Counts the adjacencies that are in graph1 but not in graph2.
- countArrowptErrors(Graph, Graph) - Static method in class edu.cmu.tetrad.graph.GraphUtils
-
Counts the arrowheads that are in graph1 but not in graph2.
- countColumn(File, char) - Static method in class edu.cmu.tetrad.util.DataUtility
- countLine(File) - Static method in class edu.cmu.tetrad.util.DataUtility
- counts(A, Map<A, V>) - Method in class edu.pitt.isp.sverchkov.data.AdTree
-
Returns the number of rows in the data set.
- cov(double[], double[], double[], double, double) - Static method in class edu.cmu.tetrad.util.StatUtils
- cov(Matrix) - Static method in class edu.cmu.tetrad.data.DataUtils
- COV_HIGH - Static variable in class edu.cmu.tetrad.util.Params
- COV_LOW - Static variable in class edu.cmu.tetrad.util.Params
- COV_SYMMETRIC - Static variable in class edu.cmu.tetrad.util.Params
- COVAR - Static variable in class edu.cmu.tetrad.sem.ParamType
-
A covariance parameter.
- covariance(double[], double[]) - Static method in class edu.cmu.tetrad.util.StatUtils
- covariance(double[], double[], int) - Static method in class edu.cmu.tetrad.util.StatUtils
- covariance(int, int) - Method in interface edu.cmu.tetrad.data.Covariances
-
Returns the covariance at (i, j).
- covariance(int, int) - Method in class edu.cmu.tetrad.data.CovariancesDoubleForkJoin
- covariance(long[], long[]) - Static method in class edu.cmu.tetrad.util.StatUtils
- covariance(long[], long[], int) - Static method in class edu.cmu.tetrad.util.StatUtils
- Covariance - Enum constant in enum class edu.cmu.tetrad.data.DataType
- Covariance - Interface in edu.cmu.tetrad.stat.correlation
-
Interface for computing covariances.
- CovarianceFunction - Interface in jgpml.covariancefunctions
- CovarianceMatrix - Class in edu.cmu.tetrad.data
-
Stores a covariance matrix together with variable names and sample size, intended as a representation of a data set.
- CovarianceMatrix - Class in edu.cmu.tetrad.stat.correlation
-
Jan 25, 2016 2:13:26 PM
- CovarianceMatrix(float[][]) - Constructor for class edu.cmu.tetrad.stat.correlation.CovarianceMatrix
- CovarianceMatrix(CovarianceMatrix) - Constructor for class edu.cmu.tetrad.data.CovarianceMatrix
-
Copy constructor.
- CovarianceMatrix(DataSet) - Constructor for class edu.cmu.tetrad.data.CovarianceMatrix
-
Constructs a new covariance matrix from the given data set.
- CovarianceMatrix(DataSet, boolean) - Constructor for class edu.cmu.tetrad.data.CovarianceMatrix
- CovarianceMatrix(ICovarianceMatrix) - Constructor for class edu.cmu.tetrad.data.CovarianceMatrix
- CovarianceMatrix(List<Node>, double[][], int) - Constructor for class edu.cmu.tetrad.data.CovarianceMatrix
- CovarianceMatrix(List<Node>, Matrix, int) - Constructor for class edu.cmu.tetrad.data.CovarianceMatrix
-
Protected constructor to construct a new covariance matrix using the supplied continuous variables and the the given symmetric, positive definite matrix and sample size.
- CovarianceMatrixOnTheFly - Class in edu.cmu.tetrad.data
-
Stores a covariance matrix together with variable names and sample size, intended as a representation of a data set.
- CovarianceMatrixOnTheFly(DataSet) - Constructor for class edu.cmu.tetrad.data.CovarianceMatrixOnTheFly
-
Constructs a new covariance matrix from the given data set.
- CovarianceMatrixOnTheFly(DataSet, boolean) - Constructor for class edu.cmu.tetrad.data.CovarianceMatrixOnTheFly
- covarianceNonparanormalDrton(DataSet) - Static method in class edu.cmu.tetrad.data.DataTransforms
- Covariances - Interface in edu.cmu.tetrad.data
-
Some comemon methods for the various covariance implementations.
- CovariancesDoubleForkJoin - Class in edu.cmu.tetrad.data
-
Computes covariances using the standard calculation.
- CovariancesDoubleForkJoin(double[][], boolean) - Constructor for class edu.cmu.tetrad.data.CovariancesDoubleForkJoin
- covered(SortedSet<ItkPredictorSearch.Gene>, SortedSet<ItkPredictorSearch.Gene>) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.ideker.ItkPredictorSearch
- coveredEdge(Node, Node) - Method in class edu.cmu.tetrad.search.utils.TeyssierScorer
-
Returns true iff x->y or y->x is a covered edge.
- CovLINard - Class in jgpml.covariancefunctions
-
Linear covariance function with Automatic Relevance Determination (ARD).
- CovLINard(int) - Constructor for class jgpml.covariancefunctions.CovLINard
-
Creates a new
CovSEard CovarianceFunction - CovLINone - Class in jgpml.covariancefunctions
-
Linear covariance function with a single hyperparameter.
- CovLINone() - Constructor for class jgpml.covariancefunctions.CovLINone
- covMatrix(double[], double[], double[][], double[], double, double) - Static method in class edu.cmu.tetrad.util.StatUtils
- CovNNone - Class in jgpml.covariancefunctions
-
Neural network covariance function with a single parameter for the distance measure.
- CovNNone() - Constructor for class jgpml.covariancefunctions.CovNNone
- CovNNoneNoise - Class in jgpml.covariancefunctions
-
Neural network covariance function with a single parameter for the distance measure and white noise.
- CovNNoneNoise() - Constructor for class jgpml.covariancefunctions.CovNNoneNoise
- CovNoise - Class in jgpml.covariancefunctions
-
Independent covariance function, ie "white noise", with specified variance.
- CovNoise() - Constructor for class jgpml.covariancefunctions.CovNoise
-
Creates a new
CovNoise CovarianceFunction - CovSEard - Class in jgpml.covariancefunctions
-
Squared Exponential covariance function with Automatic Relevance Detemination (ARD) distance measure.
- CovSEard(int) - Constructor for class jgpml.covariancefunctions.CovSEard
-
Creates a new
CovSEard CovarianceFunction - CovSEiso - Class in jgpml.covariancefunctions
-
Squared Exponential covariance function with isotropic distance measure.
- CovSEiso() - Constructor for class jgpml.covariancefunctions.CovSEiso
- CovSum - Class in jgpml.covariancefunctions
-
Composes a covariance function as the sum of other covariance functions.
- CovSum(int, CovarianceFunction...) - Constructor for class jgpml.covariancefunctions.CovSum
-
Create a new
CovarianceFunctionas sum of theCovarianceFunctions passed as input. - Cpc - Class in edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag
-
Conservative PC (CPC).
- Cpc - Class in edu.cmu.tetrad.search
-
Implements a convervative version of PC, in which the Markov condition is assumed but faithfulness is tested locally.
- Cpc() - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Cpc
- Cpc(IndependenceWrapper) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Cpc
- Cpc(IndependenceTest) - Constructor for class edu.cmu.tetrad.search.Cpc
-
Constructs a CPC algorithm that uses the given independence test as oracle.
- CPC - Enum constant in enum class edu.cmu.tetrad.study.performance.ComparisonParameters.Algorithm
- CPDAG - Enum constant in enum class edu.cmu.tetrad.algcomparison.comparegraphs.CompareTwoGraphs.CompareToType
- CPDAG - Enum constant in enum class edu.cmu.tetrad.study.performance.ComparisonParameters.ResultType
- CPDAG - Static variable in class edu.cmu.tetrad.util.Params
- CPDAG_of_the_true_DAG - Enum constant in enum class edu.cmu.tetrad.algcomparison.Comparison.ComparisonGraph
- CPDAG_of_the_true_DAG - Enum constant in enum class edu.cmu.tetrad.algcomparison.TimeoutComparison.ComparisonGraph
- cpdagForDag(Graph) - Static method in class edu.cmu.tetrad.graph.GraphTransforms
- CptInvariantMarginalCalculator - Class in edu.cmu.tetrad.bayes
-
Calculates marginals of the form P(V=v') for an updated Bayes net for purposes of the CPT Invariant Updater.
- CptInvariantMarginalCalculator(BayesIm, Evidence) - Constructor for class edu.cmu.tetrad.bayes.CptInvariantMarginalCalculator
-
Constructs a new marginal calculator for the given updated Bayes IM.
- CptInvariantUpdater - Class in edu.cmu.tetrad.bayes
-
Calculates updated probabilities for variables conditional on their parents as well as single-variable updated marginals for a Bayes IM using an algorithm that restricts expensive updating summations only to conditional probabilities of variables with respect to their parents that change from non-updated to updated values.
- CptInvariantUpdater(BayesIm) - Constructor for class edu.cmu.tetrad.bayes.CptInvariantUpdater
- CptInvariantUpdater(BayesIm, Evidence) - Constructor for class edu.cmu.tetrad.bayes.CptInvariantUpdater
-
Constructs a new updater for the given Bayes net.
- CPU - Enum constant in enum class edu.cmu.tetrad.util.MillisecondTimes.Type
- cpuTimeMillis() - Static method in class edu.cmu.tetrad.util.MillisecondTimes
- create(Class<? extends Algorithm>, IndependenceWrapper, ScoreWrapper) - Static method in class edu.cmu.tetrad.algcomparison.algorithm.AlgorithmFactory
-
Creates an algorithm.
- create(Class<? extends Algorithm>, IndependenceWrapper, ScoreWrapper, Graph) - Static method in class edu.cmu.tetrad.algcomparison.algorithm.AlgorithmFactory
-
Creates an algorithm.
- create(Class<? extends Algorithm>, Class<? extends IndependenceWrapper>, Class<? extends ScoreWrapper>) - Static method in class edu.cmu.tetrad.algcomparison.algorithm.AlgorithmFactory
-
Creates an algorithm.
- create(Class<? extends Algorithm>, Class<? extends IndependenceWrapper>, Class<? extends ScoreWrapper>, Graph) - Static method in class edu.cmu.tetrad.algcomparison.algorithm.AlgorithmFactory
-
Creates an algorithm.
- create(String, RandomGraph) - Static method in class edu.cmu.tetrad.algcomparison.simulation.SimulationUtils
- create(List<String>) - Static method in class edu.cmu.tetrad.util.ParameterUtils
-
Create parameters with their default values.
- createCellTable(BayesIm) - Static method in class edu.cmu.tetrad.bayes.StoredCellProbs
- createCellTable(MlBayesIm) - Method in class edu.cmu.tetrad.bayes.StoredCellProbsObs
- createCellTable(MlBayesImObs) - Method in class edu.cmu.tetrad.bayes.StoredCellProbsObs
- createContinuousVariables(String[]) - Static method in class edu.cmu.tetrad.data.DataUtils
- createData(Parameters, boolean) - Method in class edu.cmu.tetrad.algcomparison.simulation.BayesNetSimulation
-
Creates the data.
- createData(Parameters, boolean) - Method in class edu.cmu.tetrad.algcomparison.simulation.BooleanGlassSimulation
- createData(Parameters, boolean) - Method in class edu.cmu.tetrad.algcomparison.simulation.ConditionalGaussianSimulation
- createData(Parameters, boolean) - Method in class edu.cmu.tetrad.algcomparison.simulation.GeneralSemSimulation
- createData(Parameters, boolean) - Method in class edu.cmu.tetrad.algcomparison.simulation.GeneralSemSimulationSpecial1
- createData(Parameters, boolean) - Method in class edu.cmu.tetrad.algcomparison.simulation.LeeHastieSimulation
- createData(Parameters, boolean) - Method in class edu.cmu.tetrad.algcomparison.simulation.LinearFisherModel
- createData(Parameters, boolean) - Method in class edu.cmu.tetrad.algcomparison.simulation.LinearSineSimulation
- createData(Parameters, boolean) - Method in class edu.cmu.tetrad.algcomparison.simulation.NLSemSimulation
- createData(Parameters, boolean) - Method in class edu.cmu.tetrad.algcomparison.simulation.SemSimulation
- createData(Parameters, boolean) - Method in class edu.cmu.tetrad.algcomparison.simulation.SemThenDiscretize
- createData(Parameters, boolean) - Method in interface edu.cmu.tetrad.algcomparison.simulation.Simulation
-
Creates a data set and simulates data.
- createData(Parameters, boolean) - Method in class edu.cmu.tetrad.algcomparison.simulation.StandardizedSemSimulation
- createData(Parameters, boolean) - Method in class edu.cmu.tetrad.algcomparison.simulation.TimeSeriesSemSimulation
- createData(Parameters, boolean) - Method in class edu.cmu.tetrad.data.simulation.LoadContinuousDataAndGraphs
- createData(Parameters, boolean) - Method in class edu.cmu.tetrad.data.simulation.LoadContinuousDataAndSingleGraph
- createData(Parameters, boolean) - Method in class edu.cmu.tetrad.data.simulation.LoadContinuousDataSmithSim
- createData(Parameters, boolean) - Method in class edu.cmu.tetrad.data.simulation.LoadDataAndGraphs
- createData(Parameters, boolean) - Method in class edu.cmu.tetrad.data.simulation.LoadDataFromFileWithoutGraph
- createDescendantModels(SessionNode, boolean) - Method in class edu.cmu.tetrad.session.SimulationStudy
- createDisplayGraph(Graph, ResamplingEdgeEnsemble) - Static method in class edu.cmu.tetrad.util.GraphSampling
-
Create a graph for displaying and print out.
- createExpression(Expression...) - Method in interface edu.cmu.tetrad.calculator.expression.ExpressionDescriptor
-
Creates the actual expression that can be used to evaluate matters from the given expressions.
- createGraph(Parameters) - Method in class edu.cmu.tetrad.algcomparison.graph.Cyclic
- createGraph(Parameters) - Method in class edu.cmu.tetrad.algcomparison.graph.ErdosRenyi
- createGraph(Parameters) - Method in class edu.cmu.tetrad.algcomparison.graph.RandomForward
- createGraph(Parameters) - Method in interface edu.cmu.tetrad.algcomparison.graph.RandomGraph
- createGraph(Parameters) - Method in class edu.cmu.tetrad.algcomparison.graph.RandomSingleFactorMim
- createGraph(Parameters) - Method in class edu.cmu.tetrad.algcomparison.graph.RandomTwoFactorMim
- createGraph(Parameters) - Method in class edu.cmu.tetrad.algcomparison.graph.ScaleFree
- createGraph(Parameters) - Method in class edu.cmu.tetrad.algcomparison.graph.SingleGraph
- createGraphWithHighProbabilityEdges(List<Graph>) - Static method in class edu.cmu.tetrad.util.GraphSampling
-
Combine all the edges from the list of graphs onto one graph with the edge type that has the highest frequency probability.
- createGraphWithHighProbabilityEdges(List<Graph>, ResamplingEdgeEnsemble) - Static method in class edu.cmu.tetrad.util.GraphSampling
- createGraphWithoutNullEdges(Graph) - Static method in class edu.cmu.tetrad.util.GraphSampling
-
Create a graph from the given graph that contains no null edges.
- createLagData(DataSet, int) - Static method in class edu.cmu.tetrad.search.utils.TsUtils
-
Creates new time series dataset from the given one (fixed to deal with mixed datasets)
- createModel(boolean) - Method in class edu.cmu.tetrad.session.SessionNode
-
Creates a model, provided the class of the model can be uniquely determined without any further hints.
- createModel(Class, boolean) - Method in class edu.cmu.tetrad.session.SessionNode
-
Creates a model of the given class using models of the parent SessionNodes as constructor arguments.
- createRandomCellTable() - Method in class edu.cmu.tetrad.bayes.MlBayesImObs
- createRandomCellTable(List<Node>) - Static method in class edu.cmu.tetrad.bayes.StoredCellProbs
- createShiftedData(DataSet, int[]) - Static method in class edu.cmu.tetrad.search.utils.TsUtils
- crossTab(int, int, int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.reveal.RevealEvaluator
-
This method computes the cross tablulation (table) of values of a gene and its possible parent.
- crossTab(int, int, int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.RevealEvaluator
-
This method computes the cross tablulation (table) of values of a gene and its possible parent.
- crossTabulation() - Method in class edu.cmu.tetrad.classify.ClassifierBayesUpdaterDiscrete
-
Computes the "confusion matrix" of coefs of the number of cases associated with each combination of estimated and observed values in the test dataset.
- crossTabulation() - Method in interface edu.cmu.tetrad.classify.ClassifierDiscrete
- crossTabulation() - Method in class edu.cmu.tetrad.classify.ClassifierMbDiscrete
- cStar(LinkedList<LinkedList<Cstar.Record>>) - Static method in class edu.cmu.tetrad.search.Cstar
-
Returns a list of records for making a CSTaR table.
- Cstar - Class in edu.cmu.tetrad.algcomparison.algorithm.oracle.pattern
- Cstar - Class in edu.cmu.tetrad.search
-
Implements the CStaR algorithm (Stekhoven et al., 2012), which finds a CPDAG of that data and then tries all orientations of the undirected edges about a variable in the CPDAG to estimate a minimum bound on the effect for a given edge.
- Cstar() - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.oracle.pattern.Cstar
- Cstar(IndependenceWrapper, ScoreWrapper) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.oracle.pattern.Cstar
- Cstar(IndependenceWrapper, ScoreWrapper, Parameters) - Constructor for class edu.cmu.tetrad.search.Cstar
-
Constructor.
- CSTAR_CPDAG_ALGORITHM - Static variable in class edu.cmu.tetrad.util.Params
- Cstar.CpdagAlgorithm - Enum Class in edu.cmu.tetrad.search
-
An enumeration of the options available for determining the CPDAG used for the algorithm.
- Cstar.Record - Class in edu.cmu.tetrad.search
-
Represents a single record in the returned table for CSTaR.
- Cstar.SampleStyle - Enum Class in edu.cmu.tetrad.search
-
An enumeration of the methods for selecting samples from the full dataset.
- CsvtoMatrix - Class in jgpml
-
Simple Class to load the example data from files straight into Matrices.
- CsvtoMatrix() - Constructor for class jgpml.CsvtoMatrix
- cumulativeProbability(double) - Method in class edu.cmu.tetrad.sem.EmpiricalCdf
- cumulativeProbability(double, double) - Method in class edu.cmu.tetrad.sem.EmpiricalCdf
-
Deprecated.
- currentRepositoryVersion() - Static method in class edu.cmu.tetrad.util.Version
- currentViewableVersion() - Static method in class edu.cmu.tetrad.util.Version
- CUTOFF_CONSTRAIN_SEARCH - Static variable in class edu.cmu.tetrad.util.Params
- CUTOFF_DATA_SEARCH - Static variable in class edu.cmu.tetrad.util.Params
- CUTOFF_IND_TEST - Static variable in class edu.cmu.tetrad.util.Params
- CutoffFinder - Class in edu.cmu.tetrad.util
-
Provides a static method for finding the cutoff value for a symmetric probability distribution function about the origin.
- CutoffFinder() - Constructor for class edu.cmu.tetrad.util.CutoffFinder
- Cyclic - Class in edu.cmu.tetrad.algcomparison.graph
-
Returns a cyclic graph build up from small cyclic graph components.
- Cyclic() - Constructor for class edu.cmu.tetrad.algcomparison.graph.Cyclic
- CYCLIC_CONSTRUCTED_FROM_SMALL_LOOPS - Static variable in class edu.cmu.tetrad.algcomparison.graph.GraphTypes
D
- Dag - Class in edu.cmu.tetrad.graph
-
Represents a directed acyclic graph--that is, a graph containing only directed edges, with no cycles.
- Dag() - Constructor for class edu.cmu.tetrad.graph.Dag
-
Constructs a new directed acyclic graph (DAG).
- Dag(Graph) - Constructor for class edu.cmu.tetrad.graph.Dag
-
Constructs a new directed acyclic graph from the given graph object.
- Dag(List<Node>) - Constructor for class edu.cmu.tetrad.graph.Dag
- DAG - Enum constant in enum class edu.cmu.tetrad.algcomparison.comparegraphs.CompareTwoGraphs.CompareToType
- dagFromCPDAG(Graph) - Static method in class edu.cmu.tetrad.graph.GraphTransforms
- dagFromCPDAG(Graph, Knowledge) - Static method in class edu.cmu.tetrad.graph.GraphTransforms
- DagInCpcagIterator - Class in edu.cmu.tetrad.search.utils
-
Given a CPDAG, lists all the DAGs in that DPCAG.
- DagInCpcagIterator(Graph) - Constructor for class edu.cmu.tetrad.search.utils.DagInCpcagIterator
-
The given CPDAG must be a CPDAG.
- DagInCpcagIterator(Graph, Knowledge) - Constructor for class edu.cmu.tetrad.search.utils.DagInCpcagIterator
-
The given CPDAG must be a CPDAG.
- DagInCpcagIterator(Graph, Knowledge, boolean, boolean) - Constructor for class edu.cmu.tetrad.search.utils.DagInCpcagIterator
-
The given CPDAG must be a CPDAG.
- DagIterator - Class in edu.cmu.tetrad.search.utils
-
Given a graph, lists all DAGs that result from directing the undirected edges in that graph every possible way.
- DagIterator(Graph) - Constructor for class edu.cmu.tetrad.search.utils.DagIterator
-
The given CPDAG must be a CPDAG.
- Dagma - Class in edu.cmu.tetrad.algcomparison.algorithm.continuous.dag
-
DAGMA.
- Dagma - Class in edu.cmu.tetrad.search
-
Implements the DAGMA algorithm.
- Dagma() - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.continuous.dag.Dagma
- Dagma(DataSet) - Constructor for class edu.cmu.tetrad.search.Dagma
-
Constructor.
- DagScorer - Class in edu.cmu.tetrad.sem
-
Estimates a SemIm given a CovarianceMatrix and a SemPm.
- DagScorer - Interface in edu.cmu.tetrad.search.utils
-
Interface for a method that scores a DAG.
- DagScorer(DataSet) - Constructor for class edu.cmu.tetrad.sem.DagScorer
-
Constructs a new SemEstimator that uses the specified optimizer.
- DagScorer(ICovarianceMatrix) - Constructor for class edu.cmu.tetrad.sem.DagScorer
-
Constructs a new SemEstimator that uses the specified optimizer.
- DagSepsets - Class in edu.cmu.tetrad.search.utils
-
Determines sepsets, collider, and noncolliders by examining d-separation facts in a DAG.
- DagSepsets(Graph) - Constructor for class edu.cmu.tetrad.search.utils.DagSepsets
-
Constructs a new DagSepsets object for the given DAG.
- dagToPag(Graph) - Static method in class edu.cmu.tetrad.graph.GraphTransforms
- DagToPag - Class in edu.cmu.tetrad.search.utils
-
Converts a DAG (Directed acyclic graph) into the PAG (partial ancestral graph) which it is in the equivalence class of.
- DagToPag(Graph) - Constructor for class edu.cmu.tetrad.search.utils.DagToPag
-
Constructs a new FCI search for the given independence test and background knowledge.
- DATA_TYPE - Static variable in class edu.cmu.tetrad.util.Params
- DataBox - Interface in edu.cmu.tetrad.data
-
Stores a 2D array of data.
- DataConvertUtils - Class in edu.cmu.tetrad.util
-
Dec 15, 2018 11:10:30 AM
- DataFilter - Interface in edu.cmu.tetrad.data
-
Interface implemented by classes whose purpose is to generate modifications of data sets.
- DataForCalibrationRfci - Class in edu.cmu.tetrad.calibration
- DataForCalibrationRfci() - Constructor for class edu.cmu.tetrad.calibration.DataForCalibrationRfci
- DataGraphSearch - Class in edu.pitt.csb.stability
-
Created by ajsedgewick on 9/4/15.
- DataGraphSearch(double...) - Constructor for class edu.pitt.csb.stability.DataGraphSearch
- DataGraphUtils - Class in edu.cmu.tetrad.data
-
Sundry graph utils that need to be located in the data package to avoid package cycles.
- DataGraphUtils() - Constructor for class edu.cmu.tetrad.data.DataGraphUtils
- DataModel - Interface in edu.cmu.tetrad.data
-
Interface implemented by classes, instantiations of which can serve as data models in Tetrad.
- DataModelList - Class in edu.cmu.tetrad.data
-
Stores a list of data models and keeps track of which one is selected.
- DataModelList() - Constructor for class edu.cmu.tetrad.data.DataModelList
- DataModelList(DataModelList) - Constructor for class edu.cmu.tetrad.data.DataModelList
- DataSet - Interface in edu.cmu.tetrad.data
-
Implements a rectangular data set, in the sense of being a dataset with a fixed number of columns and a fixed number of rows, the length of each column being constant.
- DataSetProbs - Class in edu.cmu.tetrad.bayes
-
Estimates maximum likelihood probabilities directly from data on the fly.
- DataSetProbs(DataSet) - Constructor for class edu.cmu.tetrad.bayes.DataSetProbs
-
Creates a cell count table for the given data set.
- DataTable<N,
V> - Interface in edu.pitt.isp.sverchkov.data -
Data table implementation.
- dataTableFromFile(File) - Static method in class edu.pitt.isp.sverchkov.data.DataTools
- DataTableImpl<N,
V> - Class in edu.pitt.isp.sverchkov.data -
Data table implementation.
- DataTableImpl(List<? extends N>) - Constructor for class edu.pitt.isp.sverchkov.data.DataTableImpl
- DataTools - Class in edu.pitt.isp.sverchkov.data
-
Data tools.
- DataTools() - Constructor for class edu.pitt.isp.sverchkov.data.DataTools
- DataTransforms - Class in edu.cmu.tetrad.data
- DataTransforms() - Constructor for class edu.cmu.tetrad.data.DataTransforms
- dataType() - Element in annotation interface edu.cmu.tetrad.annotation.Algorithm
-
Description of the algorithm.
- dataType() - Element in annotation interface edu.cmu.tetrad.annotation.Score
- dataType() - Element in annotation interface edu.cmu.tetrad.annotation.TestOfIndependence
- DataType - Enum Class in edu.cmu.tetrad.data
-
The type of the data set--continuous if all continuous variables, discrete if all discrete variables; otherwise, mixed.
- DataUtility - Class in edu.cmu.tetrad.util
-
Fast data loader for continuous or discrete data.
- DataUtils - Class in edu.cmu.tetrad.data
-
Some static utility methods for dealing with data sets.
- DataWriter - Class in edu.cmu.tetrad.data
-
Provides static methods for saving data to files.
- DataWriter() - Constructor for class edu.cmu.tetrad.data.DataWriter
- Dci - Class in edu.cmu.tetrad.search.work_in_progress
-
Implements the DCI (Distributed Causal Inference) algorithm for learning causal structure over a set of variable from multiple datasets that each may only measure proper overlapping subsets of that sets, or datasets with some variables in common and others not.
- Dci(List<IndependenceTest>) - Constructor for class edu.cmu.tetrad.search.work_in_progress.Dci
- Dci(List<IndependenceTest>, ResolveSepsets.Method) - Constructor for class edu.cmu.tetrad.search.work_in_progress.Dci
- dd - Enum constant in enum class edu.cmu.tetrad.graph.Edge.Property
- ddpOrient(Node, Node, Node, Graph) - Method in class edu.cmu.tetrad.search.utils.FciOrient
-
a method to search "back from a" to find a DDP.
- ddpOrient(Node, Node, Node, Graph) - Method in class edu.cmu.tetrad.search.utils.SvarFciOrient
-
a method to search "back from a" to find a DDP.
- decomposition() - Method in class edu.cmu.tetrad.search.utils.GraphoidAxioms
-
Checks if decomposition holds, e.g., X ⊥⊥ (Y ∪ W) |Z ==> (X ⊥⊥ Y |Z) ∧ (X ⊥⊥ W |Z)
- deepCopy(DataSet) - Static method in class edu.pitt.csb.mgm.MixedUtils
-
Makes a deep copy of a dataset (Nodes copied as well).
- defaultCategory(int) - Static method in class edu.cmu.tetrad.data.DataUtils
- DefaultEvent(String, String) - Constructor for class edu.cmu.tetrad.util.DefaultTetradLoggerConfig.DefaultEvent
- defaultLayout(Graph) - Static method in class edu.cmu.tetrad.graph.LayoutUtil
-
Arranges the nodes in the graph in a circle if there are 20 or fewer nodes, otherwise arranges them in a square.
- DefaultTetradLoggerConfig - Class in edu.cmu.tetrad.util
-
Logger configuration.
- DefaultTetradLoggerConfig(String...) - Constructor for class edu.cmu.tetrad.util.DefaultTetradLoggerConfig
-
Constructs the config for the given event ids.
- DefaultTetradLoggerConfig(List<TetradLoggerConfig.Event>) - Constructor for class edu.cmu.tetrad.util.DefaultTetradLoggerConfig
-
Constructs the config given the events in it.
- DefaultTetradLoggerConfig.DefaultEvent - Class in edu.cmu.tetrad.util
- DefiniteDirectedPathPrecision - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- DefiniteDirectedPathPrecision() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.DefiniteDirectedPathPrecision
- DefiniteDirectedPathRecall - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- DefiniteDirectedPathRecall() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.DefiniteDirectedPathRecall
- definiteNonDescendent(Node, Node) - Method in class edu.cmu.tetrad.graph.Paths
-
added by ekorber, 2004/06/12
- DEFLATION - Static variable in class edu.cmu.tetrad.search.FastIca
-
The algorithm type where the components are extracted one at a time.
- defVisible(Edge) - Method in class edu.cmu.tetrad.graph.Paths
-
added by ekorber, 2004/06/11
- DegenerateGaussianBicScore - Class in edu.cmu.tetrad.algcomparison.score
-
Wrapper for degenerate Gaussian BIC score
- DegenerateGaussianBicScore() - Constructor for class edu.cmu.tetrad.algcomparison.score.DegenerateGaussianBicScore
- DegenerateGaussianLRT - Class in edu.cmu.tetrad.algcomparison.independence
-
Wrapper for DG LRT.
- DegenerateGaussianLRT() - Constructor for class edu.cmu.tetrad.algcomparison.independence.DegenerateGaussianLRT
- DegenerateGaussianScore - Class in edu.cmu.tetrad.search.score
-
This implements the degenerate Gaussian BIC score for FGES.
- DegenerateGaussianScore(DataSet, boolean) - Constructor for class edu.cmu.tetrad.search.score.DegenerateGaussianScore
- degree(Graph) - Static method in class edu.cmu.tetrad.graph.GraphUtils
- DelegatesEditing - Interface in edu.cmu.tetrad.session
-
An interface for editors that delegate their editing responsibilities.
- DELIMITER - Static variable in class edu.pitt.isp.sverchkov.data.DataTools
- DELIMITER_REGEX - Static variable in class edu.pitt.isp.sverchkov.data.DataTools
- DelimiterType - Class in edu.cmu.tetrad.data
-
Type-safe enum of delimiter types for parsing data.
- DelimiterUtils - Class in edu.cmu.tetrad.util
-
Jun 20, 2017 12:09:05 PM
- DeltaSextadTest - Class in edu.cmu.tetrad.search.utils
-
Implements a test for simultaneously zero sextads in the style of Bollen, K.
- DeltaSextadTest(DataSet) - Constructor for class edu.cmu.tetrad.search.utils.DeltaSextadTest
-
Constructs a test using a given data set.
- DeltaSextadTest(ICovarianceMatrix) - Constructor for class edu.cmu.tetrad.search.utils.DeltaSextadTest
-
Constructs a test using the given covariance matrix.
- DeltaTetradTest - Class in edu.cmu.tetrad.search.utils
-
Implements a test for simultaneously zero tetrads in Bollen, K.
- DeltaTetradTest(DataSet) - Constructor for class edu.cmu.tetrad.search.utils.DeltaTetradTest
-
Constructs a test using a given data set.
- DeltaTetradTest(ICovarianceMatrix) - Constructor for class edu.cmu.tetrad.search.utils.DeltaTetradTest
-
Constructs a test using the given covariance matrix.
- demean(double[][], Vector) - Static method in class edu.cmu.tetrad.data.CovarianceMatrixOnTheFly
- density(double) - Method in class edu.cmu.tetrad.sem.EmpiricalCdf
- DensityEst - Class in edu.cmu.tetrad.algcomparison.statistic
-
The adjacency precision.
- DensityEst() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.DensityEst
- DensityTrue - Class in edu.cmu.tetrad.algcomparison.statistic
-
The adjacency precision.
- DensityTrue() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.DensityTrue
- dependenceFactMsg(Node, Node, Set<Node>, double) - Static method in class edu.cmu.tetrad.search.utils.LogUtilsSearch
- dependent - Enum constant in enum class edu.pitt.dbmi.algo.bayesian.constraint.inference.BCInference.OP
- DEPENDENT - Enum constant in enum class edu.pitt.dbmi.algo.bayesian.constraint.inference.BCCausalInference.OP
- depth - Variable in class edu.cmu.tetrad.calibration.DataForCalibrationRfci
- DEPTH - Static variable in class edu.cmu.tetrad.util.Params
- description() - Element in annotation interface edu.cmu.tetrad.annotation.Score
- description() - Element in annotation interface edu.cmu.tetrad.annotation.TestOfIndependence
- deserializeArchivedVersions() - Method in class edu.cmu.tetrad.util.TetradSerializableUtils
-
Deserializes examplars stored in archives in getArchiveDirectory().
- deserializeCurrentDirectory() - Method in class edu.cmu.tetrad.util.TetradSerializableUtils
-
Deserializes all files in the given directory, as a test to make sure they can all be deserialized.
- destroyModel() - Method in class edu.cmu.tetrad.session.SessionNode
-
Sets the model to null.
- det() - Method in class edu.cmu.tetrad.util.Matrix
- det() - Method in class edu.cmu.tetrad.util.Matrix2
- determinant(double[][]) - Static method in class edu.cmu.tetrad.util.MatrixUtils
- determines(List<Node>, Node) - Method in class edu.cmu.tetrad.search.IndTestIod
-
Returns true if z contains x.
- determines(List<Node>, Node) - Method in class edu.cmu.tetrad.search.score.BdeuScore
-
This score does not implement a method to decide whehter a node is determined by its parents.
- determines(List<Node>, Node) - Method in class edu.cmu.tetrad.search.score.EbicScore
-
Return a judgment of whether the variable in z determine y exactly.
- determines(List<Node>, Node) - Method in class edu.cmu.tetrad.search.score.GicScores
- determines(List<Node>, Node) - Method in class edu.cmu.tetrad.search.score.ImagesScore
-
Returns the 'determines' judgment from the first score.
- determines(List<Node>, Node) - Method in class edu.cmu.tetrad.search.score.IndTestScore
- determines(List<Node>, Node) - Method in class edu.cmu.tetrad.search.score.MvpScore
- determines(List<Node>, Node) - Method in class edu.cmu.tetrad.search.score.PoissonPriorScore
- determines(List<Node>, Node) - Method in interface edu.cmu.tetrad.search.score.Score
-
Returns true iff the score determines the edge between x and y.
- determines(List<Node>, Node) - Method in class edu.cmu.tetrad.search.score.SemBicScore
- determines(List<Node>, Node) - Method in class edu.cmu.tetrad.search.score.ZsbScore
-
Returns true if the variable in Z determine y.
- determines(List<Node>, Node) - Method in class edu.cmu.tetrad.search.test.IndTestChiSquare
-
Returns True if the variables z determining the variable z.
- determines(List<Node>, Node) - Method in class edu.cmu.tetrad.search.test.IndTestConditionalCorrelation
- determines(List<Node>, Node) - Method in class edu.cmu.tetrad.search.test.IndTestConditionalGaussianLrt
-
Returns true if y is determined the variable in z.
- determines(List<Node>, Node) - Method in class edu.cmu.tetrad.search.test.IndTestDegenerateGaussianLrt
-
Returns true if y is determined the variable in z.
- determines(List<Node>, Node) - Method in class edu.cmu.tetrad.search.test.IndTestFisherZ
-
Returns true in case the variable in Z jointly determine x.
- determines(List<Node>, Node) - Method in class edu.cmu.tetrad.search.test.IndTestFisherZConcatenateResiduals
- determines(List<Node>, Node) - Method in class edu.cmu.tetrad.search.test.IndTestFisherZFisherPValue
- determines(List<Node>, Node) - Method in class edu.cmu.tetrad.search.test.IndTestHsic
- determines(List<Node>, Node) - Method in class edu.cmu.tetrad.search.test.IndTestIndependenceFacts
- determines(List<Node>, Node) - Method in class edu.cmu.tetrad.search.test.IndTestMulti
- determines(List<Node>, Node) - Method in class edu.cmu.tetrad.search.test.IndTestMvpLrt
- determines(List<Node>, Node) - Method in class edu.cmu.tetrad.search.test.IndTestRegression
- determines(List<Node>, Node) - Method in class edu.cmu.tetrad.search.test.IndTestTrekSep
-
If
isDeterminismAllowed(), defers to IndTestFisherZD; otherwise throws UnsupportedOperationException. - determines(List<Node>, Node) - Method in class edu.cmu.tetrad.search.test.Kci
-
Returns true if y is determined the variable in z.
- determines(List<Node>, Node) - Method in class edu.cmu.tetrad.search.test.MsepTest
- determines(List<Node>, Node) - Method in class edu.cmu.tetrad.search.test.ScoreIndTest
-
Returns true if y is determined the variable in z.
- determines(List<Node>, Node) - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestCramerT
- determines(List<Node>, Node) - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestFisherZGeneralizedInverse
-
Returns true just in case the varialbe in zList determine xVar.
- determines(List<Node>, Node) - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestMixedMultipleTTest
- determines(List<Node>, Node) - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestMnlrLr
- determines(List<Node>, Node) - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestMultinomialLogisticRegression
- determines(List<Node>, Node) - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestPositiveCorr
-
If
isDeterminismAllowed(), deters to IndTestFisherZD; otherwise throws UnsupportedOperationException. - determines(List<Node>, Node) - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestSepsetDci
- determines(List<Node>, Node) - Method in class edu.cmu.tetrad.search.work_in_progress.SemBicScoreDeterministic
- determines(List<Node>, Node) - Method in class edu.pitt.csb.mgm.IndTestMultinomialLogisticRegressionWald
- determines(List, Node) - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestFisherZPercentIndependent
- determines(Set<Node>, Node) - Method in interface edu.cmu.tetrad.search.IndependenceTest
-
Returns true if y is determined the variable in z.
- determines(Set<Node>, Node) - Method in class edu.cmu.tetrad.search.test.IndTestGSquare
-
Returns a judgment whether the variables in z determine x.
- determines(Set<Node>, Node) - Method in class edu.cmu.tetrad.search.test.IndTestProbabilistic
- determines(Set<Node>, Node) - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestFisherZRecursive
-
If
isDeterminismAllowed(), deters to IndTestFisherZD; otherwise throws UnsupportedOperationException. - determines(Set<Node>, Node) - Method in class edu.cmu.tetrad.search.work_in_progress.ProbabilisticMapIndependence
- DETERMINISM_THRESHOLD - Static variable in class edu.cmu.tetrad.util.Params
- determinismDetected(Set<Node>, Node) - Static method in class edu.cmu.tetrad.search.utils.LogUtilsSearch
- diag() - Method in class edu.cmu.tetrad.util.Matrix
- diag() - Method in class edu.cmu.tetrad.util.Matrix2
- diag() - Method in class edu.cmu.tetrad.util.Vector
- diag(Matrix) - Static method in class jgpml.covariancefunctions.MatrixOperations
-
If the argument is a row or column
Matrixit returns a new diagonalMatrixwith the input as diagonal elements. - dieToss(int) - Static method in class edu.cmu.tetrad.util.StatUtils
- differByPerturbation(int, int, int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.ideker.ItkPredictorSearch
-
This method determines whether the levels for a given gene differ between two perturbations p0 and p1 (rows of the perturbation matrix).
- difference(DataSet, int) - Static method in class edu.cmu.tetrad.search.utils.TsUtils
-
Calculates the dth difference of the given data.
- DIFFERENT_GRAPHS - Static variable in class edu.cmu.tetrad.util.Params
- differExpressions(int, int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.ideker.ItkPredictorSearch
- Digraph - Class in edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.biolingua
-
Simple implementation of a directed Graph.
- Digraph(Digraph) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.biolingua.Digraph
-
Copy constructor.
- Digraph(String) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.biolingua.Digraph
-
Creates a OldDigraph reading it from file
fname. - Digraph(String, int) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.biolingua.Digraph
-
Creates a OldDigraph with
gNamename, andnnodes. - directedEdge(Node, Node) - Static method in class edu.cmu.tetrad.graph.Edges
-
Constructs a new directed edge from nodeA to nodeB (-->).
- directedPathsFromTo(Node, Node, int) - Method in class edu.cmu.tetrad.graph.Paths
- DirectLingam - Class in edu.cmu.tetrad.algcomparison.algorithm.continuous.dag
-
Direct LiNGAM.
- DirectLingam - Class in edu.cmu.tetrad.search
-
Implements the Direct-LiNGAM algorithm.
- DirectLingam() - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.continuous.dag.DirectLingam
- DirectLingam(ScoreWrapper) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.continuous.dag.DirectLingam
- DirectLingam(DataSet, Score) - Constructor for class edu.cmu.tetrad.search.DirectLingam
-
Constructor.
- directProduct(double[][], double[][]) - Static method in class edu.cmu.tetrad.util.MatrixUtils
-
Computes the direct (Kronecker) outerProduct.
- DirichletBayesIm - Class in edu.cmu.tetrad.bayes
-
Stores Dirichlet pseudocounts for the distributions of each variable conditional on particular combinations of its parent values and, together with Bayes Pm and Dag, provides methods to manipulate these tables.
- DirichletBayesIm(DirichletBayesIm) - Constructor for class edu.cmu.tetrad.bayes.DirichletBayesIm
-
Copy constructor.
- DirichletDataSetProbs - Class in edu.cmu.tetrad.bayes
-
Estimates probabilities directly from data on the fly using maximum likelihood method.
- DirichletDataSetProbs(DataSet, double) - Constructor for class edu.cmu.tetrad.bayes.DirichletDataSetProbs
-
Creates a cell count table for the given data set.
- DirichletEstimator - Class in edu.cmu.tetrad.bayes
-
Estimates a DirichletBayesIm from a DirichletBayesIm (the prior) and a data set.
- DirichletEstimator() - Constructor for class edu.cmu.tetrad.bayes.DirichletEstimator
- disallowComplement(int, int) - Method in class edu.cmu.tetrad.bayes.Proposition
-
Without changing the status of the specified category, disallows all other categories for the given variable.
- Discrete - Class in edu.cmu.tetrad.util.dist
-
Wraps a chi square distribution for purposes of drawing random samples.
- Discrete - Enum constant in enum class edu.cmu.tetrad.data.DataType
- Discrete - Enum constant in enum class edu.cmu.tetrad.study.performance.ComparisonParameters.DataType
- DISCRETE - Enum constant in enum class edu.cmu.tetrad.search.utils.BpcTestType
- DISCRETE_LRT - Enum constant in enum class edu.cmu.tetrad.search.utils.BpcTestType
- DISCRETE_VARIATIONAL - Enum constant in enum class edu.cmu.tetrad.search.utils.BpcTestType
- DiscreteBicScore - Class in edu.cmu.tetrad.algcomparison.score
-
Wrapper for Discrete BIC test.
- DiscreteBicScore - Class in edu.cmu.tetrad.search.score
-
Calculates the discrete BIC score.
- DiscreteBicScore() - Constructor for class edu.cmu.tetrad.algcomparison.score.DiscreteBicScore
- DiscreteBicScore(DataSet) - Constructor for class edu.cmu.tetrad.search.score.DiscreteBicScore
-
Constructor.
- DiscreteBicTest - Class in edu.cmu.tetrad.algcomparison.independence
-
Wrapper for Fisher Z test.
- DiscreteBicTest() - Constructor for class edu.cmu.tetrad.algcomparison.independence.DiscreteBicTest
- DiscreteDiscretizationSpec - Class in edu.cmu.tetrad.data
-
Specifies how a column (continuous or discrete) should be discretized.
- DiscreteDiscretizationSpec(int[], List<String>) - Constructor for class edu.cmu.tetrad.data.DiscreteDiscretizationSpec
- DiscreteScore - Interface in edu.cmu.tetrad.search.score
-
Gives an interface that can be used by various discrete scores.
- discreteSerializableInstance() - Static method in class edu.cmu.tetrad.data.DataUtils
-
A discrete data set used to construct some other serializable instances.
- DiscreteVariable - Class in edu.cmu.tetrad.data
-
Represents a discrete variable as a range of integer-valued categories 0, 1, ..., m - 1, where m is the number of categories for the variable.
- DiscreteVariable(DiscreteVariable) - Constructor for class edu.cmu.tetrad.data.DiscreteVariable
-
Copy constructor.
- DiscreteVariable(String) - Constructor for class edu.cmu.tetrad.data.DiscreteVariable
-
Builds a discrete variable with the given name and an empty list of categories.
- DiscreteVariable(String, int) - Constructor for class edu.cmu.tetrad.data.DiscreteVariable
-
Builds a qualitative variable with the given name and number of categories.
- DiscreteVariable(String, List<String>) - Constructor for class edu.cmu.tetrad.data.DiscreteVariable
-
Builds a qualitative variable with the given name and array of possible categories.
- DiscreteVariableType - Class in edu.cmu.tetrad.data
-
Type-safe enum of discrete variable types.
- DiscretizationSpec - Interface in edu.cmu.tetrad.data
-
A continuous or discrete discretization spec (see).
- discretize() - Method in class edu.cmu.tetrad.data.Discretizer
- discretize(double[], double[], String, List<String>) - Static method in class edu.cmu.tetrad.data.Discretizer
-
Discretizes the continuous data in the given column using the specified cutoffs and category names.
- discretize(DataSet, int, boolean) - Static method in class edu.cmu.tetrad.data.DataTransforms
- DISCRETIZE - Static variable in class edu.cmu.tetrad.util.Params
- Discretizer - Class in edu.cmu.tetrad.data
-
Discretizes individual columns of discrete or continuous data.
- Discretizer(DataSet) - Constructor for class edu.cmu.tetrad.data.Discretizer
-
Constructs a new discretizer that discretizes every variable as binary, using evenly distributed values.
- Discretizer(DataSet, Map<Node, DiscretizationSpec>) - Constructor for class edu.cmu.tetrad.data.Discretizer
- Discretizer.Discretization - Class in edu.cmu.tetrad.data
- DishModel - Class in edu.cmu.tetrad.study.gene.tetrad.gene.history
-
Models the manner in which gene models are initialized differentially depending on the dishes that the cells are in.
- DishModel(int, double) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.history.DishModel
- display(SortedSet<ItkPredictorSearch.Gene>) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.ideker.ItkPredictorSearch
- DisplayNameHandler - Class in edu.cmu.tetrad.study.gene.tetrad.gene.graph
-
Translates display names of lagged variables (e.g.
- DisplayNameHandler() - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.graph.DisplayNameHandler
- displayParents() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.AbstractNbComponent
-
Displays the parents.
- dissimilarity(Vector, Vector) - Method in interface edu.cmu.tetrad.cluster.metrics.Dissimilarity
- dissimilarity(Vector, Vector) - Method in class edu.cmu.tetrad.cluster.metrics.SquaredErrorLoss
- Dissimilarity - Interface in edu.cmu.tetrad.cluster.metrics
-
Interface for a dissilimarity metric.
- distance(LinkedList<Double>, double) - Method in class edu.cmu.tetrad.search.Ida
-
Returns the distance between the effects and the true effect.
- distances(Graph, Graph) - Method in class edu.cmu.tetrad.simulation.Gdistance
- Distribution - Interface in edu.cmu.tetrad.util.dist
-
Interface for a statistical distribution from which random values can be drawn.
- district(Node, Graph) - Static method in class edu.cmu.tetrad.graph.GraphUtils
- DMSearch - Class in edu.cmu.tetrad.search.work_in_progress
-
Implements the DM search.
- DMSearch() - Constructor for class edu.cmu.tetrad.search.work_in_progress.DMSearch
- DMSearch.LatentStructure - Class in edu.cmu.tetrad.search.work_in_progress
- DO_COLLIDER_ORIENTATION - Static variable in class edu.cmu.tetrad.util.Params
- DO_DISCRIMINATING_PATH_COLLIDER_RULE - Static variable in class edu.cmu.tetrad.util.Params
- DO_DISCRIMINATING_PATH_RULE - Static variable in class edu.cmu.tetrad.util.Params
- DO_DISCRIMINATING_PATH_TAIL_RULE - Static variable in class edu.cmu.tetrad.util.Params
- doDdpOrientation(Node, Node, Node, Node, Graph) - Method in class edu.cmu.tetrad.search.utils.FciOrient
-
Orients the edges inside the definte discriminating path triangle.
- dof - Variable in class edu.cmu.tetrad.bayes.BayesProperties.LikelihoodRet
- doFinalOrientation(Graph) - Method in class edu.cmu.tetrad.search.utils.FciOrient
-
Orients the graph according to rules in the graph (FCI step D).
- doFinalOrientation(Graph) - Method in class edu.cmu.tetrad.search.utils.SvarFciOrient
-
Orients the graph according to rules in the graph (FCI step D).
- doLayout() - Method in class edu.cmu.tetrad.graph.LayoutUtil.FruchtermanReingoldLayout
- doLayout() - Method in class edu.cmu.tetrad.graph.LayoutUtil.KamadaKawaiLayout
- DOMAIN - Enum constant in enum class edu.cmu.tetrad.graph.NodeVariableType
- DoNotAddOldModel - Interface in edu.cmu.tetrad.session
-
Tags session nodes that should not be passed on as old models to new models.
- dot(Vector) - Method in class edu.cmu.tetrad.util.Vector
- dotProduct(Vector) - Method in class edu.cmu.tetrad.util.Vector
- DOUBLE_REMOVE - Enum constant in enum class edu.cmu.tetrad.search.work_in_progress.HbsmsBeam.Move.Type
- DoubleDataBox - Class in edu.cmu.tetrad.data
-
Stores a 2D array of double data.
- DoubleDataBox(double[][]) - Constructor for class edu.cmu.tetrad.data.DoubleDataBox
-
Constructs a new data box using the given 2D double data array as data.
- DoubleDataBox(int, int) - Constructor for class edu.cmu.tetrad.data.DoubleDataBox
-
Constructs an 2D double array consisting entirely of missing values (Double.NaN).
E
- E - Static variable in class edu.cmu.tetrad.calculator.expression.ConstantExpression
-
Constant expression for e.
- E(double[], double[], double[], double, double) - Static method in class edu.cmu.tetrad.util.StatUtils
- Eb - Class in edu.cmu.tetrad.algcomparison.algorithm.pairwise
-
EB.
- Eb() - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.pairwise.Eb
- Eb(Algorithm) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.pairwise.Eb
- EB - Enum constant in enum class edu.cmu.tetrad.search.Lofs.Rule
- EBIC_GAMMA - Static variable in class edu.cmu.tetrad.util.Params
- EbicScore - Class in edu.cmu.tetrad.algcomparison.score
-
Wrapper for linear, Gaussian Extended BIC score (Chen and Chen).
- EbicScore - Class in edu.cmu.tetrad.search.score
-
Implements the extended BIC (EBIC) score.
- EbicScore() - Constructor for class edu.cmu.tetrad.algcomparison.score.EbicScore
- EbicScore(DataSet, boolean) - Constructor for class edu.cmu.tetrad.search.score.EbicScore
-
Constructs the score using a covariance matrix.
- EbicScore(ICovarianceMatrix) - Constructor for class edu.cmu.tetrad.search.score.EbicScore
-
Constructs the score using a covariance matrix.
- Edge - Class in edu.cmu.tetrad.graph
-
Represents an edge node1 *-# node2 where * and # are endpoints of type Endpoint--that is, Endpoint.TAIL, Endpoint.ARROW, or Endpoint.CIRCLE.
- Edge(Edge) - Constructor for class edu.cmu.tetrad.graph.Edge
- Edge(Node, Node, Endpoint, Endpoint) - Constructor for class edu.cmu.tetrad.graph.Edge
-
Constructs a new edge by specifying the nodes it connects and the endpoint types.
- Edge.Property - Enum Class in edu.cmu.tetrad.graph
- EdgeListGraph - Class in edu.cmu.tetrad.graph
-
Stores a graph a list of lists of edges adjacent to each node in the graph, with an additional list storing all of the edges in the graph.
- EdgeListGraph() - Constructor for class edu.cmu.tetrad.graph.EdgeListGraph
-
Constructs a new (empty) EdgeListGraph.
- EdgeListGraph(EdgeListGraph) - Constructor for class edu.cmu.tetrad.graph.EdgeListGraph
- EdgeListGraph(Graph) - Constructor for class edu.cmu.tetrad.graph.EdgeListGraph
-
Constructs a EdgeListGraph using the nodes and edges of the given graph.
- EdgeListGraph(List<Node>) - Constructor for class edu.cmu.tetrad.graph.EdgeListGraph
-
Constructs a new graph, with no edges, using the given variable names.
- edgeMisclassificationCounts(Graph, Graph, boolean) - Static method in class edu.cmu.tetrad.graph.GraphUtils
- edgeMisclassifications(double[][], NumberFormat) - Static method in class edu.cmu.tetrad.graph.GraphUtils
- edgeMisclassifications(int[][]) - Static method in class edu.cmu.tetrad.graph.GraphUtils
- edgeMisclassifications(Graph, Graph) - Static method in class edu.cmu.tetrad.graph.MisclassificationUtils
- edgeOrientedMsg(String, Edge) - Static method in class edu.cmu.tetrad.search.utils.LogUtilsSearch
- Edges - Class in edu.cmu.tetrad.graph
-
This factory class produces edges of the types commonly used for Tetrad-style graphs.
- Edges() - Constructor for class edu.cmu.tetrad.graph.Edges
- EdgeStatHeader - Static variable in class edu.pitt.csb.mgm.MixedUtils
- EdgesToString() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.biolingua.Digraph
-
Returns a string representation of the set of edges in this graph
- EdgesToString() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.BasicGraph
-
Returns a string representation of the set of edges in this graph
- EdgeTypeProbability - Class in edu.cmu.tetrad.graph
-
Apr 13, 2017 3:56:46 PM
- EdgeTypeProbability() - Constructor for class edu.cmu.tetrad.graph.EdgeTypeProbability
- EdgeTypeProbability(EdgeTypeProbability.EdgeType, double) - Constructor for class edu.cmu.tetrad.graph.EdgeTypeProbability
- EdgeTypeProbability(EdgeTypeProbability.EdgeType, List<Edge.Property>, double) - Constructor for class edu.cmu.tetrad.graph.EdgeTypeProbability
- EdgeTypeProbability.EdgeType - Enum Class in edu.cmu.tetrad.graph
- EDGEWISE - Enum constant in enum class edu.cmu.tetrad.algcomparison.comparegraphs.CompareTwoGraphs.ComparisonType
- edu.cmu.tetrad.algcomparison - package edu.cmu.tetrad.algcomparison
- edu.cmu.tetrad.algcomparison.algorithm - package edu.cmu.tetrad.algcomparison.algorithm
- edu.cmu.tetrad.algcomparison.algorithm.cluster - package edu.cmu.tetrad.algcomparison.algorithm.cluster
- edu.cmu.tetrad.algcomparison.algorithm.continuous.dag - package edu.cmu.tetrad.algcomparison.algorithm.continuous.dag
- edu.cmu.tetrad.algcomparison.algorithm.external - package edu.cmu.tetrad.algcomparison.algorithm.external
- edu.cmu.tetrad.algcomparison.algorithm.mixed - package edu.cmu.tetrad.algcomparison.algorithm.mixed
- edu.cmu.tetrad.algcomparison.algorithm.multi - package edu.cmu.tetrad.algcomparison.algorithm.multi
- edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag - package edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag
- edu.cmu.tetrad.algcomparison.algorithm.oracle.pag - package edu.cmu.tetrad.algcomparison.algorithm.oracle.pag
- edu.cmu.tetrad.algcomparison.algorithm.oracle.pattern - package edu.cmu.tetrad.algcomparison.algorithm.oracle.pattern
- edu.cmu.tetrad.algcomparison.algorithm.other - package edu.cmu.tetrad.algcomparison.algorithm.other
- edu.cmu.tetrad.algcomparison.algorithm.pairwise - package edu.cmu.tetrad.algcomparison.algorithm.pairwise
- edu.cmu.tetrad.algcomparison.comparegraphs - package edu.cmu.tetrad.algcomparison.comparegraphs
- edu.cmu.tetrad.algcomparison.examples - package edu.cmu.tetrad.algcomparison.examples
- edu.cmu.tetrad.algcomparison.graph - package edu.cmu.tetrad.algcomparison.graph
- edu.cmu.tetrad.algcomparison.independence - package edu.cmu.tetrad.algcomparison.independence
- edu.cmu.tetrad.algcomparison.score - package edu.cmu.tetrad.algcomparison.score
- edu.cmu.tetrad.algcomparison.simulation - package edu.cmu.tetrad.algcomparison.simulation
- edu.cmu.tetrad.algcomparison.statistic - package edu.cmu.tetrad.algcomparison.statistic
- edu.cmu.tetrad.algcomparison.statistic.utils - package edu.cmu.tetrad.algcomparison.statistic.utils
- edu.cmu.tetrad.algcomparison.utils - package edu.cmu.tetrad.algcomparison.utils
- edu.cmu.tetrad.annotation - package edu.cmu.tetrad.annotation
- edu.cmu.tetrad.bayes - package edu.cmu.tetrad.bayes
- edu.cmu.tetrad.calculator - package edu.cmu.tetrad.calculator
- edu.cmu.tetrad.calculator.expression - package edu.cmu.tetrad.calculator.expression
- edu.cmu.tetrad.calculator.parser - package edu.cmu.tetrad.calculator.parser
- edu.cmu.tetrad.calibration - package edu.cmu.tetrad.calibration
- edu.cmu.tetrad.classify - package edu.cmu.tetrad.classify
- edu.cmu.tetrad.cluster - package edu.cmu.tetrad.cluster
- edu.cmu.tetrad.cluster.metrics - package edu.cmu.tetrad.cluster.metrics
- edu.cmu.tetrad.data - package edu.cmu.tetrad.data
- edu.cmu.tetrad.data.simulation - package edu.cmu.tetrad.data.simulation
- edu.cmu.tetrad.graph - package edu.cmu.tetrad.graph
- edu.cmu.tetrad.regression - package edu.cmu.tetrad.regression
- edu.cmu.tetrad.search - package edu.cmu.tetrad.search
-
Contains classes for searching for (mostly structural) causal models given data.
- edu.cmu.tetrad.search.score - package edu.cmu.tetrad.search.score
-
Contains classes for various various sorts of scores for running score-based algorithms.
- edu.cmu.tetrad.search.test - package edu.cmu.tetrad.search.test
-
Contains classes for running conditional independence tests for various sorts of data.
- edu.cmu.tetrad.search.utils - package edu.cmu.tetrad.search.utils
-
Contains some utility classes for search algorithms.
- edu.cmu.tetrad.search.work_in_progress - package edu.cmu.tetrad.search.work_in_progress
-
Contains some classes that aren't ready for prime time.
- edu.cmu.tetrad.sem - package edu.cmu.tetrad.sem
- edu.cmu.tetrad.session - package edu.cmu.tetrad.session
- edu.cmu.tetrad.simulation - package edu.cmu.tetrad.simulation
- edu.cmu.tetrad.stat - package edu.cmu.tetrad.stat
- edu.cmu.tetrad.stat.correlation - package edu.cmu.tetrad.stat.correlation
- edu.cmu.tetrad.study - package edu.cmu.tetrad.study
- edu.cmu.tetrad.study.examples.conditions - package edu.cmu.tetrad.study.examples.conditions
- edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.akutsu - package edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.akutsu
- edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.biolingua - package edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.biolingua
- edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.ideker - package edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.ideker
- edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.reveal - package edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.reveal
- edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin - package edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin
- edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util - package edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util
- edu.cmu.tetrad.study.gene.tetrad.gene.graph - package edu.cmu.tetrad.study.gene.tetrad.gene.graph
-
Contains an editable display graph for (small) lag graphs.
- edu.cmu.tetrad.study.gene.tetrad.gene.history - package edu.cmu.tetrad.study.gene.tetrad.gene.history
-
Implements a time-series simulation engine suitable for time-series gene expression studies.
- edu.cmu.tetrad.study.gene.tetrad.gene.simexp - package edu.cmu.tetrad.study.gene.tetrad.gene.simexp
-
Implements a collection of manual simulation experiments.
- edu.cmu.tetrad.study.gene.tetrad.gene.simulation - package edu.cmu.tetrad.study.gene.tetrad.gene.simulation
-
Contains classes for generating simulations of expression levels over a collection of genes.
- edu.cmu.tetrad.study.gene.tetrad.gene.util - package edu.cmu.tetrad.study.gene.tetrad.gene.util
-
Contains some utility classes needed for the edu.cmu.tetrad.gene.* packages.
- edu.cmu.tetrad.study.gene.tetradapp.model - package edu.cmu.tetrad.study.gene.tetradapp.model
- edu.cmu.tetrad.study.performance - package edu.cmu.tetrad.study.performance
- edu.cmu.tetrad.util - package edu.cmu.tetrad.util
- edu.cmu.tetrad.util.dist - package edu.cmu.tetrad.util.dist
- edu.pitt.csb.mgm - package edu.pitt.csb.mgm
- edu.pitt.csb.stability - package edu.pitt.csb.stability
- edu.pitt.dbmi.algo.bayesian.constraint.inference - package edu.pitt.dbmi.algo.bayesian.constraint.inference
- edu.pitt.dbmi.algo.bayesian.constraint.search - package edu.pitt.dbmi.algo.bayesian.constraint.search
- edu.pitt.dbmi.algo.resampling - package edu.pitt.dbmi.algo.resampling
- edu.pitt.dbmi.algo.resampling.task - package edu.pitt.dbmi.algo.resampling.task
- edu.pitt.isp.sverchkov.data - package edu.pitt.isp.sverchkov.data
- EigenDecomposition - Class in edu.pitt.csb.mgm
-
Calculates the eigen decomposition of a real matrix.
- EigenDecomposition(double[], double[]) - Constructor for class edu.pitt.csb.mgm.EigenDecomposition
-
Calculates the eigen decomposition of the symmetric tridiagonal matrix.
- EigenDecomposition(double[], double[], double) - Constructor for class edu.pitt.csb.mgm.EigenDecomposition
-
Deprecated.in 3.1 (to be removed in 4.0) due to unused parameter
- EigenDecomposition(RealMatrix) - Constructor for class edu.pitt.csb.mgm.EigenDecomposition
-
Calculates the eigen decomposition of the given real matrix.
- EigenDecomposition(RealMatrix, double) - Constructor for class edu.pitt.csb.mgm.EigenDecomposition
-
Deprecated.in 3.1 (to be removed in 4.0) due to unused parameter
- Elapsed - Enum constant in enum class edu.cmu.tetrad.study.performance.Comparison.TableColumn
- Elapsed - Enum constant in enum class edu.cmu.tetrad.study.performance.Comparison2.TableColumn
- ElapsedCpuTime - Class in edu.cmu.tetrad.algcomparison.statistic
-
Records the elapsed time of the algorithm in seconds.
- ElapsedCpuTime() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.ElapsedCpuTime
- EmBayesEstimator - Class in edu.cmu.tetrad.bayes
-
Estimates parameters of the given Bayes net from the given data using maximum likelihood method.
- EmBayesEstimator(BayesIm, DataSet) - Constructor for class edu.cmu.tetrad.bayes.EmBayesEstimator
- EmBayesEstimator(BayesPm, DataSet) - Constructor for class edu.cmu.tetrad.bayes.EmBayesEstimator
-
Provides methods for estimating a Bayes IM from an existing BayesIM and a discrete dataset using EM (Expectation Maximization).
- EmBayesProperties - Class in edu.cmu.tetrad.bayes
-
Calculates some scores for Bayes nets as a whole.
- EmBayesProperties(DataSet, Graph) - Constructor for class edu.cmu.tetrad.bayes.EmBayesProperties
- EmBayesProperties.Estimator - Interface in edu.cmu.tetrad.bayes
- EmpiricalCdf - Class in edu.cmu.tetrad.sem
-
Only the cumulativeProbability, density, setShift methods are implemented.
- EmpiricalCdf(List<Double>) - Constructor for class edu.cmu.tetrad.sem.EmpiricalCdf
- EmpiricalDistributionForExpression - Class in edu.cmu.tetrad.sem
-
Returns a sample empirical distribution for a particular expression.
- EmpiricalDistributionForExpression(GeneralizedSemPm, Node, Context) - Constructor for class edu.cmu.tetrad.sem.EmpiricalDistributionForExpression
- empiricalHSIC(Matrix, Matrix, int) - Method in class edu.cmu.tetrad.search.test.IndTestHsic
-
Empirical unconditional Hilbert-Schmidt Dependence Measure for X and Y
- empiricalHSICincompleteCholesky(Matrix, Matrix, int) - Method in class edu.cmu.tetrad.search.test.IndTestHsic
-
Empirical unconditional Hilbert-Schmidt Dependence Measure for X and Y using incomplete Cholesky decomposition to approximate Gram matrices
- empiricalHSICincompleteCholesky(Matrix, Matrix, Matrix, int) - Method in class edu.cmu.tetrad.search.test.IndTestHsic
-
Empirical unconditional Hilbert-Schmidt Dependence Measure for X and Y given Z using incomplete Cholesky decomposition to approximate Gram matrices
- EmptyConfig(boolean) - Constructor for class edu.cmu.tetrad.util.TetradLogger.EmptyConfig
- emptyGraph(int) - Static method in class edu.cmu.tetrad.graph.GraphUtils
- Endpoint - Enum Class in edu.cmu.tetrad.graph
-
A typesafe enumeration of the types of endpoints that are permitted in Tetrad-style graphs: null (-), arrow (->), circle (-o), start (-*), and null (no endpoint).
- endpointMisclassification(Graph, Graph) - Static method in class edu.cmu.tetrad.graph.MisclassificationUtils
- endpointMisclassification(List<Node>, Graph, Graph) - Static method in class edu.cmu.tetrad.study.performance.PerformanceTests
- ensureColumns(int, List<String>) - Method in class edu.cmu.tetrad.data.BoxDataSet
-
Ensures that the dataset has at least the given number of columns, adding continuous variables with unique names until that is true.
- ensureColumns(int, List<String>) - Method in interface edu.cmu.tetrad.data.DataSet
-
Ensures that the dataset has at least
columnscolumns. - ensureColumns(int, List<String>) - Method in class edu.cmu.tetrad.data.NumberObjectDataSet
-
Ensures that the dataset has at least the given number of columns, adding continuous variables with unique names until that is true.
- ensureRows(int) - Method in class edu.cmu.tetrad.data.BoxDataSet
-
Ensures that the dataset has at least the number of rows, adding rows if necessary to make that the case.
- ensureRows(int) - Method in interface edu.cmu.tetrad.data.DataSet
-
Ensures that the dataset has at least
rowsrows. - ensureRows(int) - Method in class edu.cmu.tetrad.data.NumberObjectDataSet
-
Ensures that the dataset has at least the number of rows, adding rows if necessary to make that the case.
- ensureSymmetry() - Method in class edu.cmu.tetrad.search.utils.GraphoidAxioms
-
Sets symmetry as assumed--i.e., ensures that X ⊥⊥ Y | Z ==> Y ⊥⊥ X | Z.
- ensureTriviality() - Method in class edu.cmu.tetrad.search.utils.GraphoidAxioms
-
Sets whether triviality as assumed.
- entropy - Enum constant in enum class edu.cmu.tetrad.search.Lofs.Score
- entropy(int[]) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.reveal.RevealEvaluator
-
This method computes the entropy of a binary signal stored in an int array.
- entropy(int[]) - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.LTestReveal
- entropy(int[]) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.RevealEvaluator
-
This method computes the entropy of a binary signal stored in an int array.
- entropy(int, double[]) - Static method in class edu.cmu.tetrad.util.StatUtils
- entropy(int, int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.reveal.RevealEvaluator
-
This method implements the same definition of entropy as above but this specialized version is intended to be used by the mutualInformation method (viz).
- entropy(int, int) - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.LTestReveal
- entropy(int, int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.RevealEvaluator
-
This method implements the same definition of entropy as above but this specialized version is intended to be used by the mutualInformation method (viz).
- EOF - Enum constant in enum class edu.cmu.tetrad.calculator.parser.Token
- Epinechnikov - Enum constant in enum class edu.cmu.tetrad.search.test.ConditionalCorrelationIndependence.Kernel
- EQ - Static variable in class edu.cmu.tetrad.sem.ParamComparison
-
Indicates that the first parameter is equal to the second.
- EQ - Static variable in class edu.cmu.tetrad.sem.ParamConstraintType
-
An "equal to" constraint.
- equalCounts(Node, int) - Method in class edu.cmu.tetrad.data.Discretizer
-
Sets the given node to discretized using evenly distributed values using the given number of categories.
- equalIntervals(Node, int) - Method in class edu.cmu.tetrad.data.Discretizer
-
Sets the given node to discretized using evenly spaced intervals using the given number of categories.
- equals(double[][], double[][]) - Static method in class edu.cmu.tetrad.util.MatrixUtils
-
Tests two matrices for equality.
- equals(double[][], double[][], double) - Static method in class edu.cmu.tetrad.util.MatrixUtils
-
Tests to see whether two matrices are equal within the given tolerance.
- equals(double[], double[]) - Static method in class edu.cmu.tetrad.util.MatrixUtils
-
Tests two vectors for equality.
- equals(double[], double[], double) - Static method in class edu.cmu.tetrad.util.MatrixUtils
-
Tests to see whether two vectors are equal within the given tolerance.
- equals(ScoredGraph) - Method in class edu.cmu.tetrad.search.score.ScoredGraph
- equals(Matrix2, double) - Method in class edu.cmu.tetrad.util.Matrix2
- equals(Matrix, double) - Method in class edu.cmu.tetrad.util.Matrix
- equals(Object) - Method in interface edu.cmu.tetrad.bayes.BayesIm
-
Returns true iff this Bayes net is equal to the given Bayes net.
- equals(Object) - Method in class edu.cmu.tetrad.bayes.BayesPm
-
Will return true if the argument is a BayesPm with the same graph and variables.
- equals(Object) - Method in class edu.cmu.tetrad.bayes.DirichletBayesIm
- equals(Object) - Method in class edu.cmu.tetrad.bayes.Evidence
- equals(Object) - Method in class edu.cmu.tetrad.bayes.Manipulation
- equals(Object) - Method in class edu.cmu.tetrad.bayes.MlBayesIm
- equals(Object) - Method in class edu.cmu.tetrad.bayes.MlBayesImObs
- equals(Object) - Method in class edu.cmu.tetrad.bayes.Proposition
- equals(Object) - Method in class edu.cmu.tetrad.bayes.UpdatedBayesIm
- equals(Object) - Method in class edu.cmu.tetrad.data.BoxDataSet
- equals(Object) - Method in class edu.cmu.tetrad.data.Clusters
- equals(Object) - Method in class edu.cmu.tetrad.data.ContinuousVariable
-
Two continuous variables are equal if they have the same name and the same missing value marker.
- equals(Object) - Method in class edu.cmu.tetrad.data.DataModelList
- equals(Object) - Method in interface edu.cmu.tetrad.data.DataSet
- equals(Object) - Method in class edu.cmu.tetrad.data.DiscreteVariable
- equals(Object) - Method in class edu.cmu.tetrad.data.Knowledge
-
Two Knowledge objects are equal just in case their forbidden and required edges are equal, and their tiers are equal.
- equals(Object) - Method in class edu.cmu.tetrad.data.KnowledgeEdge
-
Reteurns true if (from1, to1) == (from2, to2).
- equals(Object) - Method in class edu.cmu.tetrad.data.KnowledgeGroup
-
Equals when they are the same type and have the same edges.
- equals(Object) - Method in class edu.cmu.tetrad.data.NumberObjectDataSet
- equals(Object) - Method in class edu.cmu.tetrad.graph.Dag
- equals(Object) - Method in class edu.cmu.tetrad.graph.Edge
-
Two edges are equal just in case they connect the same nodes and have the same endpoints proximal to each node.
- equals(Object) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
- equals(Object) - Method in interface edu.cmu.tetrad.graph.Graph
-
Determines whether this graph is equal to some other graph, in the sense that they contain the same nodes and the sets of edges defined over these nodes in the two graphs are isomorphic typewise.
- equals(Object) - Method in class edu.cmu.tetrad.graph.GraphNode
-
Two continuous variables are equal if they have the same name and the same missing value marker.
- equals(Object) - Method in class edu.cmu.tetrad.graph.IndependenceFact
- equals(Object) - Method in interface edu.cmu.tetrad.graph.Node
-
Tests whether this variable is equal to the given variable.
- equals(Object) - Method in class edu.cmu.tetrad.graph.NodePair
- equals(Object) - Method in class edu.cmu.tetrad.graph.OrderedPair
- equals(Object) - Method in class edu.cmu.tetrad.graph.SemGraph
- equals(Object) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- equals(Object) - Method in class edu.cmu.tetrad.graph.Triple
- equals(Object) - Method in class edu.cmu.tetrad.search.utils.GraphoidAxioms.GraphoidIndFact
- equals(Object) - Method in class edu.cmu.tetrad.search.utils.PossibleMConnectingPath
- equals(Object) - Method in class edu.cmu.tetrad.search.utils.SepsetMap
-
Checks equality of this to another sepset map.
- equals(Object) - Method in class edu.cmu.tetrad.search.utils.Sextad
-
Returns a judgment of equality with another Sextad instance.
- equals(Object) - Method in class edu.cmu.tetrad.search.utils.Tetrad
- equals(Object) - Method in class edu.cmu.tetrad.search.work_in_progress.DMSearch
- equals(Object) - Method in class edu.cmu.tetrad.search.work_in_progress.GraphChange
-
Equals is defined such that if the internal strucs of this GraphChange all individually equal the corresponding strucs of GraphChange gc, then this "equals" gc
- equals(Object) - Method in class edu.cmu.tetrad.search.work_in_progress.HbsmsGes.GraphWithPValue
- equals(Object) - Method in class edu.cmu.tetrad.search.work_in_progress.SepsetMapDci
- equals(Object) - Method in class edu.cmu.tetrad.search.work_in_progress.Sextad
- equals(Object) - Method in class edu.cmu.tetrad.sem.ParameterPair
-
Tests whether this object pair is equal to a second object pair by looking to see whether each element a and b is equal to its corresponding element.
- equals(Object) - Method in class edu.cmu.tetrad.sem.SemEvidence
- equals(Object) - Method in class edu.cmu.tetrad.sem.SemManipulation
- equals(Object) - Method in class edu.cmu.tetrad.sem.SemProposition
- equals(Object) - Method in class edu.cmu.tetrad.session.Type1
- equals(Object) - Method in class edu.cmu.tetrad.session.Type2
- equals(Object) - Method in class edu.cmu.tetrad.session.Type3
- equals(Object) - Method in class edu.cmu.tetrad.session.Type4
- equals(Object) - Method in class edu.cmu.tetrad.session.Type5
- equals(Object) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.IndexedParent
-
Returns true iff the lags and indices are equal.
- equals(Object) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.LaggedFactor
-
Two lagged factors are equals just in case their factors are equals and their lags are equal.
- equals(Object) - Method in class edu.cmu.tetrad.util.PointXy
- equals(Object) - Method in class edu.cmu.tetrad.util.Vector
- equals(Object) - Method in class edu.cmu.tetrad.util.Version
- Equation - Class in edu.cmu.tetrad.calculator.expression
-
Represents an equation of the form Variable = Expression, where the Variable represents a column in some dataset.
- Equation(String, Expression, String) - Constructor for class edu.cmu.tetrad.calculator.expression.Equation
- EQUATION - Enum constant in enum class edu.cmu.tetrad.calculator.parser.Token
- ERDOS_RENYI_DAG - Static variable in class edu.cmu.tetrad.algcomparison.graph.GraphTypes
- ErdosRenyi - Class in edu.cmu.tetrad.algcomparison.graph
-
Creates a random graph by the Erdos-Renyi method (probabiliy of edge fixed, # edges not).
- ErdosRenyi() - Constructor for class edu.cmu.tetrad.algcomparison.graph.ErdosRenyi
- erf(double) - Static method in class edu.cmu.tetrad.util.StatUtils
-
Calculates the error function for a double
- error(String) - Method in class edu.cmu.tetrad.util.TetradLogger
-
Logs an error, this will log the message regardless of any configuration information.
- ERROR - Static variable in class edu.cmu.tetrad.graph.NodeType
- errorEval(Graph, Graph) - Static method in class edu.cmu.tetrad.simulation.HsimUtils
- ERRORS_NORMAL - Static variable in class edu.cmu.tetrad.util.Params
- esp(TeyssierScorer) - Method in class edu.cmu.tetrad.search.work_in_progress.OtherPermAlgs
- ESP - Enum constant in enum class edu.cmu.tetrad.search.work_in_progress.OtherPermAlgs.Method
- estimate() - Method in class edu.cmu.tetrad.sem.SemEstimator
-
Runs the estimator on the data and SemPm passed in through the constructor.
- estimate() - Method in class edu.cmu.tetrad.sem.SemEstimatorGibbs
-
Runs the estimator on the data and SemPm passed in through the constructor.
- estimate(BayesPm, DataSet) - Method in interface edu.cmu.tetrad.bayes.EmBayesProperties.Estimator
- estimate(BayesPm, DataSet) - Method in class edu.cmu.tetrad.bayes.MlBayesEstimator
-
33 Estimates a Bayes IM using the variables, graph, and parameters in the given Bayes PM and the data columns in the given data set.
- estimate(DirichletBayesIm, DataSet) - Static method in class edu.cmu.tetrad.bayes.DirichletEstimator
- estimate(GeneralizedSemPm, DataSet) - Method in class edu.cmu.tetrad.sem.GeneralizedSemEstimator
-
Maximizes likelihood equation by equation.
- Estimate(double[][], double[][], double) - Static method in class edu.cmu.tetrad.search.utils.EstimateRank
-
Estimate rank from data.
- Estimate(int[], int[], double[][], int, double) - Static method in class edu.cmu.tetrad.search.utils.EstimateRank
-
Estimate rank from covariance matrix.
- EstimateRank - Class in edu.cmu.tetrad.search.utils
-
Estimates the rank of a matrix.
- EstimateRank() - Constructor for class edu.cmu.tetrad.search.utils.EstimateRank
- estimateW(DataSet, int, double, double) - Static method in class edu.cmu.tetrad.search.IcaLingD
-
Estimates the W matrix using FastICA.
- eval(double, double) - Method in interface edu.cmu.tetrad.search.utils.Kernel
-
Evaluates the kernel at two points in the input space
- eval(double, double) - Method in class edu.cmu.tetrad.search.utils.KernelGaussian
-
Evaluates the kernel at two given points
- evalEdges(Graph, Set<Node>, Set<Node>) - Static method in class edu.cmu.tetrad.simulation.HsimUtils
- evaluate(double[]) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.Polynomial
-
Evaluates the term.
- evaluate(double[]) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.PolynomialTerm
-
Evaluates the term.
- evaluate(Context) - Method in class edu.cmu.tetrad.calculator.expression.ConstantExpression
- evaluate(Context) - Method in class edu.cmu.tetrad.calculator.expression.EvaluationExpression
- evaluate(Context) - Method in interface edu.cmu.tetrad.calculator.expression.Expression
-
Evaluates the expression using the given context
- evaluate(Context) - Method in class edu.cmu.tetrad.calculator.expression.VariableExpression
- evaluateGeneric(Context) - Method in class edu.cmu.tetrad.calculator.expression.VariableExpression
- EvaluationExpression - Class in edu.cmu.tetrad.calculator.expression
-
An equation expression.
- EvaluationExpression(VariableExpression, String) - Constructor for class edu.cmu.tetrad.calculator.expression.EvaluationExpression
- EVENLY_DISTRIBUTED_INTERVALS - Static variable in class edu.cmu.tetrad.data.ContinuousDiscretizationSpec
- EVENLY_DISTRIBUTED_VALUES - Static variable in class edu.cmu.tetrad.data.ContinuousDiscretizationSpec
-
The types of discretization
- evenSplitVector(double, int) - Static method in class edu.pitt.csb.mgm.MixedUtils
- Evidence - Class in edu.cmu.tetrad.bayes
-
Stores information for a variable source about evidence we have for each variable as well as whether each variable has been manipulated.
- Evidence(Evidence) - Constructor for class edu.cmu.tetrad.bayes.Evidence
-
Copy constructor.
- Evidence(Evidence, VariableSource) - Constructor for class edu.cmu.tetrad.bayes.Evidence
- Evidence(Proposition) - Constructor for class edu.cmu.tetrad.bayes.Evidence
-
Wraps the proposition.
- ExampleCompareFromFiles - Class in edu.cmu.tetrad.algcomparison.examples
-
An example script to load in data sets and graphs from files and analyze them.
- ExampleCompareFromFiles - Class in edu.cmu.tetrad.study.examples.conditions
-
An example script to load in data sets and graphs from files and analyze them.
- ExampleCompareFromFiles() - Constructor for class edu.cmu.tetrad.algcomparison.examples.ExampleCompareFromFiles
- ExampleCompareFromFiles() - Constructor for class edu.cmu.tetrad.study.examples.conditions.ExampleCompareFromFiles
- ExampleCompareSimulation - Class in edu.cmu.tetrad.algcomparison.examples
-
An example script to simulate data and run a comparison analysis on it.
- ExampleCompareSimulation - Class in edu.cmu.tetrad.study.examples.conditions
-
An example script to simulate data and run a comparison analysis on it.
- ExampleCompareSimulation() - Constructor for class edu.cmu.tetrad.algcomparison.examples.ExampleCompareSimulation
- ExampleCompareSimulation() - Constructor for class edu.cmu.tetrad.study.examples.conditions.ExampleCompareSimulation
- ExampleCompareSimulation2 - Class in edu.cmu.tetrad.algcomparison.examples
-
An example script to simulate data and run a comparison analysis on it.
- ExampleCompareSimulation2() - Constructor for class edu.cmu.tetrad.algcomparison.examples.ExampleCompareSimulation2
- ExampleCompareSimulationDiscrete - Class in edu.cmu.tetrad.study.examples.conditions
-
An example script to simulate data and run a comparison analysis on it.
- ExampleCompareSimulationDiscrete() - Constructor for class edu.cmu.tetrad.study.examples.conditions.ExampleCompareSimulationDiscrete
- ExampleCompareSimulationTimeSeries - Class in edu.cmu.tetrad.algcomparison.examples
-
An example script to simulate time series data and run a comparison analysis on it.
- ExampleCompareSimulationTimeSeries() - Constructor for class edu.cmu.tetrad.algcomparison.examples.ExampleCompareSimulationTimeSeries
- ExampleFirstInflection - Class in edu.cmu.tetrad.study.examples.conditions
-
An example script to simulate data and run a comparison analysis on it.
- ExampleFirstInflection() - Constructor for class edu.cmu.tetrad.study.examples.conditions.ExampleFirstInflection
- ExampleMixedSearch - Class in edu.pitt.csb.mgm
-
Created by ajsedgewick on 8/18/15.
- ExampleMixedSearch() - Constructor for class edu.pitt.csb.mgm.ExampleMixedSearch
- ExampleNonlinearSave - Class in edu.cmu.tetrad.algcomparison.examples
-
An example script to save out data files and graphs from a simulation.
- ExampleNonlinearSave() - Constructor for class edu.cmu.tetrad.algcomparison.examples.ExampleNonlinearSave
- ExampleSave - Class in edu.cmu.tetrad.algcomparison.examples
-
An example script to save out data files and graphs from a simulation.
- ExampleSave - Class in edu.cmu.tetrad.study.examples.conditions
-
An example script to save out data files and graphs from a simulation.
- ExampleSave() - Constructor for class edu.cmu.tetrad.algcomparison.examples.ExampleSave
- ExampleSave() - Constructor for class edu.cmu.tetrad.study.examples.conditions.ExampleSave
- ExampleStars - Class in edu.cmu.tetrad.study.examples.conditions
-
An example script to simulate data and run a comparison analysis on it.
- ExampleStars() - Constructor for class edu.cmu.tetrad.study.examples.conditions.ExampleStars
- Executable - Interface in edu.cmu.tetrad.session
-
Interface indicating that a class can be executed as an algorithm.
- execute() - Method in interface edu.cmu.tetrad.session.Executable
-
Executes the algorithm.
- execute(SessionNode, boolean) - Method in class edu.cmu.tetrad.session.SimulationStudy
-
Executes the given node the specified number of times.
- EXECUTION_STARTED - Static variable in class edu.cmu.tetrad.session.SessionEvent
- ExecutionRestarter - Interface in edu.cmu.tetrad.session
-
Interface indicating that a parameter object can and should be reinitialized at each new execution in a simulation edu.cmu.tetrad.study.
- executionStarted(SessionEvent) - Method in class edu.cmu.tetrad.session.SessionAdapter
-
Indicates that a new execution of a simulation edu.cmu.tetrad.study has begun.
- executionStarted(SessionEvent) - Method in interface edu.cmu.tetrad.session.SessionListener
-
Indicates that a new execution of a simulation edu.cmu.tetrad.study has begun.
- exhaustiveSearch(int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.reveal.RevealSearch
-
This method computes m/e values for all single regulators, pairs and triples at a given time lag.
- exhaustiveSearch(int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.RevealSearch
-
This method computes m/e values for all single regulators, pairs and triples at a given time lag.
- exhaustiveSearch(int, int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.RevealSearch
-
This method computes m/e values for all single regulators, pairs and triples between two time lags (inclusively).
- existsCombination() - Method in class edu.cmu.tetrad.bayes.Proposition
- existsCommonAncestor(Graph, Edge) - Static method in class edu.cmu.tetrad.algcomparison.statistic.CommonAncestorTruePositiveBidirected
- existsCommonAncestor(Graph, Edge) - Static method in class edu.cmu.tetrad.algcomparison.statistic.NumCommonMeasuredAncestorBidirected
- existsConstructor(Class, Class[]) - Method in class edu.cmu.tetrad.session.SessionNode
-
Tests whether the model class has an argument that takes all of the given argument classes (or more) as arguments.
- existsDirectedCycle() - Method in class edu.cmu.tetrad.graph.Paths
- existsDirectedPathFromTo(Graph, Node, Node) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumDirectedEdgeNoMeasureAncestors
- existsDirectedPathFromTo(Node, Node) - Method in class edu.cmu.tetrad.graph.Paths
- existsDirectedPathFromTo(Node, Node, int) - Method in class edu.cmu.tetrad.graph.Paths
- existsEdge(String, LaggedFactor) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ActiveLagGraph
- existsEdge(String, LaggedFactor) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ManualLagGraph
- existsEdge(String, LaggedFactor) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.BasicLagGraph
-
Determines whether the edge to 'factor' at time lag 0 from 'laggedFactor' exists in the graph.
- existsEdge(String, LaggedFactor) - Method in interface edu.cmu.tetrad.study.gene.tetrad.gene.history.LagGraph
-
Determines whether the edge to 'factor' at time lag 0 from 'laggedFactor' exists in the graph.
- existsEdgeCoef(Node, Node) - Method in class edu.cmu.tetrad.sem.SemIm
- existsFactor(String) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ActiveLagGraph
- existsFactor(String) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ManualLagGraph
- existsFactor(String) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.BasicLagGraph
-
Determines whether the given factor exists in the graph.
- existsFactor(String) - Method in interface edu.cmu.tetrad.study.gene.tetrad.gene.history.LagGraph
-
Determines whether the given factor exists in the graph.
- existsInducingPath(Node, Node) - Method in class edu.cmu.tetrad.graph.Paths
-
Determines whether an inducing path exists between node1 and node2, given a set O of observed nodes and a set sem of conditioned nodes.
- existsInducingPathInto(Node, Node, Graph) - Static method in class edu.cmu.tetrad.search.utils.DagToPag
- existsInducingPathInto(Node, Node, Graph, Knowledge) - Static method in class edu.cmu.tetrad.search.utils.TsDagToPag
- existsInducingPathVisit(Node, Node, Node, Node, LinkedList<Node>) - Method in class edu.cmu.tetrad.graph.Paths
- existsInducingPathVisitts(Graph, Node, Node, Node, Node, LinkedList<Node>, Knowledge) - Static method in class edu.cmu.tetrad.search.utils.TsDagToPag
- existsLatentCommonAncestor(Graph, Edge) - Static method in class edu.cmu.tetrad.algcomparison.statistic.LatentCommonAncestorTruePositiveBidirected
- existsMissingValue() - Method in class edu.cmu.tetrad.data.BoxDataSet
- existsMissingValue() - Method in interface edu.cmu.tetrad.data.DataSet
-
Returns true if and only if this data set contains at least one missing value.
- existsMissingValue() - Method in class edu.cmu.tetrad.data.NumberObjectDataSet
- existsParameterizedConstructor(Class) - Method in class edu.cmu.tetrad.session.SessionNode
- existsSemiDirectedPath(Node, Node) - Method in class edu.cmu.tetrad.graph.Paths
- existsSemiDirectedPath(Node, Set<Node>) - Method in class edu.cmu.tetrad.graph.Paths
- existsTrek(Node, Node) - Method in class edu.cmu.tetrad.graph.Paths
-
Determines whether a trek exists between two nodes in the graph.
- exp - Enum constant in enum class edu.cmu.tetrad.search.Lofs.Score
- exp(Matrix) - Static method in class jgpml.covariancefunctions.MatrixOperations
-
Computes the exponential of the input
Matrix - EXP - Static variable in class edu.cmu.tetrad.search.FastIca
-
The other function type that can be used to approximate negative entropy.
- expandTemplate(String, GeneralizedSemPm, Node) - Method in class edu.cmu.tetrad.sem.TemplateExpander
-
Returns the expanded template, which needs to be checked to make sure it can be used.
- experiment(String, int, int, int, double, double, boolean, boolean, double, double, String, int) - Method in class edu.cmu.tetrad.study.RBExperiments
- Experimental - Interface in edu.cmu.tetrad.util
-
Tags a file as experimental so it's not listed in the configuration.
- Experimental - Annotation Interface in edu.cmu.tetrad.annotation
-
Oct 17, 2017 11:40:50 AM
- ExploreComparison - Class in edu.cmu.tetrad.study.performance
-
Runs algorithm on data set (simulation is OK), printing out error statistics.
- ExploreComparison() - Constructor for class edu.cmu.tetrad.study.performance.ExploreComparison
- ExploreIndepTests - Class in edu.pitt.csb.mgm
-
Created by ajsedgewick on 9/10/15.
- ExploreIndepTests() - Constructor for class edu.pitt.csb.mgm.ExploreIndepTests
- Exponential - Class in edu.cmu.tetrad.util.dist
-
Wraps a chi square distribution for purposes of drawing random samples.
- Exponential(double) - Constructor for class edu.cmu.tetrad.util.dist.Exponential
- Expression - Interface in edu.cmu.tetrad.calculator.expression
-
Represents a mathematical expression.
- ExpressionDescriptor - Interface in edu.cmu.tetrad.calculator.expression
-
Represents a definition for some expression.
- ExpressionDescriptor.Position - Enum Class in edu.cmu.tetrad.calculator.expression
- ExpressionInitializationException - Exception in edu.cmu.tetrad.calculator.expression
-
Thrown if the expression can't be parsed, for instance, if it has the wrong number of arguments.
- ExpressionInitializationException(String) - Constructor for exception edu.cmu.tetrad.calculator.expression.ExpressionInitializationException
- ExpressionLexer - Class in edu.cmu.tetrad.calculator.parser
-
Parses the tokens of an expression.
- ExpressionLexer(CharSequence) - Constructor for class edu.cmu.tetrad.calculator.parser.ExpressionLexer
- ExpressionManager - Class in edu.cmu.tetrad.calculator.expression
-
Manager for expressions, this includes all implementations of expression descriptors for the calculator.
- ExpressionParser - Class in edu.cmu.tetrad.calculator.parser
-
Parses a string into a tree-like expression.
- ExpressionParser() - Constructor for class edu.cmu.tetrad.calculator.parser.ExpressionParser
-
Constructrs a parser that has no allowable parameters.
- ExpressionParser(Collection<String>, ExpressionParser.RestrictionType) - Constructor for class edu.cmu.tetrad.calculator.parser.ExpressionParser
-
Constructs the parser given a collection of allowable parameters.
- ExpressionParser.RestrictionType - Enum Class in edu.cmu.tetrad.calculator.parser
-
The type of restriction on parameters.
- ExpressionSignature - Interface in edu.cmu.tetrad.calculator.expression
-
Represents the signature of the expression, for example sqrt(number).
- expScore(double[]) - Static method in class edu.cmu.tetrad.util.StatUtils
- expUnstandardized - Enum constant in enum class edu.cmu.tetrad.search.Lofs.Score
- expUnstandardizedInverted - Enum constant in enum class edu.cmu.tetrad.search.Lofs.Score
- EXTERNAL_GRAPH - Enum constant in enum class edu.cmu.tetrad.search.Fask.AdjacencyMethod
- ExternalAlgorithm - Class in edu.cmu.tetrad.algcomparison.algorithm
-
Tags an an algorithm that loads up external graphs for inclusion in reports.
- ExternalAlgorithm() - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.ExternalAlgorithm
- ExternalAlgorithmBnlearnMmhc - Class in edu.cmu.tetrad.algcomparison.algorithm.external
-
An API to allow results from external algorithms to be included in a report through the algrorithm comparison tool.
- ExternalAlgorithmBnlearnMmhc(String) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.external.ExternalAlgorithmBnlearnMmhc
- ExternalAlgorithmBnlearnMmhc(String, String) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.external.ExternalAlgorithmBnlearnMmhc
- ExternalAlgorithmBNTPc - Class in edu.cmu.tetrad.algcomparison.algorithm.external
-
An API to allow results from external algorithms to be included in a report through the algrorithm comparison tool.
- ExternalAlgorithmBNTPc(String) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.external.ExternalAlgorithmBNTPc
- ExternalAlgorithmBNTPc(String, String) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.external.ExternalAlgorithmBNTPc
- ExternalAlgorithmIntersection - Class in edu.cmu.tetrad.algcomparison.algorithm.external
-
An API to allow results from external algorithms to be included in a report through the algrorithm comparison tool.
- ExternalAlgorithmIntersection(String, ExternalAlgorithm...) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.external.ExternalAlgorithmIntersection
- ExternalAlgorithmPcalgGes - Class in edu.cmu.tetrad.algcomparison.algorithm.external
-
An API to allow results from external algorithms to be included in a report through the algrorithm comparison tool.
- ExternalAlgorithmPcalgGes(String) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.external.ExternalAlgorithmPcalgGes
- ExternalAlgorithmPcalgGes(String, String) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.external.ExternalAlgorithmPcalgGes
- ExternalAlgorithmPcalgPc - Class in edu.cmu.tetrad.algcomparison.algorithm.external
-
An API to allow results from external algorithms to be included in a report through the algrorithm comparison tool.
- ExternalAlgorithmPcalgPc(String) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.external.ExternalAlgorithmPcalgPc
- ExternalAlgorithmPcalgPc(String, String) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.external.ExternalAlgorithmPcalgPc
- ExternalAlgorithmTetrad - Class in edu.cmu.tetrad.algcomparison.algorithm.external
-
An API to allow results from external algorithms to be included in a report through the algrorithm comparison tool.
- ExternalAlgorithmTetrad(String) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.external.ExternalAlgorithmTetrad
- ExternalAlgorithmTetrad(String, String) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.external.ExternalAlgorithmTetrad
- ExtraCategoryInterpolator - Class in edu.cmu.tetrad.bayes
-
Returns a data set in variables for columns with missing values are augmented with an extra category that represents the missing values, with missing values being reported as belong this category.
- ExtraCategoryInterpolator() - Constructor for class edu.cmu.tetrad.bayes.ExtraCategoryInterpolator
- extractFactor_Display(String) - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.DisplayNameHandler
-
Parses the given string representing a lagged factor and return the part that represents the factor.
- extractLag_Display(String) - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.DisplayNameHandler
-
Extracts the lag from the lagged factor name string.
F
- F1Adj - Class in edu.cmu.tetrad.algcomparison.statistic
-
Calculates the F1 statistic for adjacencies.
- F1Adj() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.F1Adj
- F1All - Class in edu.cmu.tetrad.algcomparison.statistic
-
Calculates the F1 statistic for adjacencies.
- F1All() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.F1All
- F1Arrow - Class in edu.cmu.tetrad.algcomparison.statistic
-
Calculates the F1 statistic for arrowheads.
- F1Arrow() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.F1Arrow
- FactorAnalysis - Class in edu.cmu.tetrad.algcomparison.algorithm.other
-
Factor analysis.
- FactorAnalysis - Class in edu.cmu.tetrad.search
-
Implements the classical Factor Analysis algorithm.
- FactorAnalysis() - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.other.FactorAnalysis
- FactorAnalysis(DataSet) - Constructor for class edu.cmu.tetrad.search.FactorAnalysis
-
Constructor.
- FactorAnalysis(ICovarianceMatrix) - Constructor for class edu.cmu.tetrad.search.FactorAnalysis
-
Constructor.
- FactoredBayesStructuralEM - Class in edu.cmu.tetrad.bayes
-
Implements the procedure Factored-Bayesian-SEM found on page 6 of "The Bayesian Structural EM Algorithm" by Nir Friedman.> 0
- FactoredBayesStructuralEM(DataSet, BayesPm) - Constructor for class edu.cmu.tetrad.bayes.FactoredBayesStructuralEM
- factorial(int) - Static method in class edu.cmu.tetrad.util.MathUtils
- factorial(int) - Static method in class edu.cmu.tetrad.util.StatUtils
- FAITHFULNESS_ASSUMED - Static variable in class edu.cmu.tetrad.util.Params
- FalseNegativesAdjacencies - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- FalseNegativesAdjacencies() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.FalseNegativesAdjacencies
- FalsePositiveAdjacencies - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- FalsePositiveAdjacencies() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.FalsePositiveAdjacencies
- Fas - Class in edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag
-
Fast Adjacency Search (FAS)--i.e., the PC adjacency step, which is used in many algorithms.
- Fas - Class in edu.cmu.tetrad.search
-
Implements the Fast Adjacency Search (FAS), which is the adjacency search of the PC algorithm (see).
- Fas() - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Fas
- Fas(IndependenceWrapper) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Fas
- Fas(IndependenceTest) - Constructor for class edu.cmu.tetrad.search.Fas
-
Constructor.
- FAS_RULE - Static variable in class edu.cmu.tetrad.util.Params
- FAS_SEPSETS - Enum constant in enum class edu.cmu.tetrad.search.utils.PcCommon.ColliderDiscovery
- FAS_STABLE - Enum constant in enum class edu.cmu.tetrad.search.Fask.AdjacencyMethod
- Fas2 - Class in edu.cmu.tetrad.search.work_in_progress
-
Implements the "fast adjacency search" used in several causal algorithm in this package.
- Fas2(Graph, IndependenceTest) - Constructor for class edu.cmu.tetrad.search.work_in_progress.Fas2
-
Constructs a new FastAdjacencySearch.
- Fas2(IndependenceTest) - Constructor for class edu.cmu.tetrad.search.work_in_progress.Fas2
- Fas3 - Class in edu.cmu.tetrad.search.work_in_progress
-
Implements the Fast Adjacency Search (FAS), which is the adjacency search of the PC algorithm (see).
- Fas3(IndependenceTest) - Constructor for class edu.cmu.tetrad.search.work_in_progress.Fas3
-
Constructor.
- Fasd - Class in edu.cmu.tetrad.search
-
Adjusts FAS (see) for the deterministic case by refusing to removed edges based on conditional independence tests that are judged to be deterministic.
- Fasd(IndependenceTest) - Constructor for class edu.cmu.tetrad.search.Fasd
-
Constructs a new FastAdjacencySearch.
- FasDci - Class in edu.cmu.tetrad.search.work_in_progress
-
Implements a modified version of the the "fast adjacency search" for use in the Distributed Causal Inference (DCI) algorithm.
- FasDci(Graph, IndependenceTest) - Constructor for class edu.cmu.tetrad.search.work_in_progress.FasDci
-
Constructs a new FastAdjacencySearch for DCI.
- FasDci(Graph, IndependenceTest, ResolveSepsets.Method, List<Set<Node>>, List<IndependenceTest>, SepsetMapDci, SepsetMapDci) - Constructor for class edu.cmu.tetrad.search.work_in_progress.FasDci
-
Constructs a new FastAdjacencySearch for DCI with independence test pooling to resolve inconsistencies.
- FasFdr - Class in edu.cmu.tetrad.search.work_in_progress
-
Implements the "fast adjacency search" used in several causal algorithm in this package.
- FasFdr(IndependenceTest, int) - Constructor for class edu.cmu.tetrad.search.work_in_progress.FasFdr
-
Constructs a new FastAdjacencySearch.
- Fask - Class in edu.cmu.tetrad.algcomparison.algorithm.multi
-
Wraps the IMaGES algorithm for continuous variables.
- Fask - Class in edu.cmu.tetrad.search
-
Implements the FASK (Fast Adjacency Skewness) algorithm, which makes decisions for adjacency and orientation using a combination of conditional independence testing, judgments of nonlinear adjacency, and pairwise orientation due to non-Gaussianity.
- Fask() - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.multi.Fask
- Fask(IndependenceWrapper, ScoreWrapper) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.multi.Fask
- Fask(DataSet, Score, IndependenceTest) - Constructor for class edu.cmu.tetrad.search.Fask
-
Constructor.
- FASK_ADJACENCY_METHOD - Static variable in class edu.cmu.tetrad.util.Params
- FASK_DELTA - Static variable in class edu.cmu.tetrad.util.Params
- FASK_LEFT_RIGHT_RULE - Static variable in class edu.cmu.tetrad.util.Params
- FASK_NONEMPIRICAL - Static variable in class edu.cmu.tetrad.util.Params
- Fask.AdjacencyMethod - Enum Class in edu.cmu.tetrad.search
-
Enumerates the alternatives to use for finding the initial adjacencies for FASK.
- Fask.LeftRight - Enum Class in edu.cmu.tetrad.search
-
Enumerates the options left-right rules to use for FASK.
- FASK1 - Enum constant in enum class edu.cmu.tetrad.search.Fask.LeftRight
- FASK2 - Enum constant in enum class edu.cmu.tetrad.search.Fask.LeftRight
- FaskConcatenated - Class in edu.cmu.tetrad.algcomparison.algorithm.multi
-
Wraps the IMaGES algorithm for continuous variables.
- FaskConcatenated() - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.multi.FaskConcatenated
- FaskConcatenated(ScoreWrapper, IndependenceWrapper) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.multi.FaskConcatenated
- faskLeftRightV1(double[], double[], boolean, double) - Static method in class edu.cmu.tetrad.search.Fask
- faskLeftRightV2(double[], double[], boolean, double) - Static method in class edu.cmu.tetrad.search.Fask
- FaskLofsConcatenated - Class in edu.cmu.tetrad.algcomparison.algorithm.multi
-
Wraps the IMaGES algorithm for continuous variables.
- FaskLofsConcatenated(Lofs.Rule) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.multi.FaskLofsConcatenated
- FaskPw - Class in edu.cmu.tetrad.algcomparison.algorithm.pairwise
-
FASK-PW (pairwise).
- FaskPw() - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.pairwise.FaskPw
- FaskPw(Algorithm) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.pairwise.FaskPw
- FaskVote - Class in edu.cmu.tetrad.algcomparison.algorithm.multi
-
Wraps the MultiFask algorithm for continuous variables.
- FaskVote - Class in edu.cmu.tetrad.search.work_in_progress
-
Runs IMaGES on a list of algorithms and then produces a graph over the ImaGES adjacencies where each edge orientation is voted on by running FASK on each dataset in turn and voting on edge orientation.
- FaskVote() - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.multi.FaskVote
- FaskVote(IndependenceWrapper, ScoreWrapper) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.multi.FaskVote
- FaskVote(ScoreWrapper) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.multi.FaskVote
- FaskVote(List<DataSet>, ScoreWrapper, IndependenceWrapper) - Constructor for class edu.cmu.tetrad.search.work_in_progress.FaskVote
-
Constructor.
- FasLofs - Class in edu.cmu.tetrad.algcomparison.algorithm.multi
-
Wraps the IMaGES algorithm for continuous variables.
- FasLofs - Class in edu.cmu.tetrad.search.work_in_progress
-
Runs Fast Adjacency Search (FAS) and then orients each edge using the robust skew orientation algorithm.
- FasLofs(DataSet, Lofs.Rule) - Constructor for class edu.cmu.tetrad.search.work_in_progress.FasLofs
- FasLofs(Lofs.Rule) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.multi.FasLofs
- FAST_ICA_A - Static variable in class edu.cmu.tetrad.util.Params
- FAST_ICA_MAX_ITER - Static variable in class edu.cmu.tetrad.util.Params
- FAST_ICA_TOLERANCE - Static variable in class edu.cmu.tetrad.util.Params
- FastIca - Class in edu.cmu.tetrad.search
-
Translates a version of the FastICA algorithm used in R from Fortran into Java for use in Tetrad.
- FastIca(Matrix, int) - Constructor for class edu.cmu.tetrad.search.FastIca
-
Constructs an instance of the Fast ICA algorithm, taking as arguments the two arguments that cannot be defaulted: the data matrix itself and the number of components to be extracted.
- FastICA - Enum constant in enum class edu.cmu.tetrad.search.Lofs.Rule
- FastIca.IcaResult - Class in edu.cmu.tetrad.search
-
A list containing the following components
- fCdf(double, double, double) - Static method in class edu.cmu.tetrad.util.ProbUtils
-
F CDF.
- Fci - Class in edu.cmu.tetrad.algcomparison.algorithm.oracle.pag
-
FCI.
- Fci - Class in edu.cmu.tetrad.search
-
Implements the Fast Causal Inference (FCI) algorithm due to Peter Spirtes, which addressed the case where latent common causes cannot be assumed not to exist with respect to the data set being analyzed.
- Fci() - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Fci
- Fci(IndependenceWrapper) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Fci
- Fci(IndependenceTest) - Constructor for class edu.cmu.tetrad.search.Fci
-
Constructor.
- Fci(IndependenceTest, List<Node>) - Constructor for class edu.cmu.tetrad.search.Fci
-
Constructor.
- FCI - Enum constant in enum class edu.cmu.tetrad.study.performance.ComparisonParameters.Algorithm
- FciIod - Class in edu.cmu.tetrad.algcomparison.algorithm.multi
-
Runs FCI on multiple datasets using the IOD pooled dataset independence test.
- FciIod() - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.multi.FciIod
- FciIod(IndependenceWrapper) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.multi.FciIod
- FciMax - Class in edu.cmu.tetrad.algcomparison.algorithm.oracle.pag
-
FCI.
- FciMax - Class in edu.cmu.tetrad.search
-
Modifies FCI to do orientation of unshielded colliders (X*-*Y*-*Z with X and Z not adjacent) using the max-P rule (see the PC-Max algorithm).
- FciMax() - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.FciMax
- FciMax(IndependenceWrapper) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.FciMax
- FciMax(IndependenceTest) - Constructor for class edu.cmu.tetrad.search.FciMax
-
Constructor.
- FciOrient - Class in edu.cmu.tetrad.search.utils
-
Performs the final orientation steps of the FCI algorithms, which is a useful tool to use in a variety of FCI-like algorithms.
- FciOrient(SepsetProducer) - Constructor for class edu.cmu.tetrad.search.utils.FciOrient
-
Constructs a new FCI search for the given independence test and background knowledge.
- fciOrientbk(Knowledge, Graph, List<Node>) - Static method in class edu.cmu.tetrad.graph.GraphUtils
-
Orients according to background knowledge
- fciOrientbk(Knowledge, Graph, List<Node>) - Method in class edu.cmu.tetrad.search.utils.FciOrient
-
Orients according to background knowledge
- fdr - Enum constant in enum class edu.cmu.tetrad.search.utils.ResolveSepsets.Method
- fdr - Enum constant in enum class edu.cmu.tetrad.search.work_in_progress.ResolveSepsetsDci.Method
- fdr(double, List<Double>) - Static method in class edu.cmu.tetrad.util.StatUtils
- fdr(double, List<Double>, boolean, boolean) - Static method in class edu.cmu.tetrad.util.StatUtils
- fdrCutoff(double, List<Double>, boolean) - Static method in class edu.cmu.tetrad.util.StatUtils
- fdrCutoff(double, List<Double>, boolean, boolean) - Static method in class edu.cmu.tetrad.util.StatUtils
-
Calculates the cutoff value for p-values using the FDR method.
- fdrCutoff(double, List<Double>, int[], boolean, boolean) - Static method in class edu.cmu.tetrad.util.StatUtils
- fdrQ(List<Double>, int) - Static method in class edu.cmu.tetrad.util.StatUtils
- Fges - Class in edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag
-
FGES (the heuristic version).
- Fges - Class in edu.cmu.tetrad.search
-
Implements the Fast Greedy Equivalence Search (FGES) algorithm.
- Fges() - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Fges
- Fges(ScoreWrapper) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Fges
- Fges(Score) - Constructor for class edu.cmu.tetrad.search.Fges
-
Constructor.
- FGES - Enum constant in enum class edu.cmu.tetrad.search.Cstar.CpdagAlgorithm
- FGES - Enum constant in enum class edu.cmu.tetrad.search.Fask.AdjacencyMethod
- FGES - Enum constant in enum class edu.cmu.tetrad.study.performance.ComparisonParameters.Algorithm
- FGES2 - Enum constant in enum class edu.cmu.tetrad.study.performance.ComparisonParameters.Algorithm
- FgesConcatenated - Class in edu.cmu.tetrad.algcomparison.algorithm.multi
-
Requires that the parameter 'randomSelectionSize' be set to indicate how many datasets should be taken at a time (randomly).
- FgesConcatenated(ScoreWrapper) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.multi.FgesConcatenated
- FgesConcatenated(ScoreWrapper, boolean) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.multi.FgesConcatenated
- FgesConcatenated(ScoreWrapper, Algorithm) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.multi.FgesConcatenated
- FgesMb - Class in edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag
-
FGES-MB (the heuristic version).
- FgesMb - Class in edu.cmu.tetrad.search
-
Implements the Fast Greedy Equivalence Search (FGES) algorithm.
- FgesMb() - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.FgesMb
- FgesMb(ScoreWrapper) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.FgesMb
- FgesMb(Score) - Constructor for class edu.cmu.tetrad.search.FgesMb
-
Constructor.
- FgesMb.TrimmingStyle - Enum Class in edu.cmu.tetrad.search
- FgesMeasurement - Class in edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag
-
FGES (the heuristic version).
- FgesMeasurement(ScoreWrapper) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.FgesMeasurement
- FgesOrienter - Class in edu.cmu.tetrad.search.utils
-
This Orients a given undirected graph such that the edges in the graph are a superset of the edges in the oriented graph, using FGES method.
- FgesOrienter(DataSet) - Constructor for class edu.cmu.tetrad.search.utils.FgesOrienter
-
The data set must either be all continuous or all discrete.
- FgesWrapper(double...) - Constructor for class edu.pitt.csb.stability.SearchWrappers.FgesWrapper
- Fgls - Enum constant in enum class edu.cmu.tetrad.sem.ScoreType
- fifthMoment - Enum constant in enum class edu.cmu.tetrad.search.Lofs.Score
- FILE_OUT_PATH - Static variable in class edu.cmu.tetrad.util.Params
- fillIn(Graph, Node[]) - Static method in class edu.cmu.tetrad.bayes.GraphTools
-
Apply Tarjan and Yannakakis (1984) fill in algorithm for graph triangulation.
- filter(DataSet) - Method in class edu.cmu.tetrad.bayes.ExtraCategoryInterpolator
- filter(DataSet) - Method in class edu.cmu.tetrad.bayes.ModeInterpolator
- filter(DataSet) - Method in class edu.cmu.tetrad.data.CaseExpander
-
Expands cases for the given dataset.
- filter(DataSet) - Method in interface edu.cmu.tetrad.data.DataFilter
-
Interpolates the given data set, producing a data set with no missing values.
- filter(DataSet) - Method in class edu.cmu.tetrad.data.MeanInterpolator
- filterByAnnotation(List<AnnotatedClass<T>>, Class<? extends Annotation>) - Method in class edu.cmu.tetrad.annotation.AbstractAnnotations
-
Filter annotated classes by annotation type.
- filterByAnnotations(Class<? extends Annotation>, List<AnnotatedClass<T>>) - Static method in class edu.cmu.tetrad.annotation.AnnotatedClassUtils
-
Filters a list of annotated classes by the given annotation.
- filterOutByAnnotation(List<AnnotatedClass<T>>, Class<? extends Annotation>) - Method in class edu.cmu.tetrad.annotation.AbstractAnnotations
-
Filter out annotated classes by annotation type.
- filterOutExperimental(List<AnnotatedClass<Algorithm>>) - Method in class edu.cmu.tetrad.annotation.AlgorithmAnnotations
-
Filters out algorithms that are not for the given data type.
- filterOutExperimental(List<AnnotatedClass<Score>>) - Method in class edu.cmu.tetrad.annotation.ScoreAnnotations
- filterOutExperimental(List<AnnotatedClass<TestOfIndependence>>) - Method in class edu.cmu.tetrad.annotation.TestOfIndependenceAnnotations
- FIND_ONE_FACTOR_CLUSTERS - Enum constant in enum class edu.cmu.tetrad.search.utils.BpcAlgorithmType
- FIND_TWO_FACTOR_CLUSTERS - Enum constant in enum class edu.cmu.tetrad.search.utils.BpcAlgorithmType
- findCliques(int[][], int) - Static method in class edu.cmu.tetrad.graph.Paths.AllCliquesAlgorithm
- findComponents() - Method in class edu.cmu.tetrad.search.FastIca
-
Runs the Fast ICA algorithm (following the R version) and returns the list of result items that the R version returns.
- findHittingSet(List<Set<GraphChange>>) - Static method in class edu.cmu.tetrad.search.work_in_progress.IonHittingSet
-
takes a List of HashSets of GraphChanges, and returns a List of GraphChanges.
- findMb(Node) - Method in class edu.cmu.tetrad.search.GrowShrink
-
Finds the Markov blanket of the given target.
- findMb(Node) - Method in interface edu.cmu.tetrad.search.IMbSearch
-
Given the target, this returns all the nodes in the Markov Blanket.
- findMb(Node) - Method in class edu.cmu.tetrad.search.PcMb
-
Returns the Markov blanket variables (not the Markov blanket DAG).
- findMb(Node) - Method in class edu.cmu.tetrad.search.work_in_progress.Iamb
- findMb(Node) - Method in class edu.cmu.tetrad.search.work_in_progress.IambnPc
- findMb(Node) - Method in class edu.cmu.tetrad.search.work_in_progress.InterIamb
- findMb(Node) - Method in class edu.cmu.tetrad.search.work_in_progress.Mmmb
-
Searches for the Markov blanket of the node by the given name.
- findMConnectingPaths(Graph, Node, Node, Collection<Node>) - Static method in class edu.cmu.tetrad.search.utils.PossibleMConnectingPath
-
Finds all possible D-connection undirectedPaths as sub-graphs of the pag given at construction time from x to y given z.
- findMConnectingPathsOfLength(Graph, Node, Node, Collection<Node>, Integer) - Static method in class edu.cmu.tetrad.search.utils.PossibleMConnectingPath
-
Finds all possible D-connection undirectedPaths as sub-graphs of the pag given at construction time from x to y given z for a particular path length.
- findOptimalAssignment() - Method in class edu.cmu.tetrad.search.utils.HungarianAlgorithm
-
find an optimal assignment
- findTerm(int[]) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.Polynomial
-
Finds the first term matching the given profile.
- fine(String) - Method in class edu.cmu.tetrad.util.LogUtils
- finer(String) - Method in class edu.cmu.tetrad.util.LogUtils
- finest(String) - Method in class edu.cmu.tetrad.util.LogUtils
- fireAddingEdge() - Method in class edu.cmu.tetrad.session.SessionSupport
-
Fires an event indicating that an edge is about to be added.
- fireExecutionStarted() - Method in class edu.cmu.tetrad.session.SessionSupport
-
Fires an event indicating that an new execution of a node has begun.
- fireModelCreated(SessionNode) - Method in class edu.cmu.tetrad.session.SessionSupport
-
Fires an event indicating that a new model has been created for the given session node in the session.
- fireModelDestroyed(SessionNode) - Method in class edu.cmu.tetrad.session.SessionSupport
-
Fires an event indicating that the model for the given session node in the session has been destroyed.
- fireModelUnclear(SessionNode) - Method in class edu.cmu.tetrad.session.SessionSupport
-
Fires an event indicating that the model for the given session node in the session has been destroyed.
- fireNodeAdded(SessionNode) - Method in class edu.cmu.tetrad.session.SessionSupport
-
Fires an event indicating that a session node has been added to the session.
- fireNodeRemoved(SessionNode) - Method in class edu.cmu.tetrad.session.SessionSupport
-
Fires an event indicating that a sesison node has been removed from the session.
- fireParentAdded(SessionNode, SessionNode) - Method in class edu.cmu.tetrad.session.SessionSupport
-
Fires an event indicating that a parent has been added from the given parent to the given child session node in the session.
- fireParentRemoved(SessionNode, SessionNode) - Method in class edu.cmu.tetrad.session.SessionSupport
-
Fires an event indicating that a parent has been removed from the given parent to the given child session node in the session.
- fireRepetitionChanged(SessionNode) - Method in class edu.cmu.tetrad.session.SessionSupport
-
Fires an event indicating that the model for the given session node in the session has been destroyed.
- fireSessionEvent(SessionEvent) - Method in class edu.cmu.tetrad.session.SessionSupport
-
Fires a session event.
- fireSessionEvent(SessionEvent, boolean) - Method in class edu.cmu.tetrad.session.SessionSupport
-
Fires a session event.
- FirstInflection - Class in edu.cmu.tetrad.algcomparison.algorithm
-
First inflection point.
- FirstInflection(Algorithm, String, double, double, double) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.FirstInflection
- fisher - Enum constant in enum class edu.cmu.tetrad.search.utils.ResolveSepsets.Method
- fisher - Enum constant in enum class edu.cmu.tetrad.search.work_in_progress.ResolveSepsetsDci.Method
- FISHER_EPSILON - Static variable in class edu.cmu.tetrad.util.Params
- fisher2 - Enum constant in enum class edu.cmu.tetrad.search.utils.ResolveSepsets.Method
- fisher2 - Enum constant in enum class edu.cmu.tetrad.search.work_in_progress.ResolveSepsetsDci.Method
- FisherZ - Class in edu.cmu.tetrad.algcomparison.independence
-
Wrapper for Fisher Z test.
- FisherZ - Enum constant in enum class edu.cmu.tetrad.study.performance.ComparisonParameters.IndependenceTestType
- FisherZ() - Constructor for class edu.cmu.tetrad.algcomparison.independence.FisherZ
- FisherZScore - Class in edu.cmu.tetrad.algcomparison.score
-
Wrapper for Fisher Z test.
- FisherZScore() - Constructor for class edu.cmu.tetrad.algcomparison.score.FisherZScore
- fit(DataSet) - Method in class edu.cmu.tetrad.search.IcaLingam
-
Fits an ICA-LiNGAM model to the given dataset using a default method for estimating W.
- fit(DataSet) - Method in class edu.cmu.tetrad.search.IcaLingD
-
Fits a LiNG-D model to the given dataset using a default method for estimating W.
- FitConGraphResult(DoubleMatrix2D, double, int, int) - Constructor for class edu.cmu.tetrad.sem.Ricf.FitConGraphResult
- fitW(Matrix) - Method in class edu.cmu.tetrad.search.IcaLingam
-
Searches given a W matrix is that is provided by the user (where WX = e).
- fitW(Matrix) - Method in class edu.cmu.tetrad.search.IcaLingD
-
Performs the LiNG-D algorithm given a W matrix, which needs to be discovered elsewhere.
- fixLatentErrorVariances() - Method in class edu.cmu.tetrad.sem.SemPm
- fixLatents1(int, Graph) - Static method in class edu.cmu.tetrad.graph.RandomGraph
- fixLatents4(int, Graph) - Static method in class edu.cmu.tetrad.graph.RandomGraph
- fixOneLoadingPerLatent() - Method in class edu.cmu.tetrad.sem.SemPm
- flatten(DoubleMatrix2D) - Static method in class edu.pitt.csb.mgm.Mgm
- FloatDataBox - Class in edu.cmu.tetrad.data
-
Stores a 2D array of float data.
- FloatDataBox(float[][]) - Constructor for class edu.cmu.tetrad.data.FloatDataBox
-
Constructs a new data box using the given 2D float data array as data.
- flush() - Method in class edu.cmu.tetrad.util.TetradLogger
-
Flushes the writers.
- Fml - Enum constant in enum class edu.cmu.tetrad.sem.ScoreType
- Fofc - Class in edu.cmu.tetrad.algcomparison.algorithm.cluster
-
Find One Factor Clusters.
- Fofc - Class in edu.cmu.tetrad.search
-
Implements the Find One Factor Clusters (FOFC) algorithm by Erich Kummerfeld, which uses reasoning about vanishing tetrads of algorithms to infer clusters of the measured variables in a dataset that each be explained by a single latent variable.
- Fofc() - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.cluster.Fofc
- Fofc(DataSet, BpcTestType, Fofc.Algorithm, double) - Constructor for class edu.cmu.tetrad.search.Fofc
-
Conctructor.
- Fofc(ICovarianceMatrix, BpcTestType, Fofc.Algorithm, double) - Constructor for class edu.cmu.tetrad.search.Fofc
-
Constructor.
- Fofc.Algorithm - Enum Class in edu.cmu.tetrad.search
-
Gives the options to be used in FOFC to sort through the various possibilities for forming clusters to find the best options.
- forbid_latent_common_causes - Enum constant in enum class edu.cmu.tetrad.annotation.AlgType
-
If an algorithm forbids latent common causes.
- FORBIDDEN - Static variable in class edu.cmu.tetrad.data.KnowledgeGroup
- forbiddenEdgesIterator() - Method in class edu.cmu.tetrad.data.Knowledge
-
Iterator over the KnowledgeEdge's representing forbidden edges.
- forceLogMessage(String) - Method in class edu.cmu.tetrad.util.TetradLogger
-
Logs the given message regardless of the logger's getModel settings.
- forgetOldModel() - Method in class edu.cmu.tetrad.session.SessionNode
-
Forgets the old model so that it can't be used to recapture parameter values.
- forgetSavedModel() - Method in class edu.cmu.tetrad.session.SessionNode
- ForkJoinPoolInstance - Class in edu.cmu.tetrad.util
-
Static instance of a ForkJoinPool.
- formatErrorsArray(double[], String) - Static method in class edu.cmu.tetrad.simulation.HsimUtils
- fPdf(double, double, double) - Static method in class edu.cmu.tetrad.util.ProbUtils
- fQuantile(double, double, double) - Static method in class edu.cmu.tetrad.util.ProbUtils
- FractionDependentUnderAlternative - Class in edu.cmu.tetrad.algcomparison.statistic
-
Estimates whether the p-values under the null are Uniform usign the Markov Checker.
- FractionDependentUnderAlternative() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.FractionDependentUnderAlternative
- FractionDependentUnderAlternative(double) - Constructor for class edu.cmu.tetrad.algcomparison.statistic.FractionDependentUnderAlternative
- FractionDependentUnderNull - Class in edu.cmu.tetrad.algcomparison.statistic
-
Estimates whether the p-values under the null are Uniform usign the Markov Checker.
- FractionDependentUnderNull() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.FractionDependentUnderNull
- FractionDependentUnderNull(double) - Constructor for class edu.cmu.tetrad.algcomparison.statistic.FractionDependentUnderNull
- fRand(double, double) - Static method in class edu.cmu.tetrad.util.ProbUtils
-
F distribution random generator.
- fruchtermanReingoldLayout(Graph) - Static method in class edu.cmu.tetrad.graph.LayoutUtil
- FruchtermanReingoldLayout(Graph) - Constructor for class edu.cmu.tetrad.graph.LayoutUtil.FruchtermanReingoldLayout
- Ftfc - Class in edu.cmu.tetrad.algcomparison.algorithm.cluster
-
FTFC.
- Ftfc - Class in edu.cmu.tetrad.search
-
Implements the Find Two Factor Clusters (FOFC) algorithm, which uses reasoning about vanishing tetrads of algorithms to infer clusters of the measured variables in a dataset that each be explained by a single latent variable.
- Ftfc() - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.cluster.Ftfc
- Ftfc(DataSet, Ftfc.Algorithm, double) - Constructor for class edu.cmu.tetrad.search.Ftfc
-
Conctructor.
- Ftfc(ICovarianceMatrix, Ftfc.Algorithm, double) - Constructor for class edu.cmu.tetrad.search.Ftfc
-
Conctructor.
- Ftfc.Algorithm - Enum Class in edu.cmu.tetrad.search
-
Gives the options to be used in FOFC to sort through the various possibilities for forming clusters to find the best options.
- fullyConnect(Endpoint) - Method in class edu.cmu.tetrad.graph.Dag
- fullyConnect(Endpoint) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
-
Resets the graph so that it is fully connects it using #-# edges, where # is the given endpoint.
- fullyConnect(Endpoint) - Method in interface edu.cmu.tetrad.graph.Graph
-
Removes all edges from the graph and fully connects it using #-# edges, where # is the given endpoint.
- fullyConnect(Endpoint) - Method in class edu.cmu.tetrad.graph.LagGraph
- fullyConnect(Endpoint) - Method in class edu.cmu.tetrad.graph.SemGraph
- fullyConnect(Endpoint) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- Function - Interface in edu.cmu.tetrad.util
-
Interface for a single-argument, double-valued function that can be passed to mathematical routines.
- futureNodeVisit(Graph, Node, LinkedList<Node>, Set<Node>) - Static method in class edu.cmu.tetrad.search.work_in_progress.SampleVcpc
- futureNodeVisit(Graph, Node, LinkedList<Node>, Set<Node>) - Static method in class edu.cmu.tetrad.search.work_in_progress.SampleVcpcFast
- futureNodeVisit(Graph, Node, LinkedList<Node>, Set<Node>) - Static method in class edu.cmu.tetrad.search.work_in_progress.VcPc
- futureNodeVisit(Graph, Node, LinkedList<Node>, Set<Node>) - Static method in class edu.cmu.tetrad.search.work_in_progress.VcPcAlt
- futureNodeVisit(Graph, Node, LinkedList<Node>, Set<Node>) - Static method in class edu.cmu.tetrad.search.work_in_progress.VcPcFast
G
- g(double) - Static method in class edu.cmu.tetrad.search.Fask
- gamma(double) - Static method in class edu.cmu.tetrad.util.StatUtils
-
GAMMA FUNCTION (From DStat, used by permission).
- Gamma - Class in edu.cmu.tetrad.util.dist
-
Wraps a chi square distribution for purposes of drawing random samples.
- gammaCdf(double, double) - Static method in class edu.cmu.tetrad.util.ProbUtils
-
compute complementary gamma cdf by its continued fraction expansion
- gammaPdf(double, double) - Static method in class edu.cmu.tetrad.util.ProbUtils
- gammaQuantile(double, double) - Static method in class edu.cmu.tetrad.util.ProbUtils
- gammaRand(double) - Static method in class edu.cmu.tetrad.util.ProbUtils
-
Gamma random generator.
- GAP - Enum constant in enum class edu.cmu.tetrad.search.Fofc.Algorithm
- GAP - Enum constant in enum class edu.cmu.tetrad.search.Ftfc.Algorithm
- GAP - Enum constant in enum class edu.cmu.tetrad.search.utils.BpcTestType
- gasp(TeyssierScorer) - Method in class edu.cmu.tetrad.search.work_in_progress.OtherPermAlgs
- Gaussian - Enum constant in enum class edu.cmu.tetrad.search.test.ConditionalCorrelationIndependence.Kernel
- Gaussian - Annotation Interface in edu.cmu.tetrad.annotation
-
Data are normal distributed.
- GAUSSIAN_FACTOR - Enum constant in enum class edu.cmu.tetrad.search.utils.BpcTestType
- GAUSSIAN_PVALUE - Enum constant in enum class edu.cmu.tetrad.search.utils.BpcTestType
- GAUSSIAN_SCORE - Enum constant in enum class edu.cmu.tetrad.search.utils.BpcTestType
- GAUSSIAN_SCORE_ITERATE - Enum constant in enum class edu.cmu.tetrad.search.utils.BpcTestType
- GAUSSIAN_SCORE_MARKS - Enum constant in enum class edu.cmu.tetrad.search.utils.BpcTestType
- GaussianCategoricalIm(GeneralizedSemPm) - Static method in class edu.pitt.csb.mgm.MixedUtils
- GaussianCategoricalIm(GeneralizedSemPm, boolean) - Static method in class edu.pitt.csb.mgm.MixedUtils
-
This method is needed to normalize edge parameters for an Instantiated Mixed Model Generates edge parameters for c-d and d-d edges from a single weight, abs(w), drawn by the normal IM constructor.
- GaussianCategoricalPm(Graph, String) - Static method in class edu.pitt.csb.mgm.MixedUtils
- GaussianPower - Class in edu.cmu.tetrad.util.dist
- GaussianPower(double) - Constructor for class edu.cmu.tetrad.util.dist.GaussianPower
- GaussianProcess - Class in jgpml
-
Main class of the package, contains the objects that constitutes a Gaussian Process as well as the algorithm to train the Hyperparameters and to do predictions.
- GaussianProcess(CovarianceFunction) - Constructor for class jgpml.GaussianProcess
-
Creates a new GP object.
- GaussianTrinaryPm(Graph, HashMap<String, String>, int, String) - Static method in class edu.pitt.csb.mgm.MixedUtils
- Gdistance - Class in edu.cmu.tetrad.simulation
-
Created by Erich on 7/3/2016.
- Gdistance(DataSet, double, double, double) - Constructor for class edu.cmu.tetrad.simulation.Gdistance
- GdistanceApply - Class in edu.cmu.tetrad.simulation
-
Created by Erich on 7/14/2016.
- GdistanceApply() - Constructor for class edu.cmu.tetrad.simulation.GdistanceApply
- GdistanceRandom - Class in edu.cmu.tetrad.simulation
-
Created by Erich on 8/6/2016.
- GdistanceRandom(DataSet) - Constructor for class edu.cmu.tetrad.simulation.GdistanceRandom
- GdistanceRandomApply - Class in edu.cmu.tetrad.simulation
-
Created by Erich on 8/6/2016.
- GdistanceRandomApply() - Constructor for class edu.cmu.tetrad.simulation.GdistanceRandomApply
- GdistanceTest - Class in edu.cmu.tetrad.simulation
-
Created by Erich on 7/6/2016.
- GdistanceTest() - Constructor for class edu.cmu.tetrad.simulation.GdistanceTest
- GdistanceUtils - Class in edu.cmu.tetrad.simulation
-
Created by Erich on 8/11/2016.
- GdistanceUtils() - Constructor for class edu.cmu.tetrad.simulation.GdistanceUtils
- Gene(int) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.ideker.ItkPredictorSearch.Gene
- GeneHistory - Class in edu.cmu.tetrad.study.gene.tetrad.gene.history
-
Implements the basic machinery used by all history objects.
- GeneHistory(Initializer, UpdateFunction) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.history.GeneHistory
-
Constructs a new history with the given initializer and the given update function.
- GenePm - Class in edu.cmu.tetrad.study.gene.tetradapp.model
-
Implements a parametric gene model.
- GenePm(LagGraph) - Constructor for class edu.cmu.tetrad.study.gene.tetradapp.model.GenePm
-
Construct a new gene pm, wrapping the given lag workbench.
- General - Annotation Interface in edu.cmu.tetrad.annotation
-
Data with variables of general distribution.
- GENERAL_SEM_ERROR_TEMPLATE - Static variable in class edu.cmu.tetrad.util.Params
- GENERAL_SEM_FUNCTION_TEMPLATE_LATENT - Static variable in class edu.cmu.tetrad.util.Params
- GENERAL_SEM_FUNCTION_TEMPLATE_MEASURED - Static variable in class edu.cmu.tetrad.util.Params
- GENERAL_SEM_PARAMETER_TEMPLATE - Static variable in class edu.cmu.tetrad.util.Params
- GENERAL_STRUCTURAL_EQUATION_MODEL - Static variable in class edu.cmu.tetrad.algcomparison.simulation.SimulationTypes
- GeneralAndersonDarlingTest - Class in edu.cmu.tetrad.data
-
Implements the Anderson-Darling test against the given CDF, with P values calculated as in R's ad.test method (in package nortest).
- GeneralAndersonDarlingTest(List<Double>, RealDistribution) - Constructor for class edu.cmu.tetrad.data.GeneralAndersonDarlingTest
-
Constructs an Anderson-Darling test for the given column of data.
- GeneralizedSemEstimator - Class in edu.cmu.tetrad.sem
-
Estimates a Generalized SEM I'M given a Generalized SEM PM and a data set.
- GeneralizedSemEstimator() - Constructor for class edu.cmu.tetrad.sem.GeneralizedSemEstimator
- GeneralizedSemEstimator.MyContext - Class in edu.cmu.tetrad.sem
- GeneralizedSemIm - Class in edu.cmu.tetrad.sem
-
Represents a generalized SEM instantiated model.
- GeneralizedSemIm(GeneralizedSemPm) - Constructor for class edu.cmu.tetrad.sem.GeneralizedSemIm
-
Constructs a new GeneralizedSemIm from the given GeneralizedSemPm by picking values for each of the freeParameters from their initial distributions.
- GeneralizedSemIm(GeneralizedSemPm, SemIm) - Constructor for class edu.cmu.tetrad.sem.GeneralizedSemIm
- GeneralizedSemPm - Class in edu.cmu.tetrad.sem
-
Parametric model for Generalized SEM model.
- GeneralizedSemPm(Graph) - Constructor for class edu.cmu.tetrad.sem.GeneralizedSemPm
-
Constructs a BayesPm from the given Graph, which must be convertible first into a ProtoSemGraph and then into a SemGraph.
- GeneralizedSemPm(SemGraph) - Constructor for class edu.cmu.tetrad.sem.GeneralizedSemPm
-
Constructs a new SemPm from the given SemGraph.
- GeneralizedSemPm(GeneralizedSemPm) - Constructor for class edu.cmu.tetrad.sem.GeneralizedSemPm
-
Copy constructor.
- GeneralizedSemPm(SemPm) - Constructor for class edu.cmu.tetrad.sem.GeneralizedSemPm
- GeneralResamplingSearch - Class in edu.pitt.dbmi.algo.resampling
-
Sep 7, 2018 1:38:50 PM
- GeneralResamplingSearch(DataSet, int) - Constructor for class edu.pitt.dbmi.algo.resampling.GeneralResamplingSearch
- GeneralResamplingSearch(List<DataSet>, int) - Constructor for class edu.pitt.dbmi.algo.resampling.GeneralResamplingSearch
- GeneralResamplingSearchRunnable - Class in edu.pitt.dbmi.algo.resampling.task
-
Mar 19, 2017 9:45:44 PM
- GeneralResamplingSearchRunnable(DataModel, Algorithm, Parameters, GeneralResamplingSearch, boolean) - Constructor for class edu.pitt.dbmi.algo.resampling.task.GeneralResamplingSearchRunnable
- GeneralResamplingSearchRunnable(List<DataModel>, MultiDataSetAlgorithm, Parameters, GeneralResamplingSearch, boolean) - Constructor for class edu.pitt.dbmi.algo.resampling.task.GeneralResamplingSearchRunnable
- GeneralResamplingTest - Class in edu.pitt.dbmi.algo.resampling
-
Created by mahdi on 1/16/17.
- GeneralResamplingTest(DataSet, Algorithm, int, double, boolean, int, boolean) - Constructor for class edu.pitt.dbmi.algo.resampling.GeneralResamplingTest
- GeneralResamplingTest(List<DataSet>, MultiDataSetAlgorithm, int, double, boolean, int, boolean) - Constructor for class edu.pitt.dbmi.algo.resampling.GeneralResamplingTest
- GeneralSemSimulation - Class in edu.cmu.tetrad.algcomparison.simulation
-
General SEM simulation.
- GeneralSemSimulation(RandomGraph) - Constructor for class edu.cmu.tetrad.algcomparison.simulation.GeneralSemSimulation
- GeneralSemSimulation(GeneralizedSemIm) - Constructor for class edu.cmu.tetrad.algcomparison.simulation.GeneralSemSimulation
- GeneralSemSimulation(GeneralizedSemPm) - Constructor for class edu.cmu.tetrad.algcomparison.simulation.GeneralSemSimulation
- GeneralSemSimulationSpecial1 - Class in edu.cmu.tetrad.algcomparison.simulation
-
This was used for a simulation to test the FTFC and FOFC algorithm and contains some carefully selected functions to test nonlinearity and non-Gaussianity.
- GeneralSemSimulationSpecial1(RandomGraph) - Constructor for class edu.cmu.tetrad.algcomparison.simulation.GeneralSemSimulationSpecial1
- generate() - Method in class edu.cmu.tetrad.graph.RandomGraph.UniformGraphGenerator
- generate(Graph) - Static method in class edu.cmu.tetrad.bayes.ModelGenerator
-
This method takes an acyclic graph as input and returns a list of graphs each of which is a modification of the original graph with either an edge deleted, added or reversed.
- generateCpdagDags(Graph, boolean) - Static method in class edu.cmu.tetrad.graph.GraphTransforms
-
Generates the list of DAGs in the given cpdag.
- generateLatentNames(int) - Static method in class edu.cmu.tetrad.search.utils.ClusterUtils
- generateMbDags(Graph, boolean, IndependenceTest, int, Node) - Static method in class edu.cmu.tetrad.search.utils.MbUtils
-
Generates the list of MB DAGs consistent with the MB CPDAG returned by the previous search.
- generateMixedEdgeParams(double, int) - Static method in class edu.pitt.csb.mgm.MixedUtils
- generateReportFromExternalAlgorithms(String, String, Algorithms, Statistics, Parameters) - Method in class edu.cmu.tetrad.algcomparison.Comparison
- generateReportFromExternalAlgorithms(String, String, Algorithms, Statistics, Parameters, long, TimeUnit) - Method in class edu.cmu.tetrad.algcomparison.TimeoutComparison
- generateReportFromExternalAlgorithms(String, String, String, Algorithms, Statistics, Parameters) - Method in class edu.cmu.tetrad.algcomparison.Comparison
- generateReportFromExternalAlgorithms(String, String, String, Algorithms, Statistics, Parameters, long, TimeUnit) - Method in class edu.cmu.tetrad.algcomparison.TimeoutComparison
- generateResults() - Method in class edu.cmu.tetrad.search.MarkovCheck
-
Generates all results, for both the local Markov and local Faithfulness checks, for each node in the graph given the parents of that node.
- generateTetradResults() - Method in class edu.cmu.tetrad.study.examples.conditions.Condition1
- generateTetradResults() - Method in class edu.cmu.tetrad.study.examples.conditions.Condition2
- GesMe - Class in edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag
-
FGES (the heuristic version).
- GesMe() - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.GesMe
- GesMe(boolean) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.GesMe
- get(int) - Method in class edu.cmu.tetrad.data.DataModelList
- get(int) - Method in class edu.cmu.tetrad.search.utils.TeyssierScorer
-
Returns the node at index j in pi.
- get(int) - Method in class edu.cmu.tetrad.util.Vector
- get(int, int) - Method in class edu.cmu.tetrad.data.ByteDataBox
- get(int, int) - Method in interface edu.cmu.tetrad.data.DataBox
- get(int, int) - Method in class edu.cmu.tetrad.data.DoubleDataBox
- get(int, int) - Method in class edu.cmu.tetrad.data.FloatDataBox
- get(int, int) - Method in class edu.cmu.tetrad.data.IntDataBox
- get(int, int) - Method in class edu.cmu.tetrad.data.LongDataBox
- get(int, int) - Method in class edu.cmu.tetrad.data.MixedDataBox
- get(int, int) - Method in class edu.cmu.tetrad.data.ShortDataBox
- get(int, int) - Method in class edu.cmu.tetrad.data.VerticalDoubleDataBox
- get(int, int) - Method in class edu.cmu.tetrad.data.VerticalIntDataBox
- get(int, int) - Method in class edu.cmu.tetrad.util.Matrix
- get(int, int) - Method in class edu.cmu.tetrad.util.Matrix2
- get(Node) - Method in class edu.cmu.tetrad.search.utils.SepsetMap
-
Returns the parents of the node x.
- get(Node) - Method in class edu.cmu.tetrad.search.work_in_progress.SepsetMapDci
- get(Node, Node) - Method in class edu.cmu.tetrad.search.utils.SepsetMap
-
Retrieves the sepset previously set for {a, b}, or null if no such set was previously set.
- get(Node, Node) - Method in class edu.cmu.tetrad.search.work_in_progress.SepsetMapDci
-
Retrieves the sepset previously set for {x, y}, or null if no such set was previously set.
- get(String) - Method in class edu.cmu.tetrad.util.AlgorithmDescriptions
-
Gets the description of the algorithm.
- get(String) - Method in class edu.cmu.tetrad.util.IndependenceTestDescriptions
- get(String) - Method in class edu.cmu.tetrad.util.ParamDescriptions
- get(String) - Method in class edu.cmu.tetrad.util.Parameters
-
Returns the object value of the given parameter, looking up its default in the ParamDescriptions map.
- get(String) - Method in class edu.cmu.tetrad.util.ScoreDescriptions
- get(String, Object) - Method in class edu.cmu.tetrad.util.Parameters
-
Returns the object value of the given parameter, using the given default.
- getA() - Method in class edu.cmu.tetrad.sem.ParameterPair
-
Method getNumObjects
- getA() - Method in class edu.cmu.tetrad.util.ChoiceGenerator
- getA() - Method in class edu.cmu.tetrad.util.dist.Split
- getA() - Method in class edu.cmu.tetrad.util.SelectionGenerator
- getA() - Method in class edu.cmu.tetrad.util.SublistGenerator
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.AdjacencyFn
-
Returns the name of the statistic.
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.AdjacencyFp
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.AdjacencyFpr
-
Returns the name of the statistic.
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.AdjacencyPrecision
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.AdjacencyRecall
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.AdjacencyTn
-
Returns the name of the statistic.
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.AdjacencyTp
-
Returns the name of the statistic.
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.AdjacencyTpr
-
Returns the name of the statistic.
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.AncestorF1
-
Returns the name of the statistic.
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.AncestorPrecision
-
Returns the name of the statistic.
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.AncestorRecall
-
Returns the name of the statistic.
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.AncestralPrecision
-
Returns the name of the statistic.
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.AncestralRecall
-
Returns the name of the statistic.
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.ArrowheadFn
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.ArrowheadFp
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.ArrowheadFpr
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.ArrowheadPrecision
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.ArrowheadPrecisionCommonEdges
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.ArrowheadRecall
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.ArrowheadRecallCommonEdges
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.ArrowheadTn
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.ArrowheadTp
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.AverageDegreeEst
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.AverageDegreeTrue
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.BicDiff
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.BicDiffPerRecord
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.BicEst
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.BicTrue
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.BidirectedEst
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.BidirectedFP
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.BidirectedLatentPrecision
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.BidirectedPrecision
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.BidirectedRecall
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.BidirectedTP
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.BidirectedTrue
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.CommonAncestorFalseNegativeBidirected
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.CommonAncestorFalsePositiveBidirected
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.CommonAncestorTruePositiveBidirected
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.CommonMeasuredAncestorRecallBidirected
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.CorrectSkeleton
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.DefiniteDirectedPathPrecision
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.DefiniteDirectedPathRecall
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.DensityEst
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.DensityTrue
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.ElapsedCpuTime
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.F1Adj
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.F1All
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.F1Arrow
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.FalseNegativesAdjacencies
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.FalsePositiveAdjacencies
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.FractionDependentUnderAlternative
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.FractionDependentUnderNull
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.GraphExactlyRight
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.LatentCommonAncestorFalseNegativeBidirected
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.LatentCommonAncestorFalsePositiveBidirected
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.LatentCommonAncestorRecallBidirected
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.LatentCommonAncestorTruePositiveBidirected
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.LegalPag
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.MarkovAdequacyScore
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.MathewsCorrAdj
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.MathewsCorrArrow
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.MaximalityCondition
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.NoAlmostCyclicPathsCondition
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.NoAlmostCyclicPathsInMagCondition
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.NoCyclicPathsCondition
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.NoCyclicPathsInMagCondition
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.NodesInCyclesPrecision
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.NodesInCyclesRecall
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.NonancestorPrecision
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.NonancestorRecall
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.NoSemidirectedF1
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.NoSemidirectedPrecision
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.NoSemidirectedRecall
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumAmbiguousTriples
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumberOfEdgesEst
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumberOfEdgesTrue
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumBidirectedBothNonancestorAncestor
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumBidirectedEdgesEst
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumBidirectedEdgesTrue
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumColoredDD
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumColoredNL
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumColoredPD
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumColoredPL
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumCommonMeasuredAncestorBidirected
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumCompatibleDefiniteDirectedEdgeAncestors
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumCompatibleDirectedEdgeConfounded
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumCompatibleDirectedEdgeNonAncestors
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumCompatibleEdges
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumCompatiblePossiblyDirectedEdgeAncestors
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumCompatiblePossiblyDirectedEdgeNonAncestors
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumCompatibleVisibleAncestors
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumCompatibleVisibleNonancestors
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumCorrectDDAncestors
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumCorrectPDAncestors
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumCorrectVisibleAncestors
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumDefinitelyDirected
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumDefinitelyNotDirectedPaths
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumDirectedEdgeAncestors
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumDirectedEdgeBnaMeasuredCounfounded
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumDirectedEdgeNoMeasureAncestors
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumDirectedEdgeNotAncNotRev
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumDirectedEdgeReversed
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumDirectedEdges
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumDirectedEdgeVisible
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumDirectedPathsEst
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumDirectedPathsTrue
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumDirectedShouldBePartiallyDirected
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumIncorrectDDAncestors
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumIncorrectPDAncestors
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumIncorrectVisibleAncestors
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumLatentCommonAncestorBidirected
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumNondirectedEdges
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumPartiallyOrientedEdges
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumPossiblyDirected
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumUndirectedEdges
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumVisibleEst
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.OrientationPrecision
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.OrientationRecall
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.PagAdjacencyPrecision
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.PagAdjacencyRecall
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.ParameterColumn
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.PercentAmbiguous
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.PercentBidirectedEdges
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.ProportionSemidirectedPathsNotReversedEst
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.ProportionSemidirectedPathsNotReversedTrue
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.PvalueDistanceToAlpha
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.PvalueUniformityUnderNull
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.SemidirectedPathF1
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.SemidirectedPrecision
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.SemidirectedRecall
- getAbbreviation() - Method in interface edu.cmu.tetrad.algcomparison.statistic.Statistic
-
The abbreviation for the statistic.
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.StructuralHammingDistance
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.TailPrecision
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.TailRecall
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.TrueDagFalseNegativesArrows
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.TrueDagFalseNegativesTails
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.TrueDagFalsePositiveArrow
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.TrueDagFalsePositiveTails
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.TrueDagPrecisionArrow
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.TrueDagPrecisionTails
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.TrueDagRecallArrows
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.TrueDagRecallTails
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.TrueDagTruePositiveArrow
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.TrueDagTruePositiveDirectedPathNonancestor
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.TrueDagTruePositiveTails
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.TwoCycleFalseNegative
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.TwoCycleFalsePositive
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.TwoCyclePrecision
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.TwoCycleRecall
- getAbbreviation() - Method in class edu.cmu.tetrad.algcomparison.statistic.TwoCycleTruePositive
- getAdjacencies() - Method in class edu.cmu.tetrad.search.Cpc
-
Returns the edges in the search graph as a set of undirected edges.
- getAdjacencies() - Method in class edu.cmu.tetrad.search.Pc
-
Returns The edges of the searched graph.
- getAdjacencies() - Method in class edu.cmu.tetrad.search.Pcd
- getAdjacencies() - Method in class edu.cmu.tetrad.search.SvarFges
- getAdjacencies() - Method in class edu.cmu.tetrad.search.utils.FgesOrienter
- getAdjacencies() - Method in class edu.cmu.tetrad.search.utils.PcCommon
-
Returns The edges in the search graph.
- getAdjacencies() - Method in class edu.cmu.tetrad.search.utils.TeyssierScorer
-
Returns a list of adjacent node pairs in the current graph.
- getAdjacencies() - Method in class edu.cmu.tetrad.search.work_in_progress.SampleVcpc
- getAdjacencies() - Method in class edu.cmu.tetrad.search.work_in_progress.SampleVcpcFast
- getAdjacencies() - Method in class edu.cmu.tetrad.search.work_in_progress.VcPc
- getAdjacencies() - Method in class edu.cmu.tetrad.search.work_in_progress.VcPcFast
- getAdjacentNodes(Node) - Method in class edu.cmu.tetrad.graph.Dag
- getAdjacentNodes(Node) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
- getAdjacentNodes(Node) - Method in interface edu.cmu.tetrad.graph.Graph
- getAdjacentNodes(Node) - Method in class edu.cmu.tetrad.graph.LagGraph
- getAdjacentNodes(Node) - Method in class edu.cmu.tetrad.graph.SemGraph
- getAdjacentNodes(Node) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- getAdjacentNodes(Node) - Method in class edu.cmu.tetrad.search.utils.TeyssierScorer
-
Returns the nodes adjacent to v.
- getAdjConfusionMatrix(Graph, Graph) - Static method in class edu.pitt.dbmi.algo.resampling.GeneralResamplingTest
- getAdjCor() - Method in class edu.cmu.tetrad.graph.GraphUtils.GraphComparison
- getAdjFn() - Method in class edu.cmu.tetrad.graph.GraphUtils.GraphComparison
- getAdjFp() - Method in class edu.cmu.tetrad.graph.GraphUtils.GraphComparison
- getAdjPrec() - Method in class edu.cmu.tetrad.graph.GraphUtils.GraphComparison
- getAdjPrecision() - Method in class edu.cmu.tetrad.simulation.PRAOerrors
- getAdjRec() - Method in class edu.cmu.tetrad.graph.GraphUtils.GraphComparison
- getAdjRecall() - Method in class edu.cmu.tetrad.simulation.PRAOerrors
- getAhdCor() - Method in class edu.cmu.tetrad.graph.GraphUtils.GraphComparison
- getAhdFn() - Method in class edu.cmu.tetrad.graph.GraphUtils.GraphComparison
- getAhdFp() - Method in class edu.cmu.tetrad.graph.GraphUtils.GraphComparison
- getAhdPrec() - Method in class edu.cmu.tetrad.graph.GraphUtils.GraphComparison
- getAhdRec() - Method in class edu.cmu.tetrad.graph.GraphUtils.GraphComparison
- getAlgorithm() - Method in class edu.cmu.tetrad.study.performance.ComparisonParameters
- getAlgorithmDescriptions() - Static method in enum class edu.cmu.tetrad.search.utils.BpcAlgorithmType
- getAlgorithmName() - Method in class edu.cmu.tetrad.search.GrowShrink
-
Returns "Grow Shrink".
- getAlgorithmName() - Method in interface edu.cmu.tetrad.search.IMbSearch
-
The name of the algorithm.
- getAlgorithmName() - Method in class edu.cmu.tetrad.search.PcMb
-
Returns "PC-MB."
- getAlgorithmName() - Method in class edu.cmu.tetrad.search.work_in_progress.Iamb
- getAlgorithmName() - Method in class edu.cmu.tetrad.search.work_in_progress.IambnPc
- getAlgorithmName() - Method in class edu.cmu.tetrad.search.work_in_progress.InterIamb
- getAlgorithmName() - Method in class edu.cmu.tetrad.search.work_in_progress.Mmmb
- getAlgorithmParameters(Algorithm) - Static method in class edu.cmu.tetrad.util.Params
- getAlgorithms() - Method in class edu.cmu.tetrad.algcomparison.algorithm.Algorithms
-
Returns the list of algorithm.
- getAllAttributes() - Method in class edu.cmu.tetrad.data.ContinuousVariable
- getAllAttributes() - Method in class edu.cmu.tetrad.data.DiscreteVariable
- getAllAttributes() - Method in class edu.cmu.tetrad.graph.Dag
- getAllAttributes() - Method in class edu.cmu.tetrad.graph.EdgeListGraph
- getAllAttributes() - Method in interface edu.cmu.tetrad.graph.Graph
- getAllAttributes() - Method in class edu.cmu.tetrad.graph.GraphNode
- getAllAttributes() - Method in class edu.cmu.tetrad.graph.LagGraph
- getAllAttributes() - Method in interface edu.cmu.tetrad.graph.Node
- getAllAttributes() - Method in class edu.cmu.tetrad.graph.SemGraph
- getAllAttributes() - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- getAllAttributes() - Method in class edu.cmu.tetrad.session.SessionNode
- getAllGraphsByDirectingUndirectedEdges(Graph) - Static method in class edu.cmu.tetrad.graph.GraphTransforms
- getAllParamSettings() - Method in interface edu.cmu.tetrad.session.SimulationParamsSource
- getAllParents(Graph, Set<Node>) - Static method in class edu.cmu.tetrad.simulation.HsimUtils
- getAllSubsetsIndependenceFacts(Graph) - Static method in class edu.cmu.tetrad.search.MarkovCheck
- getAlpha() - Method in class edu.cmu.tetrad.regression.LogisticRegression
- getAlpha() - Method in interface edu.cmu.tetrad.search.IndependenceTest
-
Returns the significance level of the independence test.
- getAlpha() - Method in class edu.cmu.tetrad.search.IndTestIod
-
Returns the alpha level for this test.
- getAlpha() - Method in class edu.cmu.tetrad.search.test.ChiSquareTest
-
Returns the model significance level being used for tests.
- getAlpha() - Method in class edu.cmu.tetrad.search.test.GSquareTest
- getAlpha() - Method in class edu.cmu.tetrad.search.test.IndTestChiSquare
-
Returns the alpha significance level of the test.
- getAlpha() - Method in class edu.cmu.tetrad.search.test.IndTestConditionalCorrelation
-
Returns the model significance level.
- getAlpha() - Method in class edu.cmu.tetrad.search.test.IndTestConditionalGaussianLrt
-
Returns the significance level of the independence test.
- getAlpha() - Method in class edu.cmu.tetrad.search.test.IndTestDegenerateGaussianLrt
-
Returns the significance level of the independence test.
- getAlpha() - Method in class edu.cmu.tetrad.search.test.IndTestFisherZ
-
Gets the model significance level.
- getAlpha() - Method in class edu.cmu.tetrad.search.test.IndTestFisherZConcatenateResiduals
-
Gets the getModel significance level.
- getAlpha() - Method in class edu.cmu.tetrad.search.test.IndTestFisherZFisherPValue
-
Gets the getModel significance level.
- getAlpha() - Method in class edu.cmu.tetrad.search.test.IndTestGSquare
-
Gets the getModel significance level.
- getAlpha() - Method in class edu.cmu.tetrad.search.test.IndTestHsic
-
Gets the getModel significance level.
- getAlpha() - Method in class edu.cmu.tetrad.search.test.IndTestIndependenceFacts
- getAlpha() - Method in class edu.cmu.tetrad.search.test.IndTestMulti
-
Gets the getModel significance level.
- getAlpha() - Method in class edu.cmu.tetrad.search.test.IndTestMvpLrt
-
Returns the significance level of the independence test.
- getAlpha() - Method in class edu.cmu.tetrad.search.test.IndTestProbabilistic
- getAlpha() - Method in class edu.cmu.tetrad.search.test.IndTestRegression
-
Gets the getModel significance level.
- getAlpha() - Method in class edu.cmu.tetrad.search.test.IndTestTrekSep
-
Gets the model significance level.
- getAlpha() - Method in class edu.cmu.tetrad.search.test.Kci
-
Returns the significance level of the independence test.
- getAlpha() - Method in class edu.cmu.tetrad.search.test.MsepTest
-
Returns an alpha level, 0.5.
- getAlpha() - Method in class edu.cmu.tetrad.search.test.ScoreIndTest
-
Returns the significance level of the independence test.
- getAlpha() - Method in class edu.cmu.tetrad.search.work_in_progress.HbsmsBeam
- getAlpha() - Method in class edu.cmu.tetrad.search.work_in_progress.HbsmsGes
- getAlpha() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestCramerT
- getAlpha() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestFisherZGeneralizedInverse
-
Gets the getModel significance level.
- getAlpha() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestFisherZPercentIndependent
-
Gets the getModel significance level.
- getAlpha() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestFisherZRecursive
-
Gets the getModel significance level.
- getAlpha() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestMixedMultipleTTest
- getAlpha() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestMnlrLr
- getAlpha() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestMultinomialLogisticRegression
- getAlpha() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestPositiveCorr
-
Gets the getModel significance level.
- getAlpha() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestSepsetDci
- getAlpha() - Method in class edu.cmu.tetrad.search.work_in_progress.Kpc
-
Gets the getModel significance level.
- getAlpha() - Method in class edu.cmu.tetrad.search.work_in_progress.ProbabilisticMapIndependence
- getAlpha() - Method in class edu.cmu.tetrad.study.performance.ComparisonParameters
- getAlpha() - Method in class edu.pitt.csb.mgm.IndTestMultinomialLogisticRegressionWald
- getAlpha1() - Method in class edu.pitt.csb.mgm.Mgm.MGMParams
- getAlpha2() - Method in class edu.pitt.csb.mgm.Mgm.MGMParams
- getAmbiguousTriples() - Method in class edu.cmu.tetrad.graph.Dag
- getAmbiguousTriples() - Method in class edu.cmu.tetrad.graph.EdgeListGraph
- getAmbiguousTriples() - Method in interface edu.cmu.tetrad.graph.Graph
- getAmbiguousTriples() - Method in class edu.cmu.tetrad.graph.LagGraph
- getAmbiguousTriples() - Method in class edu.cmu.tetrad.graph.SemGraph
- getAmbiguousTriples() - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- getAmbiguousTriples() - Method in class edu.cmu.tetrad.graph.Underlines
- getAmbiguousTriples() - Method in class edu.cmu.tetrad.search.Cfci
-
Returns the ambiguous triples found in the search.
- getAmbiguousTriples() - Method in class edu.cmu.tetrad.search.Cpc
-
Returns the set of ambiguous triples found during the most recent run of the algorithm.
- getAmbiguousTriples() - Method in class edu.cmu.tetrad.search.PcMb
-
Returns the set of triples identified as ambiguous by the CPC algorithm during the most recent search.
- getAmbiguousTriples() - Method in class edu.cmu.tetrad.search.utils.PcCommon
- getAmbiguousTriples() - Method in class edu.cmu.tetrad.search.work_in_progress.SampleVcpc
- getAmbiguousTriples() - Method in class edu.cmu.tetrad.search.work_in_progress.SampleVcpcFast
- getAmbiguousTriples() - Method in class edu.cmu.tetrad.search.work_in_progress.VcPc
- getAmbiguousTriples() - Method in class edu.cmu.tetrad.search.work_in_progress.VcPcAlt
- getAmbiguousTriples() - Method in class edu.cmu.tetrad.search.work_in_progress.VcPcFast
- getAmbiguousTriples(Node) - Method in class edu.cmu.tetrad.search.Fas
-
There are no ambiguous triples for this search, for any nodes.
- getAmbiguousTriples(Node) - Method in class edu.cmu.tetrad.search.Fasd
-
Returns an empty list.
- getAmbiguousTriples(Node) - Method in interface edu.cmu.tetrad.search.IFas
-
Returns the list of ambiguous triples found for a given node.
- getAmbiguousTriples(Node) - Method in class edu.cmu.tetrad.search.SvarFas
- getAmbiguousTriples(Node) - Method in class edu.cmu.tetrad.search.work_in_progress.Fas2
- getAmbiguousTriples(Node) - Method in class edu.cmu.tetrad.search.work_in_progress.Fas3
-
There are no ambiguous triples for this search, for any nodes.
- getAmbiguousTriples(Node) - Method in class edu.cmu.tetrad.search.work_in_progress.FasFdr
- getAmbiguousTriplesFromGraph(Node, Graph) - Static method in class edu.cmu.tetrad.graph.GraphUtils
- getAncestorMap() - Method in class edu.cmu.tetrad.graph.Paths
-
Return a map from each node to its ancestors.
- getAncestors(Node) - Method in class edu.cmu.tetrad.search.utils.TeyssierScorer
- getAncestors(List<Node>) - Method in class edu.cmu.tetrad.graph.Paths
- getAnnotatedClasses() - Method in class edu.cmu.tetrad.annotation.AbstractAnnotations
-
Get annotated classes.
- getAnnotatedClasses(String, Class<T>) - Static method in class edu.cmu.tetrad.annotation.AnnotatedClassUtils
-
Gets a list of annotated classes in the given package.
- getAnnotation() - Method in class edu.cmu.tetrad.annotation.AnnotatedClass
-
Gets the annotation.
- getApacheData() - Method in class edu.cmu.tetrad.util.Matrix
- getApacheData() - Method in class edu.cmu.tetrad.util.Matrix2
- getApparentlyNonadjacencies() - Method in class edu.cmu.tetrad.search.work_in_progress.VcFas
- getApparentNonadjacencies() - Method in class edu.cmu.tetrad.search.work_in_progress.SampleVcpc
- getApparentNonadjacencies() - Method in class edu.cmu.tetrad.search.work_in_progress.SampleVcpcFast
- getApparentNonadjacencies() - Method in class edu.cmu.tetrad.search.work_in_progress.VcPc
- getApparentNonadjacencies() - Method in class edu.cmu.tetrad.search.work_in_progress.VcPcFast
- getArea(Function, double, double, int) - Static method in class edu.cmu.tetrad.util.Integrator
-
Finds the area under function f between x1 and x2 using Simpson's rule.
- getArgument(int) - Method in interface edu.cmu.tetrad.calculator.expression.ExpressionSignature
- getArrowsFn() - Method in class edu.cmu.tetrad.algcomparison.statistic.utils.TailConfusion
- getArrowsFp() - Method in class edu.cmu.tetrad.algcomparison.statistic.utils.TailConfusion
- getArrowsTn() - Method in class edu.cmu.tetrad.algcomparison.statistic.utils.TailConfusion
- getArrowsTp() - Method in class edu.cmu.tetrad.algcomparison.statistic.utils.TailConfusion
- getASquared() - Method in class edu.cmu.tetrad.data.AndersonDarlingTest
-
Constructs an Anderson-Darling test for the given column of data.
- getASquared() - Method in class edu.cmu.tetrad.data.GeneralAndersonDarlingTest
- getASquared() - Method in class edu.cmu.tetrad.data.MultiGeneralAndersonDarlingTest
- getaSquaredStar() - Method in class edu.cmu.tetrad.sem.GeneralizedSemEstimator
- getASquaredStar() - Method in class edu.cmu.tetrad.data.AndersonDarlingTest
-
Constructs an Anderson-Darling test for the given column of data.
- getASquaredStar() - Method in class edu.cmu.tetrad.data.GeneralAndersonDarlingTest
- getASquaredStar() - Method in class edu.cmu.tetrad.data.MultiGeneralAndersonDarlingTest
- getAssignableClass(List, Class) - Method in class edu.cmu.tetrad.session.SessionNode
-
Returns the first class c in
classesthatclazzis assignable to.> 0 - getAssociatedNode(Node, Graph) - Static method in class edu.cmu.tetrad.graph.GraphUtils
- getAttribute(String) - Method in class edu.cmu.tetrad.data.ContinuousVariable
- getAttribute(String) - Method in class edu.cmu.tetrad.data.DiscreteVariable
- getAttribute(String) - Method in class edu.cmu.tetrad.graph.Dag
- getAttribute(String) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
- getAttribute(String) - Method in interface edu.cmu.tetrad.graph.Graph
- getAttribute(String) - Method in class edu.cmu.tetrad.graph.GraphNode
- getAttribute(String) - Method in class edu.cmu.tetrad.graph.LagGraph
- getAttribute(String) - Method in interface edu.cmu.tetrad.graph.Node
- getAttribute(String) - Method in class edu.cmu.tetrad.graph.SemGraph
- getAttribute(String) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- getAttribute(String) - Method in class edu.cmu.tetrad.session.SessionNode
- getAuc() - Method in class edu.cmu.tetrad.util.RocCalculator
-
Calculates the area under the ROC curve using a very clever Ramsey idea.
- getB() - Method in class edu.cmu.tetrad.search.Fask
-
Returns the coefficient matrix for the search.
- getB() - Method in class edu.cmu.tetrad.sem.ParameterPair
-
Method getNumObjects
- getB() - Method in class edu.cmu.tetrad.util.ChoiceGenerator
- getB() - Method in class edu.cmu.tetrad.util.dist.Split
- getBandwidth() - Method in interface edu.cmu.tetrad.search.utils.Kernel
-
Gets kernel bandwidth
- getBandwidth() - Method in class edu.cmu.tetrad.search.utils.KernelGaussian
- getBasalExpression() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.BooleanGlassFunction
-
Returns the basalExpression.
- getBayesIm() - Method in class edu.cmu.tetrad.bayes.ApproximateUpdater
- getBayesIm() - Method in interface edu.cmu.tetrad.bayes.BayesUpdater
-
Returns the evidence for the updater.
- getBayesIm() - Method in class edu.cmu.tetrad.bayes.CptInvariantUpdater
- getBayesIm() - Method in class edu.cmu.tetrad.bayes.Identifiability
-
The BayesIm that this updater bases its update on.
- getBayesIm() - Method in class edu.cmu.tetrad.bayes.JunctionTreeUpdater
- getBayesIm() - Method in class edu.cmu.tetrad.bayes.RowSummingExactUpdater
-
The BayesIm that this updater bases its update on.
- getBayesIm() - Method in class edu.cmu.tetrad.classify.ClassifierBayesUpdaterDiscrete
-
Returns the Bayes IM being used.
- getBayesIm(Element) - Method in class edu.cmu.tetrad.bayes.BayesXmlParser
- getBayesIm(Element) - Method in class edu.cmu.tetrad.search.utils.BayesImParser
-
Takes an xml representation of a Bayes IM and reinstantiates the IM
- getBayesImObs() - Method in class edu.cmu.tetrad.bayes.MlBayesImObs
- getBayesIms() - Method in class edu.cmu.tetrad.algcomparison.simulation.BayesNetSimulation
-
Returns the list of Bayes IMs.
- getBayesImVars() - Method in class edu.cmu.tetrad.classify.ClassifierBayesUpdaterDiscrete
-
Returns the variables of the BayesIM.
- getBayesPm() - Method in interface edu.cmu.tetrad.bayes.BayesIm
-
Returns the underlying Bayes PM.
- getBayesPm() - Method in class edu.cmu.tetrad.bayes.DirichletBayesIm
- getBayesPm() - Method in class edu.cmu.tetrad.bayes.EmBayesProperties
- getBayesPm() - Method in class edu.cmu.tetrad.bayes.MlBayesIm
- getBayesPm() - Method in class edu.cmu.tetrad.bayes.MlBayesImObs
- getBayesPm() - Method in class edu.cmu.tetrad.bayes.UpdatedBayesIm
- getBeta() - Method in class edu.pitt.csb.mgm.Mgm.MGMParams
- getBetad() - Method in class edu.pitt.csb.mgm.Mgm.MGMParams
- getBhat() - Method in class edu.cmu.tetrad.sem.Ricf.RicfResult
- getBic() - Method in class edu.cmu.tetrad.bayes.BayesProperties
-
Call after calling getLikelihoodP().
- getBic() - Method in class edu.cmu.tetrad.bayes.EmBayesProperties
-
Calculates the BIC (Bayes Information Criterion) score for a BayesPM with respect to a given discrete data set.
- getBic() - Method in class edu.cmu.tetrad.search.test.IndTestFisherZ
-
Returns the BIC score for this test.
- getBic() - Method in class edu.cmu.tetrad.search.work_in_progress.HbsmsBeam.Score
- getBic() - Method in class edu.cmu.tetrad.search.work_in_progress.HbsmsGes.Score
- getBics() - Method in class edu.cmu.tetrad.search.Boss
- getBicScore() - Method in class edu.cmu.tetrad.sem.DagScorer
- getBicScore() - Method in interface edu.cmu.tetrad.sem.ISemIm
- getBicScore() - Method in interface edu.cmu.tetrad.sem.Scorer
- getBicScore() - Method in class edu.cmu.tetrad.sem.SemIm
- getBoolean(String) - Method in class edu.cmu.tetrad.util.Parameters
-
Returns the boolean value of the given parameter, looking up its default in the ParamDescriptions map.
- getBoolean(String, boolean) - Method in class edu.cmu.tetrad.util.Parameters
-
Returns the boolean value of the given parameter, using the given default.
- getBooleanGlassFunction() - Method in class edu.cmu.tetrad.study.gene.tetradapp.model.BooleanGlassGeneIm
-
Returns the Glass function case to BooleanGlassFunction for convenience.
- getBooleanInfluenceRate() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.BooleanGlassFunction
-
Returns the rate at which Boolean Glass subfunctions tend to affect the update.
- getBootstrapGraphs() - Method in class edu.cmu.tetrad.algcomparison.algorithm.continuous.dag.Dagma
- getBootstrapGraphs() - Method in class edu.cmu.tetrad.algcomparison.algorithm.continuous.dag.DirectLingam
- getBootstrapGraphs() - Method in class edu.cmu.tetrad.algcomparison.algorithm.continuous.dag.IcaLingam
- getBootstrapGraphs() - Method in class edu.cmu.tetrad.algcomparison.algorithm.continuous.dag.IcaLingD
- getBootstrapGraphs() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Boss
- getBootstrapGraphs() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Cpc
- getBootstrapGraphs() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Fas
- getBootstrapGraphs() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Fges
- getBootstrapGraphs() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.FgesMb
- getBootstrapGraphs() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.FgesMeasurement
- getBootstrapGraphs() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.GesMe
- getBootstrapGraphs() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Grasp
- getBootstrapGraphs() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Pc
- getBootstrapGraphs() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Pcd
- getBootstrapGraphs() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.PcLingam
- getBootstrapGraphs() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.PcMb
- getBootstrapGraphs() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.RestrictedBoss
- getBootstrapGraphs() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Sp
- getBootstrapGraphs() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Bfci
- getBootstrapGraphs() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Ccd
- getBootstrapGraphs() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Cfci
- getBootstrapGraphs() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Fci
- getBootstrapGraphs() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.FciMax
- getBootstrapGraphs() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Gfci
- getBootstrapGraphs() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.GraspFci
- getBootstrapGraphs() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Rfci
- getBootstrapGraphs() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.SpFci
- getBootstrapGraphs() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.SvarFci
- getBootstrapGraphs() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.SvarGfci
- getBootstrapGraphs() - Method in interface edu.cmu.tetrad.algcomparison.algorithm.ReturnsBootstrapGraphs
- getBootstrappingParameters(Algorithm) - Static method in class edu.cmu.tetrad.util.Params
- getBootstrapSample(DataSet, int) - Static method in class edu.cmu.tetrad.data.DataTransforms
- getBootstrapSample(DataSet, int, RandomGenerator) - Static method in class edu.cmu.tetrad.data.DataTransforms
-
Get dataset sampled with replacement.
- getBootstrapSample(Matrix, int) - Static method in class edu.cmu.tetrad.data.DataTransforms
- getBoxType() - Method in class edu.cmu.tetrad.session.SessionNode
-
Gets the (optional) name of this node.
- getBreakpoints() - Method in class edu.cmu.tetrad.data.ContinuousDiscretizationSpec
- getBreakpoints() - Method in class edu.cmu.tetrad.data.SplitCasesSpec
- getBscD() - Method in class edu.pitt.dbmi.algo.bayesian.constraint.search.RfciBsc
- getBscI() - Method in class edu.pitt.dbmi.algo.bayesian.constraint.search.RfciBsc
- getC() - Method in class edu.cmu.tetrad.search.utils.ShiftSearch
- getCategories() - Method in class edu.cmu.tetrad.data.ContinuousDiscretizationSpec
- getCategories() - Method in class edu.cmu.tetrad.data.DiscreteDiscretizationSpec
- getCategories() - Method in class edu.cmu.tetrad.data.DiscreteVariable
- getCategory(int) - Method in class edu.cmu.tetrad.data.DiscreteVariable
- getCategory(Node, int) - Method in class edu.cmu.tetrad.bayes.BayesPm
-
Returns the index'th value for the given node.
- getCategory(Node, int) - Method in class edu.cmu.tetrad.bayes.Evidence
- getCategoryIndex(Node, String) - Method in class edu.cmu.tetrad.bayes.BayesPm
-
Returns the index of the given category for the given node.
- getCategoryIndex(String, String) - Method in class edu.cmu.tetrad.bayes.Evidence
- getCategoryIndex(String, String) - Method in class edu.cmu.tetrad.bayes.Proposition
- getCauseNode() - Method in class edu.cmu.tetrad.search.Cstar.Record
- getCellIndex(int[]) - Method in class edu.cmu.tetrad.util.MultiDimIntTable
- getCellLeaves(List<DiscreteVariable>) - Method in class edu.cmu.tetrad.search.utils.AdLeafTree
-
Finds the set of indices into the leaves of the tree for the given variables.
- getCellLeaves(List<DiscreteVariable>, DiscreteVariable) - Method in class edu.cmu.tetrad.search.utils.AdLeafTree
-
Finds the set of indices into the leaves of the tree for the given variables.
- getCellNumber() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.simulation.MeasurementSimulator
-
While the simulate() method is being executed, returns the cell number of the cell currently being simulated in a particular dish, zero indexed.
- getCellProb(int[]) - Method in class edu.cmu.tetrad.bayes.BayesImProbs
-
Calculates the probability in the given cell from the conditional probabilities in the BayesIm.
- getCellProb(int[]) - Method in class edu.cmu.tetrad.bayes.CellTableProbs
- getCellProb(int[]) - Method in class edu.cmu.tetrad.bayes.DataSetProbs
- getCellProb(int[]) - Method in class edu.cmu.tetrad.bayes.DirichletDataSetProbs
- getCellProb(int[]) - Method in class edu.cmu.tetrad.bayes.IntAveDataSetProbs
- getCellProb(int[]) - Method in class edu.cmu.tetrad.bayes.StoredCellProbs
- getCellProb(int[]) - Method in class edu.cmu.tetrad.bayes.StoredCellProbsObs
- getCellTable() - Method in class edu.cmu.tetrad.search.test.GSquareTest
-
Returns the cell table for this test.
- getCenteringFrame() - Static method in class edu.cmu.tetrad.util.JOptionUtils
- getCenterX() - Method in class edu.cmu.tetrad.data.ContinuousVariable
- getCenterX() - Method in class edu.cmu.tetrad.data.DiscreteVariable
- getCenterX() - Method in class edu.cmu.tetrad.graph.GraphNode
- getCenterX() - Method in interface edu.cmu.tetrad.graph.Node
-
Returns the x coordinate of the center of this node.
- getCenterX() - Method in class edu.cmu.tetrad.session.SessionNode
- getCenterY() - Method in class edu.cmu.tetrad.data.ContinuousVariable
- getCenterY() - Method in class edu.cmu.tetrad.data.DiscreteVariable
- getCenterY() - Method in class edu.cmu.tetrad.graph.GraphNode
- getCenterY() - Method in interface edu.cmu.tetrad.graph.Node
-
Returns the y coordinate of the center of this node.
- getCenterY() - Method in class edu.cmu.tetrad.session.SessionNode
- getCfi() - Method in interface edu.cmu.tetrad.sem.ISemIm
- getCfi() - Method in class edu.cmu.tetrad.sem.SemIm
- getChangedEdges() - Method in class edu.cmu.tetrad.search.utils.MeekRules
-
Returns a complete set of all the edges that were changed in the course of orientation, as a map from the previous edges in the graph to the new, changed edges for the same node pair.
- getChild() - Method in class edu.cmu.tetrad.session.SessionEvent
- getChildren() - Method in class edu.cmu.tetrad.session.SessionNode
- getChildren(int) - Method in class edu.cmu.tetrad.search.utils.TeyssierScorer
-
Returns the children of a node v.
- getChildren(Node) - Method in class edu.cmu.tetrad.graph.Dag
- getChildren(Node) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
- getChildren(Node) - Method in interface edu.cmu.tetrad.graph.Graph
- getChildren(Node) - Method in class edu.cmu.tetrad.graph.LagGraph
- getChildren(Node) - Method in class edu.cmu.tetrad.graph.SemGraph
- getChildren(Node) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- getChildren(Node) - Method in class edu.cmu.tetrad.search.utils.TeyssierScorer
-
Returns the children of a node v.
- getChipChipVariability() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.simulation.MeasurementSimulator
-
Returns the chip to chip variability.
- getChipChipVariability() - Method in class edu.cmu.tetrad.study.gene.tetradapp.model.MeasurementSimulatorParams
- getChisq() - Method in class edu.cmu.tetrad.bayes.BayesProperties
-
Call after calling getLikelihoodP().
- getChiSquare() - Method in class edu.cmu.tetrad.search.test.IndTestChiSquare
-
Returns the chi Square value.
- getChiSquare() - Method in class edu.cmu.tetrad.search.work_in_progress.HbsmsBeam.Score
- getChiSquare() - Method in class edu.cmu.tetrad.search.work_in_progress.HbsmsGes.Score
- getChiSquare() - Method in class edu.cmu.tetrad.sem.DagScorer
- getChiSquare() - Method in interface edu.cmu.tetrad.sem.ISemIm
- getChiSquare() - Method in interface edu.cmu.tetrad.sem.Scorer
- getChiSquare() - Method in class edu.cmu.tetrad.sem.SemIm
- getClassifications() - Method in class edu.cmu.tetrad.classify.ClassifierBayesUpdaterDiscrete
-
Returns the classification for the target variable.
- getClazz() - Method in class edu.cmu.tetrad.annotation.AnnotatedClass
-
Gets the class.
- getCliques(Node[], Graph) - Static method in class edu.cmu.tetrad.bayes.GraphTools
-
Get cliques in a decomposable graph.
- getCliqueTree(Node[], Map<Node, Set<Node>>, Map<Node, Set<Node>>) - Static method in class edu.cmu.tetrad.bayes.GraphTools
- getCluster(int) - Method in class edu.cmu.tetrad.cluster.KMeans
- getCluster(int) - Method in class edu.cmu.tetrad.data.Clusters
- getClustering() - Method in class edu.cmu.tetrad.search.Mimbuild
-
Returns the clustering of measured variables, each of which is explained by a single latent.
- getClustering() - Method in class edu.cmu.tetrad.search.MimbuildTrek
-
The clustering used.
- getClusterName(int) - Method in class edu.cmu.tetrad.data.Clusters
- getClusters() - Method in interface edu.cmu.tetrad.cluster.ClusteringAlgorithm
- getClusters() - Method in class edu.cmu.tetrad.cluster.KMeans
- getClusters() - Method in class edu.cmu.tetrad.data.Clusters
- getClusters() - Method in class edu.cmu.tetrad.search.Fofc
-
The clusters that are output by the algorithm from the last call to search().
- getClusters() - Method in class edu.cmu.tetrad.search.Ftfc
-
Returns clusters output by the algorithm from the last call to search().
- getCoef() - Method in class edu.cmu.tetrad.regression.RegressionResult
- getCoef() - Method in class edu.cmu.tetrad.sem.StandardizedSemIm.ParameterRange
- getCoefficient() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.PolynomialTerm
-
Returns the coefficient.
- getCoefficientMatrix() - Method in class edu.cmu.tetrad.sem.LargeScaleSimulation
- getCoefficientParameter(Node, Node) - Method in class edu.cmu.tetrad.sem.SemPm
- getCoefficientRange(Node, Node) - Method in class edu.cmu.tetrad.sem.StandardizedSemIm
- getCoefs() - Method in class edu.cmu.tetrad.regression.LogisticRegression.Result
-
The array of regression coefficients.
- getCollapsedVarGraph() - Method in class edu.cmu.tetrad.search.utils.TsUtils.VarResult
- getColliders() - Method in class edu.cmu.tetrad.search.work_in_progress.GraphChange
-
Return colliders
- getCollidersFromGraph(Node, Graph) - Static method in class edu.cmu.tetrad.graph.GraphSaveLoadUtils
- getColliderTriples() - Method in class edu.cmu.tetrad.search.utils.PcCommon
- getColliderTriples() - Method in class edu.cmu.tetrad.search.work_in_progress.SampleVcpc
- getColliderTriples() - Method in class edu.cmu.tetrad.search.work_in_progress.SampleVcpcFast
- getColliderTriples() - Method in class edu.cmu.tetrad.search.work_in_progress.VcPc
- getColliderTriples() - Method in class edu.cmu.tetrad.search.work_in_progress.VcPcAlt
- getColliderTriples() - Method in class edu.cmu.tetrad.search.work_in_progress.VcPcFast
- getColPerm() - Method in class edu.cmu.tetrad.search.utils.PermutationMatrixPair
- getColumn(int) - Method in class edu.cmu.tetrad.util.Matrix
- getColumn(int) - Method in class edu.cmu.tetrad.util.Matrix2
- getColumn(Node) - Method in class edu.cmu.tetrad.data.BoxDataSet
- getColumn(Node) - Method in interface edu.cmu.tetrad.data.DataSet
- getColumn(Node) - Method in class edu.cmu.tetrad.data.NumberObjectDataSet
- getColumnToTooltip() - Method in class edu.cmu.tetrad.data.BoxDataSet
- getColumnToTooltip() - Method in interface edu.cmu.tetrad.data.DataSet
- getColumnToTooltip() - Method in class edu.cmu.tetrad.data.NumberObjectDataSet
- getComparisonGraph() - Method in class edu.cmu.tetrad.algcomparison.Comparison
-
The type of graph the results are compared to.
- getComparisonGraph() - Method in class edu.cmu.tetrad.algcomparison.TimeoutComparison
-
The type of graph the results are compared to.
- getComparisonGraph(Graph) - Method in interface edu.cmu.tetrad.algcomparison.algorithm.Algorithm
-
Returns that graph that the result should be compared to.
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.cluster.Bpc
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.cluster.Fofc
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.cluster.Ftfc
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.continuous.dag.Dagma
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.continuous.dag.DirectLingam
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.continuous.dag.IcaLingam
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.continuous.dag.IcaLingD
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.external.ExternalAlgorithmBnlearnMmhc
-
Returns the CPDAG of the supplied DAG.
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.external.ExternalAlgorithmBNTPc
-
Returns the CPDAG of the supplied DAG.
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.external.ExternalAlgorithmIntersection
-
Returns the CPDAG of the supplied DAG.
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.external.ExternalAlgorithmPcalgGes
-
Returns the CPDAG of the supplied DAG.
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.external.ExternalAlgorithmPcalgPc
-
Returns the CPDAG of the supplied DAG.
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.external.ExternalAlgorithmTetrad
-
Returns the CPDAG of the supplied DAG.
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.FirstInflection
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.mixed.Mgm
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.Fask
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FaskConcatenated
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FaskLofsConcatenated
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FaskVote
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FasLofs
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FciIod
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FgesConcatenated
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.Images
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Boss
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Cpc
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Fas
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Fges
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.FgesMb
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.FgesMeasurement
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.GesMe
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Grasp
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Pc
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Pcd
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.PcLingam
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.PcMb
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.RestrictedBoss
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.SingleGraphAlg
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Sp
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Bfci
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Ccd
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Cfci
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Fci
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.FciMax
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Gfci
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.GraspFci
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.PagSampleRfci
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Rfci
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.RfciBsc
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.SpFci
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.SvarFci
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.SvarGfci
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pattern.Cstar
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.other.FactorAnalysis
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.other.Glasso
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.Eb
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.FaskPw
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.R1
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.R2
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.R3
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.Rskew
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.RskewE
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.Skew
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.SkewE
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.Tanh
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.StabilitySelection
- getComparisonGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.algorithm.StARS
- getComparisonGraph(Graph, Parameters) - Static method in class edu.cmu.tetrad.graph.GraphUtils
- getComparisonString() - Method in class edu.cmu.tetrad.algcomparison.comparegraphs.CompareTwoGraphs
-
Returns a string comparing 'target' to 'reference' using the given comparison method.
- getConditionalProb(Proposition, Proposition) - Method in class edu.cmu.tetrad.bayes.BayesImProbs
- getConditionalProb(Proposition, Proposition) - Method in class edu.cmu.tetrad.bayes.CellTableProbs
- getConditionalProb(Proposition, Proposition) - Method in class edu.cmu.tetrad.bayes.DataSetProbs
- getConditionalProb(Proposition, Proposition) - Method in class edu.cmu.tetrad.bayes.DirichletDataSetProbs
- getConditionalProb(Proposition, Proposition) - Method in class edu.cmu.tetrad.bayes.IntAveDataSetProbs
- getConditionalProb(Proposition, Proposition) - Method in class edu.cmu.tetrad.bayes.StoredCellProbs
- getConditionalProb(Proposition, Proposition) - Method in class edu.cmu.tetrad.bayes.StoredCellProbsObs
- getConditionalProbabilities(int[], int[], int[], int[]) - Method in class edu.cmu.tetrad.bayes.JunctionTreeAlgorithm
-
Get the joint probability of the nodes given their parents.
- getConditionalProbabilities(int, int[], int[]) - Method in class edu.cmu.tetrad.bayes.JunctionTreeAlgorithm
-
Get the conditional probability of a node for all of its values.
- getConditionalProbability(int, int, int[], int[]) - Method in class edu.cmu.tetrad.bayes.JunctionTreeAlgorithm
- getConditions() - Method in class edu.cmu.tetrad.search.utils.PossibleMConnectingPath
- getConnectivity() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ActiveLagGraph
- getConnectivity() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ManualLagGraph
- getConnectivity() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.BasicLagGraph
-
Returns (a copy of) the sorted map from factors to lagged factors which internally encodes the update graph.
- getConnectivity() - Method in interface edu.cmu.tetrad.study.gene.tetrad.gene.history.LagGraph
-
Returns (a copy of) the sorted map from factors to lagged factors which internally encodes the update graph.
- getConsistentModelClasses(boolean) - Method in class edu.cmu.tetrad.session.SessionNode
- getConstantColumns(DataSet) - Static method in class edu.cmu.tetrad.data.DataTransforms
- getContinousData(DataSet) - Static method in class edu.pitt.csb.mgm.MixedUtils
- getContinuousData() - Method in class edu.cmu.tetrad.data.MixedDataBox
- getContinuousData(String) - Method in class edu.cmu.tetrad.data.Histogram
-
A convenience method to return the data for a particular named continuous variable.
- getContinuousDataSet(DataModel) - Static method in class edu.cmu.tetrad.data.SimpleDataLoader
-
Returns the datamodel case to DataSet if it is continuous.
- getContinuousInds(List<Node>) - Static method in class edu.pitt.csb.mgm.MixedUtils
- getCoordinates(int) - Method in class edu.cmu.tetrad.util.MultiDimIntTable
- getCorrectResult() - Method in class edu.cmu.tetrad.study.performance.ComparisonResult
- getCorrelationMatrix() - Method in class edu.cmu.tetrad.data.BoxDataSet
- getCorrelationMatrix() - Method in interface edu.cmu.tetrad.data.DataSet
-
If this is a continuous data set, returns the correlation matrix.
- getCorrelationMatrix() - Method in class edu.cmu.tetrad.data.NumberObjectDataSet
- getCorrelationMatrix(DataSet) - Static method in class edu.cmu.tetrad.data.SimpleDataLoader
- getCorrespondingNodeIndex(int, BayesIm) - Method in interface edu.cmu.tetrad.bayes.BayesIm
-
Returns the index of the given node in the given BayesIm.
- getCorrespondingNodeIndex(int, BayesIm) - Method in class edu.cmu.tetrad.bayes.DirichletBayesIm
- getCorrespondingNodeIndex(int, BayesIm) - Method in class edu.cmu.tetrad.bayes.MlBayesIm
- getCorrespondingNodeIndex(int, BayesIm) - Method in class edu.cmu.tetrad.bayes.MlBayesImObs
- getCorrespondingNodeIndex(int, BayesIm) - Method in class edu.cmu.tetrad.bayes.UpdatedBayesIm
- getCounts() - Method in class edu.cmu.tetrad.graph.GraphUtils.GraphComparison
- getCov() - Method in interface edu.cmu.tetrad.search.IndependenceTest
-
Returns the covariance matrix.
- getCov() - Method in class edu.cmu.tetrad.search.test.IndTestFisherZ
-
Returns the correlation matrix being analyzed.
- getCov() - Method in class edu.cmu.tetrad.search.test.IndTestFisherZConcatenateResiduals
-
Returns teh covaraince matrix of the concatenated data.
- getCov() - Method in class edu.cmu.tetrad.search.test.IndTestFisherZFisherPValue
-
Returns the covariance matrix of the concatenated data.
- getCov() - Method in class edu.cmu.tetrad.search.test.IndTestTrekSep
-
Returns the covariance matrix.
- getCov() - Method in class edu.cmu.tetrad.search.test.Kci
- getCov() - Method in class edu.cmu.tetrad.search.test.ScoreIndTest
-
Returns the covariance matrix.
- getCov() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestFisherZPercentIndependent
- getCov() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestFisherZRecursive
- getCov() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestPositiveCorr
- getCov() - Method in class edu.cmu.tetrad.search.work_in_progress.SampleVcpc
- getCov() - Method in class edu.cmu.tetrad.search.work_in_progress.SampleVcpcFast
- getCovarianceMatrix() - Method in class edu.cmu.tetrad.data.BoxDataSet
- getCovarianceMatrix() - Method in interface edu.cmu.tetrad.data.DataSet
-
If this is a continuous data set, returns the covariance matrix.
- getCovarianceMatrix() - Method in class edu.cmu.tetrad.data.NumberObjectDataSet
- getCovarianceMatrix() - Method in class edu.cmu.tetrad.search.Bpc
-
Returns the wrapped covariance matrix.
- getCovarianceMatrix(DataModel, boolean) - Static method in class edu.cmu.tetrad.data.SimpleDataLoader
-
Returns the model cast to ICovarianceMatrix if already a covariance matric, or else returns the covariance matrix for a dataset.
- getCovarianceMatrix(DataSet, boolean) - Static method in class edu.cmu.tetrad.data.SimpleDataLoader
- getCovarianceParameter(Node, Node) - Method in class edu.cmu.tetrad.sem.SemPm
- getCovarianceRange(Node, Node) - Method in class edu.cmu.tetrad.sem.StandardizedSemIm
- getCovariances() - Method in class edu.cmu.tetrad.search.score.GicScores
-
Specialized scoring method for a single parent.
- getCovariances() - Method in class edu.cmu.tetrad.search.score.PoissonPriorScore
- getCovariances() - Method in class edu.cmu.tetrad.search.score.SemBicScore
- getCovariances() - Method in class edu.cmu.tetrad.search.score.ZsbScore
- getCovariances() - Method in class edu.cmu.tetrad.search.work_in_progress.SemBicScoreDeterministic
- getCovMatrix() - Method in interface edu.cmu.tetrad.search.utils.TetradTest
- getCovMatrix() - Method in class edu.cmu.tetrad.search.utils.TetradTestContinuous
- getCovMatrix() - Method in class edu.cmu.tetrad.search.utils.TetradTestDiscrete
- getCovMatrix() - Method in class edu.cmu.tetrad.search.utils.TetradTestPopulation
- getCovMatrix() - Method in class edu.cmu.tetrad.sem.DagScorer
- getCovMatrix() - Method in interface edu.cmu.tetrad.sem.Scorer
- getCovMatrix() - Method in class edu.cmu.tetrad.sem.SemEstimator
- getCpcTripleType(Node, Node, Node, IndependenceTest, int, Graph) - Static method in class edu.cmu.tetrad.search.utils.GraphSearchUtils
- getCpdag() - Method in class edu.cmu.tetrad.search.Dagma
- getCurrentOffset() - Method in class edu.cmu.tetrad.calculator.parser.ExpressionLexer
- getCutoff(Function, double, double, double) - Static method in class edu.cmu.tetrad.util.CutoffFinder
-
Assumes f is a positive symmetric function between x1 and x2 about 0.
- getD() - Method in class edu.pitt.csb.mgm.EigenDecomposition
-
Gets the block diagonal matrix D of the decomposition.
- getDag() - Method in interface edu.cmu.tetrad.bayes.BayesIm
-
$Description
- getDag() - Method in class edu.cmu.tetrad.bayes.BayesPm
-
Returns the DAG.
- getDag() - Method in class edu.cmu.tetrad.bayes.DirichletBayesIm
- getDag() - Method in class edu.cmu.tetrad.bayes.MlBayesIm
- getDag() - Method in class edu.cmu.tetrad.bayes.MlBayesImObs
- getDag() - Method in class edu.cmu.tetrad.bayes.UpdatedBayesIm
- getDag() - Method in class edu.cmu.tetrad.graph.RandomGraph.UniformGraphGenerator
- getDag() - Method in class edu.cmu.tetrad.search.score.GraphScore
-
Returns a copy of the DAG being searched over.
- getDag() - Method in class edu.cmu.tetrad.search.utils.DagSepsets
-
Returns the DAG being analyzed.
- getDag() - Method in class edu.cmu.tetrad.search.utils.SepsetsGreedy
- getDag(List<Node>) - Method in class edu.cmu.tetrad.graph.RandomGraph.UniformGraphGenerator
- getDagsInCpdagMeek(Graph, Knowledge) - Static method in class edu.cmu.tetrad.graph.GraphTransforms
- getData() - Method in class edu.cmu.tetrad.data.Discretizer.Discretization
- getData() - Method in class edu.cmu.tetrad.data.DoubleDataBox
- getData() - Method in class edu.cmu.tetrad.data.IntDataBox
- getData() - Method in class edu.cmu.tetrad.data.TimeSeriesData
- getData() - Method in interface edu.cmu.tetrad.search.IndependenceTest
- getData() - Method in class edu.cmu.tetrad.search.IndTestIod
-
The data set for this test is undefined, since the test is pooled over multiple datasets.
- getData() - Method in class edu.cmu.tetrad.search.score.GraphScore
- getData() - Method in class edu.cmu.tetrad.search.score.PoissonPriorScore
- getData() - Method in class edu.cmu.tetrad.search.score.SemBicScore
- getData() - Method in class edu.cmu.tetrad.search.test.IndTestChiSquare
-
Returns the data being analyzed.
- getData() - Method in class edu.cmu.tetrad.search.test.IndTestConditionalCorrelation
-
Returns the data set being analyzed.
- getData() - Method in class edu.cmu.tetrad.search.test.IndTestConditionalGaussianLrt
-
Returns the data.
- getData() - Method in class edu.cmu.tetrad.search.test.IndTestDegenerateGaussianLrt
-
Returns the dataset being analyzed.
- getData() - Method in class edu.cmu.tetrad.search.test.IndTestFisherZ
-
Returns the data set being analyzed.
- getData() - Method in class edu.cmu.tetrad.search.test.IndTestFisherZConcatenateResiduals
-
Returns the concatenated data.
- getData() - Method in class edu.cmu.tetrad.search.test.IndTestFisherZFisherPValue
-
Returns the concatenated data.
- getData() - Method in class edu.cmu.tetrad.search.test.IndTestGSquare
-
Returns the data.
- getData() - Method in class edu.cmu.tetrad.search.test.IndTestHsic
-
Returns the data set being analyzed.
- getData() - Method in class edu.cmu.tetrad.search.test.IndTestIndependenceFacts
-
Returns the facts supplied in the constructor, which constutite a data model.
- getData() - Method in class edu.cmu.tetrad.search.test.IndTestMulti
- getData() - Method in class edu.cmu.tetrad.search.test.IndTestMvpLrt
-
Returns the data.
- getData() - Method in class edu.cmu.tetrad.search.test.IndTestProbabilistic
- getData() - Method in class edu.cmu.tetrad.search.test.IndTestRegression
- getData() - Method in class edu.cmu.tetrad.search.test.IndTestTrekSep
- getData() - Method in class edu.cmu.tetrad.search.test.Kci
-
Returns The data model for the independence test.
- getData() - Method in class edu.cmu.tetrad.search.test.MsepTest
- getData() - Method in class edu.cmu.tetrad.search.test.ScoreIndTest
- getData() - Method in class edu.cmu.tetrad.search.work_in_progress.DMSearch
- getData() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestCramerT
- getData() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestFisherZGeneralizedInverse
-
Returns the data being analyzed.
- getData() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestFisherZPercentIndependent
- getData() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestFisherZRecursive
- getData() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestMixedMultipleTTest
-
Returne the original data for the method.
- getData() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestMnlrLr
-
Returns the data.
- getData() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestMultinomialLogisticRegression
- getData() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestPositiveCorr
- getData() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestSepsetDci
- getData() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestUniformScatter
- getData() - Method in class edu.cmu.tetrad.search.work_in_progress.ProbabilisticMapIndependence
- getData() - Method in class edu.pitt.csb.mgm.IndTestMultinomialLogisticRegressionWald
- getDataBox() - Method in class edu.cmu.tetrad.data.BoxDataSet
- getDataFile() - Method in class edu.cmu.tetrad.study.performance.ComparisonParameters
- getDataModel() - Method in class edu.cmu.tetrad.search.score.SemBicScore
- getDataModel(int) - Method in class edu.cmu.tetrad.algcomparison.simulation.BayesNetSimulation
-
Returns the simulated data set.
- getDataModel(int) - Method in class edu.cmu.tetrad.algcomparison.simulation.BooleanGlassSimulation
- getDataModel(int) - Method in class edu.cmu.tetrad.algcomparison.simulation.ConditionalGaussianSimulation
- getDataModel(int) - Method in class edu.cmu.tetrad.algcomparison.simulation.GeneralSemSimulation
- getDataModel(int) - Method in class edu.cmu.tetrad.algcomparison.simulation.GeneralSemSimulationSpecial1
- getDataModel(int) - Method in class edu.cmu.tetrad.algcomparison.simulation.LeeHastieSimulation
- getDataModel(int) - Method in class edu.cmu.tetrad.algcomparison.simulation.LinearFisherModel
- getDataModel(int) - Method in class edu.cmu.tetrad.algcomparison.simulation.LinearSineSimulation
- getDataModel(int) - Method in class edu.cmu.tetrad.algcomparison.simulation.NLSemSimulation
- getDataModel(int) - Method in class edu.cmu.tetrad.algcomparison.simulation.SemSimulation
- getDataModel(int) - Method in class edu.cmu.tetrad.algcomparison.simulation.SemThenDiscretize
- getDataModel(int) - Method in interface edu.cmu.tetrad.algcomparison.simulation.Simulation
-
Returns the number of data sets to simulate.
- getDataModel(int) - Method in class edu.cmu.tetrad.algcomparison.simulation.StandardizedSemSimulation
- getDataModel(int) - Method in class edu.cmu.tetrad.algcomparison.simulation.TimeSeriesSemSimulation
- getDataModel(int) - Method in class edu.cmu.tetrad.data.simulation.LoadContinuousDataAndGraphs
- getDataModel(int) - Method in class edu.cmu.tetrad.data.simulation.LoadContinuousDataAndSingleGraph
- getDataModel(int) - Method in class edu.cmu.tetrad.data.simulation.LoadContinuousDataSmithSim
- getDataModel(int) - Method in class edu.cmu.tetrad.data.simulation.LoadDataAndGraphs
- getDataModel(int) - Method in class edu.cmu.tetrad.data.simulation.LoadDataFromFileWithoutGraph
- getDataSet() - Method in class edu.cmu.tetrad.bayes.CellTableProbs
- getDataSet() - Method in class edu.cmu.tetrad.bayes.DataSetProbs
- getDataSet() - Method in class edu.cmu.tetrad.bayes.DirichletDataSetProbs
- getDataSet() - Method in class edu.cmu.tetrad.bayes.FactoredBayesStructuralEM
- getDataSet() - Method in class edu.cmu.tetrad.bayes.IntAveDataSetProbs
- getDataSet() - Method in class edu.cmu.tetrad.data.Histogram
- getDataSet() - Method in class edu.cmu.tetrad.search.score.BdeScore
-
Returns the dataset being analyzed.
- getDataSet() - Method in class edu.cmu.tetrad.search.score.BdeuScore
-
Returns the dataset being analyzed.
- getDataSet() - Method in class edu.cmu.tetrad.search.score.DiscreteBicScore
-
Returns the dataset being analyzed.
- getDataSet() - Method in interface edu.cmu.tetrad.search.score.DiscreteScore
-
Returns the dataset.
- getDataSet() - Method in class edu.cmu.tetrad.search.score.GicScores
- getDataSet() - Method in class edu.cmu.tetrad.search.score.GraphScore
- getDataSet() - Method in class edu.cmu.tetrad.search.score.IndTestScore
- getDataSet() - Method in class edu.cmu.tetrad.search.test.GSquareTest
-
Returns the dataset used for this test.
- getDataSet() - Method in interface edu.cmu.tetrad.search.utils.TetradTest
- getDataSet() - Method in class edu.cmu.tetrad.search.utils.TetradTestContinuous
- getDataSet() - Method in class edu.cmu.tetrad.search.utils.TetradTestDiscrete
- getDataSet() - Method in class edu.cmu.tetrad.search.utils.TetradTestPopulation
- getDataSet() - Method in class edu.cmu.tetrad.search.work_in_progress.SemBicScoreDeterministic
- getDataSet() - Method in class edu.cmu.tetrad.sem.DagScorer
- getDataSet() - Method in interface edu.cmu.tetrad.sem.Scorer
- getDataSet() - Method in class edu.cmu.tetrad.sem.SemEstimator
- getDataSet() - Method in class edu.cmu.tetrad.sem.SemEstimatorGibbs
- getDataSets() - Method in interface edu.cmu.tetrad.search.IndependenceTest
-
Returns the datasets for this test
- getDataSets() - Method in class edu.cmu.tetrad.search.test.IndTestFisherZ
-
Returns the (singleton) list of datasets being analyzed.
- getDataSets() - Method in class edu.cmu.tetrad.search.test.IndTestTrekSep
- getDataSets() - Method in class edu.cmu.tetrad.search.test.Kci
-
Returns a list consisting of the dataset for this test.
- getDataSets() - Method in class edu.cmu.tetrad.search.test.ScoreIndTest
- getDataSets() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestFisherZPercentIndependent
- getDataSets() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestFisherZRecursive
- getDataSets() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestPositiveCorr
- getDataType() - Method in interface edu.cmu.tetrad.algcomparison.algorithm.Algorithm
-
Returns the data type that the search requires, whether continuous, discrete, or mixed.
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.cluster.Bpc
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.cluster.Fofc
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.cluster.Ftfc
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.continuous.dag.Dagma
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.continuous.dag.DirectLingam
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.continuous.dag.IcaLingam
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.continuous.dag.IcaLingD
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.external.ExternalAlgorithmBnlearnMmhc
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.external.ExternalAlgorithmBNTPc
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.external.ExternalAlgorithmIntersection
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.external.ExternalAlgorithmPcalgGes
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.external.ExternalAlgorithmPcalgPc
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.external.ExternalAlgorithmTetrad
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.FirstInflection
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.mixed.Mgm
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.Fask
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FaskConcatenated
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FaskLofsConcatenated
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FaskVote
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FasLofs
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FciIod
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FgesConcatenated
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.Images
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Boss
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Cpc
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Fas
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Fges
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.FgesMb
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.FgesMeasurement
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.GesMe
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Grasp
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Pc
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Pcd
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.PcLingam
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.PcMb
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.RestrictedBoss
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.SingleGraphAlg
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Sp
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Bfci
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Ccd
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Cfci
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Fci
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.FciMax
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Gfci
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.GraspFci
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.PagSampleRfci
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Rfci
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.RfciBsc
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.SpFci
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.SvarFci
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.SvarGfci
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pattern.Cstar
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.other.FactorAnalysis
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.other.Glasso
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.Eb
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.FaskPw
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.R1
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.R2
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.R3
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.Rskew
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.RskewE
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.Skew
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.SkewE
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.Tanh
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.StabilitySelection
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.algorithm.StARS
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.independence.BdeuTest
-
Returns the data type of the test.
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.independence.CciTest
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.independence.ChiSquare
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.independence.ConditionalGaussianLRT
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.independence.DegenerateGaussianLRT
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.independence.DiscreteBicTest
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.independence.FisherZ
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.independence.GICScoreTests
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.independence.Gsquare
- getDataType() - Method in interface edu.cmu.tetrad.algcomparison.independence.IndependenceWrapper
-
Returns the data type that the search requires, whether continuous, discrete, or mixed.
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.independence.Kci
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.independence.MagSemBicTest
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.independence.Mnlrlrt
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.independence.MSeparationTest
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.independence.MultinomialLogisticRegressionWald
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.independence.Mvplrt
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.independence.PoissonScoreTest
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.independence.PositiveCorr
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.independence.ProbabilisticTest
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.independence.SemBicDTest
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.independence.SemBicTest
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.independence.UniformScatterTest
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.score.BdeuScore
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.score.CciScore
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.score.ConditionalGaussianBicScore
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.score.DegenerateGaussianBicScore
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.score.DiscreteBicScore
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.score.EbicScore
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.score.FisherZScore
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.score.GicScores
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.score.MagSemBicScore
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.score.MSeparationScore
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.score.MVPBicScore
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.score.PoissonPriorScore
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.score.PositiveCorrScore
- getDataType() - Method in interface edu.cmu.tetrad.algcomparison.score.ScoreWrapper
-
Returns the data type that the search requires, whether continuous, discrete, or mixed.
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.score.SemBicScore
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.score.SemBicScoreDeterministic
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.score.ZhangShenBoundScore
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.simulation.BayesNetSimulation
-
Returns the data type.
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.simulation.BooleanGlassSimulation
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.simulation.ConditionalGaussianSimulation
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.simulation.GeneralSemSimulation
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.simulation.GeneralSemSimulationSpecial1
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.simulation.LeeHastieSimulation
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.simulation.LinearFisherModel
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.simulation.LinearSineSimulation
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.simulation.NLSemSimulation
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.simulation.SemSimulation
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.simulation.SemThenDiscretize
- getDataType() - Method in interface edu.cmu.tetrad.algcomparison.simulation.Simulation
-
Returns the data type of the data.
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.simulation.StandardizedSemSimulation
- getDataType() - Method in class edu.cmu.tetrad.algcomparison.simulation.TimeSeriesSemSimulation
- getDataType() - Method in class edu.cmu.tetrad.data.simulation.LoadContinuousDataAndGraphs
- getDataType() - Method in class edu.cmu.tetrad.data.simulation.LoadContinuousDataAndSingleGraph
- getDataType() - Method in class edu.cmu.tetrad.data.simulation.LoadContinuousDataSmithSim
- getDataType() - Method in class edu.cmu.tetrad.data.simulation.LoadDataAndGraphs
- getDataType() - Method in class edu.cmu.tetrad.data.simulation.LoadDataFromFileWithoutGraph
- getDataType() - Method in class edu.cmu.tetrad.study.performance.ComparisonParameters
- getDatum(int, int) - Method in class edu.cmu.tetrad.data.TimeSeriesData
- getDecayRate() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.BooleanGlassFunction
-
Returns the rate at which expression levels tend to return to equilibrium.
- getDefaultValue() - Method in class edu.cmu.tetrad.util.ParamDescription
- getDefiniteNonadjacencies() - Method in class edu.cmu.tetrad.search.work_in_progress.SampleVcpc
- getDefiniteNonadjacencies() - Method in class edu.cmu.tetrad.search.work_in_progress.SampleVcpcFast
- getDefiniteNonadjacencies() - Method in class edu.cmu.tetrad.search.work_in_progress.VcPc
- getDefiniteNonadjacencies() - Method in class edu.cmu.tetrad.search.work_in_progress.VcPcFast
- getDegree() - Method in class edu.cmu.tetrad.graph.Dag
- getDegree() - Method in class edu.cmu.tetrad.graph.EdgeListGraph
- getDegree() - Method in interface edu.cmu.tetrad.graph.Graph
- getDegree() - Method in class edu.cmu.tetrad.graph.LagGraph
- getDegree() - Method in class edu.cmu.tetrad.graph.SemGraph
- getDegree() - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- getDegree(Graph) - Static method in class edu.cmu.tetrad.graph.GraphUtils
- getDegree(Node) - Method in class edu.cmu.tetrad.graph.Dag
- getDegree(Node) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
- getDegree(Node) - Method in interface edu.cmu.tetrad.graph.Graph
- getDegree(Node) - Method in class edu.cmu.tetrad.graph.LagGraph
- getDegree(Node) - Method in class edu.cmu.tetrad.graph.SemGraph
- getDegree(Node) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- getDepth() - Method in class edu.cmu.tetrad.search.Cpc
-
Returns the depth of the search--that is, the maximum number of variables conditioned on in any conditional independence test.
- getDepth() - Method in class edu.cmu.tetrad.search.Fask
- getDepth() - Method in class edu.cmu.tetrad.search.Pc
-
Returns the current depth of search--that is, the maximum number of conditioning nodes for any conditional independence checked.
- getDepth() - Method in class edu.cmu.tetrad.search.Pcd
- getDepth() - Method in class edu.cmu.tetrad.search.PcMb
-
Returns the depth of the search--that is, the maximum number of variables conditioned on in any conditional independence test.
- getDepth() - Method in class edu.cmu.tetrad.search.SvarFci
-
Returns the depth of search--i.e., the maximum number of conditioning variables for tests.
- getDepth() - Method in class edu.cmu.tetrad.search.utils.FgesOrienter
- getDepth() - Method in class edu.cmu.tetrad.search.utils.PcCommon
- getDepth() - Method in class edu.cmu.tetrad.search.utils.PossibleMsepFci
- getDepth() - Method in class edu.cmu.tetrad.search.work_in_progress.Dci
- getDepth() - Method in class edu.cmu.tetrad.search.work_in_progress.Fas2
- getDepth() - Method in class edu.cmu.tetrad.search.work_in_progress.FasDci
- getDepth() - Method in class edu.cmu.tetrad.search.work_in_progress.FasLofs
- getDepth() - Method in class edu.cmu.tetrad.search.work_in_progress.Kpc
- getDepth() - Method in class edu.cmu.tetrad.search.work_in_progress.Mmhc
- getDepth() - Method in class edu.cmu.tetrad.search.work_in_progress.SampleVcpc
- getDepth() - Method in class edu.cmu.tetrad.search.work_in_progress.SampleVcpcFast
- getDepth() - Method in class edu.cmu.tetrad.search.work_in_progress.VcFas
- getDepth() - Method in class edu.cmu.tetrad.search.work_in_progress.VcPc
- getDepth() - Method in class edu.cmu.tetrad.search.work_in_progress.VcPcAlt
- getDepth() - Method in class edu.cmu.tetrad.search.work_in_progress.VcPcFast
- getDescendants(SessionNode) - Static method in class edu.cmu.tetrad.session.SimulationStudy
- getDescendants(List<Node>) - Method in class edu.cmu.tetrad.graph.Paths
- getDescription() - Method in interface edu.cmu.tetrad.algcomparison.algorithm.Algorithm
-
Returns a short, one-line description of this algorithm.
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.cluster.Bpc
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.cluster.Fofc
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.cluster.Ftfc
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.continuous.dag.Dagma
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.continuous.dag.DirectLingam
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.continuous.dag.IcaLingam
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.continuous.dag.IcaLingD
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.external.ExternalAlgorithmBnlearnMmhc
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.external.ExternalAlgorithmBNTPc
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.external.ExternalAlgorithmIntersection
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.external.ExternalAlgorithmPcalgGes
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.external.ExternalAlgorithmPcalgPc
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.external.ExternalAlgorithmTetrad
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.FirstInflection
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.mixed.Mgm
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.Fask
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FaskConcatenated
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FaskLofsConcatenated
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FaskVote
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FasLofs
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FciIod
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FgesConcatenated
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.Images
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Boss
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Cpc
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Fas
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Fges
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.FgesMb
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.FgesMeasurement
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.GesMe
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Grasp
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Pc
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Pcd
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.PcLingam
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.PcMb
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.RestrictedBoss
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.SingleGraphAlg
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Sp
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Bfci
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Ccd
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Cfci
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Fci
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.FciMax
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Gfci
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.GraspFci
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.PagSampleRfci
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Rfci
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.RfciBsc
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.SpFci
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.SvarFci
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.SvarGfci
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pattern.Cstar
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.other.FactorAnalysis
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.other.Glasso
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.Eb
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.FaskPw
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.R1
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.R2
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.R3
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.Rskew
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.RskewE
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.Skew
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.SkewE
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.Tanh
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.StabilitySelection
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.algorithm.StARS
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.graph.Cyclic
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.graph.ErdosRenyi
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.graph.RandomForward
- getDescription() - Method in interface edu.cmu.tetrad.algcomparison.graph.RandomGraph
-
Returns a short, one-line description of this graph type.
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.graph.RandomSingleFactorMim
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.graph.RandomTwoFactorMim
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.graph.ScaleFree
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.graph.SingleGraph
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.independence.BdeuTest
-
Returns the description of the test.
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.independence.CciTest
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.independence.ChiSquare
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.independence.ConditionalGaussianLRT
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.independence.DegenerateGaussianLRT
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.independence.DiscreteBicTest
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.independence.FisherZ
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.independence.GICScoreTests
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.independence.Gsquare
- getDescription() - Method in interface edu.cmu.tetrad.algcomparison.independence.IndependenceWrapper
-
Returns a short of this independence test.
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.independence.Kci
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.independence.MagSemBicTest
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.independence.Mnlrlrt
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.independence.MSeparationTest
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.independence.MultinomialLogisticRegressionWald
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.independence.Mvplrt
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.independence.PoissonScoreTest
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.independence.PositiveCorr
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.independence.ProbabilisticTest
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.independence.SemBicDTest
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.independence.SemBicTest
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.independence.UniformScatterTest
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.score.BdeuScore
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.score.CciScore
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.score.ConditionalGaussianBicScore
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.score.DegenerateGaussianBicScore
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.score.DiscreteBicScore
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.score.EbicScore
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.score.FisherZScore
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.score.GicScores
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.score.MagSemBicScore
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.score.MSeparationScore
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.score.MVPBicScore
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.score.PoissonPriorScore
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.score.PositiveCorrScore
- getDescription() - Method in interface edu.cmu.tetrad.algcomparison.score.ScoreWrapper
-
Returns a short of this independence test.
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.score.SemBicScore
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.score.SemBicScoreDeterministic
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.score.ZhangShenBoundScore
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.simulation.BayesNetSimulation
-
Returns the description.
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.simulation.BooleanGlassSimulation
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.simulation.ConditionalGaussianSimulation
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.simulation.GeneralSemSimulation
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.simulation.GeneralSemSimulationSpecial1
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.simulation.LeeHastieSimulation
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.simulation.LinearFisherModel
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.simulation.LinearSineSimulation
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.simulation.NLSemSimulation
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.simulation.SemSimulation
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.simulation.SemThenDiscretize
- getDescription() - Method in interface edu.cmu.tetrad.algcomparison.simulation.Simulation
-
Returns the description of the simulation.
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.simulation.StandardizedSemSimulation
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.simulation.TimeSeriesSemSimulation
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.AdjacencyFn
-
Returns the description of the statistic.
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.AdjacencyFp
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.AdjacencyFpr
-
Returns the description of the statistic.
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.AdjacencyPrecision
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.AdjacencyRecall
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.AdjacencyTn
-
Returns the description of the statistic.
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.AdjacencyTp
-
Returns the description of the statistic.
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.AdjacencyTpr
-
Returns the description of the statistic.
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.AncestorF1
-
Returns the name of the statistic.
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.AncestorPrecision
-
Returns the description of the statistic.
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.AncestorRecall
-
Returns the description of the statistic.
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.AncestralPrecision
-
Returns the description of the statistic.
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.AncestralRecall
-
Returns the description of the statistic.
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.ArrowheadFn
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.ArrowheadFp
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.ArrowheadFpr
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.ArrowheadPrecision
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.ArrowheadPrecisionCommonEdges
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.ArrowheadRecall
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.ArrowheadRecallCommonEdges
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.ArrowheadTn
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.ArrowheadTp
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.AverageDegreeEst
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.AverageDegreeTrue
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.BicDiff
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.BicDiffPerRecord
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.BicEst
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.BicTrue
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.BidirectedEst
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.BidirectedFP
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.BidirectedLatentPrecision
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.BidirectedPrecision
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.BidirectedRecall
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.BidirectedTP
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.BidirectedTrue
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.CommonAncestorFalseNegativeBidirected
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.CommonAncestorFalsePositiveBidirected
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.CommonAncestorTruePositiveBidirected
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.CommonMeasuredAncestorRecallBidirected
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.CorrectSkeleton
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.DefiniteDirectedPathPrecision
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.DefiniteDirectedPathRecall
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.DensityEst
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.DensityTrue
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.ElapsedCpuTime
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.F1Adj
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.F1All
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.F1Arrow
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.FalseNegativesAdjacencies
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.FalsePositiveAdjacencies
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.FractionDependentUnderAlternative
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.FractionDependentUnderNull
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.GraphExactlyRight
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.LatentCommonAncestorFalseNegativeBidirected
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.LatentCommonAncestorFalsePositiveBidirected
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.LatentCommonAncestorRecallBidirected
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.LatentCommonAncestorTruePositiveBidirected
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.LegalPag
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.MarkovAdequacyScore
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.MathewsCorrAdj
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.MathewsCorrArrow
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.MaximalityCondition
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.NoAlmostCyclicPathsCondition
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.NoAlmostCyclicPathsInMagCondition
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.NoCyclicPathsCondition
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.NoCyclicPathsInMagCondition
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.NodesInCyclesPrecision
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.NodesInCyclesRecall
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.NonancestorPrecision
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.NonancestorRecall
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.NoSemidirectedF1
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.NoSemidirectedPrecision
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.NoSemidirectedRecall
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumAmbiguousTriples
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumberOfEdgesEst
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumberOfEdgesTrue
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumBidirectedBothNonancestorAncestor
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumBidirectedEdgesEst
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumBidirectedEdgesTrue
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumColoredDD
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumColoredNL
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumColoredPD
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumColoredPL
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumCommonMeasuredAncestorBidirected
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumCompatibleDefiniteDirectedEdgeAncestors
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumCompatibleDirectedEdgeConfounded
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumCompatibleDirectedEdgeNonAncestors
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumCompatibleEdges
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumCompatiblePossiblyDirectedEdgeAncestors
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumCompatiblePossiblyDirectedEdgeNonAncestors
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumCompatibleVisibleAncestors
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumCompatibleVisibleNonancestors
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumCorrectDDAncestors
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumCorrectPDAncestors
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumCorrectVisibleAncestors
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumDefinitelyDirected
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumDefinitelyNotDirectedPaths
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumDirectedEdgeAncestors
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumDirectedEdgeBnaMeasuredCounfounded
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumDirectedEdgeNoMeasureAncestors
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumDirectedEdgeNotAncNotRev
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumDirectedEdgeReversed
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumDirectedEdges
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumDirectedEdgeVisible
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumDirectedPathsEst
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumDirectedPathsTrue
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumDirectedShouldBePartiallyDirected
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumIncorrectDDAncestors
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumIncorrectPDAncestors
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumIncorrectVisibleAncestors
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumLatentCommonAncestorBidirected
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumNondirectedEdges
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumPartiallyOrientedEdges
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumPossiblyDirected
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumUndirectedEdges
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.NumVisibleEst
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.OrientationPrecision
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.OrientationRecall
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.PagAdjacencyPrecision
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.PagAdjacencyRecall
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.ParameterColumn
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.PercentAmbiguous
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.PercentBidirectedEdges
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.ProportionSemidirectedPathsNotReversedEst
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.ProportionSemidirectedPathsNotReversedTrue
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.PvalueDistanceToAlpha
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.PvalueUniformityUnderNull
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.SemidirectedPathF1
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.SemidirectedPrecision
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.SemidirectedRecall
- getDescription() - Method in interface edu.cmu.tetrad.algcomparison.statistic.Statistic
-
Returns a short one-line description of this statistic.
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.StructuralHammingDistance
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.TailPrecision
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.TailRecall
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.TrueDagFalseNegativesArrows
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.TrueDagFalseNegativesTails
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.TrueDagFalsePositiveArrow
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.TrueDagFalsePositiveTails
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.TrueDagPrecisionArrow
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.TrueDagPrecisionTails
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.TrueDagRecallArrows
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.TrueDagRecallTails
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.TrueDagTruePositiveArrow
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.TrueDagTruePositiveDirectedPathNonancestor
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.TrueDagTruePositiveTails
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.TwoCycleFalseNegative
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.TwoCycleFalsePositive
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.TwoCyclePrecision
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.TwoCycleRecall
- getDescription() - Method in class edu.cmu.tetrad.algcomparison.statistic.TwoCycleTruePositive
- getDescription() - Method in class edu.cmu.tetrad.data.simulation.LoadContinuousDataAndGraphs
- getDescription() - Method in class edu.cmu.tetrad.data.simulation.LoadContinuousDataAndSingleGraph
- getDescription() - Method in class edu.cmu.tetrad.data.simulation.LoadContinuousDataSmithSim
- getDescription() - Method in class edu.cmu.tetrad.data.simulation.LoadDataAndGraphs
- getDescription() - Method in class edu.cmu.tetrad.data.simulation.LoadDataFromFileWithoutGraph
- getDescription() - Method in class edu.cmu.tetrad.util.DefaultTetradLoggerConfig.DefaultEvent
- getDescription() - Method in interface edu.cmu.tetrad.util.TetradLoggerConfig.Event
- getDescriptorFromToken(String) - Method in class edu.cmu.tetrad.calculator.expression.ExpressionManager
- getDescriptors() - Method in class edu.cmu.tetrad.calculator.expression.ExpressionManager
- getDeterminant() - Method in class edu.pitt.csb.mgm.EigenDecomposition
-
Computes the determinant of the matrix.
- getDeterminismThreshold() - Method in class edu.cmu.tetrad.search.work_in_progress.SemBicScoreDeterministic
- getDf() - Method in class edu.cmu.tetrad.search.test.ChiSquareTest.Result
- getDf() - Method in class edu.cmu.tetrad.search.test.GSquareTest.Result
- getDf() - Method in class edu.cmu.tetrad.search.test.IndTestChiSquare
-
Returns the degrees of freedom associated with the most recent call of isIndependent.
- getDimension() - Method in class edu.cmu.tetrad.data.CorrelationMatrixOnTheFly
- getDimension() - Method in class edu.cmu.tetrad.data.CovarianceMatrix
- getDimension() - Method in class edu.cmu.tetrad.data.CovarianceMatrixOnTheFly
- getDimension() - Method in interface edu.cmu.tetrad.data.ICovarianceMatrix
- getDimension(int) - Method in class edu.cmu.tetrad.util.MultiDimIntTable
-
Describe
getDimensionmethod here. - getDimensions() - Method in class edu.cmu.tetrad.util.MultiDimIntTable
- getDims() - Method in class edu.cmu.tetrad.search.test.GSquareTest
-
Returns the dimensions of the variables, in order.
- getDims(int) - Method in class edu.cmu.tetrad.util.MultiDimIntTable
- getDir() - Method in class edu.cmu.tetrad.search.Cstar
- getDirectedEdge(Node, Node) - Method in class edu.cmu.tetrad.graph.Dag
- getDirectedEdge(Node, Node) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
- getDirectedEdge(Node, Node) - Method in interface edu.cmu.tetrad.graph.Graph
- getDirectedEdge(Node, Node) - Method in class edu.cmu.tetrad.graph.LagGraph
- getDirectedEdge(Node, Node) - Method in class edu.cmu.tetrad.graph.SemGraph
- getDirectedEdge(Node, Node) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- getDirectedEdgeHead(Edge) - Static method in class edu.cmu.tetrad.graph.Edges
-
For a directed edge, returns the node adjacent to the arrow endpoint.
- getDirectedEdgeTail(Edge) - Static method in class edu.cmu.tetrad.graph.Edges
-
For a directed edge, returns the node adjacent to the null endpoint.
- getDiscLevels(DataSet) - Static method in class edu.pitt.csb.mgm.MixedUtils
- getDiscreteData() - Method in class edu.cmu.tetrad.data.MixedDataBox
- getDiscreteData(DataSet) - Static method in class edu.pitt.csb.mgm.MixedUtils
- getDiscreteDataSet(DataModel) - Static method in class edu.cmu.tetrad.data.SimpleDataLoader
-
Returns the datamodel case to DataSet if it is discrete.
- getDiscreteInds(List<Node>) - Static method in class edu.pitt.csb.mgm.MixedUtils
- getDiscreteScore() - Method in class edu.cmu.tetrad.search.utils.FgesOrienter
- getDishBumpStDev() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.DishModel
- getDishDishVariability() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.simulation.MeasurementSimulator
-
Returns the standard deviation in percent of random dish bump values away from 100%.
- getDishDishVariability() - Method in class edu.cmu.tetrad.study.gene.tetradapp.model.MeasurementSimulatorParams
- getDishModel() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.GeneHistory
-
Gets the dish model.
- getDishNumber() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.DishModel
-
Returns the number of the getModel dish.
- getDishNumber() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.simulation.MeasurementSimulator
-
While the simulate() method is being executed, returns the dish number of the cell currently being simulated, zero indexed.
- getDisplayName() - Method in class edu.cmu.tetrad.session.SessionNode
- getDisplayString(LaggedFactor) - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.DisplayNameHandler
-
Converts the given lagged factor into a display string.
- getDisplayString(String, int) - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.DisplayNameHandler
-
Uses the given factor and lag information to construct a display string.
- getDist() - Method in class edu.cmu.tetrad.sem.EmpiricalDistributionForExpression
- getDistalEndpoint(Node) - Method in class edu.cmu.tetrad.graph.Edge
- getDistalNode(Node) - Method in class edu.cmu.tetrad.graph.Edge
-
Traverses the edge in an undirected fashion--given one node along the edge, returns the node at the opposite end of the edge.
- getDistribution() - Method in class edu.cmu.tetrad.sem.Parameter
- getDmStructure() - Method in class edu.cmu.tetrad.search.work_in_progress.DMSearch
- getDof() - Method in class edu.cmu.tetrad.bayes.BayesProperties
-
Call after calling getLikelihoodP().
- getDof() - Method in class edu.cmu.tetrad.search.score.ConditionalGaussianLikelihood.Ret
- getDof() - Method in class edu.cmu.tetrad.search.test.IndTestDegenerateGaussianLrt.Ret
- getDof() - Method in class edu.cmu.tetrad.search.work_in_progress.HbsmsBeam.Score
- getDof() - Method in class edu.cmu.tetrad.search.work_in_progress.HbsmsGes.Score
- getDof() - Method in class edu.cmu.tetrad.sem.DagScorer
- getDof() - Method in interface edu.cmu.tetrad.sem.Scorer
- getDof() - Method in class edu.cmu.tetrad.sem.SemPm
- getDoF(int, int[]) - Method in class edu.cmu.tetrad.search.score.MvpLikelihood
- getDoF(int, int[]) - Method in class edu.cmu.tetrad.search.work_in_progress.MnlrLikelihood
-
Returns the degrees of freedom of a child given its parents.
- getDottedUnderlinedTriplesFromGraph(Node, Graph) - Static method in class edu.cmu.tetrad.graph.GraphUtils
- getDottedUnderlines() - Method in class edu.cmu.tetrad.graph.Dag
- getDottedUnderlines() - Method in class edu.cmu.tetrad.graph.EdgeListGraph
- getDottedUnderlines() - Method in interface edu.cmu.tetrad.graph.Graph
- getDottedUnderlines() - Method in class edu.cmu.tetrad.graph.LagGraph
- getDottedUnderlines() - Method in class edu.cmu.tetrad.graph.SemGraph
- getDottedUnderlines() - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- getDottedUnderlines() - Method in class edu.cmu.tetrad.graph.Underlines
- getDouble(int, int) - Method in class edu.cmu.tetrad.data.BoxDataSet
- getDouble(int, int) - Method in interface edu.cmu.tetrad.data.DataSet
- getDouble(int, int) - Method in class edu.cmu.tetrad.data.NumberObjectDataSet
- getDouble(String) - Method in class edu.cmu.tetrad.util.Parameters
-
Returns the double value of the given parameter, looking up its default in the ParamDescriptions map.
- getDouble(String, double) - Method in class edu.cmu.tetrad.util.Parameters
-
Returns the object value of the given parameter, using the given default.
- getDoubleData() - Method in class edu.cmu.tetrad.data.BoxDataSet
- getDoubleData() - Method in interface edu.cmu.tetrad.data.DataSet
- getDoubleData() - Method in class edu.cmu.tetrad.data.NumberObjectDataSet
- getDoubleMissingValue() - Static method in class edu.cmu.tetrad.data.ContinuousVariable
- getDoubleValue(int, int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.BasicMatrix
-
Returns the value stored at element (r,c) as a double
- getDoubleValue(int, int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.LTMatrix
-
Returns element (r,c) as a double
- getDoubleValue(int, int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.LTMatrixF
-
Returns element (r,c) as a double
- getDoubleValue(int, int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.Matrix
-
Returns the value stored at element (r,c) as a double
- getDoubleValue(int, int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.MatrixF
-
Returns the value stored at element (r,c) as a double
- getEBICprior() - Method in class edu.cmu.tetrad.search.score.MvpLikelihood
- getEBICprior() - Method in class edu.cmu.tetrad.search.work_in_progress.MnlrLikelihood
- getEdge() - Method in class edu.cmu.tetrad.sem.StandardizedSemIm.ParameterRange
- getEdge(int, int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.biolingua.Digraph
-
Returns the value of edge between nodes i and j
- getEdge(int, int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.BasicGraph
-
Returns the value of edge between nodes i and j
- getEdge(Node, Node) - Method in class edu.cmu.tetrad.graph.Dag
- getEdge(Node, Node) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
- getEdge(Node, Node) - Method in interface edu.cmu.tetrad.graph.Graph
- getEdge(Node, Node) - Method in class edu.cmu.tetrad.graph.LagGraph
- getEdge(Node, Node) - Method in class edu.cmu.tetrad.graph.SemGraph
- getEdge(Node, Node) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- getEdgeCoef() - Method in class edu.cmu.tetrad.sem.DagScorer
- getEdgeCoef() - Method in interface edu.cmu.tetrad.sem.Scorer
- getEdgeCoef() - Method in class edu.cmu.tetrad.sem.SemIm
- getEdgeCoef(Edge) - Method in class edu.cmu.tetrad.sem.SemIm
- getEdgeCoef(Node, Node) - Method in class edu.cmu.tetrad.sem.SemIm
- getEdgeCoef(Node, Node) - Method in class edu.cmu.tetrad.sem.StandardizedSemIm
- getEdgeNodePairs(List<Graph>) - Static method in class edu.cmu.tetrad.util.GraphSampling
- getEdgeParams(Node, Node, GeneralizedSemPm) - Static method in class edu.pitt.csb.mgm.MixedUtils
- getEdgeParams(String, String, GeneralizedSemPm) - Static method in class edu.pitt.csb.mgm.MixedUtils
- getEdges() - Method in class edu.cmu.tetrad.data.KnowledgeGroup
- getEdges() - Method in class edu.cmu.tetrad.graph.Dag
- getEdges() - Method in class edu.cmu.tetrad.graph.EdgeListGraph
- getEdges() - Method in interface edu.cmu.tetrad.graph.Graph
- getEdges() - Method in class edu.cmu.tetrad.graph.LagGraph
- getEdges() - Method in class edu.cmu.tetrad.graph.SemGraph
- getEdges() - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- getEdges() - Method in class edu.cmu.tetrad.search.utils.TeyssierScorer
-
Returns a list of edges for the current graph as a list of ordered pairs.
- getEdges() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.biolingua.Digraph
-
Returns the edge matrix.
- getEdges(Node) - Method in class edu.cmu.tetrad.graph.Dag
- getEdges(Node) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
- getEdges(Node) - Method in interface edu.cmu.tetrad.graph.Graph
- getEdges(Node) - Method in class edu.cmu.tetrad.graph.LagGraph
- getEdges(Node) - Method in class edu.cmu.tetrad.graph.SemGraph
- getEdges(Node) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- getEdges(Node, Node) - Method in class edu.cmu.tetrad.graph.Dag
- getEdges(Node, Node) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
- getEdges(Node, Node) - Method in interface edu.cmu.tetrad.graph.Graph
- getEdges(Node, Node) - Method in class edu.cmu.tetrad.graph.LagGraph
- getEdges(Node, Node) - Method in class edu.cmu.tetrad.graph.SemGraph
- getEdges(Node, Node) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- getEdgesAdded() - Method in class edu.cmu.tetrad.graph.GraphUtils.GraphComparison
- getEdgesRemoved() - Method in class edu.cmu.tetrad.graph.GraphUtils.GraphComparison
- getEdgeType() - Method in class edu.cmu.tetrad.graph.EdgeTypeProbability
- getEdgeTypeConfusionMatrix(Graph, Graph) - Static method in class edu.pitt.dbmi.algo.resampling.GeneralResamplingTest
- getEdgeTypeProbabilities() - Method in class edu.cmu.tetrad.graph.Edge
- getEdgewiseComparisonString(Graph, Graph) - Static method in class edu.cmu.tetrad.algcomparison.CompareTwoGraphs
-
Returns an edgewise comparison of two graphs.
- getEdgewiseComparisonString(String, Graph, String, Graph) - Static method in class edu.cmu.tetrad.search.utils.GraphSearchUtils
- getEditDelegate() - Method in interface edu.cmu.tetrad.session.DelegatesEditing
- getEffectNode() - Method in class edu.cmu.tetrad.search.Cstar.Record
- getEffects() - Method in class edu.cmu.tetrad.search.Ida.NodeEffects
- getEigenvector(int) - Method in class edu.pitt.csb.mgm.EigenDecomposition
-
Gets a copy of the ith eigenvector of the original matrix.
- getElapsed() - Method in class edu.cmu.tetrad.study.performance.ComparisonResult
- getElapsedTime() - Method in class edu.cmu.tetrad.search.Cfci
-
Returns the elapsed time ot the search.
- getElapsedTime() - Method in class edu.cmu.tetrad.search.Cpc
-
Returns the elapsed time of search in milliseconds, after
search()has been run. - getElapsedTime() - Method in class edu.cmu.tetrad.search.Fas
-
Returns the elapsed time of the search.
- getElapsedTime() - Method in class edu.cmu.tetrad.search.Fasd
-
Returns the elapsed time.
- getElapsedTime() - Method in class edu.cmu.tetrad.search.Fask
- getElapsedTime() - Method in class edu.cmu.tetrad.search.Fci
-
Returns the elapsed time of search.
- getElapsedTime() - Method in class edu.cmu.tetrad.search.FciMax
-
Returns the elapsed time of search.
- getElapsedTime() - Method in class edu.cmu.tetrad.search.Fges
-
Returns the elapsed time of the search.
- getElapsedTime() - Method in class edu.cmu.tetrad.search.FgesMb
-
Returns the elapsed time of the search.
- getElapsedTime() - Method in interface edu.cmu.tetrad.search.IFas
-
Returns the elapsed time of the search.
- getElapsedTime() - Method in class edu.cmu.tetrad.search.Pc
-
Returns the elapsed time of the search, in milliseconds.
- getElapsedTime() - Method in class edu.cmu.tetrad.search.Pcd
- getElapsedTime() - Method in class edu.cmu.tetrad.search.PcMb
-
Returns the elapsed time of the most recent search.
- getElapsedTime() - Method in class edu.cmu.tetrad.search.Rfci
-
Returns the elapsed time of the search.
- getElapsedTime() - Method in class edu.cmu.tetrad.search.SvarFas
- getElapsedTime() - Method in class edu.cmu.tetrad.search.SvarFges
-
Returns the elapsed time of the search.
- getElapsedTime() - Method in class edu.cmu.tetrad.search.utils.FgesOrienter
- getElapsedTime() - Method in class edu.cmu.tetrad.search.utils.PcCommon
- getElapsedTime() - Method in class edu.cmu.tetrad.search.work_in_progress.Dci
- getElapsedTime() - Method in class edu.cmu.tetrad.search.work_in_progress.Fas2
- getElapsedTime() - Method in class edu.cmu.tetrad.search.work_in_progress.Fas3
-
Returns the elapsed time of the search.
- getElapsedTime() - Method in class edu.cmu.tetrad.search.work_in_progress.FasFdr
- getElapsedTime() - Method in class edu.cmu.tetrad.search.work_in_progress.FasLofs
- getElapsedTime() - Method in class edu.cmu.tetrad.search.work_in_progress.Kpc
- getElapsedTime() - Method in class edu.cmu.tetrad.search.work_in_progress.Mmhc
- getElapsedTime() - Method in class edu.cmu.tetrad.search.work_in_progress.SampleVcpc
- getElapsedTime() - Method in class edu.cmu.tetrad.search.work_in_progress.SampleVcpcFast
- getElapsedTime() - Method in class edu.cmu.tetrad.search.work_in_progress.VcPc
- getElapsedTime() - Method in class edu.cmu.tetrad.search.work_in_progress.VcPcAlt
- getElapsedTime() - Method in class edu.cmu.tetrad.search.work_in_progress.VcPcFast
- getElapsedTime() - Method in class edu.pitt.csb.mgm.Mgm
-
Return time of execution for learning.
- getElapsedTime(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.external.ExternalAlgorithmBnlearnMmhc
- getElapsedTime(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.external.ExternalAlgorithmBNTPc
- getElapsedTime(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.external.ExternalAlgorithmIntersection
- getElapsedTime(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.external.ExternalAlgorithmPcalgGes
- getElapsedTime(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.external.ExternalAlgorithmPcalgPc
- getElapsedTime(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.external.ExternalAlgorithmTetrad
- getElapsedTime(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.ExternalAlgorithm
- getElement(BayesIm) - Static method in class edu.cmu.tetrad.bayes.BayesXmlRenderer
- getElement(SemIm) - Static method in class edu.cmu.tetrad.sem.SemXmlRenderer
-
Converts a Sem Im into xml.
- getEndpoint(Node, Node) - Method in class edu.cmu.tetrad.graph.Dag
- getEndpoint(Node, Node) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
- getEndpoint(Node, Node) - Method in interface edu.cmu.tetrad.graph.Graph
- getEndpoint(Node, Node) - Method in class edu.cmu.tetrad.graph.LagGraph
- getEndpoint(Node, Node) - Method in class edu.cmu.tetrad.graph.SemGraph
- getEndpoint(Node, Node) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- getEndpoint1() - Method in class edu.cmu.tetrad.graph.Edge
- getEndpoint2() - Method in class edu.cmu.tetrad.graph.Edge
- getEqualFrequencyBreakPoints(double[], int) - Static method in class edu.cmu.tetrad.data.Discretizer
- getErrCovar() - Method in class edu.cmu.tetrad.sem.SemIm
- getErrCovar(Node, Node) - Method in class edu.cmu.tetrad.sem.SemIm
- getErrorCovar() - Method in class edu.cmu.tetrad.sem.DagScorer
- getErrorCovar() - Method in interface edu.cmu.tetrad.sem.Scorer
- getErrorCovariance(Node, Node) - Method in class edu.cmu.tetrad.sem.StandardizedSemIm
- getErrorDistribution(int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.BooleanGlassFunction
-
Returns the error distribution for the
factor'th factor. - getErrorDistribution(int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.LinearFunction
-
Returns the error distribution for the
factor'th factor. - getErrorDistribution(int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.PolynomialFunction
-
Returns the error distribution for the
factor'th factor. - getErrorDistribution(int) - Method in class edu.cmu.tetrad.study.gene.tetradapp.model.BooleanGlassGeneIm
-
Returns the error distribution for the given factor.
- getErrorNode(Node) - Method in class edu.cmu.tetrad.graph.SemGraph
- getErrorNode(Node) - Method in class edu.cmu.tetrad.sem.GeneralizedSemPm
- getErrorNodes() - Method in class edu.cmu.tetrad.sem.GeneralizedSemPm
-
Returns the list of exogenous variableNodes.
- getErrorNodes() - Method in class edu.cmu.tetrad.sem.StandardizedSemIm
- getErrorsTemplate() - Method in class edu.cmu.tetrad.sem.GeneralizedSemPm
- getErrorVariance(Node) - Method in class edu.cmu.tetrad.sem.StandardizedSemIm
- getErrVar(Node) - Method in class edu.cmu.tetrad.sem.SemIm
- getEss(ICovarianceMatrix) - Static method in class edu.cmu.tetrad.data.DataUtils
-
Returns the equivalent sample size, assuming all units are equally correlated and all unit variances are equal.
- getEstimatedIm() - Method in class edu.cmu.tetrad.bayes.EmBayesEstimator
- getEstimatedSem() - Method in class edu.cmu.tetrad.search.work_in_progress.HbsmsBeam.Score
- getEstimatedSem() - Method in class edu.cmu.tetrad.search.work_in_progress.HbsmsGes.Score
- getEstimatedSem() - Method in class edu.cmu.tetrad.sem.SemEstimator
- getEstimatedSem() - Method in class edu.cmu.tetrad.sem.SemEstimatorGibbs
- getEstimator() - Method in class edu.cmu.tetrad.bayes.EmBayesProperties
- getEstSem() - Method in class edu.cmu.tetrad.sem.DagScorer
- getEstSem() - Method in interface edu.cmu.tetrad.sem.Scorer
- getEvidence() - Method in class edu.cmu.tetrad.bayes.ApproximateUpdater
- getEvidence() - Method in class edu.cmu.tetrad.bayes.CptInvariantUpdater
- getEvidence() - Method in class edu.cmu.tetrad.bayes.Identifiability
- getEvidence() - Method in class edu.cmu.tetrad.bayes.JunctionTreeUpdater
- getEvidence() - Method in interface edu.cmu.tetrad.bayes.ManipulatingBayesUpdater
-
Returns the manipulation that was used to manipulate the Bayes IM.
- getEvidence() - Method in class edu.cmu.tetrad.bayes.RowSummingExactUpdater
- getEvidence() - Method in class edu.cmu.tetrad.bayes.UpdatedBayesIm
- getEvidence() - Method in class edu.cmu.tetrad.sem.SemUpdater
- getExampleNonsingular(ICovarianceMatrix, int) - Static method in class edu.cmu.tetrad.data.DataUtils
- getExogenous(Node) - Method in class edu.cmu.tetrad.graph.SemGraph
- getExpression() - Method in class edu.cmu.tetrad.calculator.expression.Equation
- getExpressions() - Method in class edu.cmu.tetrad.calculator.expression.ConstantExpression
- getExpressions() - Method in class edu.cmu.tetrad.calculator.expression.EvaluationExpression
- getExpressions() - Method in interface edu.cmu.tetrad.calculator.expression.Expression
- getExpressions() - Method in class edu.cmu.tetrad.calculator.expression.VariableExpression
- getExternalGraph() - Method in class edu.cmu.tetrad.search.SvarFges
- getExternalGraph() - Method in class edu.cmu.tetrad.search.utils.FgesOrienter
- getExternalGraph() - Method in class edu.pitt.dbmi.algo.resampling.task.GeneralResamplingSearchRunnable
- getFact() - Method in class edu.cmu.tetrad.search.test.IndependenceResult
-
Returns the independence fact being stored.
- getFactor() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.AbstractNbComponent
-
Returns the factor.
- getFactor() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.LaggedEdge
- getFactor() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.LaggedFactor
-
Returns the name of the lagged factor.
- getFactor(int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.IndexedConnectivity
-
Returns the (string name of) the factor at the given index.
- getFactor(int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.IndexedLagGraph
-
Returns the (string name of) the factor at the given index.
- getFactors() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ActiveLagGraph
- getFactors() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ManualLagGraph
- getFactors() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.BasicLagGraph
-
Returns a SortedSet of the factors in this graph.
- getFactors() - Method in interface edu.cmu.tetrad.study.gene.tetrad.gene.history.LagGraph
-
Returns a SortedSet of the factors in this graph.
- getFactors() - Method in class edu.cmu.tetrad.study.gene.tetradapp.model.BooleanGlassGeneIm
-
Returns the list of factors in the history.
- getFacts() - Method in class edu.cmu.tetrad.data.IndependenceFacts
- getFilename() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.StoredLagGraphParams
-
Returns the stored file.
- getFirst() - Method in class edu.cmu.tetrad.graph.NodePair
- getFirst() - Method in class edu.cmu.tetrad.graph.OrderedPair
- getFirstEdge() - Method in class edu.cmu.tetrad.search.work_in_progress.HbsmsBeam.Move
- getFirstLayer() - Method in class edu.cmu.tetrad.search.utils.GrowShrinkTree
- getFirstStepStored() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.simulation.MeasurementSimulator
-
Returns the index of the first step to actually be stored out.
- getFirstStepStored() - Method in class edu.cmu.tetrad.study.gene.tetradapp.model.MeasurementSimulatorParams
- getFixedParameters() - Method in interface edu.cmu.tetrad.sem.ISemIm
- getFixedParameters() - Method in class edu.cmu.tetrad.sem.SemIm
- getFml() - Method in class edu.cmu.tetrad.search.work_in_progress.HbsmsBeam.Score
- getFml() - Method in class edu.cmu.tetrad.search.work_in_progress.HbsmsGes.Score
- getFml() - Method in class edu.cmu.tetrad.sem.DagScorer
-
The value of the maximum likelihood function for the getModel the model (Bollen 107).
- getFml() - Method in interface edu.cmu.tetrad.sem.Scorer
- getFn() - Method in class edu.cmu.tetrad.algcomparison.statistic.utils.AdjacencyConfusion
-
Returns the false negative count.
- getFn() - Method in class edu.cmu.tetrad.algcomparison.statistic.utils.ArrowConfusion
-
False negatives.
- getFn() - Method in class edu.cmu.tetrad.algcomparison.statistic.utils.BidirectedConfusion
- getFn() - Method in class edu.cmu.tetrad.algcomparison.statistic.utils.OrientationConfusion
- getFnc() - Method in class edu.cmu.tetrad.algcomparison.statistic.utils.ArrowConfusion
-
False negatives for common edges.
- getForbidden() - Method in class edu.cmu.tetrad.search.utils.GrowShrinkTree
- getFp() - Method in class edu.cmu.tetrad.algcomparison.statistic.utils.AdjacencyConfusion
-
Returns the false positive count.
- getFp() - Method in class edu.cmu.tetrad.algcomparison.statistic.utils.ArrowConfusion
-
False positives.
- getFp() - Method in class edu.cmu.tetrad.algcomparison.statistic.utils.BidirectedConfusion
- getFp() - Method in class edu.cmu.tetrad.algcomparison.statistic.utils.OrientationConfusion
- getFpc() - Method in class edu.cmu.tetrad.algcomparison.statistic.utils.ArrowConfusion
-
False positives for common edges.
- getFractionDependent(boolean) - Method in class edu.cmu.tetrad.search.MarkovCheck
-
Returns the fraction of dependent judgments for the given list of results.
- getFreeParameters() - Method in interface edu.cmu.tetrad.sem.ISemIm
- getFreeParameters() - Method in class edu.cmu.tetrad.sem.SemIm
- getFreeParameters() - Method in class edu.cmu.tetrad.sem.SemPm
- getFreeParamValues() - Method in interface edu.cmu.tetrad.sem.ISemIm
- getFreeParamValues() - Method in class edu.cmu.tetrad.sem.SemIm
- getFrequencies() - Method in class edu.cmu.tetrad.data.Histogram
- getFrom() - Method in class edu.cmu.tetrad.data.KnowledgeEdge
- getFromVariables() - Method in class edu.cmu.tetrad.data.KnowledgeGroup
- getFullGraph() - Method in class edu.cmu.tetrad.search.Mimbuild
-
The full graph inferred, including the edges from latents to measures.
- getFullGraph() - Method in class edu.cmu.tetrad.search.MimbuildTrek
-
The full graph discovered.
- getFullTierOrdering() - Method in class edu.cmu.tetrad.graph.SemGraph
- getFValue(int, double[][]) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.BooleanGlassFunction
-
Calculates the new value for the F function, for the given factor, in light of the given history.
- getGeneralizedSemPm() - Method in class edu.cmu.tetrad.sem.GeneralizedSemIm
- getGesDepth() - Method in class edu.cmu.tetrad.search.work_in_progress.DMSearch
- getGraph() - Method in interface edu.cmu.tetrad.regression.Regression
- getGraph() - Method in class edu.cmu.tetrad.regression.RegressionCovariance
- getGraph() - Method in class edu.cmu.tetrad.regression.RegressionDataset
- getGraph() - Method in class edu.cmu.tetrad.search.Cpc
-
The graph that's constructed during the search.
- getGraph() - Method in class edu.cmu.tetrad.search.score.ScoredGraph
- getGraph() - Method in class edu.cmu.tetrad.search.test.MsepTest
-
Returns the underlying graph that is being used to calculate d-separation relationships.
- getGraph() - Method in class edu.cmu.tetrad.search.work_in_progress.HbsmsBeam
- getGraph() - Method in class edu.cmu.tetrad.search.work_in_progress.HbsmsGes
- getGraph() - Method in class edu.cmu.tetrad.search.work_in_progress.HbsmsGes.GraphWithPValue
- getGraph() - Method in class edu.cmu.tetrad.search.work_in_progress.SampleVcpc
-
The graph that's constructed during the search.
- getGraph() - Method in class edu.cmu.tetrad.search.work_in_progress.SampleVcpcFast
-
The graph that's constructed during the search.
- getGraph() - Method in class edu.cmu.tetrad.search.work_in_progress.VcPc
-
The graph that's constructed during the search.
- getGraph() - Method in class edu.cmu.tetrad.search.work_in_progress.VcPcAlt
-
The graph that's constructed during the search.
- getGraph() - Method in class edu.cmu.tetrad.search.work_in_progress.VcPcFast
-
The graph that's constructed during the search.
- getGraph() - Method in class edu.cmu.tetrad.sem.GeneralizedSemPm
-
Returns the structural model graph this SEM PM is using.
- getGraph() - Method in class edu.cmu.tetrad.sem.LargeScaleSimulation
- getGraph() - Method in class edu.cmu.tetrad.sem.SemPm
- getGraph(boolean) - Method in class edu.cmu.tetrad.search.Grasp
-
Returns the graph implied by the discovered permutation.
- getGraph(boolean) - Method in class edu.cmu.tetrad.search.utils.TeyssierScorer
-
Returns the DAG build for the current permutation, or its CPDAG.
- getGraph(boolean) - Method in class edu.cmu.tetrad.search.work_in_progress.GraspTol
- getGraph(boolean) - Method in class edu.cmu.tetrad.search.work_in_progress.OtherPermAlgs
- getGraph(List<Node>, Map<Node, Set<Node>>, boolean) - Static method in class edu.cmu.tetrad.search.PermutationSearch
-
Construct a graph given a specification of the parents for each node.
- getGraph(List<Node>, Map<Node, Set<Node>>, Knowledge, boolean) - Static method in class edu.cmu.tetrad.search.PermutationSearch
-
Construct a graph given a specification of the parents for each node.
- getGraphComparison(Graph, Graph) - Static method in class edu.cmu.tetrad.search.utils.GraphSearchUtils
-
Just counts arrowhead errors--for cyclic edges counts an arrowhead at each node.
- getGraphFile() - Method in class edu.cmu.tetrad.study.performance.ComparisonParameters
- getGraphName() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.akutsu.RevealOutputGraph
- getGraphName() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.reveal.RevealOutputGraph
- getGraphName() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.RevealOutputGraph
- getGraphName() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.BasicGraph
-
Returns the name of the graph
- getGraphName() - Method in interface edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.OutputGraph
-
Returns the name of the graph
- getGraphNum() - Method in class edu.cmu.tetrad.study.performance.ComparisonParameters
- getGraphRBD() - Method in class edu.pitt.dbmi.algo.bayesian.constraint.search.RfciBsc
- getGraphRBI() - Method in class edu.pitt.dbmi.algo.bayesian.constraint.search.RfciBsc
- getGraphs() - Method in class edu.pitt.dbmi.algo.resampling.GeneralResamplingTest
-
Returns the individual bootstrap result graphs.
- getGSquare() - Method in class edu.cmu.tetrad.search.test.GSquareTest.Result
- getGST(Node) - Method in class edu.cmu.tetrad.search.PermutationSearch
- getH() - Method in class edu.cmu.tetrad.search.test.IndTestProbabilistic
- getH() - Method in class edu.cmu.tetrad.search.work_in_progress.ProbabilisticMapIndependence
- getHigh() - Method in class edu.cmu.tetrad.sem.StandardizedSemIm.ParameterRange
- getHighPValueAlpha() - Method in class edu.cmu.tetrad.search.work_in_progress.HbsmsBeam
- getHistory() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.simulation.MeasurementSimulator
-
Returns the history that was set in the constructor.
- getHistory() - Method in class edu.cmu.tetrad.study.gene.tetradapp.model.BooleanGlassGeneIm
-
Returns the Glass history case to GlassHistory for convenience.
- getHistoryArray() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.GeneHistory
-
Returns the getModel history array.
- getI() - Method in class edu.cmu.tetrad.search.utils.Sextad
- getI() - Method in class edu.cmu.tetrad.search.utils.Tetrad
- getI() - Method in class edu.cmu.tetrad.search.work_in_progress.Sextad
- getId() - Method in class edu.cmu.tetrad.util.DefaultTetradLoggerConfig.DefaultEvent
- getId() - Method in interface edu.cmu.tetrad.util.TetradLoggerConfig.Event
- getImagEigenvalue(int) - Method in class edu.pitt.csb.mgm.EigenDecomposition
-
Gets the imaginary part of the ith eigenvalue of the original matrix.
- getImagEigenvalues() - Method in class edu.pitt.csb.mgm.EigenDecomposition
-
Gets a copy of the imaginary parts of the eigenvalues of the original matrix.
- getImplCovar() - Method in class edu.cmu.tetrad.sem.StandardizedSemIm
- getImplCovar(boolean) - Method in interface edu.cmu.tetrad.sem.ISemIm
- getImplCovar(boolean) - Method in class edu.cmu.tetrad.sem.SemIm
- getImplCovar(List<Node>) - Method in class edu.cmu.tetrad.sem.SemIm
- getImplCovarMeas() - Method in interface edu.cmu.tetrad.sem.ISemIm
- getImplCovarMeas() - Method in class edu.cmu.tetrad.sem.SemIm
- getImplCovarMeas() - Method in class edu.cmu.tetrad.sem.StandardizedSemIm
- getIms() - Method in class edu.cmu.tetrad.algcomparison.simulation.GeneralSemSimulation
- getIndegree() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.LagGraphParams
- getIndegree(Graph) - Static method in class edu.cmu.tetrad.graph.GraphUtils
- getIndegree(Node) - Method in class edu.cmu.tetrad.graph.Dag
- getIndegree(Node) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
- getIndegree(Node) - Method in interface edu.cmu.tetrad.graph.Graph
- getIndegree(Node) - Method in class edu.cmu.tetrad.graph.LagGraph
- getIndegree(Node) - Method in class edu.cmu.tetrad.graph.SemGraph
- getIndegree(Node) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- getIndegreeType() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.LagGraphParams
- getIndependenceFacts() - Method in class edu.cmu.tetrad.search.utils.GraphoidAxioms
-
Returns the independence facts in the form 1:2|3 for use in various Tetrad algorithms.
- getIndependenceTest() - Method in class edu.cmu.tetrad.search.BFci
-
The independence test being used for some steps in final orientation.
- getIndependenceTest() - Method in class edu.cmu.tetrad.search.Cpc
-
Rreturn the independence test used in the search, set in the constructor.
- getIndependenceTest() - Method in class edu.cmu.tetrad.search.Fci
-
Returns the independence test used in search.
- getIndependenceTest() - Method in class edu.cmu.tetrad.search.FciMax
-
Returns the independence test used in search.
- getIndependenceTest() - Method in class edu.cmu.tetrad.search.GFci
-
Returns the independence test used in search.
- getIndependenceTest() - Method in class edu.cmu.tetrad.search.MarkovCheck
-
Returns the independence test being used.
- getIndependenceTest() - Method in class edu.cmu.tetrad.search.Pc
-
Returns the independence test being used in the search.
- getIndependenceTest() - Method in class edu.cmu.tetrad.search.Pcd
- getIndependenceTest() - Method in class edu.cmu.tetrad.search.Rfci
-
Returns the independence test.
- getIndependenceTest() - Method in class edu.cmu.tetrad.search.SpFci
-
Returns the independence test used in search.
- getIndependenceTest() - Method in class edu.cmu.tetrad.search.SvarFci
-
Returns independence test.
- getIndependenceTest() - Method in class edu.cmu.tetrad.search.utils.PcCommon
- getIndependenceTest() - Method in class edu.cmu.tetrad.search.utils.SepsetsConservative
- getIndependenceTest() - Method in class edu.cmu.tetrad.search.work_in_progress.Kpc
- getIndependenceTest() - Method in class edu.cmu.tetrad.search.work_in_progress.Mmhc
- getIndependenceTest() - Method in class edu.cmu.tetrad.search.work_in_progress.SampleVcpc
- getIndependenceTest() - Method in class edu.cmu.tetrad.search.work_in_progress.SampleVcpcFast
- getIndependenceTest() - Method in class edu.cmu.tetrad.search.work_in_progress.VcPc
- getIndependenceTest() - Method in class edu.cmu.tetrad.search.work_in_progress.VcPcAlt
- getIndependenceTest() - Method in class edu.cmu.tetrad.search.work_in_progress.VcPcFast
- getIndependenceTest() - Method in class edu.cmu.tetrad.study.performance.ComparisonParameters
- getIndependenceWrapper() - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.Fask
- getIndependenceWrapper() - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FaskConcatenated
- getIndependenceWrapper() - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FaskVote
- getIndependenceWrapper() - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FciIod
- getIndependenceWrapper() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Cpc
- getIndependenceWrapper() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Fas
- getIndependenceWrapper() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Grasp
- getIndependenceWrapper() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Pc
- getIndependenceWrapper() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.PcMb
- getIndependenceWrapper() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Bfci
- getIndependenceWrapper() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Ccd
- getIndependenceWrapper() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Cfci
- getIndependenceWrapper() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Fci
- getIndependenceWrapper() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.FciMax
- getIndependenceWrapper() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Gfci
- getIndependenceWrapper() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.GraspFci
- getIndependenceWrapper() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Rfci
- getIndependenceWrapper() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.SpFci
- getIndependenceWrapper() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.SvarFci
- getIndependenceWrapper() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.SvarGfci
- getIndependenceWrapper() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pattern.Cstar
- getIndependenceWrapper() - Method in interface edu.cmu.tetrad.algcomparison.utils.TakesIndependenceWrapper
- getIndex() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.ideker.ItkPredictorSearch.Gene
- getIndex() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.IndexedParent
-
Returns the index of the parent.
- getIndex(int, IndexedParent) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.IndexedConnectivity
-
Returns the index of the parent of the given factor that is equal to the given IndexedParent, or -1 if the given IndexedParent is not equal to any parent.
- getIndex(int, IndexedParent) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.IndexedLagGraph
-
Returns the index of the parent of the given factor that is equal to the given IndexedParent, or -1 if the given IndexedParent is not equal to any parent.
- getIndex(DataModel) - Method in class edu.cmu.tetrad.algcomparison.algorithm.ExternalAlgorithm
- getIndex(Endpoint) - Static method in class edu.cmu.tetrad.graph.MisclassificationUtils
- getIndex(Node) - Method in class edu.cmu.tetrad.search.utils.GrowShrinkTree
- getIndex(String) - Method in class edu.cmu.tetrad.data.DiscreteVariable
- getIndex(String) - Static method in class edu.cmu.tetrad.search.utils.TsUtils
- getIndex(String) - Static method in class edu.cmu.tetrad.sem.LargeScaleSimulation
- getIndex(String) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.IndexedConnectivity
-
Returns the index of the given String factor.
- getIndex(String) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.IndexedLagGraph
-
Returns the index of the given String factor.
- getIndex(String) - Static method in class edu.cmu.tetrad.study.performance.Comparison2
- getIndex(String, LaggedFactor) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.IndexedConnectivity
-
Returns the index of the given parent for the given factor.
- getIndex(String, LaggedFactor) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.IndexedLagGraph
-
Returns the index of the given parent for the given factor.
- getIndexedLagGraph() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.BooleanGlassFunction
-
Returns the indexed connectivity.
- getIndexedLagGraph() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.LinearFunction
-
Returns the indexed connectivity.
- getIndexedLagGraph() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.PolynomialFunction
-
Returns the indexed connectivity.
- getIndexedLagGraph() - Method in interface edu.cmu.tetrad.study.gene.tetrad.gene.history.UpdateFunction
-
Returns the indexed lag graph, if one is available.
- getIndices() - Method in class edu.cmu.tetrad.util.IndexedMatrix
- getInducingPath(Node, Node) - Method in class edu.cmu.tetrad.graph.Paths
- getInhibitExcite() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.AbstractNbComponent
-
Returns the inhibit/excite.
- getInitializer() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.GeneHistory
-
Returns the initializer.
- getInitSync() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.GeneHistory
-
Determines whether initialization is synchronized.
- getInputNodes() - Method in interface edu.cmu.tetrad.sem.ConnectionFunction
- getInputs() - Method in class edu.cmu.tetrad.search.work_in_progress.DMSearch
- getInputs(Node) - Method in class edu.cmu.tetrad.search.work_in_progress.DMSearch.LatentStructure
- getInstance() - Static method in class edu.cmu.tetrad.annotation.AlgorithmAnnotations
-
Gets the instance of this class.
- getInstance() - Static method in class edu.cmu.tetrad.annotation.ScoreAnnotations
- getInstance() - Static method in class edu.cmu.tetrad.annotation.TestOfIndependenceAnnotations
- getInstance() - Static method in class edu.cmu.tetrad.calculator.expression.ExpressionManager
- getInstance() - Static method in class edu.cmu.tetrad.sem.TemplateExpander
- getInstance() - Static method in class edu.cmu.tetrad.util.AlgorithmDescriptions
-
Gets the instance of this class.
- getInstance() - Static method in class edu.cmu.tetrad.util.ForkJoinPoolInstance
- getInstance() - Static method in class edu.cmu.tetrad.util.IndependenceTestDescriptions
- getInstance() - Static method in class edu.cmu.tetrad.util.LogUtils
- getInstance() - Static method in class edu.cmu.tetrad.util.NumberFormatUtil
- getInstance() - Static method in class edu.cmu.tetrad.util.ParamDescriptions
- getInstance() - Static method in class edu.cmu.tetrad.util.RandomUtil
- getInstance() - Static method in class edu.cmu.tetrad.util.ScoreDescriptions
- getInstance() - Static method in class edu.cmu.tetrad.util.TaskManager
- getInstance() - Static method in class edu.cmu.tetrad.util.TetradLogger
- getInstance() - Static method in class edu.cmu.tetrad.util.TetradProperties
- getInt(int, int) - Method in class edu.cmu.tetrad.data.BoxDataSet
- getInt(int, int) - Method in interface edu.cmu.tetrad.data.DataSet
- getInt(int, int) - Method in class edu.cmu.tetrad.data.NumberObjectDataSet
- getInt(String) - Method in class edu.cmu.tetrad.util.Parameters
-
Returns the integer value of the given parameter, looking up its default in the ParamDescriptions map.
- getInt(String, int) - Method in class edu.cmu.tetrad.util.Parameters
-
Returns the integer value of the given parameter, looking up its default in the ParamDescriptions map.
- getIntegerDistribution(Context) - Method in class edu.cmu.tetrad.calculator.expression.ConstantExpression
- getIntegerDistribution(Context) - Method in class edu.cmu.tetrad.calculator.expression.EvaluationExpression
- getIntegerDistribution(Context) - Method in interface edu.cmu.tetrad.calculator.expression.Expression
- getIntegerDistribution(Context) - Method in class edu.cmu.tetrad.calculator.expression.VariableExpression
- getIntercept() - Method in class edu.cmu.tetrad.regression.LogisticRegression.Result
- getIntercept(Node) - Method in interface edu.cmu.tetrad.sem.ISemIm
- getIntercept(Node) - Method in class edu.cmu.tetrad.sem.SemIm
- getIntersectionComparisonString(List<Graph>) - Static method in class edu.cmu.tetrad.graph.GraphUtils
- getInterval() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.simulation.MeasurementSimulator
-
Sets the interval (in time steps) between time steps stored out.
- getInterval() - Method in class edu.cmu.tetrad.study.gene.tetradapp.model.MeasurementSimulatorParams
- getInts(int[]) - Static method in class edu.cmu.tetrad.search.utils.ClusterSignificance
-
Converts a list of indices into a list of Integers representing a cluster.
- getIterations() - Method in class edu.cmu.tetrad.search.work_in_progress.Ion
- getIterations() - Method in class edu.cmu.tetrad.sem.Ricf.RicfResult
- getJ() - Method in class edu.cmu.tetrad.search.utils.Sextad
- getJ() - Method in class edu.cmu.tetrad.search.utils.Tetrad
- getJ() - Method in class edu.cmu.tetrad.search.work_in_progress.Sextad
- getJointMarginal(int[], int[]) - Method in class edu.cmu.tetrad.bayes.ApproximateUpdater
- getJointMarginal(int[], int[]) - Method in interface edu.cmu.tetrad.bayes.BayesUpdater
-
Returns the joint marginal probability of the given variables taking the given values, given the evidence.
- getJointMarginal(int[], int[]) - Method in class edu.cmu.tetrad.bayes.CptInvariantUpdater
- getJointMarginal(int[], int[]) - Method in class edu.cmu.tetrad.bayes.Identifiability
- getJointMarginal(int[], int[]) - Method in class edu.cmu.tetrad.bayes.JunctionTreeUpdater
- getJointMarginal(int[], int[]) - Method in class edu.cmu.tetrad.bayes.RowSummingExactUpdater
- getJointProbability(int[], int[]) - Method in class edu.cmu.tetrad.bayes.JunctionTreeAlgorithm
- getJointProbabilityAll(int[]) - Method in class edu.cmu.tetrad.bayes.JunctionTreeAlgorithm
-
Get the joint probability of all nodes (variables).
- getJPD() - Method in class edu.cmu.tetrad.bayes.MlBayesImObs
- getK() - Method in class edu.cmu.tetrad.search.FastIca.IcaResult
- getK() - Method in class edu.cmu.tetrad.search.utils.Sextad
- getK() - Method in class edu.cmu.tetrad.search.utils.Tetrad
- getK() - Method in class edu.cmu.tetrad.search.work_in_progress.Sextad
- getK() - Method in class edu.cmu.tetrad.util.PartialCorrelationPdf
- getKnowledge() - Method in class edu.cmu.tetrad.algcomparison.algorithm.cluster.Fofc
- getKnowledge() - Method in class edu.cmu.tetrad.algcomparison.algorithm.cluster.Ftfc
- getKnowledge() - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.Fask
- getKnowledge() - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FaskConcatenated
- getKnowledge() - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FaskLofsConcatenated
- getKnowledge() - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FaskVote
- getKnowledge() - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FasLofs
- getKnowledge() - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FciIod
- getKnowledge() - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FgesConcatenated
- getKnowledge() - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.Images
- getKnowledge() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Boss
- getKnowledge() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Cpc
- getKnowledge() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Fas
- getKnowledge() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Fges
- getKnowledge() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.FgesMb
- getKnowledge() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.FgesMeasurement
- getKnowledge() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Grasp
- getKnowledge() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Pc
- getKnowledge() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Pcd
- getKnowledge() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.PcLingam
- getKnowledge() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.PcMb
- getKnowledge() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.SingleGraphAlg
- getKnowledge() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Sp
- getKnowledge() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Bfci
- getKnowledge() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Cfci
- getKnowledge() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Fci
- getKnowledge() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.FciMax
- getKnowledge() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Gfci
- getKnowledge() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.GraspFci
- getKnowledge() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.PagSampleRfci
- getKnowledge() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Rfci
- getKnowledge() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.RfciBsc
- getKnowledge() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.SpFci
- getKnowledge() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.SvarFci
- getKnowledge() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.SvarGfci
- getKnowledge() - Method in class edu.cmu.tetrad.algcomparison.simulation.TimeSeriesSemSimulation
- getKnowledge() - Method in interface edu.cmu.tetrad.algcomparison.utils.HasKnowledge
-
Returns a knowledge object.
- getKnowledge() - Method in class edu.cmu.tetrad.data.BoxDataSet
- getKnowledge() - Method in class edu.cmu.tetrad.data.CorrelationMatrixOnTheFly
- getKnowledge() - Method in class edu.cmu.tetrad.data.CovarianceMatrix
- getKnowledge() - Method in class edu.cmu.tetrad.data.CovarianceMatrixOnTheFly
- getKnowledge() - Method in class edu.cmu.tetrad.data.DataModelList
- getKnowledge() - Method in interface edu.cmu.tetrad.data.ICovarianceMatrix
- getKnowledge() - Method in class edu.cmu.tetrad.data.IndependenceFacts
- getKnowledge() - Method in interface edu.cmu.tetrad.data.KnowledgeTransferable
- getKnowledge() - Method in class edu.cmu.tetrad.data.NumberObjectDataSet
- getKnowledge() - Method in class edu.cmu.tetrad.data.TimeSeriesData
- getKnowledge() - Method in class edu.cmu.tetrad.search.Cpc
-
Returns the knowledge specification used in the search.
- getKnowledge() - Method in class edu.cmu.tetrad.search.Fask
- getKnowledge() - Method in class edu.cmu.tetrad.search.Fci
-
Returns the background knowledge that was set.
- getKnowledge() - Method in class edu.cmu.tetrad.search.FciMax
-
Retrieves the background knowledge that was set.
- getKnowledge() - Method in class edu.cmu.tetrad.search.Fges
-
Returns the background knowledge.
- getKnowledge() - Method in class edu.cmu.tetrad.search.FgesMb
-
Returns the background knowledge.
- getKnowledge() - Method in class edu.cmu.tetrad.search.GFci
-
Returns the knowledge used in search.
- getKnowledge() - Method in class edu.cmu.tetrad.search.Pc
-
Returns the knowledge specification used in the search.
- getKnowledge() - Method in class edu.cmu.tetrad.search.Pcd
- getKnowledge() - Method in class edu.cmu.tetrad.search.PcMb
-
Returns The knowledge used in search.
- getKnowledge() - Method in class edu.cmu.tetrad.search.Rfci
-
Returns the knowledge used in search.
- getKnowledge() - Method in class edu.cmu.tetrad.search.SpFci
-
Returns the knowledge.
- getKnowledge() - Method in class edu.cmu.tetrad.search.SvarFci
-
Returns the knowledge for the search.
- getKnowledge() - Method in class edu.cmu.tetrad.search.SvarFges
- getKnowledge() - Method in class edu.cmu.tetrad.search.utils.BesPermutation
- getKnowledge() - Method in class edu.cmu.tetrad.search.utils.DagToPag
- getKnowledge() - Method in class edu.cmu.tetrad.search.utils.FgesOrienter
- getKnowledge() - Method in class edu.cmu.tetrad.search.utils.PcCommon
- getKnowledge() - Method in class edu.cmu.tetrad.search.utils.PossibleMsepFci
- getKnowledge() - Method in class edu.cmu.tetrad.search.utils.ShiftSearch
- getKnowledge() - Method in class edu.cmu.tetrad.search.utils.SvarFciOrient
-
The background knowledge.
- getKnowledge() - Method in class edu.cmu.tetrad.search.utils.TsDagToPag
- getKnowledge() - Method in class edu.cmu.tetrad.search.work_in_progress.Fas2
- getKnowledge() - Method in class edu.cmu.tetrad.search.work_in_progress.FasDci
- getKnowledge() - Method in class edu.cmu.tetrad.search.work_in_progress.FasLofs
- getKnowledge() - Method in class edu.cmu.tetrad.search.work_in_progress.HbsmsBeam
- getKnowledge() - Method in class edu.cmu.tetrad.search.work_in_progress.HbsmsGes
- getKnowledge() - Method in class edu.cmu.tetrad.search.work_in_progress.Kpc
- getKnowledge() - Method in class edu.cmu.tetrad.search.work_in_progress.Mmhc
- getKnowledge() - Method in class edu.cmu.tetrad.search.work_in_progress.SampleVcpc
- getKnowledge() - Method in class edu.cmu.tetrad.search.work_in_progress.SampleVcpcFast
- getKnowledge() - Method in class edu.cmu.tetrad.search.work_in_progress.VcFas
- getKnowledge() - Method in class edu.cmu.tetrad.search.work_in_progress.VcPc
- getKnowledge() - Method in class edu.cmu.tetrad.search.work_in_progress.VcPcAlt
- getKnowledge() - Method in class edu.cmu.tetrad.search.work_in_progress.VcPcFast
- getKnowledge() - Method in class edu.pitt.dbmi.algo.resampling.task.GeneralResamplingSearchRunnable
- getKnowledge(Graph) - Static method in class edu.cmu.tetrad.search.utils.TsUtils
- getKnowledge(Graph) - Method in class edu.cmu.tetrad.sem.LargeScaleSimulation
- getKnowledge(Graph) - Static method in class edu.cmu.tetrad.study.performance.Comparison2
- getKnowledgeGroups() - Method in class edu.cmu.tetrad.data.Knowledge
- getKsPValue(boolean) - Method in class edu.cmu.tetrad.search.MarkovCheck
-
Returns the Kolmorogov-Smirnov p-value for the given list of results.
- getL() - Method in class edu.cmu.tetrad.search.utils.Sextad
- getL() - Method in class edu.cmu.tetrad.search.utils.Tetrad
- getL() - Method in class edu.cmu.tetrad.search.work_in_progress.Sextad
- getLag() - Method in class edu.cmu.tetrad.graph.TimeLagGraph.NodeId
- getLag() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.IndexedParent
-
Returns the lag of the parent.
- getLag() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.LaggedFactor
-
Returns the number of time steps back for this lagged factor.
- getLag(String) - Static method in class edu.cmu.tetrad.search.utils.TsUtils
- getLag(String) - Static method in class edu.cmu.tetrad.sem.LargeScaleSimulation
- getLag(String) - Static method in class edu.cmu.tetrad.study.performance.Comparison2
- getLag0Nodes() - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- getLaggedFactor() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.LaggedEdge
- getLaggedFactor(String) - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.DisplayNameHandler
-
Parses the given string and returns the LaggedFactor it represents.
- getLagGraph() - Method in class edu.cmu.tetrad.study.gene.tetradapp.model.GenePm
-
Gets the lag workbench that is wrapped.
- getLags(int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.akutsu.RevealOutputGraph
- getLags(int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.biolingua.BiolinguaDigraph
-
Returns null (no lag information is stored in a BiolinguaDigraph).
- getLags(int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.reveal.RevealOutputGraph
- getLags(int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.RevealOutputGraph
- getLags(int) - Method in interface edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.OutputGraph
-
Returns the lags of the parent variables for the given variable, provided parents have associated time lags; otherwise, returns null.
- getLambda1() - Method in class edu.cmu.tetrad.search.Dagma
- getLastModelClass() - Method in class edu.cmu.tetrad.session.SessionNode
- getLatentEffects(Node) - Method in class edu.cmu.tetrad.search.work_in_progress.DMSearch.LatentStructure
- getLatentNodes() - Method in class edu.cmu.tetrad.sem.SemPm
- getLatents() - Method in class edu.cmu.tetrad.search.work_in_progress.DMSearch.LatentStructure
- getLatents(Graph) - Static method in class edu.cmu.tetrad.sem.ReidentifyVariables
- getLatentsCov() - Method in class edu.cmu.tetrad.search.Mimbuild
-
Returns the inferred covariance matrix over the latent variables.
- getLatentsCov() - Method in class edu.cmu.tetrad.search.MimbuildTrek
-
The covariance matrix over the latents that is implied by the clustering.
- getLatestFilePath() - Method in class edu.cmu.tetrad.util.TetradLogger
- getLengthWritten() - Method in interface edu.cmu.tetrad.util.TetradLogger.LogDisplayOutputStream
-
The total string length written to the text area.
- getLhat() - Method in class edu.cmu.tetrad.sem.Ricf.RicfResult
- getLik() - Method in class edu.cmu.tetrad.search.score.ConditionalGaussianLikelihood.Ret
- getLik() - Method in class edu.cmu.tetrad.search.test.IndTestDegenerateGaussianLrt.Ret
- getLik(int, int[]) - Method in class edu.cmu.tetrad.search.score.MvpLikelihood
- getLik(int, int[]) - Method in class edu.cmu.tetrad.search.work_in_progress.MnlrLikelihood
-
Returns the likelihood of a child given its parents.
- getLikelihood() - Method in class edu.cmu.tetrad.bayes.BayesProperties
-
Call after calling getLikelihoodP().
- getLikelihood(int, int[]) - Method in class edu.cmu.tetrad.search.score.ConditionalGaussianLikelihood
-
Returns the likelihood of variable i conditional on the given parents, assuming the continuous mixedVariables index by i or by the parents are jointly Gaussian conditional on the discrete comparison.
- getLikelihoodRatioP() - Method in class edu.cmu.tetrad.bayes.EmBayesProperties
-
Calculates the p-value of the graph with respect to the given data.
- getLikelihoodRatioP(Graph) - Method in class edu.cmu.tetrad.bayes.BayesProperties
-
Calculates the p-value of the graph with respect to the given data.
- getLineColor() - Method in class edu.cmu.tetrad.graph.Edge
- getListOfExplicitlyForbiddenEdges() - Method in class edu.cmu.tetrad.data.Knowledge
- getListOfExplicitlyRequiredEdges() - Method in class edu.cmu.tetrad.data.Knowledge
- getListOfForbiddenEdges() - Method in class edu.cmu.tetrad.data.Knowledge
- getListOfRequiredEdges() - Method in class edu.cmu.tetrad.data.Knowledge
- getLocation(String) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ActiveLagGraph
- getLocation(String) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ManualLagGraph
- getLocation(String) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.BasicLagGraph
- getLocation(String) - Method in interface edu.cmu.tetrad.study.gene.tetrad.gene.history.LagGraph
-
Gets the location.
- getLocations() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ActiveLagGraph
- getLocations() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ManualLagGraph
- getLocations() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.BasicLagGraph
- getLocations() - Method in interface edu.cmu.tetrad.study.gene.tetrad.gene.history.LagGraph
-
Gets the locations.
- getLoggerConfig() - Method in class edu.cmu.tetrad.session.SessionNode
- getLoggerConfig() - Method in class edu.cmu.tetrad.util.TetradLogger
- getLoggerConfig(Class) - Method in class edu.cmu.tetrad.session.SessionNode
- getLoggerForClass(Class) - Method in class edu.cmu.tetrad.util.TetradLogger
- getLoggingDirectory() - Method in class edu.cmu.tetrad.util.TetradLogger
- getLoggingFilePrefix() - Method in class edu.cmu.tetrad.util.TetradLogger
- getLogLikelihood() - Method in class edu.cmu.tetrad.regression.LogisticRegression.Result
-
The log likelihood of the regression
- getLong(String) - Method in class edu.cmu.tetrad.util.Parameters
-
Returns the long value of the given parameter, looking up its default in the ParamDescriptions map.
- getLong(String, long) - Method in class edu.cmu.tetrad.util.Parameters
-
Returns the long value of the given parameter, looking up its default in the ParamDescriptions map.
- getLongDescription() - Method in class edu.cmu.tetrad.util.ParamDescription
- getLow() - Method in class edu.cmu.tetrad.sem.StandardizedSemIm.ParameterRange
- getLowerBoundDouble() - Method in class edu.cmu.tetrad.util.ParamDescription
- getLowerBoundInt() - Method in class edu.cmu.tetrad.util.ParamDescription
- getLowerBoundLong() - Method in class edu.cmu.tetrad.util.ParamDescription
- getLrScores() - Method in class edu.cmu.tetrad.search.Fask
-
Returns a matrix of left-right scores for the search.
- getM() - Method in class edu.cmu.tetrad.search.utils.Sextad
- getM() - Method in class edu.cmu.tetrad.search.work_in_progress.Sextad
- getMag() - Method in class edu.cmu.tetrad.search.work_in_progress.MagSemBicScore
-
Returns the wrapped MAG.
- getManipulatedBayesIm() - Method in class edu.cmu.tetrad.bayes.ApproximateUpdater
- getManipulatedBayesIm() - Method in class edu.cmu.tetrad.bayes.CptInvariantUpdater
- getManipulatedBayesIm() - Method in class edu.cmu.tetrad.bayes.Identifiability
- getManipulatedBayesIm() - Method in class edu.cmu.tetrad.bayes.JunctionTreeUpdater
- getManipulatedBayesIm() - Method in interface edu.cmu.tetrad.bayes.ManipulatingBayesUpdater
-
Returns the manipulated Bayes IM.
- getManipulatedBayesIm() - Method in class edu.cmu.tetrad.bayes.RowSummingExactUpdater
- getManipulatedGraph() - Method in class edu.cmu.tetrad.bayes.ApproximateUpdater
- getManipulatedGraph() - Method in class edu.cmu.tetrad.bayes.CptInvariantUpdater
- getManipulatedGraph() - Method in class edu.cmu.tetrad.bayes.Identifiability
- getManipulatedGraph() - Method in class edu.cmu.tetrad.bayes.JunctionTreeUpdater
- getManipulatedGraph() - Method in interface edu.cmu.tetrad.bayes.ManipulatingBayesUpdater
-
Returns the manipulated graph.
- getManipulatedGraph() - Method in class edu.cmu.tetrad.bayes.RowSummingExactUpdater
- getManipulatedGraph() - Method in class edu.cmu.tetrad.sem.SemUpdater
- getManipulatedSemIm() - Method in class edu.cmu.tetrad.sem.SemUpdater
- getMarginal(int, int) - Method in class edu.cmu.tetrad.bayes.ApproximateUpdater
- getMarginal(int, int) - Method in interface edu.cmu.tetrad.bayes.BayesUpdater
-
Returns the marginal probability of the given variable taking the given value, given the evidence.
- getMarginal(int, int) - Method in class edu.cmu.tetrad.bayes.CptInvariantMarginalCalculator
- getMarginal(int, int) - Method in class edu.cmu.tetrad.bayes.CptInvariantUpdater
- getMarginal(int, int) - Method in class edu.cmu.tetrad.bayes.Identifiability
- getMarginal(int, int) - Method in class edu.cmu.tetrad.bayes.JunctionTreeUpdater
- getMarginal(int, int) - Method in interface edu.cmu.tetrad.bayes.ManipulatingBayesUpdater
-
Returns the updated graph.
- getMarginal(int, int) - Method in class edu.cmu.tetrad.bayes.RowSummingExactUpdater
- getMarginalProbability(int) - Method in class edu.cmu.tetrad.bayes.JunctionTreeAlgorithm
- getMarginalProbability(int, int) - Method in class edu.cmu.tetrad.bayes.JunctionTreeAlgorithm
- getMarginals() - Method in class edu.cmu.tetrad.classify.ClassifierBayesUpdaterDiscrete
-
Returns the marginals.
- getMarkovAdequacyScore(double) - Method in class edu.cmu.tetrad.search.MarkovCheck
-
Returns the Markov Adequacy Score for the graph.
- getMatrix() - Method in class edu.cmu.tetrad.data.CorrelationMatrixOnTheFly
- getMatrix() - Method in class edu.cmu.tetrad.data.CovarianceMatrix
- getMatrix() - Method in class edu.cmu.tetrad.data.CovarianceMatrixOnTheFly
- getMatrix() - Method in interface edu.cmu.tetrad.data.Covariances
-
Returns the underlying covariance matrix.
- getMatrix() - Method in class edu.cmu.tetrad.data.CovariancesDoubleForkJoin
- getMatrix() - Method in interface edu.cmu.tetrad.data.ICovarianceMatrix
- getMatrix(int[]) - Method in class edu.cmu.tetrad.data.CovarianceMatrixOnTheFly
- getMax() - Method in class edu.cmu.tetrad.data.Histogram
-
For a continuous target, returns the maximum value of the values histogrammed, for the unconditioned data.
- getMaxDegree() - Method in class edu.cmu.tetrad.search.Fges
-
The maximum of parents any nodes can have in the output pattern.
- getMaxDegree() - Method in class edu.cmu.tetrad.search.FgesMb
-
The maximum of parents any nodes can have in the output pattern.
- getMaxDegree() - Method in class edu.cmu.tetrad.search.score.BdeScore
-
Returns the maximum degree of the graphs as they're searched.
- getMaxDegree() - Method in class edu.cmu.tetrad.search.score.BdeuScore
-
Returns the needed max degree for some searches.
- getMaxDegree() - Method in class edu.cmu.tetrad.search.score.ConditionalGaussianScore
-
Returns the max degree recommended for the search form the MagSemBicScore and Fges.
- getMaxDegree() - Method in class edu.cmu.tetrad.search.score.DegenerateGaussianScore
- getMaxDegree() - Method in class edu.cmu.tetrad.search.score.DiscreteBicScore
-
Returns the maximum degree for some algorithms.
- getMaxDegree() - Method in class edu.cmu.tetrad.search.score.EbicScore
-
Returns an estimate of max degree of the graph for some algorithms.
- getMaxDegree() - Method in class edu.cmu.tetrad.search.score.GicScores
- getMaxDegree() - Method in class edu.cmu.tetrad.search.score.GraphScore
-
Returns the maximum degree, which is set to 1000.
- getMaxDegree() - Method in class edu.cmu.tetrad.search.score.ImagesScore
-
Returns the max degree from teh first score.
- getMaxDegree() - Method in class edu.cmu.tetrad.search.score.IndTestScore
- getMaxDegree() - Method in class edu.cmu.tetrad.search.score.MvpScore
- getMaxDegree() - Method in class edu.cmu.tetrad.search.score.PoissonPriorScore
- getMaxDegree() - Method in interface edu.cmu.tetrad.search.score.Score
-
Returns the max degree, by default 1000.
- getMaxDegree() - Method in class edu.cmu.tetrad.search.score.SemBicScore
- getMaxDegree() - Method in class edu.cmu.tetrad.search.score.ZsbScore
-
Returns a judgment of max degree for some algorithms.
- getMaxDegree() - Method in class edu.cmu.tetrad.search.SpFci
-
Returns The maximum indegree of the output graph.
- getMaxDegree() - Method in class edu.cmu.tetrad.search.work_in_progress.MagSemBicScore
-
Returns a judgment of the max degree needed for this score.
- getMaxDegree() - Method in class edu.cmu.tetrad.search.work_in_progress.MnlrScore
-
Returns a maximum degree used by some algorithms.
- getMaxDegree() - Method in class edu.cmu.tetrad.search.work_in_progress.SemBicScoreDeterministic
- getMaximumCardinalityOrdering(Graph) - Static method in class edu.cmu.tetrad.bayes.GraphTools
-
Perform Tarjan and Yannakakis (1984) maximum cardinality search (MCS) to get the maximum cardinality ordering.
- getMaxIndegree() - Method in class edu.cmu.tetrad.search.SvarFges
-
The maximum of parents any nodes can have in the output pattern.
- getMaxIndex() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.Polynomial
-
Returns the highest variable index in any term.
- getMaxIndex() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.PolynomialTerm
-
Returns the highest variable index in this term.
- getMaxit() - Method in class edu.cmu.tetrad.search.work_in_progress.Glasso
- getMaxIterations() - Method in class edu.cmu.tetrad.cluster.KMeans
-
Return the maximum number of iterations, or -1 if the algorithm is allowed to run unconstrainted.
- getMaxLag() - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- getMaxLag() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ActiveLagGraph
- getMaxLag() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ManualLagGraph
- getMaxLag() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.BasicLagGraph
-
Maximum lag needed to fully represent the graph, which is the largest lag of any of the lagged factors stored in the graph.
- getMaxLag() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.BooleanGlassFunction
-
Returns the max lag of the history.
- getMaxLag() - Method in interface edu.cmu.tetrad.study.gene.tetrad.gene.history.LagGraph
-
Maximum lag needed to fully represent the graph, which is the largest lag of any of the lagged factors stored in the graph.
- getMaxLag() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.LinearFunction
-
Returns the max lag of the history.
- getMaxLag() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.PolynomialFunction
-
Returns the max lag of the history.
- getMaxLag() - Method in interface edu.cmu.tetrad.study.gene.tetrad.gene.history.UpdateFunction
-
Returns the max lag of the gene history.
- getMaxLagAllowable() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ActiveLagGraph
- getMaxLagAllowable() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ManualLagGraph
- getMaxLagAllowable() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.BasicLagGraph
-
Gets the maximum allowable lag.
- getMaxLagAllowable() - Method in interface edu.cmu.tetrad.study.gene.tetrad.gene.history.LagGraph
-
Gets the maximum allowable lag.
- getMaxMemUsage() - Method in class edu.cmu.tetrad.search.work_in_progress.Ion
- getMaxNumShifts() - Method in class edu.cmu.tetrad.search.utils.ShiftSearch
- getMaxPathLength() - Method in class edu.cmu.tetrad.search.Rfci
-
Returns the maximum length of any discriminating path, or -1 of unlimited.
- getMaxPathLength() - Method in class edu.cmu.tetrad.search.SpFci
-
Returns the maximum length of any discriminating path, or -1 of unlimited.
- getMaxPathLength() - Method in class edu.cmu.tetrad.search.SvarFci
-
Returns the maximum length of any discriminating path, or -1 of unlimited.
- getMaxPathLength() - Method in class edu.cmu.tetrad.search.utils.FciOrient
- getMaxPathLength() - Method in class edu.cmu.tetrad.search.utils.SvarFciOrient
- getMaxPathLength() - Method in class edu.cmu.tetrad.search.utils.TsDagToPag
- getMaxReachablePathLength() - Method in class edu.cmu.tetrad.search.Cfci
- getMaxShift() - Method in class edu.cmu.tetrad.search.utils.ShiftSearch
- getMaxTierForbiddenWithin() - Method in class edu.cmu.tetrad.data.Knowledge
- getMConnectedVars(Node, Set<Node>) - Method in class edu.cmu.tetrad.graph.Paths
- getMConnectedVars(Node, Set<Node>, Map<Node, Set<Node>>) - Method in class edu.cmu.tetrad.graph.Paths
- getMean(Node) - Method in interface edu.cmu.tetrad.sem.ISemIm
- getMean(Node) - Method in class edu.cmu.tetrad.sem.SemIm
- getMeanParameter(Node) - Method in class edu.cmu.tetrad.sem.SemPm
- getMeans() - Method in class edu.cmu.tetrad.sem.SemIm
- getMeanStdDev(Node) - Method in interface edu.cmu.tetrad.sem.ISemIm
- getMeanStdDev(Node) - Method in class edu.cmu.tetrad.sem.SemIm
- getMeasuredData() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.simulation.MeasurementSimulator
-
Returns the measured data that is the result of a simulation, in the form of a three-dimensional double array.
- getMeasuredData() - Method in class edu.cmu.tetrad.study.gene.tetradapp.model.MeasurementSimulatorParams
- getMeasuredNodes() - Method in interface edu.cmu.tetrad.bayes.BayesIm
-
Returns the list of measured variables.
- getMeasuredNodes() - Method in class edu.cmu.tetrad.bayes.BayesPm
-
Returns the measured nodes.
- getMeasuredNodes() - Method in class edu.cmu.tetrad.bayes.DirichletBayesIm
- getMeasuredNodes() - Method in class edu.cmu.tetrad.bayes.MlBayesIm
- getMeasuredNodes() - Method in class edu.cmu.tetrad.bayes.MlBayesImObs
- getMeasuredNodes() - Method in class edu.cmu.tetrad.bayes.UpdatedBayesIm
- getMeasuredNodes() - Method in class edu.cmu.tetrad.sem.DagScorer
- getMeasuredNodes() - Method in class edu.cmu.tetrad.sem.GeneralizedSemPm
- getMeasuredNodes() - Method in interface edu.cmu.tetrad.sem.ISemIm
- getMeasuredNodes() - Method in interface edu.cmu.tetrad.sem.Scorer
- getMeasuredNodes() - Method in class edu.cmu.tetrad.sem.SemIm
-
The list of measured nodes for the semPm.
- getMeasuredNodes() - Method in class edu.cmu.tetrad.sem.SemPm
- getMeasuredNodes() - Method in class edu.cmu.tetrad.sem.StandardizedSemIm
-
The list of measured nodes for the semPm.
- getMeasuredVarNames() - Method in class edu.cmu.tetrad.sem.SemPm
- getMessage() - Method in exception edu.cmu.tetrad.session.CouldNotCreateModelException
- getMethod() - Method in class edu.cmu.tetrad.data.ContinuousDiscretizationSpec
- getMethod() - Method in class edu.cmu.tetrad.search.work_in_progress.OtherPermAlgs
- getMin() - Method in class edu.cmu.tetrad.data.Histogram
-
For a continuous target, returns the minimum value of the values histogrammed, for the unconditioned data.
- getMinChunk(int) - Method in class edu.cmu.tetrad.search.SvarFges
- getMinClusterSize() - Method in class edu.cmu.tetrad.search.Mimbuild
-
jf Clusters smaller than this size will be tossed out.
- getMinClusterSize() - Method in class edu.cmu.tetrad.search.MimbuildTrek
-
jf Clusters smaller than this size will be tossed out.
- getMinDepth() - Method in class edu.cmu.tetrad.search.work_in_progress.DMSearch
- getMinimum() - Method in class edu.cmu.tetrad.search.Mimbuild
- getMisclassificationTable(Graph, Graph) - Static method in class edu.cmu.tetrad.algcomparison.CompareTwoGraphs
-
Returns a misclassification comparison of two graphs.
- getMissingValueMarker() - Method in class edu.cmu.tetrad.data.AbstractVariable
- getMissingValueMarker() - Method in class edu.cmu.tetrad.data.ContinuousVariable
- getMissingValueMarker() - Method in class edu.cmu.tetrad.data.DiscreteVariable
- getMissingValueMarker() - Method in interface edu.cmu.tetrad.data.Variable
-
Returns the name of the variable.
- getMixedDataSet() - Method in class edu.cmu.tetrad.bayes.EmBayesEstimator
- getMixedDataSet(DataModel) - Static method in class edu.cmu.tetrad.data.SimpleDataLoader
-
Returns the datamodel case to DataSet if it is mixed.
- getMlag() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.LagGraphParams
- getMlag() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ManualLagGraphParams
-
Returns the maximum lag.
- getModel() - Method in class edu.cmu.tetrad.session.SessionNode
- getModelClass() - Method in exception edu.cmu.tetrad.session.CouldNotCreateModelException
- getModelClasses() - Method in class edu.cmu.tetrad.session.SessionNode
- getModelConstructorArguments(Class) - Method in class edu.cmu.tetrad.session.SessionNode
- getModelList() - Method in class edu.cmu.tetrad.data.DataModelList
- getModelPValue(List<List<Integer>>) - Method in class edu.cmu.tetrad.search.utils.ClusterSignificance
- getModelScore() - Method in class edu.cmu.tetrad.search.Fges
-
Returns the score of the final search model.
- getModelScore() - Method in class edu.cmu.tetrad.search.FgesMb
-
Returns the score of the final search model.
- getN() - Method in class edu.cmu.tetrad.data.Histogram
-
For a continuous target, returns the number of values histogrammed.
- getN() - Method in class edu.cmu.tetrad.regression.RegressionResult
- getN() - Method in class edu.cmu.tetrad.search.utils.Sextad
- getN() - Method in class edu.cmu.tetrad.search.work_in_progress.Glasso
- getN() - Method in class edu.cmu.tetrad.search.work_in_progress.Sextad
- getName() - Method in class edu.cmu.tetrad.calculator.expression.ConstantExpression
- getName() - Method in interface edu.cmu.tetrad.calculator.expression.ExpressionDescriptor
- getName() - Method in class edu.cmu.tetrad.data.AbstractVariable
- getName() - Method in class edu.cmu.tetrad.data.BoxDataSet
-
Gets the name of the data set.
- getName() - Method in class edu.cmu.tetrad.data.CorrelationMatrixOnTheFly
-
Gets the name of the covariance matrix.
- getName() - Method in class edu.cmu.tetrad.data.CovarianceMatrix
-
Gets the name of the covariance matrix.
- getName() - Method in class edu.cmu.tetrad.data.CovarianceMatrixOnTheFly
-
Gets the name of the covariance matrix.
- getName() - Method in interface edu.cmu.tetrad.data.DataModel
- getName() - Method in class edu.cmu.tetrad.data.DataModelList
-
Gets the name of the data model list.
- getName() - Method in interface edu.cmu.tetrad.data.DataSet
- getName() - Method in interface edu.cmu.tetrad.data.ICovarianceMatrix
- getName() - Method in class edu.cmu.tetrad.data.IndependenceFacts
- getName() - Method in class edu.cmu.tetrad.data.NumberObjectDataSet
-
Gets the name of the data set.
- getName() - Method in class edu.cmu.tetrad.data.TimeSeriesData
- getName() - Method in class edu.cmu.tetrad.graph.GraphNode
- getName() - Method in interface edu.cmu.tetrad.graph.Node
-
Returns the name of this node.
- getName() - Method in class edu.cmu.tetrad.graph.TimeLagGraph.NodeId
- getName() - Method in class edu.cmu.tetrad.sem.Parameter
- getName() - Method in class edu.cmu.tetrad.session.Session
-
Gets the name.
- getName() - Method in interface edu.cmu.tetrad.session.SessionModel
- getName() - Method in class edu.cmu.tetrad.session.SessionNode
- getName() - Method in class edu.cmu.tetrad.session.Type1
- getName() - Method in class edu.cmu.tetrad.session.Type10
- getName() - Method in class edu.cmu.tetrad.session.Type11
- getName() - Method in class edu.cmu.tetrad.session.Type12
- getName() - Method in class edu.cmu.tetrad.session.Type2
- getName() - Method in class edu.cmu.tetrad.session.Type3
- getName() - Method in class edu.cmu.tetrad.session.Type4
- getName() - Method in class edu.cmu.tetrad.session.Type5
- getName() - Method in class edu.cmu.tetrad.session.Type6
- getName() - Method in class edu.cmu.tetrad.session.Type7
- getName() - Method in class edu.cmu.tetrad.session.Type8
- getName() - Method in class edu.cmu.tetrad.session.Type9
- getName() - Method in class edu.cmu.tetrad.simulation.PRAOerrors
- getName() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.AbstractNbComponent
- getName() - Method in interface edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.NbComponent
-
Returns the name.
- getName() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.BasicMatrix
-
Returns name of this matrix
- getName() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ManualActiveLagGraph
- getName() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.RandomActiveLagGraph
- getName() - Method in class edu.cmu.tetrad.study.gene.tetradapp.model.BooleanGlassGeneIm
- getName() - Method in class edu.cmu.tetrad.study.gene.tetradapp.model.BooleanGlassGenePm
- getName() - Method in class edu.cmu.tetrad.util.dist.Beta
-
Please don't make me say it...
- getName() - Method in class edu.cmu.tetrad.util.dist.ChiSquare
- getName() - Method in class edu.cmu.tetrad.util.dist.Discrete
- getName() - Method in interface edu.cmu.tetrad.util.dist.Distribution
-
Returns the name of the distribution.
- getName() - Method in class edu.cmu.tetrad.util.dist.Exponential
- getName() - Method in class edu.cmu.tetrad.util.dist.Gamma
- getName() - Method in class edu.cmu.tetrad.util.dist.GaussianPower
- getName() - Method in class edu.cmu.tetrad.util.dist.Indicator
- getName() - Method in class edu.cmu.tetrad.util.dist.LogNormal
- getName() - Method in class edu.cmu.tetrad.util.dist.MixtureOfGaussians
- getName() - Method in class edu.cmu.tetrad.util.dist.Normal
- getName() - Method in class edu.cmu.tetrad.util.dist.Poisson
- getName() - Method in class edu.cmu.tetrad.util.dist.SingleValue
- getName() - Method in class edu.cmu.tetrad.util.dist.Split
- getName() - Method in class edu.cmu.tetrad.util.dist.TruncatedNormal
- getName() - Method in class edu.cmu.tetrad.util.dist.Uniform
- getNameNoLag(Object) - Method in class edu.cmu.tetrad.search.SvarFci
- getNameNoLag(Object) - Method in class edu.cmu.tetrad.search.SvarFges
- getNameNoLag(Object) - Method in class edu.cmu.tetrad.search.utils.SvarFciOrient
- getNameNoLag(Object) - Static method in class edu.cmu.tetrad.search.utils.TsUtils
- getNameNoLag(Object) - Method in class edu.cmu.tetrad.sem.LargeScaleSimulation
- getNameNoLag(Object) - Static method in class edu.cmu.tetrad.study.performance.Comparison2
- getNames() - Method in class edu.cmu.tetrad.util.ParamDescriptions
- getNewSemIm() - Method in interface edu.cmu.tetrad.search.work_in_progress.Hbsms
- getNewSemIm() - Method in class edu.cmu.tetrad.search.work_in_progress.HbsmsBeam
- getNewSemIm() - Method in class edu.cmu.tetrad.search.work_in_progress.HbsmsGes
- getNextOffset() - Method in class edu.cmu.tetrad.calculator.parser.ExpressionLexer
- getNextOffset() - Method in class edu.cmu.tetrad.calculator.parser.ExpressionParser
- getNode() - Method in class edu.cmu.tetrad.search.utils.GrowShrinkTree
- getNode() - Method in class edu.cmu.tetrad.session.SessionEvent
- getNode(int) - Method in interface edu.cmu.tetrad.bayes.BayesIm
-
Returns the name of the given node.
- getNode(int) - Method in class edu.cmu.tetrad.bayes.BayesPm
-
Returns the node at the given index.
- getNode(int) - Method in class edu.cmu.tetrad.bayes.DirichletBayesIm
- getNode(int) - Method in class edu.cmu.tetrad.bayes.Evidence
- getNode(int) - Method in class edu.cmu.tetrad.bayes.MlBayesIm
- getNode(int) - Method in class edu.cmu.tetrad.bayes.MlBayesImObs
- getNode(int) - Method in class edu.cmu.tetrad.bayes.UpdatedBayesIm
- getNode(int) - Method in class edu.cmu.tetrad.sem.SemEvidence
- getNode(int) - Method in class edu.cmu.tetrad.sem.SemManipulation
- getNode(Node) - Method in class edu.cmu.tetrad.search.IndTestIod
-
Return the node associated with the given variable in the graph.
- getNode(Node) - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestSepsetDci
- getNode(String) - Method in interface edu.cmu.tetrad.bayes.BayesIm
-
Returns the name of the given node.
- getNode(String) - Method in class edu.cmu.tetrad.bayes.BayesPm
-
Returns the node by the given name.
- getNode(String) - Method in class edu.cmu.tetrad.bayes.DirichletBayesIm
- getNode(String) - Method in class edu.cmu.tetrad.bayes.MlBayesIm
- getNode(String) - Method in class edu.cmu.tetrad.bayes.MlBayesImObs
- getNode(String) - Method in class edu.cmu.tetrad.bayes.UpdatedBayesIm
- getNode(String) - Method in class edu.cmu.tetrad.graph.Dag
- getNode(String) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
- getNode(String) - Method in interface edu.cmu.tetrad.graph.Graph
- getNode(String) - Method in class edu.cmu.tetrad.graph.LagGraph
- getNode(String) - Method in class edu.cmu.tetrad.graph.SemGraph
- getNode(String) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- getNode(String) - Method in class edu.cmu.tetrad.sem.GeneralizedSemPm
- getNode(String, int) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- getNode1() - Method in class edu.cmu.tetrad.graph.Edge
- getNode2() - Method in class edu.cmu.tetrad.graph.Edge
- getNodeA() - Method in class edu.cmu.tetrad.sem.Parameter
- getNodeB() - Method in class edu.cmu.tetrad.sem.Parameter
- getNodeDists(Graph) - Static method in class edu.pitt.csb.mgm.MixedUtils
- getNodeExpression(Node) - Method in class edu.cmu.tetrad.sem.GeneralizedSemPm
- getNodeExpressionString(Node) - Method in class edu.cmu.tetrad.sem.GeneralizedSemPm
- getNodeId(Node) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- getNodeIndex() - Method in class edu.cmu.tetrad.bayes.BayesPm
-
Returns the node index.
- getNodeIndex() - Method in class edu.cmu.tetrad.sem.SemProposition
- getNodeIndex(Node) - Method in interface edu.cmu.tetrad.bayes.BayesIm
-
Returns the index of the given node.
- getNodeIndex(Node) - Method in class edu.cmu.tetrad.bayes.DirichletBayesIm
- getNodeIndex(Node) - Method in class edu.cmu.tetrad.bayes.MlBayesIm
- getNodeIndex(Node) - Method in class edu.cmu.tetrad.bayes.MlBayesImObs
- getNodeIndex(Node) - Method in class edu.cmu.tetrad.bayes.UpdatedBayesIm
- getNodeIndex(Node) - Method in class edu.cmu.tetrad.sem.SemEvidence
- getNodeIndex(String) - Method in class edu.cmu.tetrad.bayes.Evidence
- getNodeIndex(String) - Method in class edu.cmu.tetrad.bayes.Proposition
- getNodeIndex(String) - Method in class edu.cmu.tetrad.sem.SemEvidence
- getNodeIndex(String) - Method in class edu.cmu.tetrad.sem.SemManipulation
- getNodeName(int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.akutsu.RevealOutputGraph
- getNodeName(int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.reveal.RevealOutputGraph
- getNodeName(int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.RevealOutputGraph
- getNodeName(int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.BasicGraph
-
Returns the name of node
iin this graph - getNodeName(int) - Method in interface edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.OutputGraph
-
Returns the name of the variable at the given index.
- getNodeNames() - Method in class edu.cmu.tetrad.graph.Dag
- getNodeNames() - Method in class edu.cmu.tetrad.graph.EdgeListGraph
- getNodeNames() - Method in interface edu.cmu.tetrad.graph.Graph
- getNodeNames() - Method in class edu.cmu.tetrad.graph.LagGraph
- getNodeNames() - Method in class edu.cmu.tetrad.graph.SemGraph
- getNodeNames() - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- getNodes() - Method in class edu.cmu.tetrad.bayes.JunctionTreeAlgorithm
- getNodes() - Method in class edu.cmu.tetrad.graph.Dag
- getNodes() - Method in class edu.cmu.tetrad.graph.EdgeListGraph
- getNodes() - Method in interface edu.cmu.tetrad.graph.Graph
- getNodes() - Method in class edu.cmu.tetrad.graph.LagGraph
- getNodes() - Method in class edu.cmu.tetrad.graph.SemGraph
- getNodes() - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- getNodes() - Method in class edu.cmu.tetrad.search.Fas
-
Returns the nodes from the test.
- getNodes() - Method in class edu.cmu.tetrad.search.Fasd
-
Returns the nodes being searched over.
- getNodes() - Method in class edu.cmu.tetrad.search.Ida.NodeEffects
- getNodes() - Method in interface edu.cmu.tetrad.search.IFas
-
Returns the nodes searched over.
- getNodes() - Method in class edu.cmu.tetrad.search.Pcd
- getNodes() - Method in class edu.cmu.tetrad.search.SvarFas
-
Returns the nodes of the test.
- getNodes() - Method in class edu.cmu.tetrad.search.utils.Sextad
-
Returns the list of nodes.
- getNodes() - Method in class edu.cmu.tetrad.search.utils.Tetrad
- getNodes() - Method in class edu.cmu.tetrad.search.work_in_progress.Fas2
- getNodes() - Method in class edu.cmu.tetrad.search.work_in_progress.Fas3
-
Returns the nodes from the test.
- getNodes() - Method in class edu.cmu.tetrad.search.work_in_progress.FasFdr
- getNodes() - Method in class edu.cmu.tetrad.search.work_in_progress.Sextad
- getNodes() - Method in class edu.cmu.tetrad.search.work_in_progress.VcFas
- getNodes() - Method in class edu.cmu.tetrad.sem.GeneralizedSemPm
- getNodes() - Method in class edu.cmu.tetrad.session.Session
- getNodesInEvidence() - Method in class edu.cmu.tetrad.sem.SemEvidence
- getNodesInTo(Node, Endpoint) - Method in class edu.cmu.tetrad.graph.Dag
- getNodesInTo(Node, Endpoint) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
-
Nodes adjacent to the given node with the given proximal endpoint.
- getNodesInTo(Node, Endpoint) - Method in interface edu.cmu.tetrad.graph.Graph
-
Nodes adjacent to the given node with the given proximal endpoint.
- getNodesInTo(Node, Endpoint) - Method in class edu.cmu.tetrad.graph.LagGraph
- getNodesInTo(Node, Endpoint) - Method in class edu.cmu.tetrad.graph.SemGraph
- getNodesInTo(Node, Endpoint) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- getNodesOutTo(Node, Endpoint) - Method in class edu.cmu.tetrad.graph.Dag
- getNodesOutTo(Node, Endpoint) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
-
Nodes adjacent to the given node with the given distal endpoint.
- getNodesOutTo(Node, Endpoint) - Method in interface edu.cmu.tetrad.graph.Graph
-
Nodes adjacent to the given node with the given distal endpoint.
- getNodesOutTo(Node, Endpoint) - Method in class edu.cmu.tetrad.graph.LagGraph
- getNodesOutTo(Node, Endpoint) - Method in class edu.cmu.tetrad.graph.SemGraph
- getNodesOutTo(Node, Endpoint) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- getNodeSubstitutedString(Node) - Method in class edu.cmu.tetrad.sem.GeneralizedSemIm
- getNodeSubstitutedString(Node, Map<String, Double>) - Method in class edu.cmu.tetrad.sem.GeneralizedSemIm
- getNodeType() - Method in class edu.cmu.tetrad.data.ContinuousVariable
- getNodeType() - Method in class edu.cmu.tetrad.data.DiscreteVariable
- getNodeType() - Method in class edu.cmu.tetrad.graph.GraphNode
- getNodeType() - Method in interface edu.cmu.tetrad.graph.Node
-
Returns the node type for this node.
- getNodeType() - Method in class edu.cmu.tetrad.session.SessionNode
- getNodeVariableType() - Method in class edu.cmu.tetrad.data.ContinuousVariable
- getNodeVariableType() - Method in class edu.cmu.tetrad.data.DiscreteVariable
- getNodeVariableType() - Method in class edu.cmu.tetrad.graph.GraphNode
- getNodeVariableType() - Method in interface edu.cmu.tetrad.graph.Node
-
Returns the node shape for this node.
- getNodeVariableType() - Method in class edu.cmu.tetrad.session.SessionNode
- getNonadjacencies() - Method in class edu.cmu.tetrad.search.Pc
-
Returns the non-adjacencies of the searched graph.
- getNoncolliders() - Method in class edu.cmu.tetrad.search.work_in_progress.GraphChange
-
Return noncolliders
- getNoncolliderTriples() - Method in class edu.cmu.tetrad.search.utils.PcCommon
- getNoncolliderTriples() - Method in class edu.cmu.tetrad.search.work_in_progress.SampleVcpc
- getNoncolliderTriples() - Method in class edu.cmu.tetrad.search.work_in_progress.SampleVcpcFast
- getNoncolliderTriples() - Method in class edu.cmu.tetrad.search.work_in_progress.VcPc
- getNoncolliderTriples() - Method in class edu.cmu.tetrad.search.work_in_progress.VcPcAlt
- getNoncolliderTriples() - Method in class edu.cmu.tetrad.search.work_in_progress.VcPcFast
- getNonparanormalTransformed(DataSet) - Static method in class edu.cmu.tetrad.data.DataTransforms
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.AdjacencyFn
-
Returns a mapping of the statistic to the interval [0, 1], with higher being better.
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.AdjacencyFp
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.AdjacencyFpr
-
Returns a mapping of the statistic to the interval [0, 1], with higher being better.
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.AdjacencyPrecision
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.AdjacencyRecall
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.AdjacencyTn
-
Returns a mapping of the statistic to the interval [0, 1], with higher being better.
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.AdjacencyTp
-
Returns a mapping of the statistic to the interval [0, 1], with higher being better.
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.AdjacencyTpr
-
Returns a mapping of the statistic to the interval [0, 1], with higher being better.
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.AncestorF1
-
Returns the norm value of the statistic.
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.AncestorPrecision
-
Returns the norm value of the statistic.
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.AncestorRecall
-
Returns the norm value of the statistic.
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.AncestralPrecision
-
Returns the norm value of the statistic.
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.AncestralRecall
-
Returns the norm value of the statistic.
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.ArrowheadFn
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.ArrowheadFp
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.ArrowheadFpr
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.ArrowheadPrecision
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.ArrowheadPrecisionCommonEdges
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.ArrowheadRecall
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.ArrowheadRecallCommonEdges
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.ArrowheadTn
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.ArrowheadTp
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.AverageDegreeEst
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.AverageDegreeTrue
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.BicDiff
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.BicDiffPerRecord
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.BicEst
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.BicTrue
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.BidirectedEst
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.BidirectedFP
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.BidirectedLatentPrecision
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.BidirectedPrecision
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.BidirectedRecall
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.BidirectedTP
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.BidirectedTrue
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.CommonAncestorFalseNegativeBidirected
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.CommonAncestorFalsePositiveBidirected
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.CommonAncestorTruePositiveBidirected
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.CommonMeasuredAncestorRecallBidirected
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.CorrectSkeleton
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.DefiniteDirectedPathPrecision
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.DefiniteDirectedPathRecall
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.DensityEst
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.DensityTrue
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.ElapsedCpuTime
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.F1Adj
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.F1All
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.F1Arrow
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.FalseNegativesAdjacencies
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.FalsePositiveAdjacencies
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.FractionDependentUnderAlternative
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.FractionDependentUnderNull
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.GraphExactlyRight
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.LatentCommonAncestorFalseNegativeBidirected
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.LatentCommonAncestorFalsePositiveBidirected
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.LatentCommonAncestorRecallBidirected
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.LatentCommonAncestorTruePositiveBidirected
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.LegalPag
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.MarkovAdequacyScore
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.MathewsCorrAdj
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.MathewsCorrArrow
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.MaximalityCondition
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.NoAlmostCyclicPathsCondition
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.NoAlmostCyclicPathsInMagCondition
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.NoCyclicPathsCondition
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.NoCyclicPathsInMagCondition
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.NodesInCyclesPrecision
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.NodesInCyclesRecall
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.NonancestorPrecision
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.NonancestorRecall
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.NoSemidirectedF1
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.NoSemidirectedPrecision
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.NoSemidirectedRecall
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumAmbiguousTriples
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumberOfEdgesEst
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumberOfEdgesTrue
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumBidirectedBothNonancestorAncestor
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumBidirectedEdgesEst
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumBidirectedEdgesTrue
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumColoredDD
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumColoredNL
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumColoredPD
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumColoredPL
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumCommonMeasuredAncestorBidirected
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumCompatibleDefiniteDirectedEdgeAncestors
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumCompatibleDirectedEdgeConfounded
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumCompatibleDirectedEdgeNonAncestors
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumCompatibleEdges
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumCompatiblePossiblyDirectedEdgeAncestors
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumCompatiblePossiblyDirectedEdgeNonAncestors
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumCompatibleVisibleAncestors
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumCompatibleVisibleNonancestors
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumCorrectDDAncestors
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumCorrectPDAncestors
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumCorrectVisibleAncestors
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumDefinitelyDirected
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumDefinitelyNotDirectedPaths
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumDirectedEdgeAncestors
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumDirectedEdgeBnaMeasuredCounfounded
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumDirectedEdgeNoMeasureAncestors
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumDirectedEdgeNotAncNotRev
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumDirectedEdgeReversed
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumDirectedEdges
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumDirectedEdgeVisible
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumDirectedPathsEst
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumDirectedPathsTrue
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumDirectedShouldBePartiallyDirected
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumIncorrectDDAncestors
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumIncorrectPDAncestors
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumIncorrectVisibleAncestors
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumLatentCommonAncestorBidirected
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumNondirectedEdges
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumPartiallyOrientedEdges
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumPossiblyDirected
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumUndirectedEdges
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumVisibleEst
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.OrientationPrecision
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.OrientationRecall
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.PagAdjacencyPrecision
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.PagAdjacencyRecall
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.ParameterColumn
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.PercentAmbiguous
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.PercentBidirectedEdges
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.ProportionSemidirectedPathsNotReversedEst
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.ProportionSemidirectedPathsNotReversedTrue
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.PvalueDistanceToAlpha
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.PvalueUniformityUnderNull
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.SemidirectedPathF1
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.SemidirectedPrecision
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.SemidirectedRecall
- getNormValue(double) - Method in interface edu.cmu.tetrad.algcomparison.statistic.Statistic
-
Returns a mapping of the statistic to the interval [0, 1], with higher being better.
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.StructuralHammingDistance
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.TailPrecision
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.TailRecall
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.TrueDagFalseNegativesArrows
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.TrueDagFalseNegativesTails
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.TrueDagFalsePositiveArrow
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.TrueDagFalsePositiveTails
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.TrueDagPrecisionArrow
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.TrueDagPrecisionTails
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.TrueDagRecallArrows
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.TrueDagRecallTails
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.TrueDagTruePositiveArrow
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.TrueDagTruePositiveDirectedPathNonancestor
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.TrueDagTruePositiveTails
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.TwoCycleFalseNegative
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.TwoCycleFalsePositive
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.TwoCyclePrecision
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.TwoCycleRecall
- getNormValue(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.TwoCycleTruePositive
- getNparents() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.AbstractNbComponent
-
Sets the number of parents.
- getNumAllowed(int) - Method in class edu.cmu.tetrad.bayes.Proposition
- getNumAllowedCategories(int) - Method in class edu.cmu.tetrad.bayes.Proposition
- getNumber() - Method in class edu.cmu.tetrad.sem.ParamConstraint
- getNumberFormat() - Method in class edu.cmu.tetrad.data.BoxDataSet
- getNumberFormat() - Method in interface edu.cmu.tetrad.data.DataSet
-
The number format of the dataset.
- getNumberFormat() - Method in class edu.cmu.tetrad.data.NumberObjectDataSet
- getNumberFormat() - Method in class edu.cmu.tetrad.util.NumberFormatUtil
- getNumberOfArguments() - Method in interface edu.cmu.tetrad.calculator.expression.ExpressionSignature
- getNumberOfColumns(DataModel) - Static method in class edu.cmu.tetrad.util.MultidataUtils
- getNumberOfNodes() - Method in class edu.cmu.tetrad.bayes.JunctionTreeAlgorithm
- getNumCases() - Method in class edu.cmu.tetrad.classify.ClassifierBayesUpdaterDiscrete
-
Returns the number of cases for the data.
- getNumCategories() - Method in class edu.cmu.tetrad.data.DiscreteVariable
- getNumCategories(int) - Method in class edu.cmu.tetrad.bayes.Evidence
- getNumCategories(int) - Method in class edu.cmu.tetrad.bayes.Proposition
- getNumCategories(Node) - Method in class edu.cmu.tetrad.bayes.BayesPm
-
Returns the number of values for the given node.
- getNumCauses() - Method in class edu.cmu.tetrad.search.Cstar.Record
- getNumCells() - Method in class edu.cmu.tetrad.util.MultiDimIntTable
- getNumCellsPerDish() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.simulation.MeasurementSimulator
-
Returns the number of cells per dish.
- getNumCellsPerDish() - Method in class edu.cmu.tetrad.study.gene.tetradapp.model.MeasurementSimulatorParams
- getNumChildren() - Method in class edu.cmu.tetrad.session.SessionNode
- getNumClusters() - Method in class edu.cmu.tetrad.cluster.KMeans
- getNumClusters() - Method in class edu.cmu.tetrad.data.Clusters
- getNumColumns() - Method in class edu.cmu.tetrad.data.BoxDataSet
- getNumColumns() - Method in interface edu.cmu.tetrad.data.DataSet
- getNumColumns() - Method in class edu.cmu.tetrad.data.NumberObjectDataSet
- getNumColumns() - Method in class edu.cmu.tetrad.util.Matrix
- getNumColumns() - Method in class edu.cmu.tetrad.util.Matrix2
- getNumColumns() - Method in class edu.cmu.tetrad.util.TextTable
- getNumColumns(int) - Method in interface edu.cmu.tetrad.bayes.BayesIm
-
Returns the number of columns.
- getNumColumns(int) - Method in class edu.cmu.tetrad.bayes.DirichletBayesIm
- getNumColumns(int) - Method in class edu.cmu.tetrad.bayes.MlBayesIm
- getNumColumns(int) - Method in class edu.cmu.tetrad.bayes.MlBayesImObs
- getNumColumns(int) - Method in class edu.cmu.tetrad.bayes.UpdatedBayesIm
- getNumCombinations(int, int) - Static method in class edu.cmu.tetrad.util.ChoiceGenerator
- getNumCombinations(int, int) - Static method in class edu.cmu.tetrad.util.SublistGenerator
- getNumCorrectArrowpts(Graph, Graph) - Static method in class edu.cmu.tetrad.graph.GraphUtils
- getnumCPDAGsToStore() - Method in class edu.cmu.tetrad.search.SvarFges
- getNumDataModels() - Method in class edu.cmu.tetrad.algcomparison.algorithm.ExternalAlgorithm
- getNumDataModels() - Method in class edu.cmu.tetrad.algcomparison.simulation.BayesNetSimulation
-
Returns the number of data sets.
- getNumDataModels() - Method in class edu.cmu.tetrad.algcomparison.simulation.BooleanGlassSimulation
- getNumDataModels() - Method in class edu.cmu.tetrad.algcomparison.simulation.ConditionalGaussianSimulation
- getNumDataModels() - Method in class edu.cmu.tetrad.algcomparison.simulation.GeneralSemSimulation
- getNumDataModels() - Method in class edu.cmu.tetrad.algcomparison.simulation.GeneralSemSimulationSpecial1
- getNumDataModels() - Method in class edu.cmu.tetrad.algcomparison.simulation.LeeHastieSimulation
- getNumDataModels() - Method in class edu.cmu.tetrad.algcomparison.simulation.LinearFisherModel
- getNumDataModels() - Method in class edu.cmu.tetrad.algcomparison.simulation.LinearSineSimulation
- getNumDataModels() - Method in class edu.cmu.tetrad.algcomparison.simulation.NLSemSimulation
- getNumDataModels() - Method in class edu.cmu.tetrad.algcomparison.simulation.SemSimulation
- getNumDataModels() - Method in class edu.cmu.tetrad.algcomparison.simulation.SemThenDiscretize
- getNumDataModels() - Method in interface edu.cmu.tetrad.algcomparison.simulation.Simulation
-
Returns the number of data models.
- getNumDataModels() - Method in class edu.cmu.tetrad.algcomparison.simulation.StandardizedSemSimulation
- getNumDataModels() - Method in class edu.cmu.tetrad.algcomparison.simulation.TimeSeriesSemSimulation
- getNumDataModels() - Method in class edu.cmu.tetrad.data.simulation.LoadContinuousDataAndGraphs
- getNumDataModels() - Method in class edu.cmu.tetrad.data.simulation.LoadContinuousDataAndSingleGraph
- getNumDataModels() - Method in class edu.cmu.tetrad.data.simulation.LoadContinuousDataSmithSim
- getNumDataModels() - Method in class edu.cmu.tetrad.data.simulation.LoadDataAndGraphs
- getNumDataModels() - Method in class edu.cmu.tetrad.data.simulation.LoadDataFromFileWithoutGraph
- getNumDimensions() - Method in class edu.cmu.tetrad.util.MultiDimIntTable
- getNumDishes() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.simulation.MeasurementSimulator
-
Returns the number of dishes that are to be simulated.
- getNumDishes() - Method in class edu.cmu.tetrad.study.gene.tetradapp.model.MeasurementSimulatorParams
- getNumEdges() - Method in class edu.cmu.tetrad.graph.Dag
- getNumEdges() - Method in class edu.cmu.tetrad.graph.EdgeListGraph
- getNumEdges() - Method in interface edu.cmu.tetrad.graph.Graph
- getNumEdges() - Method in class edu.cmu.tetrad.graph.LagGraph
- getNumEdges() - Method in class edu.cmu.tetrad.graph.SemGraph
- getNumEdges() - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- getNumEdges() - Method in class edu.cmu.tetrad.search.Grasp
-
Returns the number of edges in the DAG implied by the discovered permutation.
- getNumEdges() - Method in class edu.cmu.tetrad.search.utils.TeyssierScorer
- getNumEdges() - Method in class edu.cmu.tetrad.search.work_in_progress.GraspTol
- getNumEdges() - Method in class edu.cmu.tetrad.search.work_in_progress.OtherPermAlgs
- getNumEdges() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.BasicGraph
-
Returns the Total # of edges in this graph
- getNumEdges() - Method in class edu.cmu.tetrad.study.performance.ComparisonParameters
- getNumEdges(Node) - Method in class edu.cmu.tetrad.graph.Dag
- getNumEdges(Node) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
- getNumEdges(Node) - Method in interface edu.cmu.tetrad.graph.Graph
- getNumEdges(Node) - Method in class edu.cmu.tetrad.graph.LagGraph
- getNumEdges(Node) - Method in class edu.cmu.tetrad.graph.SemGraph
- getNumEdges(Node) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- getNumEffects() - Method in class edu.cmu.tetrad.search.Cstar.Record
- getNumericalMean() - Method in class edu.cmu.tetrad.sem.EmpiricalCdf
- getNumericalVariance() - Method in class edu.cmu.tetrad.sem.EmpiricalCdf
- getNumFactors() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ActiveLagGraph
- getNumFactors() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ManualLagGraph
- getNumFactors() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.BasicLagGraph
-
Returns the number of factors represented in the graph.
- getNumFactors() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.BooleanGlassFunction
-
Returns the number of factors in the history.
- getNumFactors() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.IndexedConnectivity
-
Returns the number of factors.
- getNumFactors() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.IndexedLagGraph
-
Returns the number of factors.
- getNumFactors() - Method in interface edu.cmu.tetrad.study.gene.tetrad.gene.history.LagGraph
-
Returns the number of factors represented in the graph.
- getNumFactors() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.LinearFunction
-
Returns the number of factors in the history.
- getNumFactors() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.PolynomialFunction
-
Returns the number of factors in the history.
- getNumFactors() - Method in interface edu.cmu.tetrad.study.gene.tetrad.gene.history.UpdateFunction
-
Returns the number of factors in the history.
- getNumFixedParams() - Method in class edu.cmu.tetrad.sem.SemIm
- getNumFreeParams() - Method in class edu.cmu.tetrad.sem.DagScorer
- getNumFreeParams() - Method in interface edu.cmu.tetrad.sem.ISemIm
- getNumFreeParams() - Method in interface edu.cmu.tetrad.sem.Scorer
- getNumFreeParams() - Method in class edu.cmu.tetrad.sem.SemIm
- getNumIndependenceTests() - Method in class edu.cmu.tetrad.search.Fas
-
Returns the number of independence tests that were done.
- getNumIndependenceTests() - Method in class edu.cmu.tetrad.search.Fasd
-
Returns the number of conditional independence tests done in the course of search.
- getNumIndependenceTests() - Method in class edu.cmu.tetrad.search.GrowShrink
- getNumIndependenceTests() - Method in interface edu.cmu.tetrad.search.IFas
-
Returns the number of independence tests done in the search.
- getNumIndependenceTests() - Method in interface edu.cmu.tetrad.search.IMbSearch
-
Number of independent tests.
- getNumIndependenceTests() - Method in class edu.cmu.tetrad.search.Pc
-
Returns the number of independence tests performed in the search.
- getNumIndependenceTests() - Method in class edu.cmu.tetrad.search.Pcd
- getNumIndependenceTests() - Method in class edu.cmu.tetrad.search.PcMb
-
Returns the number of independence tests performed during the most recent search.
- getNumIndependenceTests() - Method in class edu.cmu.tetrad.search.SvarFas
-
Returns the number of independence tests.
- getNumIndependenceTests() - Method in class edu.cmu.tetrad.search.work_in_progress.Fas2
- getNumIndependenceTests() - Method in class edu.cmu.tetrad.search.work_in_progress.Fas3
-
Returns the number of independence tests that were done.
- getNumIndependenceTests() - Method in class edu.cmu.tetrad.search.work_in_progress.FasDci
- getNumIndependenceTests() - Method in class edu.cmu.tetrad.search.work_in_progress.FasFdr
-
Returns the nubmer of independence tests done in the course of the search.
- getNumIndependenceTests() - Method in class edu.cmu.tetrad.search.work_in_progress.Iamb
- getNumIndependenceTests() - Method in class edu.cmu.tetrad.search.work_in_progress.IambnPc
- getNumIndependenceTests() - Method in class edu.cmu.tetrad.search.work_in_progress.InterIamb
- getNumIndependenceTests() - Method in class edu.cmu.tetrad.search.work_in_progress.Mmmb
- getNumIndependenceTests() - Method in class edu.cmu.tetrad.search.work_in_progress.VcFas
- getNumInitialLags() - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- getNumIterations() - Method in class edu.cmu.tetrad.sem.SemEstimatorGibbsParams
- getNumNodes() - Method in interface edu.cmu.tetrad.bayes.BayesIm
-
Returns the name of the given node.
- getNumNodes() - Method in class edu.cmu.tetrad.bayes.BayesPm
-
Returns the number of nodes.
- getNumNodes() - Method in class edu.cmu.tetrad.bayes.DirichletBayesIm
- getNumNodes() - Method in class edu.cmu.tetrad.bayes.Evidence
- getNumNodes() - Method in class edu.cmu.tetrad.bayes.MlBayesIm
- getNumNodes() - Method in class edu.cmu.tetrad.bayes.MlBayesImObs
- getNumNodes() - Method in class edu.cmu.tetrad.bayes.UpdatedBayesIm
- getNumNodes() - Method in class edu.cmu.tetrad.graph.Dag
- getNumNodes() - Method in class edu.cmu.tetrad.graph.EdgeListGraph
- getNumNodes() - Method in interface edu.cmu.tetrad.graph.Graph
- getNumNodes() - Method in class edu.cmu.tetrad.graph.LagGraph
- getNumNodes() - Method in class edu.cmu.tetrad.graph.SemGraph
- getNumNodes() - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- getNumNodes() - Method in class edu.cmu.tetrad.sem.SemEvidence
- getNumNograph() - Method in class edu.pitt.dbmi.algo.resampling.GeneralResamplingSearch
- getNumParameters() - Method in class edu.cmu.tetrad.util.dist.Beta
-
Uh, there are 2 parameters...
- getNumParameters() - Method in class edu.cmu.tetrad.util.dist.ChiSquare
- getNumParameters() - Method in class edu.cmu.tetrad.util.dist.Discrete
- getNumParameters() - Method in interface edu.cmu.tetrad.util.dist.Distribution
-
Returns the number of parameters in the distribution.
- getNumParameters() - Method in class edu.cmu.tetrad.util.dist.Exponential
- getNumParameters() - Method in class edu.cmu.tetrad.util.dist.Gamma
- getNumParameters() - Method in class edu.cmu.tetrad.util.dist.GaussianPower
- getNumParameters() - Method in class edu.cmu.tetrad.util.dist.Indicator
- getNumParameters() - Method in class edu.cmu.tetrad.util.dist.LogNormal
- getNumParameters() - Method in class edu.cmu.tetrad.util.dist.MixtureOfGaussians
- getNumParameters() - Method in class edu.cmu.tetrad.util.dist.Normal
- getNumParameters() - Method in class edu.cmu.tetrad.util.dist.Poisson
- getNumParameters() - Method in class edu.cmu.tetrad.util.dist.SingleValue
- getNumParameters() - Method in class edu.cmu.tetrad.util.dist.Split
- getNumParameters() - Method in class edu.cmu.tetrad.util.dist.TruncatedNormal
- getNumParameters() - Method in class edu.cmu.tetrad.util.dist.Uniform
- getNumParents() - Method in class edu.cmu.tetrad.session.SessionNode
- getNumParents(int) - Method in interface edu.cmu.tetrad.bayes.BayesIm
-
Returns the number of parents for the given node.
- getNumParents(int) - Method in class edu.cmu.tetrad.bayes.DirichletBayesIm
- getNumParents(int) - Method in class edu.cmu.tetrad.bayes.MlBayesIm
- getNumParents(int) - Method in class edu.cmu.tetrad.bayes.MlBayesImObs
- getNumParents(int) - Method in class edu.cmu.tetrad.bayes.UpdatedBayesIm
- getNumParents(int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.biolingua.Digraph
-
Returns the number of parents of node i.
- getNumParents(int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.IndexedConnectivity
-
Returns the number of parents of the given factor.
- getNumParents(int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.IndexedLagGraph
-
Returns the number of parents of the given factor.
- getNumParents(int) - Method in class edu.cmu.tetrad.study.gene.tetradapp.model.BooleanGlassGeneIm
-
Returns the number of parents that a given factor has.
- getNumRandomCalls() - Method in class edu.cmu.tetrad.sem.SemIm
- getNumRegressors() - Method in class edu.cmu.tetrad.regression.LogisticRegression.Result
-
The number of regressors.
- getNumRegressors() - Method in class edu.cmu.tetrad.regression.RegressionResult
- getNumRestarts() - Method in interface edu.cmu.tetrad.sem.SemOptimizer
- getNumRestarts() - Method in class edu.cmu.tetrad.sem.SemOptimizerEm
- getNumRestarts() - Method in class edu.cmu.tetrad.sem.SemOptimizerPowell
- getNumRestarts() - Method in class edu.cmu.tetrad.sem.SemOptimizerRegression
- getNumRestarts() - Method in class edu.cmu.tetrad.sem.SemOptimizerRicf
- getNumRestarts() - Method in class edu.cmu.tetrad.sem.SemOptimizerScattershot
- getNumRows() - Method in class edu.cmu.tetrad.bayes.MlBayesImObs
- getNumRows() - Method in class edu.cmu.tetrad.bayes.StoredCellProbsObs
- getNumRows() - Method in class edu.cmu.tetrad.data.BoxDataSet
- getNumRows() - Method in interface edu.cmu.tetrad.data.DataSet
- getNumRows() - Method in class edu.cmu.tetrad.data.NumberObjectDataSet
- getNumRows() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.BooleanFunction
-
Returns the number of rows in the table.
- getNumRows() - Method in class edu.cmu.tetrad.util.Matrix
- getNumRows() - Method in class edu.cmu.tetrad.util.Matrix2
- getNumRows() - Method in class edu.cmu.tetrad.util.TextTable
- getNumRows(int) - Method in interface edu.cmu.tetrad.bayes.BayesIm
-
Returns the number of rows.
- getNumRows(int) - Method in class edu.cmu.tetrad.bayes.DirichletBayesIm
- getNumRows(int) - Method in class edu.cmu.tetrad.bayes.MlBayesIm
- getNumRows(int) - Method in class edu.cmu.tetrad.bayes.MlBayesImObs
- getNumRows(int) - Method in class edu.cmu.tetrad.bayes.UpdatedBayesIm
- getNumSamplesPerDish() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.simulation.MeasurementSimulator
-
Returns the number of samples generated per dish in the measurement model.
- getNumSamplesPerDish() - Method in class edu.cmu.tetrad.study.gene.tetradapp.model.MeasurementSimulatorParams
- getNumTerms() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.Polynomial
-
Returns the number of terms.
- getNumTiers() - Method in class edu.cmu.tetrad.data.Knowledge
- getNumTimePoints() - Method in class edu.cmu.tetrad.data.TimeSeriesData
- getNumValues(int) - Method in class edu.cmu.tetrad.data.CellTable
- getNumValues(String) - Method in class edu.cmu.tetrad.util.Parameters
-
Returns the number of values for the parameter.
- getNumVariables() - Method in class edu.cmu.tetrad.bayes.Proposition
- getNumVariables() - Method in class edu.cmu.tetrad.sem.SemProposition
- getNumVariables() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.PolynomialTerm
-
Returns the number of variables in this term.
- getNumVars() - Method in class edu.cmu.tetrad.data.TimeSeriesData
- getNumVars() - Method in class edu.cmu.tetrad.study.performance.ComparisonParameters
- getNy0() - Method in class edu.cmu.tetrad.regression.LogisticRegression.Result
-
The number of data points with target = 0.
- getNy1() - Method in class edu.cmu.tetrad.regression.LogisticRegression.Result
-
The number of data points with target = 1.
- getObject(int, int) - Method in class edu.cmu.tetrad.data.BoxDataSet
- getObject(int, int) - Method in interface edu.cmu.tetrad.data.DataSet
- getObject(int, int) - Method in class edu.cmu.tetrad.data.NumberObjectDataSet
- getObservedCounts(Node, BayesPm, BayesIm) - Method in class edu.cmu.tetrad.bayes.BdeMetricCache
-
This method is used in testing and debugging and not in the BDe metric calculations.
- getOhat() - Method in class edu.cmu.tetrad.sem.Ricf.RicfResult
- getOneMbDag(Graph) - Static method in class edu.cmu.tetrad.search.utils.MbUtils
-
Returns an example DAG from the given MB CPDAG.
- getOrder() - Method in class edu.cmu.tetrad.search.PermutationSearch
- getOrder() - Method in class edu.cmu.tetrad.search.work_in_progress.MagSemBicScore
-
Returns the order.
- getOrderShallow() - Method in class edu.cmu.tetrad.search.utils.TeyssierScorer
-
Returns the current permutation without making a copy.
- getOrientPrecision() - Method in class edu.cmu.tetrad.simulation.PRAOerrors
- getOrientRecall() - Method in class edu.cmu.tetrad.simulation.PRAOerrors
- getOrients() - Method in class edu.cmu.tetrad.search.work_in_progress.GraphChange
-
Return orients
- getOriginalSemIm() - Method in interface edu.cmu.tetrad.search.work_in_progress.Hbsms
- getOriginalSemIm() - Method in class edu.cmu.tetrad.search.work_in_progress.HbsmsBeam
- getOriginalSemIm() - Method in class edu.cmu.tetrad.search.work_in_progress.HbsmsGes
- getOut() - Method in class edu.cmu.tetrad.search.Fges
- getOut() - Method in class edu.cmu.tetrad.search.FgesMb
- getOut() - Method in class edu.cmu.tetrad.search.SvarFges
- getOut() - Method in class edu.cmu.tetrad.search.utils.FgesOrienter
- getOut() - Method in class edu.cmu.tetrad.sem.LargeScaleSimulation
- getOut() - Method in class edu.pitt.dbmi.algo.bayesian.constraint.search.RfciBsc
- getOut() - Method in class edu.pitt.dbmi.algo.resampling.GeneralResamplingSearch
- getOut() - Method in class edu.pitt.dbmi.algo.resampling.GeneralResamplingTest
- getOut() - Method in class edu.pitt.dbmi.algo.resampling.task.GeneralResamplingSearchRunnable
- getOutdegree(Node) - Method in class edu.cmu.tetrad.graph.Dag
- getOutdegree(Node) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
- getOutdegree(Node) - Method in interface edu.cmu.tetrad.graph.Graph
- getOutdegree(Node) - Method in class edu.cmu.tetrad.graph.LagGraph
- getOutdegree(Node) - Method in class edu.cmu.tetrad.graph.SemGraph
- getOutdegree(Node) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- getOutputs() - Method in class edu.cmu.tetrad.search.work_in_progress.DMSearch
- getOutputs(Node) - Method in class edu.cmu.tetrad.search.work_in_progress.DMSearch.LatentStructure
- getP() - Method in class edu.cmu.tetrad.data.AndersonDarlingTest
-
Constructs an Anderson-Darling test for the given column of data.
- getP() - Method in class edu.cmu.tetrad.data.GeneralAndersonDarlingTest
- getP() - Method in class edu.cmu.tetrad.data.MultiGeneralAndersonDarlingTest
- getP() - Method in class edu.cmu.tetrad.regression.RegressionResult
- getPag() - Method in class edu.cmu.tetrad.search.utils.PossibleMConnectingPath
- getParam(Class) - Method in class edu.cmu.tetrad.session.SessionNode
-
Gets the parameter object for the givem model class.
- getParam2() - Method in class edu.cmu.tetrad.sem.ParamConstraint
- getParamComparison(Parameter, Parameter) - Method in class edu.cmu.tetrad.sem.SemPm
- getParameter() - Method in class edu.cmu.tetrad.sem.Mapping
- getParameter(int) - Method in class edu.cmu.tetrad.util.dist.Beta
-
The order of parameters is alpha = 0, beta = 1.
- getParameter(int) - Method in class edu.cmu.tetrad.util.dist.ChiSquare
- getParameter(int) - Method in class edu.cmu.tetrad.util.dist.Discrete
- getParameter(int) - Method in interface edu.cmu.tetrad.util.dist.Distribution
-
Returns the index'th parameter.
- getParameter(int) - Method in class edu.cmu.tetrad.util.dist.Exponential
- getParameter(int) - Method in class edu.cmu.tetrad.util.dist.Gamma
- getParameter(int) - Method in class edu.cmu.tetrad.util.dist.GaussianPower
- getParameter(int) - Method in class edu.cmu.tetrad.util.dist.Indicator
- getParameter(int) - Method in class edu.cmu.tetrad.util.dist.LogNormal
- getParameter(int) - Method in class edu.cmu.tetrad.util.dist.MixtureOfGaussians
- getParameter(int) - Method in class edu.cmu.tetrad.util.dist.Normal
- getParameter(int) - Method in class edu.cmu.tetrad.util.dist.Poisson
- getParameter(int) - Method in class edu.cmu.tetrad.util.dist.SingleValue
- getParameter(int) - Method in class edu.cmu.tetrad.util.dist.Split
- getParameter(int) - Method in class edu.cmu.tetrad.util.dist.TruncatedNormal
- getParameter(int) - Method in class edu.cmu.tetrad.util.dist.Uniform
- getParameter(Node, Node) - Method in class edu.cmu.tetrad.sem.SemPm
- getParameter(String) - Method in class edu.cmu.tetrad.sem.SemPm
- getParameterEstimationInitializationExpression(String) - Method in class edu.cmu.tetrad.sem.GeneralizedSemPm
- getParameterEstimationInitializationExpressionString(String) - Method in class edu.cmu.tetrad.sem.GeneralizedSemPm
- getParameterExpression(String) - Method in class edu.cmu.tetrad.sem.GeneralizedSemPm
- getParameterExpressionString(String) - Method in class edu.cmu.tetrad.sem.GeneralizedSemPm
- getParameterName(int) - Method in class edu.cmu.tetrad.util.dist.Beta
-
The order of parameters is alpha = 0, beta = 1.
- getParameterName(int) - Method in class edu.cmu.tetrad.util.dist.ChiSquare
- getParameterName(int) - Method in class edu.cmu.tetrad.util.dist.Discrete
- getParameterName(int) - Method in interface edu.cmu.tetrad.util.dist.Distribution
-
The name of the index'th parameter, for display purposes.
- getParameterName(int) - Method in class edu.cmu.tetrad.util.dist.Exponential
- getParameterName(int) - Method in class edu.cmu.tetrad.util.dist.Gamma
- getParameterName(int) - Method in class edu.cmu.tetrad.util.dist.GaussianPower
- getParameterName(int) - Method in class edu.cmu.tetrad.util.dist.Indicator
- getParameterName(int) - Method in class edu.cmu.tetrad.util.dist.LogNormal
- getParameterName(int) - Method in class edu.cmu.tetrad.util.dist.MixtureOfGaussians
- getParameterName(int) - Method in class edu.cmu.tetrad.util.dist.Normal
- getParameterName(int) - Method in class edu.cmu.tetrad.util.dist.Poisson
- getParameterName(int) - Method in class edu.cmu.tetrad.util.dist.SingleValue
- getParameterName(int) - Method in class edu.cmu.tetrad.util.dist.Split
- getParameterName(int) - Method in class edu.cmu.tetrad.util.dist.TruncatedNormal
- getParameterName(int) - Method in class edu.cmu.tetrad.util.dist.Uniform
- getParameterNames() - Static method in class edu.cmu.tetrad.bayes.BayesPm
-
Returns the parameter names.
- getParameterNames() - Static method in class edu.cmu.tetrad.bayes.MlBayesIm
- getParameterNames() - Static method in class edu.cmu.tetrad.sem.GeneralizedSemPm
- getParameterNames() - Static method in class edu.cmu.tetrad.sem.SemIm
- getParameterRange(Edge) - Method in class edu.cmu.tetrad.sem.StandardizedSemIm
- getParameters() - Method in interface edu.cmu.tetrad.algcomparison.algorithm.Algorithm
-
Returns the parameters that this search uses.
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.cluster.Bpc
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.cluster.Fofc
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.cluster.Ftfc
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.continuous.dag.Dagma
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.continuous.dag.DirectLingam
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.continuous.dag.IcaLingam
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.continuous.dag.IcaLingD
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.ExternalAlgorithm
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.FirstInflection
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.mixed.Mgm
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.Fask
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FaskConcatenated
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FaskLofsConcatenated
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FaskVote
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FasLofs
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FciIod
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FgesConcatenated
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.Images
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Boss
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Cpc
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Fas
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Fges
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.FgesMb
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.FgesMeasurement
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.GesMe
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Grasp
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Pc
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Pcd
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.PcLingam
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.PcMb
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.RestrictedBoss
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.SingleGraphAlg
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Sp
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Bfci
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Ccd
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Cfci
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Fci
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.FciMax
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Gfci
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.GraspFci
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.PagSampleRfci
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Rfci
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.RfciBsc
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.SpFci
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.SvarFci
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.SvarGfci
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pattern.Cstar
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.other.FactorAnalysis
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.other.Glasso
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.Eb
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.FaskPw
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.R1
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.R2
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.R3
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.Rskew
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.RskewE
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.Skew
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.SkewE
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.Tanh
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.StabilitySelection
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.algorithm.StARS
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.graph.Cyclic
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.graph.ErdosRenyi
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.graph.RandomForward
- getParameters() - Method in interface edu.cmu.tetrad.algcomparison.graph.RandomGraph
-
Returns the parameters that this graph uses.
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.graph.RandomSingleFactorMim
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.graph.RandomTwoFactorMim
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.graph.ScaleFree
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.graph.SingleGraph
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.independence.BdeuTest
-
Returns the parameters of the test.
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.independence.CciTest
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.independence.ChiSquare
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.independence.ConditionalGaussianLRT
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.independence.DegenerateGaussianLRT
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.independence.DiscreteBicTest
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.independence.FisherZ
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.independence.GICScoreTests
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.independence.Gsquare
- getParameters() - Method in interface edu.cmu.tetrad.algcomparison.independence.IndependenceWrapper
-
Returns the parameters that this search uses.
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.independence.Kci
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.independence.MagSemBicTest
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.independence.Mnlrlrt
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.independence.MSeparationTest
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.independence.MultinomialLogisticRegressionWald
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.independence.Mvplrt
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.independence.PoissonScoreTest
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.independence.PositiveCorr
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.independence.ProbabilisticTest
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.independence.SemBicDTest
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.independence.SemBicTest
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.independence.UniformScatterTest
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.score.BdeuScore
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.score.CciScore
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.score.ConditionalGaussianBicScore
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.score.DegenerateGaussianBicScore
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.score.DiscreteBicScore
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.score.EbicScore
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.score.FisherZScore
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.score.GicScores
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.score.MagSemBicScore
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.score.MSeparationScore
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.score.MVPBicScore
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.score.PoissonPriorScore
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.score.PositiveCorrScore
- getParameters() - Method in interface edu.cmu.tetrad.algcomparison.score.ScoreWrapper
-
Returns the parameters that this search uses.
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.score.SemBicScore
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.score.SemBicScoreDeterministic
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.score.ZhangShenBoundScore
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.simulation.BayesNetSimulation
-
Returns the parameters.
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.simulation.BooleanGlassSimulation
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.simulation.ConditionalGaussianSimulation
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.simulation.GeneralSemSimulation
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.simulation.GeneralSemSimulationSpecial1
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.simulation.LeeHastieSimulation
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.simulation.LinearFisherModel
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.simulation.LinearSineSimulation
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.simulation.NLSemSimulation
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.simulation.SemSimulation
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.simulation.SemThenDiscretize
- getParameters() - Method in interface edu.cmu.tetrad.algcomparison.simulation.Simulation
-
Returns the list of parameters used in the simulation.
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.simulation.StandardizedSemSimulation
- getParameters() - Method in class edu.cmu.tetrad.algcomparison.simulation.TimeSeriesSemSimulation
- getParameters() - Method in interface edu.cmu.tetrad.algcomparison.utils.HasParameters
-
Returns the list of parameter names that are used.
- getParameters() - Method in class edu.cmu.tetrad.calculator.parser.ExpressionParser
- getParameters() - Method in class edu.cmu.tetrad.data.simulation.LoadContinuousDataAndGraphs
- getParameters() - Method in class edu.cmu.tetrad.data.simulation.LoadContinuousDataAndSingleGraph
- getParameters() - Method in class edu.cmu.tetrad.data.simulation.LoadContinuousDataSmithSim
- getParameters() - Method in class edu.cmu.tetrad.data.simulation.LoadDataAndGraphs
- getParameters() - Method in class edu.cmu.tetrad.data.simulation.LoadDataFromFileWithoutGraph
- getParameters() - Method in class edu.cmu.tetrad.sem.GeneralizedSemPm
- getParameters() - Method in class edu.cmu.tetrad.sem.SemPm
- getParameters() - Method in class edu.cmu.tetrad.session.SessionNode
- getParameters() - Static method in class edu.cmu.tetrad.util.Params
- getParametersEstimationInitializationTemplate() - Method in class edu.cmu.tetrad.sem.GeneralizedSemPm
- getParametersNames() - Method in class edu.cmu.tetrad.util.Parameters
- getParametersTemplate() - Method in class edu.cmu.tetrad.sem.GeneralizedSemPm
- getParameterValue(Edge) - Method in class edu.cmu.tetrad.sem.StandardizedSemIm
- getParameterValue(String) - Method in class edu.cmu.tetrad.sem.GeneralizedSemIm
- getParameterValues() - Method in interface edu.cmu.tetrad.algcomparison.utils.HasParameterValues
- getParameterValues() - Method in class edu.cmu.tetrad.data.simulation.LoadContinuousDataAndSingleGraph
- getParameterValues() - Method in class edu.cmu.tetrad.data.simulation.LoadContinuousDataSmithSim
- getParamName() - Method in class edu.cmu.tetrad.util.ParamDescription
- getParams() - Method in class edu.cmu.tetrad.sem.SemIm
- getParams() - Method in class edu.cmu.tetrad.study.performance.ComparisonResult
- getParamSettings() - Method in interface edu.cmu.tetrad.session.SimulationParamsSource
- getParamsWithUnsupportedValueType() - Method in class edu.cmu.tetrad.util.ParamDescriptions
- getParamValue(Node, Node) - Method in interface edu.cmu.tetrad.sem.ISemIm
- getParamValue(Node, Node) - Method in class edu.cmu.tetrad.sem.SemIm
-
Gets the value of a single free parameter to the given value, where the free parameter is specified by the endpoint nodes of its edge in the w graph.
- getParamValue(Parameter) - Method in interface edu.cmu.tetrad.sem.ISemIm
- getParamValue(Parameter) - Method in class edu.cmu.tetrad.sem.SemIm
-
Gets the value of a single free parameter, or Double.NaN if the parameter is not in this
- getParent() - Method in class edu.cmu.tetrad.session.SessionEvent
- getParent(int, int) - Method in interface edu.cmu.tetrad.bayes.BayesIm
-
Returns the ith parent of the givne node.
- getParent(int, int) - Method in class edu.cmu.tetrad.bayes.DirichletBayesIm
- getParent(int, int) - Method in class edu.cmu.tetrad.bayes.MlBayesIm
- getParent(int, int) - Method in class edu.cmu.tetrad.bayes.MlBayesImObs
- getParent(int, int) - Method in class edu.cmu.tetrad.bayes.UpdatedBayesIm
- getParent(int, int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.IndexedConnectivity
-
Returns the given parent as an IndexedParent.
- getParent(int, int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.IndexedLagGraph
-
Returns the given parent as an IndexedParent.
- getParentDim(int, int) - Method in interface edu.cmu.tetrad.bayes.BayesIm
-
Returns the dimension of the given parent for the given node.
- getParentDim(int, int) - Method in class edu.cmu.tetrad.bayes.DirichletBayesIm
- getParentDim(int, int) - Method in class edu.cmu.tetrad.bayes.MlBayesIm
- getParentDim(int, int) - Method in class edu.cmu.tetrad.bayes.MlBayesImObs
- getParentDim(int, int) - Method in class edu.cmu.tetrad.bayes.UpdatedBayesIm
- getParentDims(int) - Method in interface edu.cmu.tetrad.bayes.BayesIm
-
Returns the dimensions of the pararents of the given node.
- getParentDims(int) - Method in class edu.cmu.tetrad.bayes.DirichletBayesIm
- getParentDims(int) - Method in class edu.cmu.tetrad.bayes.MlBayesIm
- getParentDims(int) - Method in class edu.cmu.tetrad.bayes.MlBayesImObs
- getParentDims(int) - Method in class edu.cmu.tetrad.bayes.UpdatedBayesIm
- getParents() - Method in class edu.cmu.tetrad.search.Boss
- getParents() - Method in class edu.cmu.tetrad.search.Sp
- getParents() - Method in interface edu.cmu.tetrad.search.SuborderSearch
-
The map from nodes to parents resulting from the search.
- getParents() - Method in class edu.cmu.tetrad.session.SessionNode
- getParents() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.AbstractNbComponent
-
Returns the parents.
- getParents() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.BooleanFunction
-
Returns the parents of this function.
- getParents(int) - Method in interface edu.cmu.tetrad.bayes.BayesIm
-
Returns the parents of the given node.
- getParents(int) - Method in class edu.cmu.tetrad.bayes.DirichletBayesIm
- getParents(int) - Method in class edu.cmu.tetrad.bayes.MlBayesIm
- getParents(int) - Method in class edu.cmu.tetrad.bayes.MlBayesImObs
- getParents(int) - Method in class edu.cmu.tetrad.bayes.UpdatedBayesIm
- getParents(int) - Method in class edu.cmu.tetrad.search.utils.TeyssierScorer
-
Returns the parents of the node at index p.
- getParents(int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.akutsu.RevealOutputGraph
- getParents(int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.biolingua.Digraph
-
Returns an array with the indexes of the parents of node i.
- getParents(int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.reveal.RevealOutputGraph
- getParents(int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.RevealOutputGraph
- getParents(int) - Method in interface edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.OutputGraph
-
Returns the indices of the parent variables for the given variable.
- getParents(int) - Method in class edu.cmu.tetrad.study.gene.tetradapp.model.BooleanGlassGeneIm
-
Returns the list of parents of the given factor as String's formatted in the style used by the Tetrad IV display-- e.g.
- getParents(Node) - Method in class edu.cmu.tetrad.graph.Dag
- getParents(Node) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
- getParents(Node) - Method in interface edu.cmu.tetrad.graph.Graph
- getParents(Node) - Method in class edu.cmu.tetrad.graph.LagGraph
- getParents(Node) - Method in class edu.cmu.tetrad.graph.SemGraph
- getParents(Node) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- getParents(Node) - Method in class edu.cmu.tetrad.search.utils.TeyssierScorer
-
Returns the parents of a node v.
- getParents(Node) - Method in class edu.cmu.tetrad.sem.GeneralizedSemPm
- getParents(String) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ActiveLagGraph
- getParents(String) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ManualLagGraph
- getParents(String) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.BasicLagGraph
-
Returns the lagged factors which are into the given factor.
- getParents(String) - Method in interface edu.cmu.tetrad.study.gene.tetrad.gene.history.LagGraph
-
Returns the lagged factors which are into the given factor.
- getParentValue(int, int, int) - Method in interface edu.cmu.tetrad.bayes.BayesIm
-
Returns the given parent value.
- getParentValue(int, int, int) - Method in class edu.cmu.tetrad.bayes.DirichletBayesIm
- getParentValue(int, int, int) - Method in class edu.cmu.tetrad.bayes.MlBayesIm
- getParentValue(int, int, int) - Method in class edu.cmu.tetrad.bayes.MlBayesImObs
- getParentValue(int, int, int) - Method in class edu.cmu.tetrad.bayes.UpdatedBayesIm
- getParentValues(int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.BooleanFunction
-
Returns the combination of parent values represented by a given row in the table.
- getParentValues(int, int) - Method in interface edu.cmu.tetrad.bayes.BayesIm
-
Returns the parents values of the given node.
- getParentValues(int, int) - Method in class edu.cmu.tetrad.bayes.DirichletBayesIm
- getParentValues(int, int) - Method in class edu.cmu.tetrad.bayes.MlBayesIm
- getParentValues(int, int) - Method in class edu.cmu.tetrad.bayes.MlBayesImObs
- getParentValues(int, int) - Method in class edu.cmu.tetrad.bayes.UpdatedBayesIm
- getPart(int, int, int, int) - Method in class edu.cmu.tetrad.util.Matrix
- getPart(int, int, int, int) - Method in class edu.cmu.tetrad.util.Matrix2
- getPath() - Method in interface edu.cmu.tetrad.algcomparison.statistic.utils.SimulationPath
- getPath() - Method in class edu.cmu.tetrad.data.simulation.LoadDataFromFileWithoutGraph
- getPath() - Method in class edu.cmu.tetrad.search.utils.PossibleMConnectingPath
- getPattern() - Method in class edu.cmu.tetrad.data.DelimiterType
- getPc(Node) - Method in class edu.cmu.tetrad.search.work_in_progress.Mmmb
- getPcs() - Method in class edu.cmu.tetrad.graph.EdgeListGraph
- getPenaltyDiscount() - Method in class edu.cmu.tetrad.search.score.ConditionalGaussianScore
-
Returns the penalty discount for this score, which is a multiplier on the penatly term of the BIC score.
- getPenaltyDiscount() - Method in class edu.cmu.tetrad.search.score.DegenerateGaussianScore
- getPenaltyDiscount() - Method in class edu.cmu.tetrad.search.score.GicScores
- getPenaltyDiscount() - Method in class edu.cmu.tetrad.search.score.SemBicScore
-
Specialized scoring method for a single parent.
- getPenaltyDiscount() - Method in class edu.cmu.tetrad.search.SvarFges
-
Deprecated.Use the getters on the individual scores instead.
- getPenaltyDiscount() - Method in class edu.cmu.tetrad.search.utils.FgesOrienter
-
For BIC score, a multiplier on the penalty term.
- getPenaltyDiscount() - Method in interface edu.cmu.tetrad.search.utils.HasPenaltyDiscount
- getPenaltyDiscount() - Method in class edu.cmu.tetrad.search.work_in_progress.FasLofs
- getPenaltyDiscount() - Method in class edu.cmu.tetrad.search.work_in_progress.MagSemBicScore
- getPenaltyDiscount() - Method in class edu.cmu.tetrad.search.work_in_progress.SemBicScoreDeterministic
-
Specialized scoring method for a single parent.
- getPenaltyDiscount() - Method in class edu.cmu.tetrad.study.performance.ComparisonParameters
- getPercent() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestFisherZPercentIndependent
- getPercentCorrect() - Method in class edu.cmu.tetrad.classify.ClassifierBayesUpdaterDiscrete
- getPercentCorrect() - Method in interface edu.cmu.tetrad.classify.ClassifierDiscrete
- getPercentCorrect() - Method in class edu.cmu.tetrad.classify.ClassifierMbDiscrete
- getPercentUnregulated() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.LagGraphParams
- getPerms() - Method in class edu.cmu.tetrad.search.work_in_progress.Kpc
-
Gets the getModel number of bootstrap samples used
- getPermutedMatrix() - Method in class edu.cmu.tetrad.search.utils.PermutationMatrixPair
-
Returns W, permuted rowwise by the permutation passed in through the constructor.
- getPhi() - Method in class edu.pitt.csb.mgm.Mgm.MGMParams
- getPi() - Method in class edu.cmu.tetrad.search.Cstar.Record
- getPi() - Method in class edu.cmu.tetrad.search.utils.TeyssierScorer
- getPixelDigitalization() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.simulation.MeasurementSimulator
-
Returns the pixel digitalization error.
- getPixelDigitalization() - Method in class edu.cmu.tetrad.study.gene.tetradapp.model.MeasurementSimulatorParams
- getPolynomial(int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.PolynomialFunction
-
Returns the polynomial for the given factor.
- getPool() - Method in class edu.cmu.tetrad.util.ForkJoinPoolInstance
- getPopulationTripleType(Node, Node, Node, IndependenceTest, int, Graph, boolean) - Method in class edu.cmu.tetrad.search.work_in_progress.VcPc
- getPopulationTripleType(Node, Node, Node, IndependenceTest, int, Graph, boolean) - Method in class edu.cmu.tetrad.search.work_in_progress.VcPcFast
- getPosition() - Method in class edu.cmu.tetrad.calculator.expression.ConstantExpression
- getPosition() - Method in class edu.cmu.tetrad.calculator.expression.EvaluationExpression
- getPosition() - Method in interface edu.cmu.tetrad.calculator.expression.Expression
- getPosition() - Method in interface edu.cmu.tetrad.calculator.expression.ExpressionDescriptor
- getPosition() - Method in class edu.cmu.tetrad.calculator.expression.VariableExpression
- getPosterior() - Method in class edu.cmu.tetrad.search.test.IndTestProbabilistic
- getPosterior() - Method in class edu.cmu.tetrad.search.work_in_progress.ProbabilisticMapIndependence
- getPower() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.AbstractNbComponent
-
Returns the power.
- getPreamble() - Method in class edu.cmu.tetrad.regression.RegressionResult
- getPrecision() - Method in class edu.cmu.tetrad.search.work_in_progress.Kpc
-
Gets the getModel precision for the Incomplete Cholesky
- getPredictedValue(double[]) - Method in class edu.cmu.tetrad.regression.RegressionResult
- getPrefix(int) - Method in class edu.cmu.tetrad.search.utils.TeyssierScorer
- getPrefix(String) - Static method in class edu.cmu.tetrad.search.utils.TsUtils
- getPrefix(String) - Static method in class edu.cmu.tetrad.sem.LargeScaleSimulation
- getPrefix(String) - Static method in class edu.cmu.tetrad.study.performance.Comparison2
- getProb(Proposition) - Method in class edu.cmu.tetrad.bayes.BayesImProbs
- getProb(Proposition) - Method in class edu.cmu.tetrad.bayes.CellTableProbs
- getProb(Proposition) - Method in class edu.cmu.tetrad.bayes.DataSetProbs
- getProb(Proposition) - Method in class edu.cmu.tetrad.bayes.DirichletDataSetProbs
- getProb(Proposition) - Method in class edu.cmu.tetrad.bayes.IntAveDataSetProbs
- getProb(Proposition) - Method in class edu.cmu.tetrad.bayes.StoredCellProbs
- getProb(Proposition) - Method in class edu.cmu.tetrad.bayes.StoredCellProbsObs
- getProbability() - Method in class edu.cmu.tetrad.graph.Edge
- getProbability() - Method in class edu.cmu.tetrad.graph.EdgeTypeProbability
- getProbability(int) - Method in class edu.cmu.tetrad.bayes.MlBayesImObs
- getProbability(int, int, int) - Method in interface edu.cmu.tetrad.bayes.BayesIm
-
Returns the probability for the given cell in the given CPT.
- getProbability(int, int, int) - Method in class edu.cmu.tetrad.bayes.DirichletBayesIm
- getProbability(int, int, int) - Method in class edu.cmu.tetrad.bayes.MlBayesIm
- getProbability(int, int, int) - Method in class edu.cmu.tetrad.bayes.MlBayesImObs
- getProbability(int, int, int) - Method in class edu.cmu.tetrad.bayes.UpdatedBayesIm
-
Calculates the probability for the given node, at the given row and column of the conditional probability table (CPT), updated for the evidence provided in the constuctor.
- getProbs() - Method in class edu.cmu.tetrad.regression.LogisticRegression.Result
-
The array of coefP-values for the regression coefficients.
- getProduct(int[]) - Method in class edu.cmu.tetrad.session.SessionNode
- getProperties() - Method in class edu.cmu.tetrad.graph.Edge
- getProperties() - Method in class edu.cmu.tetrad.graph.EdgeTypeProbability
- getProperties() - Method in class edu.cmu.tetrad.util.TetradProperties
- getProposition() - Method in class edu.cmu.tetrad.bayes.Evidence
- getProposition() - Method in class edu.cmu.tetrad.sem.SemEvidence
- getProtocolDescription() - Static method in class edu.cmu.tetrad.util.NamingProtocol
- getProximalEndpoint(Node) - Method in class edu.cmu.tetrad.graph.Edge
- getPseudocount(int, int, int) - Method in class edu.cmu.tetrad.bayes.DirichletBayesIm
- getPurifyTestDescriptions() - Static method in enum class edu.cmu.tetrad.search.utils.BpcTestType
- getpValue() - Method in class edu.cmu.tetrad.search.Mimbuild
- getpValue() - Method in class edu.cmu.tetrad.search.MimbuildTrek
-
The p-value of the model.
- getPValue() - Method in class edu.cmu.tetrad.search.test.ChiSquareTest.Result
- getPValue() - Method in class edu.cmu.tetrad.search.test.GSquareTest.Result
- getPValue() - Method in class edu.cmu.tetrad.search.test.IndependenceResult
-
Returns the p-value of the fact under the null hypothesis of independence.
- getPValue() - Method in class edu.cmu.tetrad.search.test.IndTestConditionalCorrelation
-
Returns the p-value of the test.
- getPValue() - Method in class edu.cmu.tetrad.search.test.IndTestDegenerateGaussianLrt
-
Returns the probability associated with the most recently executed independence test, of Double.NaN if p value is not meaningful for this test.
- getPValue() - Method in class edu.cmu.tetrad.search.test.IndTestGSquare
-
Returns the p value associated with the most recent call of isIndependent.
- getPValue() - Method in class edu.cmu.tetrad.search.test.IndTestIndependenceFacts
-
No p-values are available.
- getPValue() - Method in class edu.cmu.tetrad.search.utils.DeltaTetradTest
- getPValue() - Method in class edu.cmu.tetrad.search.utils.Tetrad
- getPValue() - Method in class edu.cmu.tetrad.search.work_in_progress.HbsmsBeam.Score
- getPValue() - Method in class edu.cmu.tetrad.search.work_in_progress.HbsmsGes.GraphWithPValue
- getPValue() - Method in class edu.cmu.tetrad.search.work_in_progress.HbsmsGes.Score
- getPValue() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestCramerT
- getPValue() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestFisherZGeneralizedInverse
- getPValue() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestFisherZRecursive
- getPValue() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestMixedMultipleTTest
- getPValue() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestMultinomialLogisticRegression
- getPValue() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestPositiveCorr
- getPValue() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestSepsetDci
-
Needed for IndependenceTest interface.
- getPValue() - Method in class edu.cmu.tetrad.sem.DagScorer
- getPValue() - Method in interface edu.cmu.tetrad.sem.ISemIm
- getPValue() - Method in interface edu.cmu.tetrad.sem.Scorer
- getPValue() - Method in class edu.cmu.tetrad.sem.SemIm
- getPValue() - Method in class edu.pitt.csb.mgm.IndTestMultinomialLogisticRegressionWald
- getPValue(double) - Method in class edu.cmu.tetrad.search.Lofs
- getPValue(double) - Method in class edu.cmu.tetrad.search.test.ConditionalCorrelationIndependence
-
Returns the p-value of the score.
- getPValue(double) - Method in class edu.cmu.tetrad.search.work_in_progress.InverseCorrelation
- getPValue(Node, Node) - Method in class edu.cmu.tetrad.search.utils.SepsetMap
-
Looks up the p-value for {x, y}
- getPValue(Sextad...) - Method in class edu.cmu.tetrad.search.utils.DeltaSextadTest
-
Takes a list of tetrads for the given data set and returns the chi square value for the test.
- getPValue(Tetrad...) - Method in class edu.cmu.tetrad.search.utils.DeltaTetradTest
-
Returns a p-value for the given list of tetrad.
- getPValue(Parameter, int) - Method in interface edu.cmu.tetrad.sem.ISemIm
- getPValue(Parameter, int) - Method in class edu.cmu.tetrad.sem.SemIm
- getPValue(List<Double>) - Static method in class edu.cmu.tetrad.util.UniformityTest
- getPValueChisq() - Method in class edu.cmu.tetrad.bayes.EmBayesProperties
- getPValueDf() - Method in class edu.cmu.tetrad.bayes.EmBayesProperties
- getPValues() - Method in class edu.cmu.tetrad.search.PcLingam
-
Returns the p-values of the search.
- getPValues(List<IndependenceResult>) - Method in class edu.cmu.tetrad.search.MarkovCheck
-
Returns the list of p-values for the given list of results.
- getRandomGenerator() - Method in class edu.cmu.tetrad.util.RandomUtil
- getRanks(double[]) - Static method in class edu.cmu.tetrad.util.StatUtils
- getRawData() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.simulation.MeasurementSimulator
-
Returns the raw data that is the result of a simulation, in the form of a three-dimensional double array.
- getRawData() - Method in class edu.cmu.tetrad.study.gene.tetradapp.model.MeasurementSimulatorParams
- getReachableNodes(List<Node>, LegalPairs, List<Node>, List<Node>, Graph, int) - Static method in class edu.cmu.tetrad.search.utils.GraphSearchUtils
- getRealDistribution(Context) - Method in class edu.cmu.tetrad.calculator.expression.ConstantExpression
- getRealDistribution(Context) - Method in class edu.cmu.tetrad.calculator.expression.EvaluationExpression
- getRealDistribution(Context) - Method in interface edu.cmu.tetrad.calculator.expression.Expression
- getRealDistribution(Context) - Method in class edu.cmu.tetrad.calculator.expression.VariableExpression
- getRealEigenvalue(int) - Method in class edu.pitt.csb.mgm.EigenDecomposition
-
Returns the real part of the ith eigenvalue of the original matrix.
- getRealEigenvalues() - Method in class edu.pitt.csb.mgm.EigenDecomposition
-
Gets a copy of the real parts of the eigenvalues of the original matrix.
- getReason() - Method in class edu.cmu.tetrad.search.utils.GraphSearchUtils.LegalMagRet
- getReason() - Method in class edu.cmu.tetrad.search.utils.GraphSearchUtils.LegalPagRet
- getRecords() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pattern.Cstar
- getRecords(DataSet, List<Node>, List<Node>, int, String) - Method in class edu.cmu.tetrad.search.Cstar
-
Returns records for a set of variables with expected number of false positives bounded by q.
- getReferencedNodes(Node) - Method in class edu.cmu.tetrad.sem.GeneralizedSemPm
- getReferencedParameters(Node) - Method in class edu.cmu.tetrad.sem.GeneralizedSemPm
- getReferencingNodes(Node) - Method in class edu.cmu.tetrad.sem.GeneralizedSemPm
- getReferencingNodes(String) - Method in class edu.cmu.tetrad.sem.GeneralizedSemPm
- getRegressorNames() - Method in class edu.cmu.tetrad.regression.LogisticRegression.Result
-
The variables.
- getRegressorNames() - Method in class edu.cmu.tetrad.regression.RegressionResult
- getRemap() - Method in class edu.cmu.tetrad.data.DiscreteDiscretizationSpec
- getRemoves() - Method in class edu.cmu.tetrad.search.work_in_progress.GraphChange
-
Return removes
- getRepetition() - Method in class edu.cmu.tetrad.session.SessionNode
- getRepetition(SessionNode) - Static method in class edu.cmu.tetrad.session.SimulationStudy
-
Gets the repeition of the given node.
- getReport() - Method in class edu.cmu.tetrad.sem.GeneralizedSemEstimator
- getRequired() - Method in class edu.cmu.tetrad.search.utils.GrowShrinkTree
- getResamplingDataset(DataSet, int) - Static method in class edu.cmu.tetrad.data.DataTransforms
- getResamplingDataset(DataSet, int, RandomGenerator) - Static method in class edu.cmu.tetrad.data.DataTransforms
-
Get dataset sampled without replacement.
- getResettableParams() - Method in interface edu.cmu.tetrad.session.ParamsResettable
- getResidual() - Method in class edu.cmu.tetrad.search.FactorAnalysis
-
Returns the matrix of residuals.
- getResiduals() - Method in class edu.cmu.tetrad.regression.RegressionResult
- getResiduals() - Method in class edu.cmu.tetrad.search.utils.TsUtils.VarResult
- getResidualsWithoutFirstRegressor() - Method in class edu.cmu.tetrad.regression.RegressionDataset
- getResultGraph() - Method in interface edu.cmu.tetrad.data.KnowledgeBoxInput
- getResultGraph() - Method in class edu.cmu.tetrad.study.performance.ComparisonResult
- getResults(boolean) - Method in class edu.cmu.tetrad.search.MarkovCheck
-
After the generateResults method has been called, this method returns the results for the local Markov or local Faithfulness check, depending on the value of the indep parameter.
- getResultsTable() - Method in class edu.cmu.tetrad.regression.RegressionResult
- getResultType() - Method in class edu.cmu.tetrad.study.performance.ComparisonParameters
- getRho() - Method in class edu.cmu.tetrad.search.work_in_progress.Glasso
- getRmsea() - Method in interface edu.cmu.tetrad.sem.ISemIm
- getRmsea() - Method in class edu.cmu.tetrad.sem.SemIm
- getRootElement(File) - Static method in class edu.cmu.tetrad.graph.GraphSaveLoadUtils
- getRow(boolean[]) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.BooleanFunction
-
Returns the row for the given combination of parent values.
- getRow(int) - Method in class edu.cmu.tetrad.util.Matrix
- getRow(int) - Method in class edu.cmu.tetrad.util.Matrix2
- getRowCounts(List<DataModel>) - Static method in class edu.cmu.tetrad.util.MultidataUtils
- getRowIndex(int, int[]) - Method in interface edu.cmu.tetrad.bayes.BayesIm
-
Returns a row index.
- getRowIndex(int, int[]) - Method in class edu.cmu.tetrad.bayes.DirichletBayesIm
- getRowIndex(int, int[]) - Method in class edu.cmu.tetrad.bayes.MlBayesIm
- getRowIndex(int, int[]) - Method in class edu.cmu.tetrad.bayes.MlBayesImObs
- getRowIndex(int, int[]) - Method in class edu.cmu.tetrad.bayes.UpdatedBayesIm
- getRowPerm() - Method in class edu.cmu.tetrad.search.utils.PermutationMatrixPair
- getRowPseudocount(int, int) - Method in class edu.cmu.tetrad.bayes.DirichletBayesIm
- getRows() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestFisherZPercentIndependent
- getRows(double[], double[], double, double) - Static method in class edu.cmu.tetrad.util.StatUtils
- getRows(double[], double, double) - Static method in class edu.cmu.tetrad.util.StatUtils
- getRowValueAt(int, int) - Method in class edu.cmu.tetrad.study.gene.tetradapp.model.BooleanGlassGeneIm
-
Returns the value in the given row of the boolean table for the given factor.
- getRowValues(int) - Method in class edu.cmu.tetrad.bayes.MlBayesImObs
- getRuntime() - Method in class edu.cmu.tetrad.search.work_in_progress.Ion
- getS() - Method in class edu.cmu.tetrad.search.FastIca.IcaResult
- getSampleCovar() - Method in class edu.cmu.tetrad.sem.DagScorer
- getSampleCovar() - Method in interface edu.cmu.tetrad.sem.Scorer
- getSampleCovar() - Method in class edu.cmu.tetrad.sem.SemIm
- getSamplePrior() - Method in class edu.cmu.tetrad.search.score.BdeuScore
-
Returns the smaple prior.
- getSamplePrior() - Method in class edu.cmu.tetrad.study.performance.ComparisonParameters
- getSampleSampleVariability() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.simulation.MeasurementSimulator
-
Returns the sample to sample variability, which is the standard deviation of a normal distribution with mean 0 from which errors in measured expression levels due to the microarray being used for measurement are drawn.
- getSampleSampleVariability() - Method in class edu.cmu.tetrad.study.gene.tetradapp.model.MeasurementSimulatorParams
- getSampleSize() - Method in class edu.cmu.tetrad.bayes.BayesProperties
- getSampleSize() - Method in class edu.cmu.tetrad.data.CorrelationMatrixOnTheFly
-
The size of the sample used to calculated this covariance matrix.
- getSampleSize() - Method in class edu.cmu.tetrad.data.CovarianceMatrix
-
The size of the sample used to calculated this covariance matrix.
- getSampleSize() - Method in class edu.cmu.tetrad.data.CovarianceMatrixOnTheFly
-
The size of the sample used to calculated this covariance matrix.
- getSampleSize() - Method in interface edu.cmu.tetrad.data.ICovarianceMatrix
- getSampleSize() - Method in class edu.cmu.tetrad.data.SplitCasesSpec
- getSampleSize() - Method in interface edu.cmu.tetrad.search.IndependenceTest
-
Returns the sample size.
- getSampleSize() - Method in class edu.cmu.tetrad.search.score.BdeScore
-
Returns the sample size of the data.
- getSampleSize() - Method in class edu.cmu.tetrad.search.score.BdeuScore
-
Returns the sample size of the data.
- getSampleSize() - Method in class edu.cmu.tetrad.search.score.ConditionalGaussianScore
-
Reurns the sample size of the data.
- getSampleSize() - Method in class edu.cmu.tetrad.search.score.DegenerateGaussianScore
- getSampleSize() - Method in class edu.cmu.tetrad.search.score.DiscreteBicScore
-
Returns the sample size.
- getSampleSize() - Method in class edu.cmu.tetrad.search.score.EbicScore
-
Returns the sample size.
- getSampleSize() - Method in class edu.cmu.tetrad.search.score.GicScores
- getSampleSize() - Method in class edu.cmu.tetrad.search.score.GraphScore
- getSampleSize() - Method in class edu.cmu.tetrad.search.score.ImagesScore
-
Returns the sample size from the first score.
- getSampleSize() - Method in class edu.cmu.tetrad.search.score.IndTestScore
- getSampleSize() - Method in class edu.cmu.tetrad.search.score.MvpScore
-
Returns the sample size.
- getSampleSize() - Method in class edu.cmu.tetrad.search.score.PoissonPriorScore
- getSampleSize() - Method in interface edu.cmu.tetrad.search.score.Score
-
The sample size of the data.
- getSampleSize() - Method in class edu.cmu.tetrad.search.score.SemBicScore
- getSampleSize() - Method in class edu.cmu.tetrad.search.score.ZsbScore
-
Returns the sample size.
- getSampleSize() - Method in class edu.cmu.tetrad.search.test.IndTestFisherZ
-
Returns the sample size.
- getSampleSize() - Method in class edu.cmu.tetrad.search.test.IndTestTrekSep
-
Returns the sample size.
- getSampleSize() - Method in class edu.cmu.tetrad.search.test.Kci
-
Returns the sample size.
- getSampleSize() - Method in class edu.cmu.tetrad.search.test.ScoreIndTest
-
Returns the sample size.
- getSampleSize() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestFisherZPercentIndependent
- getSampleSize() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestFisherZRecursive
- getSampleSize() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestPositiveCorr
- getSampleSize() - Method in class edu.cmu.tetrad.search.work_in_progress.MagSemBicScore
-
Returns the sample size.
- getSampleSize() - Method in class edu.cmu.tetrad.search.work_in_progress.MnlrScore
-
Returns the sample size.
- getSampleSize() - Method in class edu.cmu.tetrad.search.work_in_progress.SemBicScoreDeterministic
- getSampleSize() - Method in class edu.cmu.tetrad.sem.DagScorer
- getSampleSize() - Method in interface edu.cmu.tetrad.sem.ISemIm
- getSampleSize() - Method in interface edu.cmu.tetrad.sem.Scorer
- getSampleSize() - Method in class edu.cmu.tetrad.sem.SemIm
- getSampleSize() - Method in class edu.cmu.tetrad.sem.StandardizedSemIm
- getSampleSize() - Method in class edu.cmu.tetrad.study.performance.ComparisonParameters
- getScaledBHat(PermutationMatrixPair, double) - Static method in class edu.cmu.tetrad.search.IcaLingD
-
Returns the BHat matrix, permuted to the variable order of the original data and scaled so that the diagonal consists only of 1's.
- getScaledRocPlot() - Method in class edu.cmu.tetrad.util.RocCalculator
- getScore() - Method in class edu.cmu.tetrad.search.Boss
- getScore() - Method in class edu.cmu.tetrad.search.score.ScoredGraph
- getScore() - Method in class edu.cmu.tetrad.search.Sp
- getScore() - Method in interface edu.cmu.tetrad.search.SuborderSearch
-
The score being used.
- getScore() - Method in class edu.cmu.tetrad.search.test.ConditionalCorrelationIndependence
-
Returns the minimal scores value calculated by the method for the most recent independence check, less the cutoff so that negative scores correspond to independence.
- getScore() - Method in class edu.cmu.tetrad.search.test.IndependenceResult
- getScore() - Method in class edu.cmu.tetrad.search.utils.DagSepsets
-
Not implemented; required for an interface.
- getScore() - Method in interface edu.cmu.tetrad.search.utils.SepsetProducer
- getScore() - Method in class edu.cmu.tetrad.search.utils.SepsetsConservative
- getScore() - Method in class edu.cmu.tetrad.search.utils.SepsetsGreedy
- getScore() - Method in class edu.cmu.tetrad.search.utils.SepsetsPossibleMsep
- getScore() - Method in class edu.cmu.tetrad.search.utils.SepsetsSet
- getScore() - Method in class edu.cmu.tetrad.search.work_in_progress.HbsmsBeam.Score
- getScore() - Method in class edu.cmu.tetrad.search.work_in_progress.HbsmsGes.Score
- getScore() - Method in interface edu.cmu.tetrad.sem.ISemIm
- getScore() - Method in class edu.cmu.tetrad.sem.SemIm
-
The value of the maximum likelihood function for the getModel the model (Bollen 107).
- getScore() - Method in class edu.cmu.tetrad.study.performance.ComparisonParameters
- getScore(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.score.BdeuScore
- getScore(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.score.CciScore
- getScore(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.score.ConditionalGaussianBicScore
- getScore(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.score.DegenerateGaussianBicScore
- getScore(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.score.DiscreteBicScore
- getScore(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.score.EbicScore
- getScore(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.score.FisherZScore
- getScore(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.score.GicScores
- getScore(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.score.MagSemBicScore
- getScore(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.score.MSeparationScore
- getScore(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.score.MVPBicScore
- getScore(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.score.PoissonPriorScore
- getScore(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.score.PositiveCorrScore
- getScore(DataModel, Parameters) - Method in interface edu.cmu.tetrad.algcomparison.score.ScoreWrapper
-
Returns true iff x and y are independent conditional on z for the given data set.
- getScore(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.score.SemBicScore
- getScore(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.score.SemBicScoreDeterministic
- getScore(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.score.ZhangShenBoundScore
- getScore(Graph) - Method in class edu.cmu.tetrad.search.SvarFges
- getScore(Graph) - Method in class edu.cmu.tetrad.search.utils.FgesOrienter
- getScore(IndependenceResult) - Method in class edu.cmu.tetrad.search.test.Kci
-
Returns alpha - p.
- getScoreCount(Node, Set<Node>) - Method in class edu.cmu.tetrad.bayes.BdeMetricCache
-
This is just for testing the operation of the inner class and the map from nodes and parent sets to scores.
- getScoreFact(int, int[], List<Node>) - Static method in class edu.cmu.tetrad.search.utils.LogUtilsSearch
- getScoreFact(Node, List<Node>) - Static method in class edu.cmu.tetrad.search.utils.LogUtilsSearch
- getScoreParameters(Algorithm) - Static method in class edu.cmu.tetrad.util.Params
- getScoreWrapper() - Method in class edu.cmu.tetrad.algcomparison.algorithm.continuous.dag.DirectLingam
- getScoreWrapper() - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.Fask
- getScoreWrapper() - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FaskVote
- getScoreWrapper() - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.Images
- getScoreWrapper() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Boss
- getScoreWrapper() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Fges
- getScoreWrapper() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.FgesMb
- getScoreWrapper() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Grasp
- getScoreWrapper() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.PcLingam
- getScoreWrapper() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.RestrictedBoss
- getScoreWrapper() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Sp
- getScoreWrapper() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Bfci
- getScoreWrapper() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Gfci
- getScoreWrapper() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.GraspFci
- getScoreWrapper() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.SpFci
- getScoreWrapper() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.SvarGfci
- getScoreWrapper() - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pattern.Cstar
- getScoreWrapper() - Method in interface edu.cmu.tetrad.algcomparison.utils.UsesScoreWrapper
- getSd() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.AbstractNbComponent
-
Returns the standard deviation.
- getSe() - Method in class edu.cmu.tetrad.regression.RegressionResult
- getSecond() - Method in class edu.cmu.tetrad.graph.NodePair
- getSecond() - Method in class edu.cmu.tetrad.graph.OrderedPair
- getSecondEdge() - Method in class edu.cmu.tetrad.search.work_in_progress.HbsmsBeam.Move
- getSelectedIndices() - Method in class edu.cmu.tetrad.data.BoxDataSet
- getSelectedIndices() - Method in interface edu.cmu.tetrad.data.DataSet
- getSelectedIndices() - Method in class edu.cmu.tetrad.data.NumberObjectDataSet
- getSelectedModel() - Method in class edu.cmu.tetrad.data.DataModelList
- getSelectedVariableNames() - Method in class edu.cmu.tetrad.data.CorrelationMatrixOnTheFly
- getSelectedVariableNames() - Method in class edu.cmu.tetrad.data.CovarianceMatrix
- getSelectedVariableNames() - Method in class edu.cmu.tetrad.data.CovarianceMatrixOnTheFly
- getSelectedVariableNames() - Method in interface edu.cmu.tetrad.data.ICovarianceMatrix
- getSelectedVariables() - Method in class edu.cmu.tetrad.data.NumberObjectDataSet
- getSelection(int[], int[]) - Method in class edu.cmu.tetrad.data.CorrelationMatrix
- getSelection(int[], int[]) - Method in class edu.cmu.tetrad.data.CorrelationMatrixOnTheFly
- getSelection(int[], int[]) - Method in class edu.cmu.tetrad.data.CovarianceMatrix
- getSelection(int[], int[]) - Method in class edu.cmu.tetrad.data.CovarianceMatrixOnTheFly
- getSelection(int[], int[]) - Method in interface edu.cmu.tetrad.data.ICovarianceMatrix
- getSelection(int[], int[]) - Method in class edu.cmu.tetrad.util.Matrix
- getSelection(int[], int[]) - Method in class edu.cmu.tetrad.util.Matrix2
- getSelection(int[], int[], int[]) - Method in class edu.cmu.tetrad.data.CovarianceMatrixOnTheFly
- getSelfLoopCoef() - Method in class edu.cmu.tetrad.sem.LargeScaleSimulation
- getSelfLoopCoefs(DataSet) - Static method in class edu.cmu.tetrad.search.utils.TsUtils
- getSemIm() - Method in class edu.cmu.tetrad.search.work_in_progress.SampleVcpc
- getSemIm() - Method in class edu.cmu.tetrad.search.work_in_progress.SampleVcpcFast
- getSemIm() - Method in class edu.cmu.tetrad.sem.ParamConstraint
- getSemIm() - Method in class edu.cmu.tetrad.sem.SemEvidence
- getSemIm() - Method in class edu.cmu.tetrad.sem.SemProposition
- getSemIm() - Method in class edu.cmu.tetrad.sem.SemUpdater
- getSemIm(Element) - Static method in class edu.cmu.tetrad.sem.SemXmlParser
-
Takes an xml representation of a SEM IM and reinstantiates the IM
- getSemIms() - Method in class edu.cmu.tetrad.algcomparison.simulation.SemSimulation
- getSemPm() - Method in class edu.cmu.tetrad.search.work_in_progress.SampleVcpc
- getSemPm() - Method in class edu.cmu.tetrad.search.work_in_progress.SampleVcpcFast
- getSemPm() - Method in class edu.cmu.tetrad.sem.GeneralizedSemIm
- getSemPm() - Method in interface edu.cmu.tetrad.sem.ISemIm
- getSemPm() - Method in class edu.cmu.tetrad.sem.SemEstimator
- getSemPm() - Method in class edu.cmu.tetrad.sem.SemEstimatorGibbs
- getSemPm() - Method in class edu.cmu.tetrad.sem.SemIm
- getSemPm() - Method in class edu.cmu.tetrad.sem.StandardizedSemIm
- getSeparatedPairs() - Method in class edu.cmu.tetrad.search.work_in_progress.SepsetMapDci
- getSeparators(Node[], Map<Node, Set<Node>>) - Static method in class edu.cmu.tetrad.bayes.GraphTools
-
Calculate separator sets in clique tree.
- getSepset() - Method in class edu.cmu.tetrad.search.work_in_progress.Dci
-
Gets the resulting sepsets
- getSepset() - Method in class edu.cmu.tetrad.search.work_in_progress.Kpc
- getSepset(Node, Node) - Method in class edu.cmu.tetrad.graph.Dag
- getSepset(Node, Node) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
- getSepset(Node, Node) - Method in interface edu.cmu.tetrad.graph.Graph
- getSepset(Node, Node) - Method in class edu.cmu.tetrad.graph.LagGraph
- getSepset(Node, Node) - Method in class edu.cmu.tetrad.graph.Paths
- getSepset(Node, Node) - Method in class edu.cmu.tetrad.graph.SemGraph
- getSepset(Node, Node) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- getSepset(Node, Node) - Method in class edu.cmu.tetrad.search.utils.DagSepsets
-
Returns the list of sepset for {a, b}.
- getSepset(Node, Node) - Method in interface edu.cmu.tetrad.search.utils.SepsetProducer
- getSepset(Node, Node) - Method in class edu.cmu.tetrad.search.utils.SepsetsConservative
-
Pick out the sepset from among adj(i) or adj(k) with the highest p value.
- getSepset(Node, Node) - Method in class edu.cmu.tetrad.search.utils.SepsetsGreedy
-
Pick out the sepset from among adj(i) or adj(k) with the highest score value.
- getSepset(Node, Node) - Method in class edu.cmu.tetrad.search.utils.SepsetsPossibleMsep
-
Pick out the sepset from among adj(i) or adj(k) with the highest p value.
- getSepset(Node, Node) - Method in class edu.cmu.tetrad.search.utils.SepsetsSet
- getSepset(IndependenceTest, Node, Node) - Method in class edu.cmu.tetrad.search.utils.PossibleMsepFci
- getSepsets() - Method in class edu.cmu.tetrad.search.Cfci
-
Returns the map from nodes to their sepsets.
- getSepsets() - Method in class edu.cmu.tetrad.search.Cpc
-
Returns a map for x _||_ y | z1,..,zn from {x, y} to {z1,...,zn}.
- getSepsets() - Method in class edu.cmu.tetrad.search.Fas
-
Returns the sepsets that were discovered in the search.
- getSepsets() - Method in class edu.cmu.tetrad.search.Fasd
-
Returns the map of node pairs to sepsets from the search.
- getSepsets() - Method in class edu.cmu.tetrad.search.Fci
-
Returns the sepset map from FAS.
- getSepsets() - Method in class edu.cmu.tetrad.search.FciMax
-
Retrieves the map from variable pairs to sepsets from the FAS search.
- getSepsets() - Method in interface edu.cmu.tetrad.search.IFas
-
Returns the sepset map discovered during search--that is, the map from node pairs to the sepsets used in the search to remove the corresponding edges from the complete graph.
- getSepsets() - Method in class edu.cmu.tetrad.search.Pc
-
Returns the sepset map from the most recent search.
- getSepsets() - Method in class edu.cmu.tetrad.search.Pcd
- getSepsets() - Method in class edu.cmu.tetrad.search.Rfci
-
Returns the map from node pairs to sepsets found in search.
- getSepsets() - Method in class edu.cmu.tetrad.search.SvarFas
-
Returns a map for x _||_ y | Z from {x, y} to Z.
- getSepsets() - Method in class edu.cmu.tetrad.search.SvarFci
-
Returns the map from node pairs to sepsets.
- getSepsets() - Method in class edu.cmu.tetrad.search.utils.FciOrient
-
Returns the map from {x,y} to {z1,...,zn} for x _||_ y | z1,..,zn.
- getSepsets() - Method in class edu.cmu.tetrad.search.utils.SvarFciOrient
- getSepsets() - Method in class edu.cmu.tetrad.search.work_in_progress.Fas2
- getSepsets() - Method in class edu.cmu.tetrad.search.work_in_progress.Fas3
-
Returns the sepsets that were discovered in the search.
- getSepsets() - Method in class edu.cmu.tetrad.search.work_in_progress.FasFdr
-
Returns a map for x _||_ y | z1,...,zn of {x, y} to {z1,...,zn},
- getSepsetsLists(Node, Node, Node, IndependenceTest, int, boolean) - Method in class edu.cmu.tetrad.search.utils.SepsetsConservative
- getSession() - Method in class edu.cmu.tetrad.session.SimulationStudy
- getSet(Node, Node) - Method in class edu.cmu.tetrad.search.work_in_progress.SepsetMapDci
-
Retrieves the set of all condioning sets for {x, y} or null if no such set was ever set
- getSetType() - Method in class edu.cmu.tetrad.search.MarkovCheck
-
Returns type of conditioning sets to use in the Markov check.
- getShat() - Method in class edu.cmu.tetrad.sem.Ricf.RicfResult
- getShd() - Method in class edu.cmu.tetrad.graph.GraphUtils.GraphComparison
- getShortDescription() - Method in class edu.cmu.tetrad.util.ParamDescription
- getShuffledVariables() - Method in class edu.cmu.tetrad.search.utils.TeyssierScorer
- getSignature() - Method in interface edu.cmu.tetrad.calculator.expression.ExpressionDescriptor
- getSignature() - Method in interface edu.cmu.tetrad.calculator.expression.ExpressionSignature
- getSignificance() - Method in interface edu.cmu.tetrad.search.utils.TetradTest
- getSignificance() - Method in class edu.cmu.tetrad.search.utils.TetradTestContinuous
- getSignificance() - Method in class edu.cmu.tetrad.search.utils.TetradTestDiscrete
- getSignificance() - Method in class edu.cmu.tetrad.search.utils.TetradTestPopulation
- getSignificantModels() - Method in class edu.cmu.tetrad.search.work_in_progress.HbsmsGes
- getSimulation() - Method in class edu.cmu.tetrad.algcomparison.algorithm.ExternalAlgorithm
- getSimulationParams() - Method in class edu.cmu.tetrad.study.gene.tetradapp.model.BooleanGlassGeneIm
-
Returns the MeasurementSimulator.
- getSimulations() - Method in class edu.cmu.tetrad.algcomparison.simulation.Simulations
-
Returns the list of simulations.
- getSimulator() - Method in class edu.cmu.tetrad.study.gene.tetradapp.model.MeasurementSimulatorParams
- getSingleCategory(int) - Method in class edu.cmu.tetrad.bayes.Proposition
- getSize() - Method in class edu.cmu.tetrad.data.CorrelationMatrixOnTheFly
- getSize() - Method in class edu.cmu.tetrad.data.CovarianceMatrix
- getSize() - Method in class edu.cmu.tetrad.data.CovarianceMatrixOnTheFly
- getSize() - Method in interface edu.cmu.tetrad.data.ICovarianceMatrix
- getSize() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.akutsu.RevealOutputGraph
- getSize() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.reveal.RevealOutputGraph
- getSize() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.RevealOutputGraph
- getSize() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.BasicGraph
-
Returns the # nodes in this graph
- getSize() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.BasicMatrix
-
Returns # rows ( == # columns) of this matrix
- getSize() - Method in interface edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.OutputGraph
-
Returns the number of variables over which the graph is defined.
- getSize() - Method in class edu.cmu.tetrad.util.Point
- getSkeleton() - Method in class edu.cmu.tetrad.search.utils.TeyssierScorer
- getSoCalledPoissonShocks(int) - Method in class edu.cmu.tetrad.sem.LargeScaleSimulation
- getSolver() - Method in class edu.pitt.csb.mgm.EigenDecomposition
-
Gets a solver for finding the A × X = B solution in exact linear sense.
- getSortedMinEffects(Node) - Method in class edu.cmu.tetrad.search.Ida
-
Returns the minimum effects of X on Y for X in V \ {Y}, sorted downward by minimum effect
- getSourceGraph() - Method in interface edu.cmu.tetrad.data.KnowledgeBoxInput
- getSplitNames() - Method in class edu.cmu.tetrad.data.SplitCasesSpec
- getSquareRoot() - Method in class edu.pitt.csb.mgm.EigenDecomposition
-
Computes the square-root of the matrix.
- getSs() - Method in class edu.cmu.tetrad.search.work_in_progress.Glasso
- getStandardError(Parameter, int) - Method in interface edu.cmu.tetrad.sem.ISemIm
- getStandardError(Parameter, int) - Method in class edu.cmu.tetrad.sem.SemIm
- getStartIm() - Method in class edu.cmu.tetrad.sem.SemEstimatorGibbsParams
- getStartingValue() - Method in class edu.cmu.tetrad.sem.Parameter
- getStartsWithParameterEstimationInitializatonTemplate(String) - Method in class edu.cmu.tetrad.sem.GeneralizedSemPm
- getStartsWithParameterTemplate(String) - Method in class edu.cmu.tetrad.sem.GeneralizedSemPm
- getStatistics() - Method in class edu.cmu.tetrad.algcomparison.statistic.Statistics
-
Return the list of statistics.
- getStats() - Method in class edu.cmu.tetrad.search.work_in_progress.Ion
-
Summarizes time and hitting set time and size information for latex
- getStatsListTable(Graph, Graph) - Static method in class edu.cmu.tetrad.algcomparison.CompareTwoGraphs
-
Returns a string representing a table of statistics that can be printed.
- getStatsListTable(Graph, Graph, DataModel) - Static method in class edu.cmu.tetrad.algcomparison.CompareTwoGraphs
-
Returns a string representing a table of statistics that can be printed.
- getStdDev(Node, Matrix) - Method in interface edu.cmu.tetrad.sem.ISemIm
- getStdDev(Node, Matrix) - Method in class edu.cmu.tetrad.sem.SemIm
- getStdErrors() - Method in class edu.cmu.tetrad.sem.SemStdErrorEstimator
- getStdErrs() - Method in class edu.cmu.tetrad.regression.LogisticRegression.Result
-
The array of standard errors for the regression coefficients.
- getStep() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.GeneHistory
-
Returns the getModel step.
- getStepsGenerated() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.simulation.MeasurementSimulator
-
Returns the number of steps generated.
- getStepsGenerated() - Method in class edu.cmu.tetrad.study.gene.tetradapp.model.MeasurementSimulatorParams
- getStretch() - Method in class edu.cmu.tetrad.sem.SemEstimatorGibbsParams
- getString(String) - Method in class edu.cmu.tetrad.util.Parameters
-
Returns the string value of the given parameter, looking up its default in the ParamDescriptions map.
- getString(String, String) - Method in class edu.cmu.tetrad.util.Parameters
-
Returns the string value of the given parameter, using the given default.
- getStructurePrior() - Method in class edu.cmu.tetrad.search.score.BdeuScore
-
Returns the structure prior.
- getStructurePrior() - Method in class edu.cmu.tetrad.search.score.SemBicScore
- getStructurePrior() - Method in class edu.cmu.tetrad.study.performance.ComparisonParameters
- getStructurePrior(int) - Method in class edu.cmu.tetrad.search.score.MvpLikelihood
- getStructurePrior(int) - Method in class edu.cmu.tetrad.search.work_in_progress.MnlrLikelihood
-
Returns the structur prior for k parents.
- getSubCorrMatrix(String[]) - Method in class edu.cmu.tetrad.data.CorrelationMatrix
- getSubFunction(int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.BooleanGlassFunction
-
Returns the boolean function for the given factor.
- getSubmatrix(int[]) - Method in class edu.cmu.tetrad.data.CorrelationMatrixOnTheFly
- getSubmatrix(int[]) - Method in class edu.cmu.tetrad.data.CovarianceMatrix
- getSubmatrix(int[]) - Method in class edu.cmu.tetrad.data.CovarianceMatrixOnTheFly
- getSubmatrix(int[]) - Method in interface edu.cmu.tetrad.data.ICovarianceMatrix
- getSubmatrix(int[], int[]) - Method in class edu.cmu.tetrad.data.CovarianceMatrixOnTheFly
- getSubmatrix(String[]) - Method in class edu.cmu.tetrad.data.CorrelationMatrixOnTheFly
- getSubmatrix(String[]) - Method in class edu.cmu.tetrad.data.CovarianceMatrix
- getSubmatrix(String[]) - Method in class edu.cmu.tetrad.data.CovarianceMatrixOnTheFly
- getSubmatrix(String[]) - Method in interface edu.cmu.tetrad.data.ICovarianceMatrix
- getSubmatrix(List<String>) - Method in class edu.cmu.tetrad.data.CorrelationMatrixOnTheFly
- getSubmatrix(List<String>) - Method in class edu.cmu.tetrad.data.CovarianceMatrix
- getSubmatrix(List<String>) - Method in class edu.cmu.tetrad.data.CovarianceMatrixOnTheFly
- getSubmatrix(List<String>) - Method in interface edu.cmu.tetrad.data.ICovarianceMatrix
- getSubMatrix(int[], int[]) - Method in interface edu.cmu.tetrad.data.Covariances
-
Returns a submatrix of the covariance matrix for the given rows and columns.
- getSubMatrix(int[], int[]) - Method in class edu.cmu.tetrad.data.CovariancesDoubleForkJoin
- getSupportedEvents() - Method in class edu.cmu.tetrad.util.DefaultTetradLoggerConfig
- getSupportedEvents() - Method in class edu.cmu.tetrad.util.TetradLogger.EmptyConfig
- getSupportedEvents() - Method in interface edu.cmu.tetrad.util.TetradLoggerConfig
- getSupportLowerBound() - Method in class edu.cmu.tetrad.sem.EmpiricalCdf
- getSupportUpperBound() - Method in class edu.cmu.tetrad.sem.EmpiricalCdf
- getT() - Method in class edu.cmu.tetrad.regression.RegressionResult
- getTarget() - Method in class edu.cmu.tetrad.data.Histogram
- getTarget() - Method in class edu.cmu.tetrad.regression.LogisticRegression.Result
-
The target.
- getTargetNode() - Method in class edu.cmu.tetrad.data.Histogram
- getTargets() - Method in class edu.cmu.tetrad.search.PcMb
-
Return the targets of the most recent search.
- getTargetVariable() - Method in class edu.cmu.tetrad.classify.ClassifierBayesUpdaterDiscrete
- getTerm(int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.Polynomial
-
Returns the coefficient.
- getTest() - Method in class edu.cmu.tetrad.search.PcMb
-
Returns the test used in search.
- getTest(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.independence.BdeuTest
-
Returns the test.
- getTest(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.independence.CciTest
- getTest(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.independence.ChiSquare
- getTest(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.independence.ConditionalGaussianLRT
- getTest(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.independence.DegenerateGaussianLRT
- getTest(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.independence.DiscreteBicTest
- getTest(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.independence.FisherZ
- getTest(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.independence.GICScoreTests
- getTest(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.independence.Gsquare
- getTest(DataModel, Parameters) - Method in interface edu.cmu.tetrad.algcomparison.independence.IndependenceWrapper
-
Returns true iff x and y are independent conditional on z for the given data set.
- getTest(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.independence.Kci
- getTest(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.independence.MagSemBicTest
- getTest(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.independence.Mnlrlrt
- getTest(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.independence.MSeparationTest
- getTest(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.independence.MultinomialLogisticRegressionWald
- getTest(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.independence.Mvplrt
- getTest(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.independence.PoissonScoreTest
- getTest(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.independence.PositiveCorr
- getTest(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.independence.ProbabilisticTest
- getTest(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.independence.SemBicDTest
- getTest(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.independence.SemBicTest
- getTest(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.independence.UniformScatterTest
- getTestData() - Method in class edu.cmu.tetrad.classify.ClassifierBayesUpdaterDiscrete
-
Returns the test data being used.
- getTestDescriptions() - Static method in enum class edu.cmu.tetrad.search.utils.BpcTestType
- getTestParameters(Algorithm) - Static method in class edu.cmu.tetrad.util.Params
- getTestType() - Method in class edu.cmu.tetrad.search.utils.TetradTestContinuous
- getTetradLoggerConfig() - Method in class edu.cmu.tetrad.util.TetradLoggerEvent
- getTheta() - Method in class edu.pitt.csb.mgm.Mgm.MGMParams
- getThr() - Method in class edu.cmu.tetrad.search.work_in_progress.Glasso
- getTier(int) - Method in class edu.cmu.tetrad.data.Knowledge
- getTimeLagGraph() - Method in class edu.cmu.tetrad.graph.Dag
- getTimeLagGraph() - Method in class edu.cmu.tetrad.graph.EdgeListGraph
- getTimeLagGraph() - Method in interface edu.cmu.tetrad.graph.Graph
- getTimeLagGraph() - Method in class edu.cmu.tetrad.graph.LagGraph
- getTimeLagGraph() - Method in class edu.cmu.tetrad.graph.SemGraph
- getTimeLagGraph() - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- getTimes() - Method in class edu.cmu.tetrad.search.Boss
- getTimeSteps() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.simulation.MeasurementSimulator
-
Returns the time steps that will be stored in the simulation.
- getTimeSteps() - Method in class edu.cmu.tetrad.study.gene.tetradapp.model.MeasurementSimulatorParams
- getTn() - Method in class edu.cmu.tetrad.algcomparison.statistic.utils.AdjacencyConfusion
-
Returns the true negative count.
- getTn() - Method in class edu.cmu.tetrad.algcomparison.statistic.utils.ArrowConfusion
-
True negatives.
- getTn() - Method in class edu.cmu.tetrad.algcomparison.statistic.utils.BidirectedConfusion
- getTn() - Method in class edu.cmu.tetrad.algcomparison.statistic.utils.OrientationConfusion
- getTnc() - Method in class edu.cmu.tetrad.algcomparison.statistic.utils.ArrowConfusion
-
True Negatives for common edges.
- getTo() - Method in class edu.cmu.tetrad.data.KnowledgeEdge
- getToken() - Method in class edu.cmu.tetrad.calculator.expression.ConstantExpression
- getToken() - Method in class edu.cmu.tetrad.calculator.expression.EvaluationExpression
- getToken() - Method in interface edu.cmu.tetrad.calculator.expression.Expression
- getToken() - Method in interface edu.cmu.tetrad.calculator.expression.ExpressionDescriptor
- getToken() - Method in class edu.cmu.tetrad.calculator.expression.VariableExpression
- getTokenAt(int, int) - Method in class edu.cmu.tetrad.util.TextTable
- getTokenString() - Method in class edu.cmu.tetrad.calculator.parser.ExpressionLexer
- getTolerance() - Method in class edu.cmu.tetrad.sem.SemEstimatorGibbsParams
- getTotalUsableCases() - Method in class edu.cmu.tetrad.classify.ClassifierBayesUpdaterDiscrete
-
Returns the number of usable cases for the data.
- getToVariables() - Method in class edu.cmu.tetrad.data.KnowledgeGroup
- getTp() - Method in class edu.cmu.tetrad.algcomparison.statistic.utils.AdjacencyConfusion
-
Returns the true positive count.
- getTp() - Method in class edu.cmu.tetrad.algcomparison.statistic.utils.ArrowConfusion
-
True positives.
- getTp() - Method in class edu.cmu.tetrad.algcomparison.statistic.utils.BidirectedConfusion
- getTp() - Method in class edu.cmu.tetrad.algcomparison.statistic.utils.OrientationConfusion
- getTpc() - Method in class edu.cmu.tetrad.algcomparison.statistic.utils.ArrowConfusion
-
True positives for common edges.
- getTrial() - Method in class edu.cmu.tetrad.study.performance.ComparisonParameters
- getTriplesClassificationTypes() - Method in class edu.cmu.tetrad.graph.EdgeListGraph
- getTriplesClassificationTypes() - Method in interface edu.cmu.tetrad.graph.TripleClassifier
- getTriplesClassificationTypes() - Method in class edu.cmu.tetrad.graph.Underlines
- getTriplesLists(Node) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
- getTriplesLists(Node) - Method in interface edu.cmu.tetrad.graph.TripleClassifier
- getTriplesLists(Node) - Method in class edu.cmu.tetrad.graph.Underlines
- getTrueDag() - Method in class edu.cmu.tetrad.study.performance.ComparisonResult
- getTrueGraph(int) - Method in class edu.cmu.tetrad.algcomparison.simulation.BayesNetSimulation
-
Returns the true graph.
- getTrueGraph(int) - Method in class edu.cmu.tetrad.algcomparison.simulation.BooleanGlassSimulation
- getTrueGraph(int) - Method in class edu.cmu.tetrad.algcomparison.simulation.ConditionalGaussianSimulation
- getTrueGraph(int) - Method in class edu.cmu.tetrad.algcomparison.simulation.GeneralSemSimulation
- getTrueGraph(int) - Method in class edu.cmu.tetrad.algcomparison.simulation.GeneralSemSimulationSpecial1
- getTrueGraph(int) - Method in class edu.cmu.tetrad.algcomparison.simulation.LeeHastieSimulation
- getTrueGraph(int) - Method in class edu.cmu.tetrad.algcomparison.simulation.LinearFisherModel
- getTrueGraph(int) - Method in class edu.cmu.tetrad.algcomparison.simulation.LinearSineSimulation
- getTrueGraph(int) - Method in class edu.cmu.tetrad.algcomparison.simulation.NLSemSimulation
- getTrueGraph(int) - Method in class edu.cmu.tetrad.algcomparison.simulation.SemSimulation
- getTrueGraph(int) - Method in class edu.cmu.tetrad.algcomparison.simulation.SemThenDiscretize
- getTrueGraph(int) - Method in interface edu.cmu.tetrad.algcomparison.simulation.Simulation
-
Returns the true graph at the given index.
- getTrueGraph(int) - Method in class edu.cmu.tetrad.algcomparison.simulation.StandardizedSemSimulation
- getTrueGraph(int) - Method in class edu.cmu.tetrad.algcomparison.simulation.TimeSeriesSemSimulation
- getTrueGraph(int) - Method in class edu.cmu.tetrad.data.simulation.LoadContinuousDataAndGraphs
- getTrueGraph(int) - Method in class edu.cmu.tetrad.data.simulation.LoadContinuousDataAndSingleGraph
- getTrueGraph(int) - Method in class edu.cmu.tetrad.data.simulation.LoadContinuousDataSmithSim
- getTrueGraph(int) - Method in class edu.cmu.tetrad.data.simulation.LoadDataAndGraphs
- getTrueGraph(int) - Method in class edu.cmu.tetrad.data.simulation.LoadDataFromFileWithoutGraph
- getTrueInputs() - Method in class edu.cmu.tetrad.search.work_in_progress.DMSearch
- getTruePag() - Method in class edu.cmu.tetrad.search.utils.FciOrient
-
The true PAG if available.
- getTruePag() - Method in class edu.cmu.tetrad.search.utils.SvarFciOrient
-
The true PAG if available.
- getTruePag() - Method in class edu.cmu.tetrad.search.utils.TsDagToPag
- getTruncLL() - Method in class edu.cmu.tetrad.sem.SemIm
-
The negative of the log likelihood function for the getModel model, with the constant chopped off.
- getTValue(Parameter, int) - Method in interface edu.cmu.tetrad.sem.ISemIm
- getTValue(Parameter, int) - Method in class edu.cmu.tetrad.sem.SemIm
- getTwoCycleErrors(Graph, Graph) - Static method in class edu.cmu.tetrad.graph.GraphUtils
- getTwoCycleFn() - Method in class edu.cmu.tetrad.algcomparison.statistic.utils.ArrowConfusion
-
False negatives for two-cycles.
- getTwoCycleFn() - Method in class edu.cmu.tetrad.algcomparison.statistic.utils.TailConfusion
- getTwoCycleFp() - Method in class edu.cmu.tetrad.algcomparison.statistic.utils.ArrowConfusion
-
False positives for two-cycles.
- getTwoCycleFp() - Method in class edu.cmu.tetrad.algcomparison.statistic.utils.TailConfusion
- getTwoCycleTp() - Method in class edu.cmu.tetrad.algcomparison.statistic.utils.ArrowConfusion
-
Two positives for two-cycles.
- getTwoCycleTp() - Method in class edu.cmu.tetrad.algcomparison.statistic.utils.TailConfusion
- getType() - Method in class edu.cmu.tetrad.data.KnowledgeGroup
- getType() - Method in class edu.cmu.tetrad.search.work_in_progress.HbsmsBeam.Move
- getType() - Method in class edu.cmu.tetrad.sem.ParamConstraint
- getType() - Method in class edu.cmu.tetrad.sem.Parameter
- getType() - Method in class edu.cmu.tetrad.session.SessionEvent
- getUcCirclePaths(Node, Node, Graph) - Static method in class edu.cmu.tetrad.search.utils.FciOrient
-
Gets a list of every uncovered circle path between two nodes in the graph by iterating through the uncovered partially directed undirectedPaths and only keeping the circle undirectedPaths.
- getUcPdPaths(Node, Node, Graph) - Static method in class edu.cmu.tetrad.search.utils.FciOrient
-
Gets a list of every uncovered partially directed path between two nodes in the graph.
- getUncorrelatedShocks(int) - Method in class edu.cmu.tetrad.sem.LargeScaleSimulation
- getUnderlinedTriplesFromGraph(Node, Graph) - Static method in class edu.cmu.tetrad.graph.GraphUtils
- getUnderLines() - Method in class edu.cmu.tetrad.graph.Dag
- getUnderLines() - Method in class edu.cmu.tetrad.graph.EdgeListGraph
- getUnderLines() - Method in interface edu.cmu.tetrad.graph.Graph
- getUnderLines() - Method in class edu.cmu.tetrad.graph.LagGraph
- getUnderLines() - Method in class edu.cmu.tetrad.graph.SemGraph
- getUnderLines() - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- getUnderLines() - Method in class edu.cmu.tetrad.graph.Underlines
- getUnparsedExpression() - Method in class edu.cmu.tetrad.calculator.expression.Equation
- getUnshieldedColliders() - Method in class edu.cmu.tetrad.search.Pcd
- getUnshieldedColliders() - Method in class edu.cmu.tetrad.search.work_in_progress.Kpc
- getUnshieldedNoncolliders() - Method in class edu.cmu.tetrad.search.Pcd
- getUnshieldedNoncolliders() - Method in class edu.cmu.tetrad.search.work_in_progress.Kpc
- getUpdatedBayesIm() - Method in class edu.cmu.tetrad.bayes.ApproximateUpdater
- getUpdatedBayesIm() - Method in class edu.cmu.tetrad.bayes.CptInvariantMarginalCalculator
- getUpdatedBayesIm() - Method in class edu.cmu.tetrad.bayes.CptInvariantUpdater
- getUpdatedBayesIm() - Method in class edu.cmu.tetrad.bayes.Identifiability
-
The updated BayesIm.
- getUpdatedBayesIm() - Method in class edu.cmu.tetrad.bayes.JunctionTreeUpdater
- getUpdatedBayesIm() - Method in interface edu.cmu.tetrad.bayes.ManipulatingBayesUpdater
-
Returns the updated Bayes IM.
- getUpdatedBayesIm() - Method in class edu.cmu.tetrad.bayes.RowSummingExactUpdater
-
The updated BayesIm.
- getUpdatedSemIm() - Method in class edu.cmu.tetrad.sem.SemUpdater
-
See http://en.wikipedia.org/wiki/Multivariate_normal_distribution.
- getUpdateFunction() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.GeneHistory
-
Returns the update function.
- getUpperBoundDouble() - Method in class edu.cmu.tetrad.util.ParamDescription
- getUpperBoundInt() - Method in class edu.cmu.tetrad.util.ParamDescription
- getUpperBoundLong() - Method in class edu.cmu.tetrad.util.ParamDescription
- getV() - Method in class edu.pitt.csb.mgm.EigenDecomposition
-
Gets the matrix V of the decomposition.
- getValidOrder(List<Node>, boolean) - Method in class edu.cmu.tetrad.graph.Paths
-
Returns a valid causal order for either a DAG or a CPDAG.
- getValue() - Method in class edu.cmu.tetrad.sem.Mapping
- getValue() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.AbstractNbComponent
- getValue() - Method in interface edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.NbComponent
-
Returns the parents of this component.
- getValue(int) - Method in class edu.cmu.tetrad.sem.SemProposition
- getValue(int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.BooleanFunction
-
Returns the boolean value in a given row of the table.
- getValue(int) - Method in class edu.cmu.tetrad.util.Point
- getValue(int[]) - Method in class edu.cmu.tetrad.data.CellTable
- getValue(int[]) - Method in class edu.cmu.tetrad.util.MultiDimIntTable
- getValue(int, double[][]) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.BooleanGlassFunction
-
Returns the value of the function.
- getValue(int, double[][]) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.LinearFunction
-
Returns the value of the function.
- getValue(int, double[][]) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.PolynomialFunction
-
Returns the value of the function.
- getValue(int, double[][]) - Method in interface edu.cmu.tetrad.study.gene.tetrad.gene.history.UpdateFunction
-
Returns the value of the glass function for a given factor.
- getValue(int, int) - Method in class edu.cmu.tetrad.data.CorrelationMatrixOnTheFly
- getValue(int, int) - Method in class edu.cmu.tetrad.data.CovarianceMatrix
- getValue(int, int) - Method in class edu.cmu.tetrad.data.CovarianceMatrixOnTheFly
- getValue(int, int) - Method in interface edu.cmu.tetrad.data.ICovarianceMatrix
- getValue(int, int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.LTMatrix
-
Returns element (r,c)
- getValue(int, int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.LTMatrixF
-
Returns element (r,c)
- getValue(int, int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.Matrix
-
Returns the value stored at element (r,c)
- getValue(int, int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.MatrixF
-
Returns the value stored at element (r,c)
- getValue(int, int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.SymMatrix
-
Returns the value of element at (
row,col) - getValue(int, int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.SymMatrixF
-
Returns the value of element at (
row,col) - getValue(int, int) - Method in class edu.cmu.tetrad.util.IndexedMatrix
- getValue(int, int, int[]) - Method in class edu.cmu.tetrad.data.CovarianceMatrixOnTheFly
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.AdjacencyFn
-
Returns the value of the statistic, given the true graph and the estimated graph.
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.AdjacencyFp
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.AdjacencyFpr
-
Returns the value of the statistic, given the true graph and the estimated graph.
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.AdjacencyPrecision
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.AdjacencyRecall
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.AdjacencyTn
-
Returns the value of the statistic, given the true graph and the estimated graph.
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.AdjacencyTp
-
Returns the value of the statistic, given the true graph and the estimated graph.
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.AdjacencyTpr
-
Returns the value of the statistic, given the true graph and the estimated graph.
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.AncestorF1
-
Calculates the F1 statistic for adjacencies.
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.AncestorPrecision
-
Calculates the statistic.
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.AncestorRecall
-
Calculates the statistic.
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.AncestralPrecision
-
Calculates the statistic.
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.AncestralRecall
-
Calculates the statistic.
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.ArrowheadFn
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.ArrowheadFp
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.ArrowheadFpr
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.ArrowheadPrecision
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.ArrowheadPrecisionCommonEdges
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.ArrowheadRecall
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.ArrowheadRecallCommonEdges
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.ArrowheadTn
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.ArrowheadTp
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.AverageDegreeEst
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.AverageDegreeTrue
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.BicDiff
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.BicDiffPerRecord
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.BicEst
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.BicTrue
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.BidirectedEst
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.BidirectedFP
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.BidirectedLatentPrecision
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.BidirectedPrecision
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.BidirectedRecall
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.BidirectedTP
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.BidirectedTrue
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.CommonAncestorFalseNegativeBidirected
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.CommonAncestorFalsePositiveBidirected
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.CommonAncestorTruePositiveBidirected
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.CommonMeasuredAncestorRecallBidirected
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.CorrectSkeleton
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.DefiniteDirectedPathPrecision
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.DefiniteDirectedPathRecall
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.DensityEst
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.DensityTrue
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.ElapsedCpuTime
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.F1Adj
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.F1All
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.F1Arrow
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.FalseNegativesAdjacencies
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.FalsePositiveAdjacencies
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.FractionDependentUnderAlternative
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.FractionDependentUnderNull
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.GraphExactlyRight
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.LatentCommonAncestorFalseNegativeBidirected
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.LatentCommonAncestorFalsePositiveBidirected
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.LatentCommonAncestorRecallBidirected
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.LatentCommonAncestorTruePositiveBidirected
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.LegalPag
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.MarkovAdequacyScore
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.MathewsCorrAdj
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.MathewsCorrArrow
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.MaximalityCondition
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.NoAlmostCyclicPathsCondition
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.NoAlmostCyclicPathsInMagCondition
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.NoCyclicPathsCondition
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.NoCyclicPathsInMagCondition
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.NodesInCyclesPrecision
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.NodesInCyclesRecall
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.NonancestorPrecision
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.NonancestorRecall
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.NoSemidirectedF1
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.NoSemidirectedPrecision
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.NoSemidirectedRecall
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumAmbiguousTriples
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumberOfEdgesEst
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumberOfEdgesTrue
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumBidirectedBothNonancestorAncestor
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumBidirectedEdgesEst
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumBidirectedEdgesTrue
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumColoredDD
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumColoredNL
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumColoredPD
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumColoredPL
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumCommonMeasuredAncestorBidirected
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumCompatibleDefiniteDirectedEdgeAncestors
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumCompatibleDirectedEdgeConfounded
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumCompatibleDirectedEdgeNonAncestors
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumCompatibleEdges
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumCompatiblePossiblyDirectedEdgeAncestors
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumCompatiblePossiblyDirectedEdgeNonAncestors
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumCompatibleVisibleAncestors
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumCompatibleVisibleNonancestors
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumCorrectDDAncestors
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumCorrectPDAncestors
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumCorrectVisibleAncestors
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumDefinitelyDirected
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumDefinitelyNotDirectedPaths
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumDirectedEdgeAncestors
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumDirectedEdgeBnaMeasuredCounfounded
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumDirectedEdgeNoMeasureAncestors
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumDirectedEdgeNotAncNotRev
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumDirectedEdgeReversed
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumDirectedEdges
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumDirectedEdgeVisible
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumDirectedPathsEst
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumDirectedPathsTrue
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumDirectedShouldBePartiallyDirected
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumIncorrectDDAncestors
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumIncorrectPDAncestors
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumIncorrectVisibleAncestors
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumLatentCommonAncestorBidirected
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumNondirectedEdges
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumPartiallyOrientedEdges
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumPossiblyDirected
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumUndirectedEdges
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.NumVisibleEst
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.OrientationPrecision
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.OrientationRecall
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.PagAdjacencyPrecision
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.PagAdjacencyRecall
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.ParameterColumn
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.PercentAmbiguous
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.PercentBidirectedEdges
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.ProportionSemidirectedPathsNotReversedEst
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.ProportionSemidirectedPathsNotReversedTrue
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.PvalueDistanceToAlpha
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.PvalueUniformityUnderNull
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.SemidirectedPathF1
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.SemidirectedPrecision
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.SemidirectedRecall
- getValue(Graph, Graph, DataModel) - Method in interface edu.cmu.tetrad.algcomparison.statistic.Statistic
-
Returns the value of this statistic, given the true graph and the estimated graph.
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.StructuralHammingDistance
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.TailPrecision
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.TailRecall
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.TrueDagFalseNegativesArrows
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.TrueDagFalseNegativesTails
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.TrueDagFalsePositiveArrow
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.TrueDagFalsePositiveTails
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.TrueDagPrecisionArrow
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.TrueDagPrecisionTails
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.TrueDagRecallArrows
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.TrueDagRecallTails
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.TrueDagTruePositiveArrow
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.TrueDagTruePositiveDirectedPathNonancestor
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.TrueDagTruePositiveTails
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.TwoCycleFalseNegative
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.TwoCycleFalsePositive
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.TwoCyclePrecision
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.TwoCycleRecall
- getValue(Graph, Graph, DataModel) - Method in class edu.cmu.tetrad.algcomparison.statistic.TwoCycleTruePositive
- getValue(Node) - Method in class edu.cmu.tetrad.sem.SemProposition
- getValue(String) - Method in interface edu.cmu.tetrad.calculator.expression.Context
- getValue(String) - Method in class edu.cmu.tetrad.sem.GeneralizedSemEstimator.MyContext
- getValue(String) - Method in class edu.cmu.tetrad.util.TetradProperties
- getValueCombination(int, int[]) - Method in class edu.cmu.tetrad.session.SessionNode
- getValues(String) - Method in class edu.cmu.tetrad.util.Parameters
-
Returns the values set for the given parameter.
- getVariable() - Method in class edu.cmu.tetrad.calculator.expression.Equation
- getVariable() - Method in class edu.cmu.tetrad.calculator.expression.VariableExpression
- getVariable() - Method in class edu.cmu.tetrad.data.Discretizer.Discretization
- getVariable(int) - Method in class edu.cmu.tetrad.data.BoxDataSet
- getVariable(int) - Method in interface edu.cmu.tetrad.data.DataSet
- getVariable(int) - Method in class edu.cmu.tetrad.data.NumberObjectDataSet
- getVariable(int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.PolynomialTerm
-
Returns the index'th variable.
- getVariable(Node) - Method in class edu.cmu.tetrad.bayes.BayesPm
-
Returns the variable for the given node.
- getVariable(Node) - Method in class edu.cmu.tetrad.search.IndTestIod
-
Returns the variable associated with the given node in the graph.
- getVariable(Node) - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestSepsetDci
- getVariable(String) - Method in class edu.cmu.tetrad.algcomparison.score.BdeuScore
- getVariable(String) - Method in class edu.cmu.tetrad.algcomparison.score.CciScore
- getVariable(String) - Method in class edu.cmu.tetrad.algcomparison.score.ConditionalGaussianBicScore
- getVariable(String) - Method in class edu.cmu.tetrad.algcomparison.score.DegenerateGaussianBicScore
- getVariable(String) - Method in class edu.cmu.tetrad.algcomparison.score.DiscreteBicScore
- getVariable(String) - Method in class edu.cmu.tetrad.algcomparison.score.EbicScore
- getVariable(String) - Method in class edu.cmu.tetrad.algcomparison.score.FisherZScore
- getVariable(String) - Method in class edu.cmu.tetrad.algcomparison.score.GicScores
- getVariable(String) - Method in class edu.cmu.tetrad.algcomparison.score.MagSemBicScore
- getVariable(String) - Method in class edu.cmu.tetrad.algcomparison.score.MSeparationScore
- getVariable(String) - Method in class edu.cmu.tetrad.algcomparison.score.MVPBicScore
- getVariable(String) - Method in class edu.cmu.tetrad.algcomparison.score.PoissonPriorScore
- getVariable(String) - Method in class edu.cmu.tetrad.algcomparison.score.PositiveCorrScore
- getVariable(String) - Method in interface edu.cmu.tetrad.algcomparison.score.ScoreWrapper
-
Returns the variable with the given name.
- getVariable(String) - Method in class edu.cmu.tetrad.algcomparison.score.SemBicScore
- getVariable(String) - Method in class edu.cmu.tetrad.algcomparison.score.SemBicScoreDeterministic
- getVariable(String) - Method in class edu.cmu.tetrad.algcomparison.score.ZhangShenBoundScore
- getVariable(String) - Method in class edu.cmu.tetrad.bayes.BayesProperties
- getVariable(String) - Method in class edu.cmu.tetrad.bayes.Evidence
- getVariable(String) - Method in class edu.cmu.tetrad.data.BoxDataSet
- getVariable(String) - Method in class edu.cmu.tetrad.data.CorrelationMatrixOnTheFly
- getVariable(String) - Method in class edu.cmu.tetrad.data.CovarianceMatrix
- getVariable(String) - Method in class edu.cmu.tetrad.data.CovarianceMatrixOnTheFly
- getVariable(String) - Method in interface edu.cmu.tetrad.data.DataModel
- getVariable(String) - Method in class edu.cmu.tetrad.data.DataModelList
- getVariable(String) - Method in interface edu.cmu.tetrad.data.DataSet
- getVariable(String) - Method in interface edu.cmu.tetrad.data.ICovarianceMatrix
- getVariable(String) - Method in class edu.cmu.tetrad.data.IndependenceFacts
- getVariable(String) - Method in class edu.cmu.tetrad.data.NumberObjectDataSet
- getVariable(String) - Method in class edu.cmu.tetrad.data.TimeSeriesData
- getVariable(String) - Method in interface edu.cmu.tetrad.search.IndependenceTest
-
Returns The variable by the given name.
- getVariable(String) - Method in class edu.cmu.tetrad.search.IndTestIod
-
Returns the variable associated with the given name in the graph.
- getVariable(String) - Method in class edu.cmu.tetrad.search.MarkovCheck
-
Returns the variable with the given name.
- getVariable(String) - Method in interface edu.cmu.tetrad.search.score.Score
-
Returns the variable with the given name.
- getVariable(String) - Method in class edu.cmu.tetrad.search.test.IndTestFisherZ
-
Returns the variable with the given name.
- getVariable(String) - Method in class edu.cmu.tetrad.search.test.IndTestHsic
-
Returns the variable with the given name.
- getVariable(String) - Method in class edu.cmu.tetrad.search.test.IndTestIndependenceFacts
-
Returns the node with the given name.
- getVariable(String) - Method in class edu.cmu.tetrad.search.test.IndTestProbabilistic
- getVariable(String) - Method in class edu.cmu.tetrad.search.test.IndTestTrekSep
-
Returns the variable with the given name.
- getVariable(String) - Method in class edu.cmu.tetrad.search.test.Kci
-
Returns the variable by the given name.
- getVariable(String) - Method in class edu.cmu.tetrad.search.test.MsepTest
-
Returns the variable with the given name.
- getVariable(String) - Method in class edu.cmu.tetrad.search.test.ScoreIndTest
-
Returns the variable by the given name.
- getVariable(String) - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestFisherZRecursive
- getVariable(String) - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestPositiveCorr
- getVariable(String) - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestSepsetDci
- getVariable(String) - Method in class edu.cmu.tetrad.search.work_in_progress.ProbabilisticMapIndependence
- getVariableMeans() - Method in class edu.cmu.tetrad.sem.SemIm
- getVariableName(int) - Method in class edu.cmu.tetrad.data.CorrelationMatrixOnTheFly
- getVariableName(int) - Method in class edu.cmu.tetrad.data.CovarianceMatrix
- getVariableName(int) - Method in class edu.cmu.tetrad.data.CovarianceMatrixOnTheFly
- getVariableName(int) - Method in interface edu.cmu.tetrad.data.ICovarianceMatrix
- getVariableNames() - Method in interface edu.cmu.tetrad.bayes.BayesIm
-
Returns the list of variable names.
- getVariableNames() - Method in class edu.cmu.tetrad.bayes.BayesPm
-
Returns the variable names.
- getVariableNames() - Method in class edu.cmu.tetrad.bayes.DirichletBayesIm
- getVariableNames() - Method in class edu.cmu.tetrad.bayes.MlBayesIm
- getVariableNames() - Method in class edu.cmu.tetrad.bayes.MlBayesImObs
- getVariableNames() - Method in class edu.cmu.tetrad.bayes.UpdatedBayesIm
- getVariableNames() - Method in class edu.cmu.tetrad.data.BoxDataSet
- getVariableNames() - Method in class edu.cmu.tetrad.data.CorrelationMatrixOnTheFly
- getVariableNames() - Method in class edu.cmu.tetrad.data.CovarianceMatrix
- getVariableNames() - Method in class edu.cmu.tetrad.data.CovarianceMatrixOnTheFly
- getVariableNames() - Method in class edu.cmu.tetrad.data.DataModelList
- getVariableNames() - Method in interface edu.cmu.tetrad.data.DataSet
- getVariableNames() - Method in interface edu.cmu.tetrad.data.ICovarianceMatrix
- getVariableNames() - Method in class edu.cmu.tetrad.data.IndependenceFacts
- getVariableNames() - Method in class edu.cmu.tetrad.data.NumberObjectDataSet
- getVariableNames() - Method in class edu.cmu.tetrad.data.TimeSeriesData
- getVariableNames() - Method in interface edu.cmu.tetrad.data.VariableSource
-
Returns the variable names associated with this getVariableNames.
- getVariableNames() - Method in interface edu.cmu.tetrad.search.IndependenceTest
-
Returns the list of names for the variables in getNodesInEvidence.
- getVariableNode(String) - Method in class edu.cmu.tetrad.sem.SemIm
- getVariableNodes() - Method in class edu.cmu.tetrad.sem.GeneralizedSemPm
-
Returns the list of variable nodes--that is, node that are not error nodes.
- getVariableNodes() - Method in interface edu.cmu.tetrad.sem.ISemIm
- getVariableNodes() - Method in class edu.cmu.tetrad.sem.LargeScaleSimulation
- getVariableNodes() - Method in class edu.cmu.tetrad.sem.SemIm
-
The list of measured and latent nodes for the semPm.
- getVariableNodes() - Method in class edu.cmu.tetrad.sem.SemPm
- getVariableNodes() - Method in class edu.cmu.tetrad.sem.StandardizedSemIm
- getVariables() - Method in interface edu.cmu.tetrad.bayes.BayesIm
-
Returns the list of variables.
- getVariables() - Method in class edu.cmu.tetrad.bayes.BayesImProbs
- getVariables() - Method in class edu.cmu.tetrad.bayes.BayesPm
- getVariables() - Method in class edu.cmu.tetrad.bayes.CellTableProbs
- getVariables() - Method in class edu.cmu.tetrad.bayes.DataSetProbs
- getVariables() - Method in class edu.cmu.tetrad.bayes.DirichletBayesIm
- getVariables() - Method in class edu.cmu.tetrad.bayes.DirichletDataSetProbs
- getVariables() - Method in class edu.cmu.tetrad.bayes.IntAveDataSetProbs
- getVariables() - Method in class edu.cmu.tetrad.bayes.MlBayesIm
- getVariables() - Method in class edu.cmu.tetrad.bayes.MlBayesImObs
- getVariables() - Method in class edu.cmu.tetrad.bayes.StoredCellProbs
- getVariables() - Method in class edu.cmu.tetrad.bayes.StoredCellProbsObs
- getVariables() - Method in class edu.cmu.tetrad.bayes.UpdatedBayesIm
- getVariables() - Method in class edu.cmu.tetrad.data.BoxDataSet
- getVariables() - Method in class edu.cmu.tetrad.data.CorrelationMatrixOnTheFly
- getVariables() - Method in class edu.cmu.tetrad.data.CovarianceMatrix
- getVariables() - Method in class edu.cmu.tetrad.data.CovarianceMatrixOnTheFly
- getVariables() - Method in class edu.cmu.tetrad.data.DataModelList
- getVariables() - Method in interface edu.cmu.tetrad.data.DataSet
- getVariables() - Method in interface edu.cmu.tetrad.data.ICovarianceMatrix
- getVariables() - Method in class edu.cmu.tetrad.data.IndependenceFacts
- getVariables() - Method in class edu.cmu.tetrad.data.Knowledge
-
Get a list of variables.
- getVariables() - Method in class edu.cmu.tetrad.data.NumberObjectDataSet
- getVariables() - Method in class edu.cmu.tetrad.data.TimeSeriesData
- getVariables() - Method in interface edu.cmu.tetrad.data.VariableSource
-
Returns the list of variables associated with this object.
- getVariables() - Method in class edu.cmu.tetrad.search.Boss
- getVariables() - Method in class edu.cmu.tetrad.search.Grasp
-
Returns the variables.
- getVariables() - Method in interface edu.cmu.tetrad.search.IndependenceTest
- getVariables() - Method in class edu.cmu.tetrad.search.IndTestIod
-
Returns the list of TetradNodes over which this independence checker is capable of determining independence relations-- that is, all the variables in the given graph or the given data set.
- getVariables() - Method in class edu.cmu.tetrad.search.MarkovCheck
-
Returns the variables of the independence test.
- getVariables() - Method in class edu.cmu.tetrad.search.PermutationSearch
-
Returns the variables.
- getVariables() - Method in class edu.cmu.tetrad.search.score.BdeScore
-
Returns the variables of the dataset.
- getVariables() - Method in class edu.cmu.tetrad.search.score.BdeuScore
-
Returns the variables of the data.
- getVariables() - Method in class edu.cmu.tetrad.search.score.ConditionalGaussianScore
-
Returns the variables of the data.
- getVariables() - Method in class edu.cmu.tetrad.search.score.DegenerateGaussianScore
- getVariables() - Method in class edu.cmu.tetrad.search.score.DiscreteBicScore
-
Returns the variables.
- getVariables() - Method in class edu.cmu.tetrad.search.score.EbicScore
-
Returns the variables for this score.
- getVariables() - Method in class edu.cmu.tetrad.search.score.GicScores
- getVariables() - Method in class edu.cmu.tetrad.search.score.GraphScore
-
Returns the list of variables.
- getVariables() - Method in class edu.cmu.tetrad.search.score.ImagesScore
-
Returns the variables.
- getVariables() - Method in class edu.cmu.tetrad.search.score.IndTestScore
- getVariables() - Method in class edu.cmu.tetrad.search.score.MvpScore
- getVariables() - Method in class edu.cmu.tetrad.search.score.PoissonPriorScore
- getVariables() - Method in interface edu.cmu.tetrad.search.score.Score
-
The variables of the score.
- getVariables() - Method in class edu.cmu.tetrad.search.score.SemBicScore
- getVariables() - Method in class edu.cmu.tetrad.search.score.ZsbScore
-
Returns the variables.
- getVariables() - Method in class edu.cmu.tetrad.search.Sp
- getVariables() - Method in interface edu.cmu.tetrad.search.SuborderSearch
-
The list of all variables, in order.
- getVariables() - Method in class edu.cmu.tetrad.search.test.IndTestChiSquare
-
Returns the list of variables over which this independence checker is capable of determining independence relations-- that is, all the variables in the given graph or the given data set.
- getVariables() - Method in class edu.cmu.tetrad.search.test.IndTestConditionalCorrelation
-
Returns the list of variables over which this independence checker is capable of determining independence relations-- that is, all the variables in the given graph or the given data set.
- getVariables() - Method in class edu.cmu.tetrad.search.test.IndTestConditionalGaussianLrt
-
Returns the list of variables over which this independence checker is capable of determining independence relations.
- getVariables() - Method in class edu.cmu.tetrad.search.test.IndTestDegenerateGaussianLrt
-
Returns the list of searchVariables over which this independence checker is capable of determinining independence relations.
- getVariables() - Method in class edu.cmu.tetrad.search.test.IndTestFisherZ
-
Returns the list of variables over which this independence checker is capable of determinine independence relations-- that is, all the variables in the given graph or the given data set.
- getVariables() - Method in class edu.cmu.tetrad.search.test.IndTestFisherZConcatenateResiduals
- getVariables() - Method in class edu.cmu.tetrad.search.test.IndTestFisherZFisherPValue
-
Returns the list of variables over which this independence checker is capable of determinine independence relations-- that is, all the variables in the given graph or the given data set.
- getVariables() - Method in class edu.cmu.tetrad.search.test.IndTestGSquare
-
Return the list of variables over which this independence checker is capable of determinine independence relations-- that is, all the variables in the given graph or the given data set.
- getVariables() - Method in class edu.cmu.tetrad.search.test.IndTestHsic
-
Returns the list of variables over which this independence checker is capable of determinine independence relations-- that is, all the variables in the given graph or the given data set.
- getVariables() - Method in class edu.cmu.tetrad.search.test.IndTestIndependenceFacts
-
Returns the list of variables for the facts.
- getVariables() - Method in class edu.cmu.tetrad.search.test.IndTestMulti
- getVariables() - Method in class edu.cmu.tetrad.search.test.IndTestMvpLrt
-
Returns the list of searchVariables over which this independence checker is capable of determinining independence relations.
- getVariables() - Method in class edu.cmu.tetrad.search.test.IndTestProbabilistic
- getVariables() - Method in class edu.cmu.tetrad.search.test.IndTestRegression
- getVariables() - Method in class edu.cmu.tetrad.search.test.IndTestTrekSep
-
Returns the list of variables over which this independence checker is capable of determinine independence relations-- that is, all the variables in the given graph or the given data set.
- getVariables() - Method in class edu.cmu.tetrad.search.test.Kci
-
Returns the list of variables over which this independence checker is capable of determinining independence relations.
- getVariables() - Method in class edu.cmu.tetrad.search.test.MsepTest
-
Return the list of TetradNodes over which this independence checker is capable of determinine independence relations-- that is, all the variables in the given graph or the given data set.
- getVariables() - Method in class edu.cmu.tetrad.search.test.ScoreIndTest
-
Returns the list of variables over which this independence checker is capable of determinining independence relations.
- getVariables() - Method in class edu.cmu.tetrad.search.utils.Bes
-
Returns the variables being searched over.
- getVariables() - Method in class edu.cmu.tetrad.search.utils.BesPermutation
-
Returns the variables.
- getVariables() - Method in class edu.cmu.tetrad.search.utils.DagSepsets
-
Returns the nodes in the DAG.
- getVariables() - Method in class edu.cmu.tetrad.search.utils.DeltaSextadTest
-
Returns the variables of the data being used.
- getVariables() - Method in class edu.cmu.tetrad.search.utils.GrowShrinkTree
- getVariables() - Method in interface edu.cmu.tetrad.search.utils.SepsetProducer
- getVariables() - Method in class edu.cmu.tetrad.search.utils.SepsetsConservative
- getVariables() - Method in class edu.cmu.tetrad.search.utils.SepsetsGreedy
- getVariables() - Method in class edu.cmu.tetrad.search.utils.SepsetsPossibleMsep
- getVariables() - Method in class edu.cmu.tetrad.search.utils.SepsetsSet
- getVariables() - Method in interface edu.cmu.tetrad.search.utils.TetradTest
- getVariables() - Method in class edu.cmu.tetrad.search.utils.TetradTestContinuous
- getVariables() - Method in class edu.cmu.tetrad.search.utils.TetradTestDiscrete
- getVariables() - Method in class edu.cmu.tetrad.search.utils.TetradTestPopulation
- getVariables() - Method in class edu.cmu.tetrad.search.work_in_progress.GraspTol
- getVariables() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestCramerT
- getVariables() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestFisherZGeneralizedInverse
- getVariables() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestFisherZPercentIndependent
- getVariables() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestFisherZRecursive
- getVariables() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestMixedMultipleTTest
- getVariables() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestMnlrLr
- getVariables() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestMultinomialLogisticRegression
- getVariables() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestPositiveCorr
- getVariables() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestSepsetDci
- getVariables() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestUniformScatter
- getVariables() - Method in class edu.cmu.tetrad.search.work_in_progress.MagSemBicScore
-
Returns the list of variables.
- getVariables() - Method in class edu.cmu.tetrad.search.work_in_progress.MnlrScore
-
Returns the variables.
- getVariables() - Method in class edu.cmu.tetrad.search.work_in_progress.OtherPermAlgs
- getVariables() - Method in class edu.cmu.tetrad.search.work_in_progress.ProbabilisticMapIndependence
- getVariables() - Method in class edu.cmu.tetrad.search.work_in_progress.SemBicScoreDeterministic
- getVariables() - Method in class edu.cmu.tetrad.sem.DagScorer
- getVariables() - Method in interface edu.cmu.tetrad.sem.Scorer
- getVariables() - Method in class edu.pitt.csb.mgm.IndTestMultinomialLogisticRegressionWald
- getVariablesInEvidence() - Method in class edu.cmu.tetrad.bayes.Evidence
- getVariablesNotInTiers() - Method in class edu.cmu.tetrad.data.Knowledge
- getVariableSource() - Method in class edu.cmu.tetrad.bayes.Evidence
- getVariableSource() - Method in class edu.cmu.tetrad.bayes.Proposition
- getVariablesTemplate() - Method in class edu.cmu.tetrad.sem.GeneralizedSemPm
- getVariableValues(int) - Method in class edu.cmu.tetrad.bayes.StoredCellProbsObs
- getVariableVectors() - Method in class edu.cmu.tetrad.data.VerticalDoubleDataBox
- getVariableVectors() - Method in class edu.cmu.tetrad.data.VerticalIntDataBox
- getVariance(Node, Matrix) - Method in interface edu.cmu.tetrad.sem.ISemIm
- getVariance(Node, Matrix) - Method in class edu.cmu.tetrad.sem.SemIm
- getVarianceParameter(Node) - Method in class edu.cmu.tetrad.sem.SemPm
-
Return the parameter for the variance of the error term for the given node, which is the variance of the node if the node is an error term, and the variance of the node's error term if not.
- getVarNames() - Method in interface edu.cmu.tetrad.search.utils.TetradTest
- getVarNames() - Method in class edu.cmu.tetrad.search.utils.TetradTestContinuous
- getVarNames() - Method in class edu.cmu.tetrad.search.utils.TetradTestDiscrete
- getVarNames() - Method in class edu.cmu.tetrad.search.utils.TetradTestPopulation
- getVarNode(Node) - Method in class edu.cmu.tetrad.graph.SemGraph
- getVarRy(int, int[], Matrix, ICovarianceMatrix, boolean) - Static method in class edu.cmu.tetrad.search.score.SemBicScore
- getVarsNotInCluster(List<String>) - Method in class edu.cmu.tetrad.data.Clusters
- getVarsPerInd() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.LagGraphParams
- getVarsPerInd() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ManualLagGraphParams
-
Returns the number of variables per individual.
- getVector() - Method in class edu.cmu.tetrad.util.Point
- getVicinity(Edge, int) - Method in class edu.cmu.tetrad.simulation.Vicinity
- getVT() - Method in class edu.pitt.csb.mgm.EigenDecomposition
-
Gets the transpose of the matrix V of the decomposition.
- getW() - Method in class edu.cmu.tetrad.search.FastIca.IcaResult
- getWeight(Statistic) - Method in class edu.cmu.tetrad.algcomparison.statistic.Statistics
-
The utility weight for the statistic.
- getWidth() - Method in class edu.cmu.tetrad.search.test.ConditionalCorrelationIndependence
-
Returns the kernel width.
- getWidth() - Method in class edu.cmu.tetrad.search.test.IndTestConditionalCorrelation
-
Returns the kernel width.
- getWrappedScore() - Method in class edu.cmu.tetrad.search.test.ScoreIndTest
-
Returns the score object that this test wraps.
- getWThreshold() - Method in class edu.cmu.tetrad.search.Dagma
- getWwi() - Method in class edu.cmu.tetrad.search.work_in_progress.Glasso.Result
- getX() - Method in class edu.cmu.tetrad.graph.IndependenceFact
- getX() - Method in class edu.cmu.tetrad.graph.Triple
- getX() - Method in class edu.cmu.tetrad.search.FastIca.IcaResult
- getX() - Method in class edu.cmu.tetrad.search.utils.GraphoidAxioms.GraphoidIndFact
- getX() - Method in class edu.cmu.tetrad.util.PointXy
- getxMeans() - Method in class edu.cmu.tetrad.regression.LogisticRegression.Result
-
THe array of means.
- getXSquare() - Method in class edu.cmu.tetrad.search.test.ChiSquareTest.Result
- getxStdDevs() - Method in class edu.cmu.tetrad.regression.LogisticRegression.Result
-
The array of standard devs.
- getY() - Method in class edu.cmu.tetrad.graph.IndependenceFact
- getY() - Method in class edu.cmu.tetrad.graph.Triple
- getY() - Method in class edu.cmu.tetrad.search.utils.GraphoidAxioms.GraphoidIndFact
- getY() - Method in class edu.cmu.tetrad.util.PointXy
- getZ() - Method in class edu.cmu.tetrad.graph.IndependenceFact
- getZ() - Method in class edu.cmu.tetrad.graph.Triple
- getZ() - Method in class edu.cmu.tetrad.search.utils.GraphoidAxioms.GraphoidIndFact
- getZForAlpha(double) - Static method in class edu.cmu.tetrad.util.StatUtils
- Gfci - Class in edu.cmu.tetrad.algcomparison.algorithm.oracle.pag
-
GFCI.
- Gfci() - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Gfci
- Gfci(IndependenceWrapper, ScoreWrapper) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Gfci
- GFci - Class in edu.cmu.tetrad.search
-
Implements a modification of FCI that started by running the FGES algorithm and then fixes that result to be correct for latent variables models.
- GFci(IndependenceTest, Score) - Constructor for class edu.cmu.tetrad.search.GFci
-
Constructs a new GFci algorithm with the given independence test and score.
- GFCI - Enum constant in enum class edu.cmu.tetrad.study.performance.ComparisonParameters.Algorithm
- gfciExtraEdgeRemovalStep(Graph, Graph, List<Node>, SepsetProducer) - Static method in class edu.cmu.tetrad.graph.GraphUtils
-
The extra edge removal step for GFCI.
- gfciR0(Graph, Graph, SepsetProducer, Knowledge) - Static method in class edu.cmu.tetrad.graph.GraphUtils
- GIC2 - Enum constant in enum class edu.cmu.tetrad.search.score.GicScores.RuleType
- GIC5 - Enum constant in enum class edu.cmu.tetrad.search.score.GicScores.RuleType
- GIC6 - Enum constant in enum class edu.cmu.tetrad.search.score.GicScores.RuleType
- GicScores - Class in edu.cmu.tetrad.algcomparison.score
-
Wrapper for linear, Gaussian Extended BIC score (Chen and Chen).
- GicScores - Class in edu.cmu.tetrad.search.score
-
Implements scores motivated by the Generalized Information Criterion (GIC) approach as given in Kim et al.
- GicScores() - Constructor for class edu.cmu.tetrad.algcomparison.score.GicScores
- GicScores(DataSet, boolean) - Constructor for class edu.cmu.tetrad.search.score.GicScores
-
Constructs the score using a covariance matrix.
- GicScores(ICovarianceMatrix) - Constructor for class edu.cmu.tetrad.search.score.GicScores
-
Constructs the score using a covariance matrix.
- GicScores.RuleType - Enum Class in edu.cmu.tetrad.search.score
-
Gives the options for the rules to use for calculating the scores.
- GICScoreTests - Class in edu.cmu.tetrad.algcomparison.independence
-
Wrapper for Fisher Z test.
- GICScoreTests() - Constructor for class edu.cmu.tetrad.algcomparison.independence.GICScoreTests
- ginverse() - Method in class edu.cmu.tetrad.util.Matrix
- ginverse() - Method in class edu.cmu.tetrad.util.Matrix2
- Glasso - Class in edu.cmu.tetrad.algcomparison.algorithm.other
-
GLASSO.
- Glasso - Class in edu.cmu.tetrad.search.work_in_progress
-
A translation from Tibshirani's 2008 Fortran implementation of glasso.
- Glasso() - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.other.Glasso
- Glasso(Matrix) - Constructor for class edu.cmu.tetrad.search.work_in_progress.Glasso
- Glasso.Result - Class in edu.cmu.tetrad.search.work_in_progress
-
Return value of the algorithm.
- goToBookmark() - Method in class edu.cmu.tetrad.search.utils.TeyssierScorer
-
Retries the bookmark with key = Integer.MIN_VALUE and removes the bookmark.
- goToBookmark(int) - Method in class edu.cmu.tetrad.search.utils.TeyssierScorer
-
Retrieves the bookmarked state for index 'key' and removes that bookmark.
- grabLayout(List<Node>) - Static method in class edu.cmu.tetrad.graph.GraphSaveLoadUtils
- Graph - Enum constant in enum class edu.cmu.tetrad.data.DataType
- Graph - Interface in edu.cmu.tetrad.graph
-
Implements a graph capable of storing edges of type N1 *-# N2 where * and # are endpoints of type Endpoint.
- graphAttributesToText(Graph, String) - Static method in class edu.cmu.tetrad.graph.GraphUtils
- GraphChange - Class in edu.cmu.tetrad.search.work_in_progress
-
Provides s a data structure created mainly for use in the ION search algorithm.
- GraphChange() - Constructor for class edu.cmu.tetrad.search.work_in_progress.GraphChange
-
Default constructor, holds no changes.
- GraphChange(GraphChange) - Constructor for class edu.cmu.tetrad.search.work_in_progress.GraphChange
-
Copy constructor.
- graphComparison(Graph, Graph, PrintStream) - Static method in class edu.cmu.tetrad.search.utils.GraphSearchUtils
- GraphComparison(int, int, int, int, int, int, double, double, double, double, int, List<Edge>, List<Edge>, int[][]) - Constructor for class edu.cmu.tetrad.graph.GraphUtils.GraphComparison
- graphEdgesToText(Graph, String) - Static method in class edu.cmu.tetrad.graph.GraphUtils
- GraphExactlyRight - Class in edu.cmu.tetrad.algcomparison.statistic
-
Return a 1 if the graph is exactly right, 0 otherwise.
- GraphExactlyRight() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.GraphExactlyRight
- graphFromMGM() - Method in class edu.pitt.csb.mgm.Mgm
-
Converts MGM object to Graph object with edges if edge parameters are non-zero.
- GraphInitializer - Interface in edu.cmu.tetrad.study.gene.tetrad.gene.history
-
Instantiations of this interface know how to randomize lag graphs in particular ways.
- GraphInPag - Class in edu.cmu.tetrad.search.utils
-
Contains methods which can be used to determine whether a directed graph is in the equivalence class determined by the given PAG.
- GraphInPag() - Constructor for class edu.cmu.tetrad.search.utils.GraphInPag
- graphInPagStep0(Graph, Graph) - Static method in class edu.cmu.tetrad.search.utils.GraphInPag
-
This method implements step (1) of the definition.
- graphInPagStep1(Graph, Graph) - Static method in class edu.cmu.tetrad.search.utils.GraphInPag
- graphInPagStep2(Graph, Graph) - Static method in class edu.cmu.tetrad.search.utils.GraphInPag
- graphInPagStep3(Graph, Graph) - Static method in class edu.cmu.tetrad.search.utils.GraphInPag
- graphInPagStep4(Graph, Graph) - Static method in class edu.cmu.tetrad.search.utils.GraphInPag
- graphInPagStep5(Graph, Graph) - Static method in class edu.cmu.tetrad.search.utils.GraphInPag
- graphName - Variable in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.BasicGraph
-
Name of this graph object
- GraphNode - Class in edu.cmu.tetrad.graph
-
Implements a basic node in a graph--that is, a node that is not itself a variable.
- GraphNode(GraphNode) - Constructor for class edu.cmu.tetrad.graph.GraphNode
-
Copy constructor.
- GraphNode(String) - Constructor for class edu.cmu.tetrad.graph.GraphNode
-
Constructs a new Tetrad node with the given (non-null) string.
- graphNodeAttributesToText(Graph, String, char) - Static method in class edu.cmu.tetrad.graph.GraphUtils
- graphNodesToText(Graph, String, char) - Static method in class edu.cmu.tetrad.graph.GraphUtils
- graphoid() - Method in class edu.cmu.tetrad.search.utils.GraphoidAxioms
-
Checks whether teh IM is a semigraphoid.
- GraphoidAxioms - Class in edu.cmu.tetrad.search.utils
-
Checks the graphoid axioms for a set of Independence Model statements.
- GraphoidAxioms(Set<GraphoidAxioms.GraphoidIndFact>, List<Node>) - Constructor for class edu.cmu.tetrad.search.utils.GraphoidAxioms
-
Constructor.
- GraphoidAxioms(Set<GraphoidAxioms.GraphoidIndFact>, List<Node>, Map<GraphoidAxioms.GraphoidIndFact, String>) - Constructor for class edu.cmu.tetrad.search.utils.GraphoidAxioms
-
Constructor.
- GraphoidAxioms.GraphoidIndFact - Class in edu.cmu.tetrad.search.utils
-
Represents a graphoid independence fact--i.e., a fact in a general independence model (IM) X _||_Y | Z.
- GraphoidIndFact(Set<Node>, Set<Node>, Set<Node>) - Constructor for class edu.cmu.tetrad.search.utils.GraphoidAxioms.GraphoidIndFact
- GraphRandomizer - Interface in edu.cmu.tetrad.study.gene.tetrad.gene.history
-
Instantiations of this interface know how to randomize update graphs in particular ways.
- graphRMatrixTxt(Graph) - Static method in class edu.cmu.tetrad.graph.GraphSaveLoadUtils
- GraphSampling - Class in edu.cmu.tetrad.util
-
A utility for computing frequency probabilities.
- GraphSaveLoadUtils - Class in edu.cmu.tetrad.graph
-
Methods to load or save graphs.
- GraphSaveLoadUtils() - Constructor for class edu.cmu.tetrad.graph.GraphSaveLoadUtils
- GraphScore - Class in edu.cmu.tetrad.search.score
-
Implements a pscudo-"score" that implmenets implements Chickering and Meek's (2002) locally consistent score criterion.
- GraphScore(IndependenceFacts) - Constructor for class edu.cmu.tetrad.search.score.GraphScore
-
Constructor.
- GraphScore(Graph) - Constructor for class edu.cmu.tetrad.search.score.GraphScore
-
Constructor
- GraphSearchUtils - Class in edu.cmu.tetrad.search.utils
-
Provides some graph utilities for search algorithm.
- GraphSearchUtils() - Constructor for class edu.cmu.tetrad.search.utils.GraphSearchUtils
- GraphSearchUtils.CpcTripleType - Enum Class in edu.cmu.tetrad.search.utils
-
Gives the options for triple type for a conservative unshielded collider orientation, which may be "collider" or "noncollider" or "ambiguous".
- GraphSearchUtils.LegalMagRet - Class in edu.cmu.tetrad.search.utils
-
Stores a result for checking whether a graph is a legal MAG--(a) whether it is (a boolean), and (b) the reason why it is not, if it is not (a String).
- GraphSearchUtils.LegalPagRet - Class in edu.cmu.tetrad.search.utils
-
Stores a result for checking whether a graph is a legal PAG--(a) whether it is (a boolean), and (b) the reason why it is not, if it is not (a String).
- graphToDot(Graph) - Static method in class edu.cmu.tetrad.graph.GraphSaveLoadUtils
-
Converts a graph to a Graphviz .dot file
- graphToDot(Graph, File) - Static method in class edu.cmu.tetrad.graph.GraphSaveLoadUtils
- graphToLagGraph(Graph, int) - Static method in class edu.cmu.tetrad.search.utils.TsUtils
- graphToLavaan(Graph) - Static method in class edu.cmu.tetrad.graph.GraphSaveLoadUtils
- graphToMatrix(Graph) - Static method in class edu.pitt.csb.mgm.MixedUtils
- graphToMatrix(Graph, double, double) - Static method in class edu.pitt.csb.mgm.MixedUtils
- GraphTools - Class in edu.cmu.tetrad.bayes
-
A utility class containing graph function from graph theory.
- graphToPcalg(Graph) - Static method in class edu.cmu.tetrad.graph.GraphSaveLoadUtils
- graphToText(Graph, boolean) - Static method in class edu.cmu.tetrad.graph.GraphUtils
- graphToXml(Graph) - Static method in class edu.cmu.tetrad.graph.GraphSaveLoadUtils
- GraphTransforms - Class in edu.cmu.tetrad.graph
-
Transformations that transform one graph into another.
- GraphTransforms() - Constructor for class edu.cmu.tetrad.graph.GraphTransforms
- GraphTypes - Class in edu.cmu.tetrad.algcomparison.graph
-
Jun 4, 2019 3:21:47 PM
- GraphUtils - Class in edu.cmu.tetrad.graph
-
Basic graph utilities.
- GraphUtils() - Constructor for class edu.cmu.tetrad.graph.GraphUtils
- GraphUtils.GraphComparison - Class in edu.cmu.tetrad.graph
- GraphUtils.TwoCycleErrors - Class in edu.cmu.tetrad.graph
- GraphWithPValue(Graph, double) - Constructor for class edu.cmu.tetrad.search.work_in_progress.HbsmsGes.GraphWithPValue
- grasp(TeyssierScorer) - Method in class edu.cmu.tetrad.search.work_in_progress.GraspTol
- Grasp - Class in edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag
-
GRaSP (Greedy Relaxations of Sparsest Permutation)
- Grasp - Class in edu.cmu.tetrad.search
-
Implements the GRaSP algorithms, which uses a certain procedure to search in the space of permutations of variables for ones that imply CPDAGs that are especially close to the CPDAG of the true model.
- Grasp() - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Grasp
- Grasp(IndependenceTest) - Constructor for class edu.cmu.tetrad.search.Grasp
-
Constructor for a test.
- Grasp(IndependenceTest, Score) - Constructor for class edu.cmu.tetrad.search.Grasp
-
Constructor that takes both a test and a score; only one is used-- the parameter setting will decide which.
- Grasp(Score) - Constructor for class edu.cmu.tetrad.search.Grasp
-
Constructor for a score.
- Grasp(IndependenceWrapper, ScoreWrapper) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Grasp
- GRASP - Enum constant in enum class edu.cmu.tetrad.search.Fask.AdjacencyMethod
- GRASP_ALG - Static variable in class edu.cmu.tetrad.util.Params
- GRASP_BREAK_AFTER_IMPROVEMENT - Static variable in class edu.cmu.tetrad.util.Params
- GRASP_CHECK_COVERING - Static variable in class edu.cmu.tetrad.util.Params
- GRASP_DEPTH - Static variable in class edu.cmu.tetrad.util.Params
- GRASP_FORWARD_TUCK_ONLY - Static variable in class edu.cmu.tetrad.util.Params
- GRASP_NONSINGULAR_DEPTH - Static variable in class edu.cmu.tetrad.util.Params
- GRASP_ORDERED_ALG - Static variable in class edu.cmu.tetrad.util.Params
- GRASP_SINGULAR_DEPTH - Static variable in class edu.cmu.tetrad.util.Params
- GRASP_TOLERANCE_DEPTH - Static variable in class edu.cmu.tetrad.util.Params
- GRASP_USE_RASKUTTI_UHLER - Static variable in class edu.cmu.tetrad.util.Params
- GRASP_USE_SCORE - Static variable in class edu.cmu.tetrad.util.Params
- GRASP_USE_VP_SCORING - Static variable in class edu.cmu.tetrad.util.Params
- GraspFci - Class in edu.cmu.tetrad.algcomparison.algorithm.oracle.pag
-
Adjusts GFCI to use a permutation algorithm (such as BOSS-Tuck) to do the initial steps of finding adjacencies and unshielded colliders.
- GraspFci - Class in edu.cmu.tetrad.search
-
Uses GRaSP in place of FGES for the initial step in the GFCI algorithm.
- GraspFci() - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.GraspFci
- GraspFci(IndependenceWrapper, ScoreWrapper) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.GraspFci
- GraspFci(IndependenceTest, Score) - Constructor for class edu.cmu.tetrad.search.GraspFci
- GraspTol - Class in edu.cmu.tetrad.search.work_in_progress
-
Implements the GRASP algorithms, with various execution flags.
- GraspTol(IndependenceTest) - Constructor for class edu.cmu.tetrad.search.work_in_progress.GraspTol
- GraspTol(IndependenceTest, Score) - Constructor for class edu.cmu.tetrad.search.work_in_progress.GraspTol
- GraspTol(Score) - Constructor for class edu.cmu.tetrad.search.work_in_progress.GraspTol
- GraspTol(List<Node>) - Constructor for class edu.cmu.tetrad.search.work_in_progress.GraspTol
- GrowShrink - Class in edu.cmu.tetrad.search
-
Implements the Grow-Shrink algorithm of Margaritis and Thrun, a simple yet correct and useful Markov blanket search.
- GrowShrink(IndependenceTest) - Constructor for class edu.cmu.tetrad.search.GrowShrink
-
Constructs a new search.
- GrowShrinkTree - Class in edu.cmu.tetrad.search.utils
- GrowShrinkTree(Score, Map<Node, Integer>, Node) - Constructor for class edu.cmu.tetrad.search.utils.GrowShrinkTree
- GSP - Enum constant in enum class edu.cmu.tetrad.search.work_in_progress.OtherPermAlgs.Method
- Gsquare - Class in edu.cmu.tetrad.algcomparison.independence
-
Wrapper for Fisher Z test.
- Gsquare() - Constructor for class edu.cmu.tetrad.algcomparison.independence.Gsquare
- GSquareTest - Class in edu.cmu.tetrad.search.test
-
Performs conditional independence tests of discrete data using the G Square method.
- GSquareTest(DataSet, double) - Constructor for class edu.cmu.tetrad.search.test.GSquareTest
-
Constructor
- GSquareTest.Result - Class in edu.cmu.tetrad.search.test
-
Stores the parameters of the result returned by the G Square test and its p-value.
- GT - Static variable in class edu.cmu.tetrad.sem.ParamConstraintType
-
A "greater than" constraint.
- GUARANTEE_ACYCLIC - Static variable in class edu.cmu.tetrad.util.Params
- GUARANTEE_IID - Static variable in class edu.cmu.tetrad.util.Params
H
- handlesUnmeasuredConfounder(Class) - Method in class edu.cmu.tetrad.annotation.AlgorithmAnnotations
-
Checks if the algorithm handles unmeasured confounders.
- HandleyConvert - Class in edu.cmu.tetrad.study.gene.tetrad.gene.util
-
The purpose of this little converter is to convert "effect" files into "cause" (BasicLagGraph) files.
- HandleyConvert() - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.util.HandleyConvert
- hasComplexEigenvalues() - Method in class edu.pitt.csb.mgm.EigenDecomposition
-
Returns whether the calculated eigen values are complex or real.
- hasDimensions(double[][], int, int) - Static method in class edu.cmu.tetrad.util.MatrixUtils
- hashCode() - Method in class edu.cmu.tetrad.bayes.Evidence
- hashCode() - Method in class edu.cmu.tetrad.bayes.Manipulation
- hashCode() - Method in class edu.cmu.tetrad.bayes.Proposition
- hashCode() - Method in class edu.cmu.tetrad.data.Clusters
-
Computes a hashcode.
- hashCode() - Method in class edu.cmu.tetrad.data.ContinuousVariable
- hashCode() - Method in class edu.cmu.tetrad.data.DataModelList
- hashCode() - Method in class edu.cmu.tetrad.data.DiscreteVariable
- hashCode() - Method in class edu.cmu.tetrad.data.Knowledge
-
Computes a hashcode.
- hashCode() - Method in class edu.cmu.tetrad.data.KnowledgeEdge
- hashCode() - Method in class edu.cmu.tetrad.data.KnowledgeGroup
-
Computes a hashcode.
- hashCode() - Method in class edu.cmu.tetrad.graph.Edge
- hashCode() - Method in class edu.cmu.tetrad.graph.EdgeListGraph
- hashCode() - Method in class edu.cmu.tetrad.graph.GraphNode
- hashCode() - Method in class edu.cmu.tetrad.graph.IndependenceFact
- hashCode() - Method in interface edu.cmu.tetrad.graph.Node
-
Removes a property change listener.
- hashCode() - Method in class edu.cmu.tetrad.graph.NodePair
- hashCode() - Method in class edu.cmu.tetrad.graph.OrderedPair
- hashCode() - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- hashCode() - Method in class edu.cmu.tetrad.graph.Triple
- hashCode() - Method in class edu.cmu.tetrad.search.score.ScoredGraph
- hashCode() - Method in class edu.cmu.tetrad.search.utils.GraphoidAxioms.GraphoidIndFact
- hashCode() - Method in class edu.cmu.tetrad.search.utils.Sextad
- hashCode() - Method in class edu.cmu.tetrad.search.utils.Tetrad
- hashCode() - Method in class edu.cmu.tetrad.search.work_in_progress.GraphChange
- hashCode() - Method in class edu.cmu.tetrad.search.work_in_progress.HbsmsGes.GraphWithPValue
- hashCode() - Method in class edu.cmu.tetrad.search.work_in_progress.Sextad
- hashCode() - Method in class edu.cmu.tetrad.sem.ParameterPair
- hashCode() - Method in class edu.cmu.tetrad.sem.SemEvidence
- hashCode() - Method in class edu.cmu.tetrad.sem.SemManipulation
- hashCode() - Method in class edu.cmu.tetrad.sem.SemProposition
- hashCode() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.LaggedFactor
-
Probably should recheck this later.
- hashCode() - Method in class edu.cmu.tetrad.util.Version
- HasKnowledge - Interface in edu.cmu.tetrad.algcomparison.utils
-
Stores a knowledge object.
- hasMoreTokens() - Method in class edu.cmu.tetrad.data.RegexTokenizer
- hasNext() - Method in class edu.cmu.tetrad.search.utils.DagInCpcagIterator
- hasNext() - Method in class edu.cmu.tetrad.search.utils.DagIterator
- hasNext() - Method in class edu.cmu.tetrad.util.CombinationIterator
- hasNoEvidence(int) - Method in class edu.cmu.tetrad.bayes.Evidence
- HasParameters - Interface in edu.cmu.tetrad.algcomparison.utils
-
Tags a gadget as having parameters
- HasParameterValues - Interface in edu.cmu.tetrad.algcomparison.utils
-
Tags a gadget as having parameters values.
- HasPenaltyDiscount - Interface in edu.cmu.tetrad.search.utils
-
Provides an interface for an algorithm can can get/set a value for penalty disoucnt.
- Hbsms - Interface in edu.cmu.tetrad.search.work_in_progress
-
Interface for Bff (Heuristic Best Significant Model Search) algorithm.
- HbsmsBeam - Class in edu.cmu.tetrad.search.work_in_progress
-
Heuristic Best Significant Model Search using a beam search.
- HbsmsBeam(Graph, CovarianceMatrix, Knowledge) - Constructor for class edu.cmu.tetrad.search.work_in_progress.HbsmsBeam
- HbsmsBeam(Graph, DataSet, Knowledge) - Constructor for class edu.cmu.tetrad.search.work_in_progress.HbsmsBeam
- HbsmsBeam.Move - Class in edu.cmu.tetrad.search.work_in_progress
- HbsmsBeam.Move.Type - Enum Class in edu.cmu.tetrad.search.work_in_progress
- HbsmsBeam.Score - Class in edu.cmu.tetrad.search.work_in_progress
- HbsmsGes - Class in edu.cmu.tetrad.search.work_in_progress
-
Heuristic Best Significant Model Search using the GES algorithm.
- HbsmsGes(Graph, DataSet) - Constructor for class edu.cmu.tetrad.search.work_in_progress.HbsmsGes
- HbsmsGes.GraphWithPValue - Class in edu.cmu.tetrad.search.work_in_progress
- HbsmsGes.Score - Class in edu.cmu.tetrad.search.work_in_progress
- HEURISTIC_1 - Enum constant in enum class edu.cmu.tetrad.search.utils.PcCommon.PcHeuristicType
- HEURISTIC_2 - Enum constant in enum class edu.cmu.tetrad.search.utils.PcCommon.PcHeuristicType
- HEURISTIC_3 - Enum constant in enum class edu.cmu.tetrad.search.utils.PcCommon.PcHeuristicType
- Highest - Enum constant in enum class edu.pitt.dbmi.algo.resampling.ResamplingEdgeEnsemble
- histogram(List<Double>, double[]) - Static method in class edu.cmu.tetrad.simulation.GdistanceUtils
- Histogram - Class in edu.cmu.tetrad.data
-
Model for a conditional histogram for mixed continuous and discrete variables.
- Histogram(DataSet, String, boolean) - Constructor for class edu.cmu.tetrad.data.Histogram
-
This histogram is for variables in a particular data set.
- Hsim - Class in edu.cmu.tetrad.simulation
- Hsim(Dag, Set<Node>, DataSet) - Constructor for class edu.cmu.tetrad.simulation.Hsim
- HsimAutoC - Class in edu.cmu.tetrad.simulation
-
Created by Erich on 3/28/2016.
- HsimAutoC(DataSet) - Constructor for class edu.cmu.tetrad.simulation.HsimAutoC
- HsimAutoC(String, char) - Constructor for class edu.cmu.tetrad.simulation.HsimAutoC
- HsimAutoRun - Class in edu.cmu.tetrad.simulation
-
Created by Erich on 3/28/2016.
- HsimAutoRun(DataSet) - Constructor for class edu.cmu.tetrad.simulation.HsimAutoRun
- HsimAutoRun(String, char) - Constructor for class edu.cmu.tetrad.simulation.HsimAutoRun
- HsimCompareRepeat - Class in edu.cmu.tetrad.simulation
-
Created by Erich on 7/15/2016.
- HsimCompareRepeat() - Constructor for class edu.cmu.tetrad.simulation.HsimCompareRepeat
- HsimContinuous - Class in edu.cmu.tetrad.simulation
-
Created by Erich on 3/27/2016.
- HsimContinuous(Dag, Set<Node>, DataSet) - Constructor for class edu.cmu.tetrad.simulation.HsimContinuous
- HsimEvalFromData - Class in edu.cmu.tetrad.simulation
-
Created by ekummerfeld on 1/26/2017.
- HsimEvalFromData() - Constructor for class edu.cmu.tetrad.simulation.HsimEvalFromData
- HsimRepeatAC - Class in edu.cmu.tetrad.simulation
-
Created by Erich on 4/29/2016.
- HsimRepeatAC(DataSet) - Constructor for class edu.cmu.tetrad.simulation.HsimRepeatAC
- HsimRepeatAC(String, char) - Constructor for class edu.cmu.tetrad.simulation.HsimRepeatAC
- HsimRepeatAuto - Class in edu.cmu.tetrad.simulation
-
Created by Erich on 3/28/2016.
- HsimRepeatAuto() - Constructor for class edu.cmu.tetrad.simulation.HsimRepeatAuto
- HsimRepeatAutoRun - Class in edu.cmu.tetrad.simulation
-
Created by Erich on 4/29/2016.
- HsimRepeatAutoRun(DataSet) - Constructor for class edu.cmu.tetrad.simulation.HsimRepeatAutoRun
- HsimRepeatAutoRun(String, char) - Constructor for class edu.cmu.tetrad.simulation.HsimRepeatAutoRun
- HsimRobustCompare - Class in edu.cmu.tetrad.simulation
-
generate data from random graph, generated from parameters.
- HsimRobustCompare() - Constructor for class edu.cmu.tetrad.simulation.HsimRobustCompare
- HsimRun - Class in edu.cmu.tetrad.simulation
-
Created by Erich on 3/28/2016.
- HsimRun() - Constructor for class edu.cmu.tetrad.simulation.HsimRun
- HsimSchedule - Class in edu.cmu.tetrad.simulation
-
Created by Erich on 4/29/2016.
- HsimSchedule() - Constructor for class edu.cmu.tetrad.simulation.HsimSchedule
- HsimStudy - Class in edu.cmu.tetrad.simulation
-
Created by Erich on 3/28/2016.
- HsimStudy() - Constructor for class edu.cmu.tetrad.simulation.HsimStudy
- HsimStudyAuto - Class in edu.cmu.tetrad.simulation
-
Created by Erich on 3/28/2016.
- HsimStudyAuto() - Constructor for class edu.cmu.tetrad.simulation.HsimStudyAuto
- HsimUtils - Class in edu.cmu.tetrad.simulation
-
Created by Erich on 4/22/2016.
- HsimUtils() - Constructor for class edu.cmu.tetrad.simulation.HsimUtils
- HungarianAlgorithm - Class in edu.cmu.tetrad.search.utils
-
Provides an implemetation of the Kuhn–Munkres assignment algorithm of the year 1957.
- HungarianAlgorithm(double[][]) - Constructor for class edu.cmu.tetrad.search.utils.HungarianAlgorithm
-
Trying to find lowest-cost assignment.
- hungarianDiagonal(Matrix) - Static method in class edu.cmu.tetrad.search.IcaLingD
-
Finds a column permutation of the W matrix that maximizes the sum of 1 / |Wii| for diagonal elements Wii in W.
- hybridsimulate() - Method in class edu.cmu.tetrad.simulation.Hsim
- hybridsimulate() - Method in class edu.cmu.tetrad.simulation.HsimContinuous
I
- IA - Static variable in class edu.cmu.tetrad.util.Params
- Iamb - Class in edu.cmu.tetrad.search.work_in_progress
-
Implements IAMB.
- Iamb(IndependenceTest) - Constructor for class edu.cmu.tetrad.search.work_in_progress.Iamb
-
Constructs a new search.
- IambnPc - Class in edu.cmu.tetrad.search.work_in_progress
-
Created by IntelliJ IDEA.
- IambnPc(IndependenceTest) - Constructor for class edu.cmu.tetrad.search.work_in_progress.IambnPc
-
Constructs a new search.
- ICA_ALGORITHM - Static variable in class edu.cmu.tetrad.util.Params
- ICA_FUNCTION - Static variable in class edu.cmu.tetrad.util.Params
- IcaLingam - Class in edu.cmu.tetrad.algcomparison.algorithm.continuous.dag
-
LiNGAM.
- IcaLingam - Class in edu.cmu.tetrad.search
-
Implements the ICA-LiNGAM algorithm.
- IcaLingam() - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.continuous.dag.IcaLingam
- IcaLingam() - Constructor for class edu.cmu.tetrad.search.IcaLingam
-
Constructor..
- IcaLingD - Class in edu.cmu.tetrad.algcomparison.algorithm.continuous.dag
-
LiNG-D.
- IcaLingD - Class in edu.cmu.tetrad.search
-
Implements the ICA-LiNG-D algorithm as well as a number of ancillary methods for LiNG-D and LiNGAM.
- IcaLingD() - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.continuous.dag.IcaLingD
- IcaLingD() - Constructor for class edu.cmu.tetrad.search.IcaLingD
-
Constructor.
- IcaResult(Matrix, Matrix, Matrix, Matrix) - Constructor for class edu.cmu.tetrad.search.FastIca.IcaResult
- ICovarianceMatrix - Interface in edu.cmu.tetrad.data
-
Interface for covariance matrices.
- Ida - Class in edu.cmu.tetrad.search
-
Implements the IDA algorithm.
- Ida(DataSet, Graph, List<Node>) - Constructor for class edu.cmu.tetrad.search.Ida
-
Constructor.
- Ida.NodeEffects - Class in edu.cmu.tetrad.search
-
Gives a list of nodes (parents or children) and corresponding minimum effects for the IDA algorithm.
- IDataReader - Interface in edu.cmu.tetrad.data
-
Identifies a class that can read data from a file.
- Identifiability - Class in edu.cmu.tetrad.bayes
-
Identifiability, based on RowSummingExactUpdater
- Identifiability(BayesIm) - Constructor for class edu.cmu.tetrad.bayes.Identifiability
-
Constructs a new updater for the given Bayes net.
- Identifiability(BayesIm, Evidence) - Constructor for class edu.cmu.tetrad.bayes.Identifiability
- identity(int) - Static method in class edu.cmu.tetrad.util.Matrix
- identity(int) - Static method in class edu.cmu.tetrad.util.Matrix2
- identity(int) - Static method in class edu.cmu.tetrad.util.MatrixUtils
- identity(int) - Static method in class edu.cmu.tetrad.util.TetradAlgebra
- IFas - Interface in edu.cmu.tetrad.search
-
Gives an interface for fast adjacency searches (i.e., PC adjacency searches).
- igamma(double, double) - Static method in class edu.cmu.tetrad.util.StatUtils
-
Calculates the incomplete gamma function for two doubles
- IGCI - Enum constant in enum class edu.cmu.tetrad.search.Lofs.Rule
- IGraphSearch - Interface in edu.cmu.tetrad.search
-
Gives an interface for a search method that searches and returns a graph.
- Im - Interface in edu.cmu.tetrad.util
-
Tagging interface for instantiated models.
- Images - Class in edu.cmu.tetrad.algcomparison.algorithm.multi
-
Wraps the IMaGES algorithm for continuous variables.
- Images() - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.multi.Images
- Images(ScoreWrapper) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.multi.Images
- IMAGES_META_ALG - Static variable in class edu.cmu.tetrad.util.Params
- ImagesScore - Class in edu.cmu.tetrad.search.score
-
Implements a score to average results over multiple scores.
- ImagesScore(List<Score>) - Constructor for class edu.cmu.tetrad.search.score.ImagesScore
-
Constructs an IMaGES score using the given list of individual scores.
- IMbSearch - Interface in edu.cmu.tetrad.search
-
Gives an interface for Markov blanket searches.
- impliedCovar(Matrix, Matrix) - Static method in class edu.cmu.tetrad.util.MatrixUtils
- impliedCovar2(Matrix, Matrix) - Static method in class edu.cmu.tetrad.util.MatrixUtils
- INCLUDE_NEGATIVE_COEFS - Static variable in class edu.cmu.tetrad.util.Params
- INCLUDE_NEGATIVE_SKEWS_FOR_BETA - Static variable in class edu.cmu.tetrad.util.Params
- INCLUDE_POSITIVE_COEFS - Static variable in class edu.cmu.tetrad.util.Params
- INCLUDE_POSITIVE_SKEWS_FOR_BETA - Static variable in class edu.cmu.tetrad.util.Params
- INCLUDE_STRUCTURE_MODEL - Static variable in class edu.cmu.tetrad.util.Params
- incompleteCholeskyGramMatrix(List<Kernel>, DataSet, List<Node>, double) - Static method in class edu.cmu.tetrad.search.utils.KernelUtils
-
Approximates Gram matrix using incomplete Cholesky factorization
- increment(int[], int) - Method in class edu.cmu.tetrad.util.MultiDimIntTable
-
Increments the value at the given coordinates by the specified amount, returning the new value.
- independenceFact(Node, Node, Set<Node>) - Static method in class edu.cmu.tetrad.search.utils.LogUtilsSearch
- IndependenceFact - Class in edu.cmu.tetrad.graph
-
Stores a triple (x, y, z) of nodes.
- IndependenceFact(Node, Node, Node...) - Constructor for class edu.cmu.tetrad.graph.IndependenceFact
- IndependenceFact(Node, Node, Set<Node>) - Constructor for class edu.cmu.tetrad.graph.IndependenceFact
- independenceFactMsg(Node, Node, Set<Node>, double) - Static method in class edu.cmu.tetrad.search.utils.LogUtilsSearch
- IndependenceFacts - Class in edu.cmu.tetrad.data
-
Stores a list of independence facts.
- IndependenceFacts() - Constructor for class edu.cmu.tetrad.data.IndependenceFacts
- IndependenceFacts(IndependenceFacts) - Constructor for class edu.cmu.tetrad.data.IndependenceFacts
- IndependenceFacts(Graph) - Constructor for class edu.cmu.tetrad.data.IndependenceFacts
- IndependenceResult - Class in edu.cmu.tetrad.search.test
-
Stores a single conditional independence result, e.g., whether X _||_ Y | Z1,..,Zn holds or does not, and the p-value of the test.
- IndependenceResult(IndependenceFact, boolean, double, double) - Constructor for class edu.cmu.tetrad.search.test.IndependenceResult
-
Constructor.
- IndependenceTest - Interface in edu.cmu.tetrad.search
-
Gives an interface that can be implemented by classes that do conditional independence testing.
- IndependenceTestDescriptions - Class in edu.cmu.tetrad.util
-
May 14, 2019 11:25:02 AM
- IndependenceWrapper - Interface in edu.cmu.tetrad.algcomparison.independence
-
Interface that algorithm must implement.
- independent - Enum constant in enum class edu.pitt.dbmi.algo.bayesian.constraint.inference.BCInference.OP
- INDEPENDENT - Enum constant in enum class edu.pitt.dbmi.algo.bayesian.constraint.inference.BCCausalInference.OP
- index(Node) - Method in class edu.cmu.tetrad.search.utils.TeyssierScorer
-
Return the index of v in the current permutation.
- IndexedConnectivity - Class in edu.cmu.tetrad.study.gene.tetrad.gene.history
-
Stores a "shapshot" of the indexedConnectivity of a lag graph, using indices rather than Strings to refer to factors.
- IndexedConnectivity(LagGraph) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.history.IndexedConnectivity
-
Constructs an indexed connectivity for the getModel state of the given lag graph, including all edges.
- IndexedConnectivity(LagGraph, boolean) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.history.IndexedConnectivity
-
Constructs an indexed connectivity for the getModel state of the given lag graph.
- IndexedLagGraph - Class in edu.cmu.tetrad.study.gene.tetrad.gene.history
-
Stores a "shapshot" of the indexedLagGraph of a lag graph, using indices rather than Strings to refer to factors.
- IndexedLagGraph(LagGraph) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.history.IndexedLagGraph
-
Constructs an indexed lag graph for the getModel state of the given lag graph, including all edges.
- IndexedLagGraph(LagGraph, boolean) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.history.IndexedLagGraph
-
Constructs an indexed lag graph for the getModel state of the given lag graph.
- IndexedMatrix - Class in edu.cmu.tetrad.util
-
Indexed matrix.
- IndexedMatrix(double[][]) - Constructor for class edu.cmu.tetrad.util.IndexedMatrix
-
Constructs a new IndexedMatrix for the given matrix.
- IndexedParent - Class in edu.cmu.tetrad.study.gene.tetrad.gene.history
-
Holds an ordered pair (index, lag) to represent a causal parent of a factor, where the factor at the given index is independently known.
- IndexedParent(int, int) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.history.IndexedParent
-
Constructs a new index parent.
- Indicator - Class in edu.cmu.tetrad.util.dist
-
Created by IntelliJ IDEA.
- IndTestChiSquare - Class in edu.cmu.tetrad.search.test
-
Checks the conditional independence X _||_ Y | S, where S is a set of discrete variable, and X and Y are discrete variable not in S, by applying a conditional Chi Square test.
- IndTestChiSquare(DataSet, double) - Constructor for class edu.cmu.tetrad.search.test.IndTestChiSquare
-
Constructs a new independence checker to check conditional independence facts for discrete data using a g square test.
- IndTestConditionalCorrelation - Class in edu.cmu.tetrad.search.test
-
Checks conditional independence of variable in a continuous data set using a conditional correlation test for the nonlinear nonGaussian with the additive error case.
- IndTestConditionalCorrelation(DataSet, double) - Constructor for class edu.cmu.tetrad.search.test.IndTestConditionalCorrelation
-
Constructs a new Independence test which checks independence facts based on the correlation data implied by the given data set (must be continuous).
- IndTestConditionalGaussianLrt - Class in edu.cmu.tetrad.search.test
-
Performs a test of conditional independence X _||_ Y | Z1...Zn where all searchVariables are either continuous or discrete.
- IndTestConditionalGaussianLrt(DataSet, double, boolean) - Constructor for class edu.cmu.tetrad.search.test.IndTestConditionalGaussianLrt
-
Constructor.
- IndTestCramerT - Class in edu.cmu.tetrad.search.work_in_progress
-
Checks conditional independence for continuous variables using Cramer's T-test formula (Cramer, Mathematical Methods of Statistics (1951), page 413).
- IndTestCramerT(CorrelationMatrix, double) - Constructor for class edu.cmu.tetrad.search.work_in_progress.IndTestCramerT
-
Constructs a new independence test that will determine conditional independence facts using the given correlation matrix and the given significance level.
- IndTestCramerT(DataSet, double) - Constructor for class edu.cmu.tetrad.search.work_in_progress.IndTestCramerT
-
Constructs a new Independence test which checks independence facts based on the correlation matrix implied by the given data set (must be continuous).
- IndTestCramerT(ICovarianceMatrix, double) - Constructor for class edu.cmu.tetrad.search.work_in_progress.IndTestCramerT
-
Constructs a new independence test that will determine conditional independence facts using the given correlation matrix and the given significance level.
- IndTestDegenerateGaussianLrt - Class in edu.cmu.tetrad.search.test
-
Implements a degenerate Gaussian score as a LRT.
- IndTestDegenerateGaussianLrt(DataSet) - Constructor for class edu.cmu.tetrad.search.test.IndTestDegenerateGaussianLrt
-
Constructs the score using a covariance matrix.
- IndTestDegenerateGaussianLrt.Ret - Class in edu.cmu.tetrad.search.test
-
Stores a return value for a likelihood--i.e., a likelihood value and the degrees of freedom for it.
- IndTestFisherZ - Class in edu.cmu.tetrad.search.test
-
Checks conditional independence of variable in a continuous data set using Fisher's Z test.
- IndTestFisherZ(DataSet, double) - Constructor for class edu.cmu.tetrad.search.test.IndTestFisherZ
-
Constructs a new Independence test which checks independence facts based on the correlation matrix implied by the given data set (must be continuous).
- IndTestFisherZ(ICovarianceMatrix, double) - Constructor for class edu.cmu.tetrad.search.test.IndTestFisherZ
-
Constructs a new independence test that will determine conditional independence facts using the given correlation matrix and the given significance level.
- IndTestFisherZ(Matrix, List<Node>, double) - Constructor for class edu.cmu.tetrad.search.test.IndTestFisherZ
-
Constructs a new Fisher Z independence test with the listed arguments.
- IndTestFisherZConcatenateResiduals - Class in edu.cmu.tetrad.search.test
-
Calculates independence from pooled residuals using the Fisher Z method.
- IndTestFisherZConcatenateResiduals(List<DataSet>, double) - Constructor for class edu.cmu.tetrad.search.test.IndTestFisherZConcatenateResiduals
-
Constructor.
- IndTestFisherZFisherPValue - Class in edu.cmu.tetrad.search.test
-
Calculates independence from multiple datasets from using the Fisher method of pooling independence results.
- IndTestFisherZFisherPValue(List<DataSet>, double) - Constructor for class edu.cmu.tetrad.search.test.IndTestFisherZFisherPValue
-
Constructor.
- IndTestFisherZGeneralizedInverse - Class in edu.cmu.tetrad.search.work_in_progress
-
Checks independence of X _||_ Y | Z for variables X and Y and list Z of variables.
- IndTestFisherZGeneralizedInverse(DataSet, double) - Constructor for class edu.cmu.tetrad.search.work_in_progress.IndTestFisherZGeneralizedInverse
-
Constructs a new Independence test which checks independence facts based on the correlation matrix implied by the given data set (must be continuous).
- IndTestFisherZPercentIndependent - Class in edu.cmu.tetrad.search.work_in_progress
-
Calculates independence from pooled residuals.
- IndTestFisherZPercentIndependent(List<DataSet>, double) - Constructor for class edu.cmu.tetrad.search.work_in_progress.IndTestFisherZPercentIndependent
- IndTestFisherZRecursive - Class in edu.cmu.tetrad.search.work_in_progress
-
Checks conditional independence of variable in a continuous data set using Fisher's Z test.
- IndTestFisherZRecursive(DataSet, double) - Constructor for class edu.cmu.tetrad.search.work_in_progress.IndTestFisherZRecursive
-
Constructs a new Independence test which checks independence facts based on the correlation matrix implied by the given data set (must be continuous).
- IndTestFisherZRecursive(ICovarianceMatrix, double) - Constructor for class edu.cmu.tetrad.search.work_in_progress.IndTestFisherZRecursive
-
Constructs a new independence test that will determine conditional independence facts using the given correlation matrix and the given significance level.
- IndTestFisherZRecursive(Matrix, List<Node>, double) - Constructor for class edu.cmu.tetrad.search.work_in_progress.IndTestFisherZRecursive
-
Constructs a new Fisher Z independence test with the listed arguments.
- IndTestFromString(String, DataSet, double) - Static method in class edu.pitt.csb.mgm.MixedUtils
-
Returns independence tests by name located in edu.cmu.tetrad.search and edu.pitt.csb.mgm also supports shorthand for LRT ("lrt) and t-tests ("tlin" for prefer linear (fastest) or "tlog" for prefer logistic)
- IndTestGSquare - Class in edu.cmu.tetrad.search.test
-
Checks the conditional independence X _||_ Y | S, where S is a set of discrete variable, and X and Y are discrete variable not in S, by applying a conditional G Square test.
- IndTestGSquare(DataSet, double) - Constructor for class edu.cmu.tetrad.search.test.IndTestGSquare
-
Constructs a new independence checker to check conditional independence facts for discrete data using a g square test.
- IndTestHsic - Class in edu.cmu.tetrad.search.test
-
Checks the conditional independence X _||_ Y | S, where S is a set of continuous variable, and X and Y are discrete variable not in S, using the Hilbert-Schmidth Independence Criterion (HSIC), a kernel based nonparametric test for conditional independence.
- IndTestHsic(DataSet, double) - Constructor for class edu.cmu.tetrad.search.test.IndTestHsic
-
Constructs a new HSIC Independence test.
- IndTestHsic(Matrix, List<Node>, double) - Constructor for class edu.cmu.tetrad.search.test.IndTestHsic
-
Constructs a new HSIC Independence test.
- IndTestIndependenceFacts - Class in edu.cmu.tetrad.search.test
-
Checks conditional independence against a list of conditional independence facts, manually entered.
- IndTestIndependenceFacts(IndependenceFacts) - Constructor for class edu.cmu.tetrad.search.test.IndTestIndependenceFacts
-
Constructor.
- IndTestIod - Class in edu.cmu.tetrad.search
-
Checks independence result by listing all tests with those variables, testing each one, and returning the resolution of these test results.
- IndTestIod(List<IndependenceTest>) - Constructor for class edu.cmu.tetrad.search.IndTestIod
-
Constructs a new pooled independence test from the given list of independence tests.
- IndTestMixedMultipleTTest - Class in edu.cmu.tetrad.search.work_in_progress
-
Performs a test of conditional independence X _||_ Y | Z1...Zn where all searchVariables are either continuous or discrete.
- IndTestMixedMultipleTTest(DataSet, double) - Constructor for class edu.cmu.tetrad.search.work_in_progress.IndTestMixedMultipleTTest
- IndTestMnlrLr - Class in edu.cmu.tetrad.search.work_in_progress
-
Performs a test of conditional independence X _||_ Y | Z1...Zn where all searchVariables are either continuous or discrete.
- IndTestMnlrLr(DataSet, double) - Constructor for class edu.cmu.tetrad.search.work_in_progress.IndTestMnlrLr
- IndTestMulti - Class in edu.cmu.tetrad.search.test
-
Pools together a set of independence tests using a specified method.
- IndTestMulti(List<IndependenceTest>, ResolveSepsets.Method) - Constructor for class edu.cmu.tetrad.search.test.IndTestMulti
- IndTestMultinomialLogisticRegression - Class in edu.cmu.tetrad.search.work_in_progress
-
Performs a test of conditional independence X _||_ Y | Z1...Zn where all searchVariables are either continuous or discrete.
- IndTestMultinomialLogisticRegression(DataSet, double) - Constructor for class edu.cmu.tetrad.search.work_in_progress.IndTestMultinomialLogisticRegression
- IndTestMultinomialLogisticRegressionWald - Class in edu.pitt.csb.mgm
-
Performs a test of conditional independence X _||_ Y | Z1...Zn where all searchVariables are either continuous or discrete.
- IndTestMultinomialLogisticRegressionWald(DataSet, double, boolean) - Constructor for class edu.pitt.csb.mgm.IndTestMultinomialLogisticRegressionWald
- IndTestMvpLrt - Class in edu.cmu.tetrad.search.test
-
Performs a test of conditional independence X _||_ Y | Z1...Zn where all variables are either continuous or discrete.
- IndTestMvpLrt(DataSet, double, int, boolean) - Constructor for class edu.cmu.tetrad.search.test.IndTestMvpLrt
-
Constructor.
- IndTestPositiveCorr - Class in edu.cmu.tetrad.search.work_in_progress
-
Checks conditional independence of variable in a continuous data set using Fisher's Z test.
- IndTestPositiveCorr(DataSet, double) - Constructor for class edu.cmu.tetrad.search.work_in_progress.IndTestPositiveCorr
-
Constructs a new Independence test which checks independence facts based on the correlation matrix implied by the given data set (must be continuous).
- IndTestProbabilistic - Class in edu.cmu.tetrad.search.test
-
Uses BCInference by Cooper and Bui to calculate probabilistic conditional independence judgments.
- IndTestProbabilistic(DataSet) - Constructor for class edu.cmu.tetrad.search.test.IndTestProbabilistic
-
Initializes the test using a discrete data sets.
- IndTestRegression - Class in edu.cmu.tetrad.search.test
-
Checks independence of X _||_ Y | Z for variables X and Y and list Z of variables by regressing X on {Y} U Z and testing whether the coefficient for Y is zero.
- IndTestRegression(DataSet, double) - Constructor for class edu.cmu.tetrad.search.test.IndTestRegression
-
Constructs a new Independence test which checks independence facts based on the correlation matrix implied by the given data set (must be continuous).
- IndTestScore - Class in edu.cmu.tetrad.search.score
-
Gives a method of interpreting a test as a score.
- IndTestScore(IndependenceTest) - Constructor for class edu.cmu.tetrad.search.score.IndTestScore
-
Constructs the score using a covariance matrix.
- IndTestSepsetDci - Class in edu.cmu.tetrad.search.work_in_progress
-
Checks independence facts for variables associated with a sepset by simply querying the sepset
- IndTestSepsetDci(SepsetMapDci, List<Node>) - Constructor for class edu.cmu.tetrad.search.work_in_progress.IndTestSepsetDci
-
Constructs a new independence test that returns d-separation facts for the given graph as independence results.
- indTestSubset(List<Node>) - Method in interface edu.cmu.tetrad.search.IndependenceTest
-
Returns an Independence test for a sublist of the variables.
- indTestSubset(List<Node>) - Method in class edu.cmu.tetrad.search.IndTestIod
- indTestSubset(List<Node>) - Method in class edu.cmu.tetrad.search.test.IndTestChiSquare
-
Creates a new IndTestChiSquare for a subset of the nodes.
- indTestSubset(List<Node>) - Method in class edu.cmu.tetrad.search.test.IndTestConditionalCorrelation
- indTestSubset(List<Node>) - Method in class edu.cmu.tetrad.search.test.IndTestConditionalGaussianLrt
- indTestSubset(List<Node>) - Method in class edu.cmu.tetrad.search.test.IndTestDegenerateGaussianLrt
- indTestSubset(List<Node>) - Method in class edu.cmu.tetrad.search.test.IndTestFisherZ
-
Creates a new independence test instance for a subset of the variables.
- indTestSubset(List<Node>) - Method in class edu.cmu.tetrad.search.test.IndTestFisherZConcatenateResiduals
- indTestSubset(List<Node>) - Method in class edu.cmu.tetrad.search.test.IndTestFisherZFisherPValue
- indTestSubset(List<Node>) - Method in class edu.cmu.tetrad.search.test.IndTestGSquare
-
Creates a new IndTestGSquare for a sublist of the variables.
- indTestSubset(List<Node>) - Method in class edu.cmu.tetrad.search.test.IndTestHsic
-
Creates a new IndTestHsic instance for a subset of the variables.
- indTestSubset(List<Node>) - Method in class edu.cmu.tetrad.search.test.IndTestIndependenceFacts
- indTestSubset(List<Node>) - Method in class edu.cmu.tetrad.search.test.IndTestMulti
- indTestSubset(List<Node>) - Method in class edu.cmu.tetrad.search.test.IndTestMvpLrt
-
Returns an independence test for a sublist of the searchVariables.
- indTestSubset(List<Node>) - Method in class edu.cmu.tetrad.search.test.IndTestProbabilistic
- indTestSubset(List<Node>) - Method in class edu.cmu.tetrad.search.test.IndTestRegression
-
Creates a new IndTestCramerT instance for a subset of the variables.
- indTestSubset(List<Node>) - Method in class edu.cmu.tetrad.search.test.IndTestTrekSep
-
Creates a new independence test instance for a sublist of the variables.
- indTestSubset(List<Node>) - Method in class edu.cmu.tetrad.search.test.Kci
- indTestSubset(List<Node>) - Method in class edu.cmu.tetrad.search.test.MsepTest
-
Returns a test over a subset of the variables.
- indTestSubset(List<Node>) - Method in class edu.cmu.tetrad.search.test.ScoreIndTest
- indTestSubset(List<Node>) - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestCramerT
-
Creates a new IndTestCramerT instance for a subset of the variables.
- indTestSubset(List<Node>) - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestFisherZGeneralizedInverse
-
Creates a new IndTestCramerT instance for a subset of the variables.
- indTestSubset(List<Node>) - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestFisherZPercentIndependent
- indTestSubset(List<Node>) - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestFisherZRecursive
-
Creates a new independence test instance for a subset of the variables.
- indTestSubset(List<Node>) - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestMixedMultipleTTest
- indTestSubset(List<Node>) - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestMnlrLr
- indTestSubset(List<Node>) - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestMultinomialLogisticRegression
- indTestSubset(List<Node>) - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestPositiveCorr
-
Creates a new independence test instance for a subset of the variables.
- indTestSubset(List<Node>) - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestSepsetDci
-
Required by IndependenceTest.
- indTestSubset(List<Node>) - Method in class edu.cmu.tetrad.search.work_in_progress.ProbabilisticMapIndependence
- indTestSubset(List<Node>) - Method in class edu.pitt.csb.mgm.IndTestMultinomialLogisticRegressionWald
- IndTestTrekSep - Class in edu.cmu.tetrad.search.test
-
Checks d-separations in structural model using t-separations over indicators.
- IndTestTrekSep(ICovarianceMatrix, double, List<List<Node>>, List<Node>) - Constructor for class edu.cmu.tetrad.search.test.IndTestTrekSep
-
Constructs a new independence test that will determine conditional independence facts using the given correlation matrix and the given significance level.
- IndTestUniformScatter - Class in edu.cmu.tetrad.search.work_in_progress
- IndTestUniformScatter(DataSet, double, double, int) - Constructor for class edu.cmu.tetrad.search.work_in_progress.IndTestUniformScatter
- inferFunction(int, SortedSet<ItkPredictorSearch.Gene>) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.ideker.ItkPredictorSearch
- INFIX - Enum constant in enum class edu.cmu.tetrad.calculator.expression.ExpressionDescriptor.Position
- info(String) - Method in class edu.cmu.tetrad.util.LogUtils
- initialize() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.GeneHistory
-
Initializes the history array.
- initialize(double[][]) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.BasalInitializer
-
Sets the expression of each unregulated gene in the given history at time step 0 to a random value drawn from N(basalExpression, initStDev), sets the expression level at time step 0 of each regulated gene to zero, and then copies the values at history[0][j] to history[i][j] for all i > 0 less than the maximum time lag.
- initialize(double[][]) - Method in interface edu.cmu.tetrad.study.gene.tetrad.gene.history.Initializer
-
Initializes a history array.
- initialize(LagGraph) - Method in interface edu.cmu.tetrad.study.gene.tetrad.gene.history.GraphInitializer
-
Randomizes the given lag graph--in other words, chooses random edges for the graph according to a particlar scheme (see instantiations).
- initialize(LagGraph) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.PreviousStepOnly
-
Randomizes the graph.
- initialize(LagGraph) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.SimpleRandomizer
-
Randomizes the graph.
- INITIALIZE_FROM_DATA - Enum constant in enum class edu.cmu.tetrad.sem.StandardizedSemIm.Initialization
- initializeEdges() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.biolingua.Digraph
-
Initializes the edges matrix
- initializeEdges() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.BasicGraph
-
Initializes the data structure that holds the set of edges
- Initializer - Interface in edu.cmu.tetrad.study.gene.tetrad.gene.history
-
Initializes a history array.
- initializeValues() - Method in class edu.cmu.tetrad.sem.SemIm
-
Iterates through all freeParameters, picking values for them from the distributions that have been set for them.
- initMatrixStorage() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.BasicMatrix
-
Initializes the data structure used to hold the contents of the matrix
- initMatrixStorage() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.LTMatrix
-
Initializes the data structure used to hold the contents of the matrix
- initMatrixStorage() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.LTMatrixF
-
Initializes the data structure used to hold the contents of the matrix
- initMatrixStorage() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.Matrix
-
Initializes the data structure used to hold the contents of the matrix
- initMatrixStorage() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.MatrixF
-
Initializes the data structure used to hold the contents of the matrix
- innerProduct(double[], double[]) - Static method in class edu.cmu.tetrad.util.MatrixUtils
- IntAveDataSetProbs - Class in edu.cmu.tetrad.bayes
-
Estimates probabilities directly from data on the fly using maximum likelihood method, with the exception that if rows do not exist in the data satisfying a required condition because certain values are unattested, an attempt is made to remove each relevant column in turn, record the estimated probability with column removed from the condition (if it is defined), and then return the average over the estimated probabilities calculated this way.
- IntAveDataSetProbs(DataSet) - Constructor for class edu.cmu.tetrad.bayes.IntAveDataSetProbs
-
Creates a cell count table for the given data set.
- IntDataBox - Class in edu.cmu.tetrad.data
-
Stores a 2D array of integer data.
- IntDataBox(int[][]) - Constructor for class edu.cmu.tetrad.data.IntDataBox
-
Constructs a new data box using the given 2D short data array as data.
- IntDataBox(int, int) - Constructor for class edu.cmu.tetrad.data.IntDataBox
-
Constructs an 2D short array consisting entirely of missing values (-99).
- Integrator - Class in edu.cmu.tetrad.util
-
Integrates under a function from one endpoint to another.
- Integrator() - Constructor for class edu.cmu.tetrad.util.Integrator
- InterIamb - Class in edu.cmu.tetrad.search.work_in_progress
-
Implements the Inter-IAMB algorithm.
- InterIamb(IndependenceTest) - Constructor for class edu.cmu.tetrad.search.work_in_progress.InterIamb
-
Constructs a new search.
- intersection() - Method in class edu.cmu.tetrad.search.utils.GraphoidAxioms
-
Checks if intersection holds--e.g., (X ⊥⊥ Y | (Z ∪ W)) ∧ (X ⊥⊥ W | (Z ∪ Y)) ==> X ⊥⊥ (Y ∪ W) |Z
- INTERVAL_BETWEEN_RECORDINGS - Static variable in class edu.cmu.tetrad.util.Params
- INTERVAL_BETWEEN_SHOCKS - Static variable in class edu.cmu.tetrad.util.Params
- INTERVENTION_STATUS - Enum constant in enum class edu.cmu.tetrad.graph.NodeVariableType
- INTERVENTION_VALUE - Enum constant in enum class edu.cmu.tetrad.graph.NodeVariableType
- inverse() - Method in class edu.cmu.tetrad.util.Matrix
- inverse() - Method in class edu.cmu.tetrad.util.Matrix2
- inverse(double[][]) - Static method in class edu.cmu.tetrad.util.MatrixUtils
- InverseCorrelation - Class in edu.cmu.tetrad.search.work_in_progress
-
Returns edges whose entries in the precision matrix exceed a certain threshold.
- InverseCorrelation(DataSet, double) - Constructor for class edu.cmu.tetrad.search.work_in_progress.InverseCorrelation
- inverseCumulativeProbability(double) - Method in class edu.cmu.tetrad.sem.EmpiricalCdf
- invVech(double[]) - Static method in class edu.cmu.tetrad.util.MatrixUtils
- Ion - Class in edu.cmu.tetrad.search.work_in_progress
-
Implements the ION (Integration of Overlapping Networks) algorithm for distributed causal inference.
- Ion(List<Graph>) - Constructor for class edu.cmu.tetrad.search.work_in_progress.Ion
-
Constructs a new instance of the ION search from the input PAGs
- IonHittingSet - Class in edu.cmu.tetrad.search.work_in_progress
-
Provides a static method which implements a correct version of Reiter's hitting set algorithm as described by Greiner, Smith, and Wilkerson in "A Correction to the Algorithm in Reiter's Theory of Diagnosis" Artificial Intellegence 41 (1989) (see for detailed specification).
- IonHittingSet() - Constructor for class edu.cmu.tetrad.search.work_in_progress.IonHittingSet
- IPEN - Static variable in class edu.cmu.tetrad.util.Params
- IPurify - Interface in edu.cmu.tetrad.search.utils
-
Provides an interface for Purify algorithm.
- IS - Static variable in class edu.cmu.tetrad.util.Params
- isAccommodateNewCategories() - Method in class edu.cmu.tetrad.data.DiscreteVariable
- isActive() - Method in class edu.cmu.tetrad.util.DefaultTetradLoggerConfig
- isActive() - Method in class edu.cmu.tetrad.util.TetradLogger.EmptyConfig
- isActive() - Method in interface edu.cmu.tetrad.util.TetradLoggerConfig
-
States whether the config is active or not.
- isAcyclic(Matrix) - Static method in class edu.cmu.tetrad.search.IcaLingD
-
Determines whether a BHat matrix parses to an acyclic graph.
- isAdjacentTo(Node, Node) - Method in class edu.cmu.tetrad.graph.Dag
- isAdjacentTo(Node, Node) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
-
Determines whether some edge or other exists between two nodes.
- isAdjacentTo(Node, Node) - Method in interface edu.cmu.tetrad.graph.Graph
- isAdjacentTo(Node, Node) - Method in class edu.cmu.tetrad.graph.LagGraph
- isAdjacentTo(Node, Node) - Method in class edu.cmu.tetrad.graph.SemGraph
- isAdjacentTo(Node, Node) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- isAllowed(int, int) - Method in class edu.cmu.tetrad.bayes.Proposition
- isAmbiguousTriple(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.Dag
-
States whether r-s-r is an underline triple or not.
- isAmbiguousTriple(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
-
States whether r-s-r is an underline triple or not.
- isAmbiguousTriple(Node, Node, Node) - Method in interface edu.cmu.tetrad.graph.Graph
-
States whether r-s-r is an underline triple or not.
- isAmbiguousTriple(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.LagGraph
-
States whether r-s-r is an underline triple or not.
- isAmbiguousTriple(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.SemGraph
-
States whether r-s-r is an underline triple or not.
- isAmbiguousTriple(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
-
States whether r-s-r is an underline triple or not.
- isAmbiguousTriple(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.Underlines
-
States whether r-s-r is an underline triple or not.
- isAncestorOf(Node, Node) - Method in class edu.cmu.tetrad.graph.LagGraph
- isAncestorOf(Node, Node) - Method in class edu.cmu.tetrad.graph.Paths
-
Determines whether one node is an ancestor of another.
- isAntilogCalculated() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.simulation.MeasurementSimulator
-
Returns true iff the antilog of each expression level should be calculated.
- isAntilogCalculated() - Method in class edu.cmu.tetrad.study.gene.tetradapp.model.MeasurementSimulatorParams
- isApplyR1() - Method in class edu.cmu.tetrad.search.Ccd
-
Returns true iff the R1 rule should be applied.
- isArrowheadAllowed(Node, Node, Graph, Knowledge) - Static method in class edu.cmu.tetrad.search.utils.FciOrient
- isArrowheadAllowed(Object, Object, Knowledge) - Static method in class edu.cmu.tetrad.search.utils.GraphSearchUtils
-
Checks if an arrowhead is allowed by background knowledge.
- isArrowheadAllowed1(Node, Node, Knowledge) - Static method in class edu.cmu.tetrad.search.work_in_progress.SampleVcpcFast
- isArrowheadAllowed1(Node, Node, Knowledge) - Static method in class edu.cmu.tetrad.search.work_in_progress.VcPc
- isAutomaticLogDisplayEnabled() - Method in class edu.cmu.tetrad.util.TetradLogger
-
States whether the automatic log display is enabled or not, or returns null if there is no value stored in the user's prefs.
- isBidirectedEdge(Edge) - Static method in class edu.cmu.tetrad.graph.Edges
- isBinary(DataSet, int) - Static method in class edu.cmu.tetrad.data.DataUtils
-
States whether the given column of the given data set is binary.
- isBoundsEnforced() - Method in class edu.cmu.tetrad.bayes.DirichletDataSetProbs
-
True iff bounds checking is performed on variable values indices.
- isCanalyzing() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.BooleanFunction
-
Determines whether the getModel function is canalyzing, according to Kaufmann's definition in Oridins of Order: "I define as a canalyzing Boolean function any Boolean function having the property that it has at least one input having at least one value (1 or 0) which suffices to guarantee that the regulated element assumes a specific value (1 or 0)" (page 203-4).
- isCanceled() - Method in class edu.cmu.tetrad.util.TaskManager
- isCategoryNamesDisplayed() - Method in class edu.cmu.tetrad.data.DiscreteVariable
- isChangeFlag() - Method in class edu.cmu.tetrad.search.utils.FciOrient
-
Change flag for repeat rules
- isCheckingCycles() - Method in class edu.cmu.tetrad.search.work_in_progress.HbsmsBeam
- isChildOf(Node, Node) - Method in class edu.cmu.tetrad.graph.Dag
- isChildOf(Node, Node) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
-
Determines whether one node is a child of another.
- isChildOf(Node, Node) - Method in interface edu.cmu.tetrad.graph.Graph
- isChildOf(Node, Node) - Method in class edu.cmu.tetrad.graph.LagGraph
- isChildOf(Node, Node) - Method in class edu.cmu.tetrad.graph.SemGraph
- isChildOf(Node, Node) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- isClique(Collection<Node>, Graph) - Static method in class edu.cmu.tetrad.graph.GraphUtils
- isColinear(DataSet, boolean) - Static method in class edu.pitt.csb.mgm.MixedUtils
-
Check each pair of variables to see if correlation is 1.
- isCompleteRuleSetUsed() - Method in class edu.cmu.tetrad.search.Cfci
-
Returns true if Zhang's complete rule set should be used, false if only R1-T1 (the rule set of the original FCI) should be used.
- isCompleteRuleSetUsed() - Method in class edu.cmu.tetrad.search.SpFci
-
Returns whether the complete rule set is used.
- isCompleteRuleSetUsed() - Method in class edu.cmu.tetrad.search.SvarFci
-
Returns whether Zhang's complete rule set is to be used.
- isCompleteRuleSetUsed() - Method in class edu.cmu.tetrad.search.utils.DagToPag
- isCompleteRuleSetUsed() - Method in class edu.cmu.tetrad.search.utils.FciOrient
- isCompleteRuleSetUsed() - Method in class edu.cmu.tetrad.search.utils.SvarFciOrient
- isCompleteRuleSetUsed() - Method in class edu.cmu.tetrad.search.utils.TsDagToPag
- isConditioned(int) - Method in class edu.cmu.tetrad.bayes.Proposition
- isConsistent(GraphChange) - Method in class edu.cmu.tetrad.search.work_in_progress.GraphChange
-
Consistency check, nonexhaustive, but catches the most blatant inconsistencies.
- isConsistentModelClass(Class<Type1>, List, boolean) - Method in class edu.cmu.tetrad.session.SessionNode
-
Determines whether a given model class is consistent with the models contained in the given List of nodes, in the sense that the model class has a constructor that can take the models of the nodes as arguments.
- isConsistentParent(SessionNode) - Method in class edu.cmu.tetrad.session.SessionNode
- isConsistentParent(SessionNode, List<SessionNode>) - Method in class edu.cmu.tetrad.session.SessionNode
- isContinuous() - Method in class edu.cmu.tetrad.data.BoxDataSet
- isContinuous() - Method in class edu.cmu.tetrad.data.CorrelationMatrixOnTheFly
- isContinuous() - Method in class edu.cmu.tetrad.data.CovarianceMatrix
- isContinuous() - Method in class edu.cmu.tetrad.data.CovarianceMatrixOnTheFly
- isContinuous() - Method in interface edu.cmu.tetrad.data.DataModel
- isContinuous() - Method in class edu.cmu.tetrad.data.DataModelList
- isContinuous() - Method in interface edu.cmu.tetrad.data.DataSet
- isContinuous() - Method in class edu.cmu.tetrad.data.IndependenceFacts
- isContinuous() - Method in class edu.cmu.tetrad.data.NumberObjectDataSet
- isContinuous() - Method in class edu.cmu.tetrad.data.TimeSeriesData
- isCopyData() - Method in class edu.cmu.tetrad.algcomparison.TimeoutComparison
- isCyclic() - Method in interface edu.cmu.tetrad.sem.ISemIm
- isCyclic() - Method in class edu.cmu.tetrad.sem.SemIm
- isDag(Graph) - Static method in class edu.cmu.tetrad.graph.GraphUtils
- isDataFromFile() - Method in class edu.cmu.tetrad.study.performance.ComparisonParameters
- isDefaultToKnowledgeLayout() - Method in class edu.cmu.tetrad.data.Knowledge
- isDefCollider(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.Dag
- isDefCollider(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
- isDefCollider(Node, Node, Node) - Method in interface edu.cmu.tetrad.graph.Graph
-
Added by ekorber, 2004/6/9.
- isDefCollider(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.LagGraph
- isDefCollider(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.SemGraph
- isDefCollider(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- isDefNoncollider(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.Dag
- isDefNoncollider(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
-
IllegalArgument exception raised (by isDirectedFromTo(getEndpoint) or by getEdge) if there are multiple edges between any of the node pairs.
- isDefNoncollider(Node, Node, Node) - Method in interface edu.cmu.tetrad.graph.Graph
-
Added by ekorber, 2004/6/9.
- isDefNoncollider(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.LagGraph
- isDefNoncollider(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.SemGraph
- isDefNoncollider(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- isDependent() - Method in class edu.cmu.tetrad.search.test.IndependenceResult
-
Returns whether the fact fails to hold--i.e., if the judgment is for dependence.
- isDescendentOf(Node, Node) - Method in class edu.cmu.tetrad.graph.Paths
-
Determines whether one node is a descendent of another.
- isDetermined(int[], double) - Method in class edu.cmu.tetrad.search.test.ChiSquareTest
-
Returns a judgment of whether a set of parent variables determines a child variables.
- isDetermined(int[], double) - Method in class edu.cmu.tetrad.search.test.GSquareTest
-
Returns a judgement of whether the variables index by 'testIndices' determine the variable index by 'p'.
- isDirected() - Method in class edu.cmu.tetrad.graph.Edge
- isDirectedEdge(Edge) - Static method in class edu.cmu.tetrad.graph.Edges
- isDirectedFromTo(Node, Node) - Method in class edu.cmu.tetrad.graph.Paths
- isDiscrete() - Method in class edu.cmu.tetrad.data.BoxDataSet
- isDiscrete() - Method in class edu.cmu.tetrad.data.CorrelationMatrixOnTheFly
- isDiscrete() - Method in class edu.cmu.tetrad.data.CovarianceMatrix
- isDiscrete() - Method in class edu.cmu.tetrad.data.CovarianceMatrixOnTheFly
- isDiscrete() - Method in interface edu.cmu.tetrad.data.DataModel
- isDiscrete() - Method in class edu.cmu.tetrad.data.DataModelList
- isDiscrete() - Method in interface edu.cmu.tetrad.data.DataSet
- isDiscrete() - Method in class edu.cmu.tetrad.data.IndependenceFacts
- isDiscrete() - Method in class edu.cmu.tetrad.data.NumberObjectDataSet
- isDiscrete() - Method in class edu.cmu.tetrad.data.TimeSeriesData
- isDisplayLogEnabled() - Method in class edu.cmu.tetrad.util.TetradLogger
-
States whether to display the log display.
- isDoOrientation() - Method in class edu.cmu.tetrad.search.work_in_progress.SampleVcpc
- isDoOrientation() - Method in class edu.cmu.tetrad.search.work_in_progress.SampleVcpcFast
- isDoOrientation() - Method in class edu.cmu.tetrad.search.work_in_progress.VcPcAlt
- isDoubleMissingValue(double) - Static method in class edu.cmu.tetrad.data.ContinuousVariable
-
Determines whether the argument is equal to the missing value marker.
- isEffectEdge(double) - Method in class edu.cmu.tetrad.search.score.BdeScore
-
Returns a judgment of whether the given bump in score allows one to conclude that the edge is an "effect edge" for FGES.
- isEffectEdge(double) - Method in class edu.cmu.tetrad.search.score.BdeuScore
-
For FGES, this determines whether an edge counts as an effect edge.
- isEffectEdge(double) - Method in class edu.cmu.tetrad.search.score.ConditionalGaussianScore
-
A method for FGES for determining whether an edge counts as an effect edges for this score bump.
- isEffectEdge(double) - Method in class edu.cmu.tetrad.search.score.DegenerateGaussianScore
- isEffectEdge(double) - Method in class edu.cmu.tetrad.search.score.DiscreteBicScore
-
Must be called directly after the corresponding scoring call.
- isEffectEdge(double) - Method in class edu.cmu.tetrad.search.score.EbicScore
-
Returns a judgement for FGES of whether the given bump implies an effect edge.
- isEffectEdge(double) - Method in class edu.cmu.tetrad.search.score.GicScores
- isEffectEdge(double) - Method in class edu.cmu.tetrad.search.score.GraphScore
-
Returns a judgment for FGES as to whether a score with the bump is for an effect edge.
- isEffectEdge(double) - Method in class edu.cmu.tetrad.search.score.ImagesScore
- isEffectEdge(double) - Method in class edu.cmu.tetrad.search.score.IndTestScore
- isEffectEdge(double) - Method in class edu.cmu.tetrad.search.score.MvpScore
-
A method for FGES returning a judgment of whether an edge with a given bump counts as a effect edge.
- isEffectEdge(double) - Method in class edu.cmu.tetrad.search.score.PoissonPriorScore
- isEffectEdge(double) - Method in interface edu.cmu.tetrad.search.score.Score
-
Returns true iff the edge between x and y is an effect edge.
- isEffectEdge(double) - Method in class edu.cmu.tetrad.search.score.SemBicScore
- isEffectEdge(double) - Method in class edu.cmu.tetrad.search.score.ZsbScore
-
Returns a judgement for FGES for whether a certain bump in score gives efidence of an effect edges.
- isEffectEdge(double) - Method in class edu.cmu.tetrad.search.work_in_progress.MagSemBicScore
-
Returns a judgment for FGES as to whether an edges with this bump (for this score) counts as an effect edge.
- isEffectEdge(double) - Method in class edu.cmu.tetrad.search.work_in_progress.MnlrScore
-
A method for FGES returning a judgment of whether an edge with a given bump counts as a effect edge.
- isEffectEdge(double) - Method in class edu.cmu.tetrad.search.work_in_progress.SemBicScoreDeterministic
- isEffective() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.BooleanFunction
-
Determines whether each input parent has an influence on the outcome--that is, whether for each parent there is a combination of states for the other parents for which the function would be different if the given parent were true as opposed to false.
- ISemIm - Interface in edu.cmu.tetrad.sem
-
An interface for SemIM's; see implementations.
- isEmpty() - Method in class edu.cmu.tetrad.data.Clusters
- isEmpty() - Method in class edu.cmu.tetrad.data.DataModelList
-
Check if the modeList is empty Need to override this since this class is extending AbstractList.
- isEmpty() - Method in class edu.cmu.tetrad.data.Knowledge
-
true if there is no background knowledge recorded.
- isEmpty() - Method in class edu.cmu.tetrad.data.KnowledgeGroup
-
States whether this group is empty, that is there is no edges in it (Note there may be some partial information though).
- isEmpty() - Method in class edu.cmu.tetrad.session.Session
- isErrorEdge(Edge) - Static method in class edu.cmu.tetrad.graph.SemGraph
- isEstimated() - Method in interface edu.cmu.tetrad.sem.ISemIm
- isEstimated() - Method in class edu.cmu.tetrad.sem.SemIm
- isEventActive(String) - Method in class edu.cmu.tetrad.util.DefaultTetradLoggerConfig
- isEventActive(String) - Method in class edu.cmu.tetrad.util.TetradLogger.EmptyConfig
- isEventActive(String) - Method in class edu.cmu.tetrad.util.TetradLogger
-
States whether the given event is active or not.
- isEventActive(String) - Method in interface edu.cmu.tetrad.util.TetradLoggerConfig
-
States whether the event associated with the given id is active, that is whether it should be logged or not.
- isExogenous(Node) - Method in class edu.cmu.tetrad.graph.Dag
- isExogenous(Node) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
-
Determines whether a node in a graph is exogenous.
- isExogenous(Node) - Method in interface edu.cmu.tetrad.graph.Graph
- isExogenous(Node) - Method in class edu.cmu.tetrad.graph.LagGraph
- isExogenous(Node) - Method in class edu.cmu.tetrad.graph.SemGraph
- isExogenous(Node) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- isFaithfulnessAssumed() - Method in class edu.cmu.tetrad.search.utils.FgesOrienter
- isFdr() - Method in class edu.cmu.tetrad.search.Pcd
-
True iff the algorithm should be run with False Discovery Rate tests.
- isFileLoggingEnabled() - Method in class edu.cmu.tetrad.util.TetradLogger
-
States whether file logging is enabled or not.
- isFixed() - Method in class edu.cmu.tetrad.sem.Parameter
- isFlatPrior() - Method in class edu.cmu.tetrad.sem.SemEstimatorGibbsParams
- isForbidden(Node) - Method in class edu.cmu.tetrad.search.utils.GrowShrinkTree
- isForbidden(String, String) - Method in class edu.cmu.tetrad.data.Knowledge
-
Determines whether the edge var1 --> var2 is forbidden.
- isForbiddenByGroups(String, String) - Method in class edu.cmu.tetrad.data.Knowledge
-
Legacy.
- isForbiddenByTiers(String, String) - Method in class edu.cmu.tetrad.data.Knowledge
-
Determines whether the edge var1 --> var2 is forbidden by the temporal tiers.
- isFreshlyCreated() - Method in class edu.cmu.tetrad.session.SessionNode
- isHighlighted() - Method in class edu.cmu.tetrad.graph.Edge
- isIa() - Method in class edu.cmu.tetrad.search.work_in_progress.Glasso
- isIncludeDishAndChipColumns() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.simulation.MeasurementSimulator
- isIncludeDishAndChipVariables() - Method in class edu.cmu.tetrad.study.gene.tetradapp.model.MeasurementSimulatorParams
- isIncompatibleWith(VariableSource) - Method in class edu.cmu.tetrad.bayes.Evidence
-
Returna true just in case this evidence has a list of variables equal to those of the given variable source.
- isIncomplete(int) - Method in interface edu.cmu.tetrad.bayes.BayesIm
-
Returns true iff the given node has a Double.NaN value in it.
- isIncomplete(int) - Method in class edu.cmu.tetrad.bayes.DirichletBayesIm
- isIncomplete(int) - Method in class edu.cmu.tetrad.bayes.MlBayesIm
- isIncomplete(int) - Method in class edu.cmu.tetrad.bayes.MlBayesImObs
- isIncomplete(int) - Method in class edu.cmu.tetrad.bayes.UpdatedBayesIm
- isIncomplete(int, int) - Method in interface edu.cmu.tetrad.bayes.BayesIm
-
Returns true iff the given row in the given node has a Double.NaN value in it.
- isIncomplete(int, int) - Method in class edu.cmu.tetrad.bayes.DirichletBayesIm
- isIncomplete(int, int) - Method in class edu.cmu.tetrad.bayes.MlBayesIm
- isIncomplete(int, int) - Method in class edu.cmu.tetrad.bayes.MlBayesImObs
- isIncomplete(int, int) - Method in class edu.cmu.tetrad.bayes.UpdatedBayesIm
- isIndep() - Method in class edu.cmu.tetrad.search.test.ChiSquareTest.Result
- isIndep() - Method in class edu.cmu.tetrad.search.test.GSquareTest.Result
- isIndependent() - Method in class edu.cmu.tetrad.search.test.IndependenceResult
-
Returns whether the fact holds--i.e., if the judgment is for independence.
- isIndependent(Node, Node, Node...) - Method in class edu.cmu.tetrad.data.IndependenceFacts
- isIndependent(Node, Node, Set<Node>) - Method in class edu.cmu.tetrad.data.IndependenceFacts
- isIndependent(Node, Node, Set<Node>) - Method in class edu.cmu.tetrad.search.test.ConditionalCorrelationIndependence
-
Returns the p-value of the test, x _||_ y | z.
- isIndependent(Node, Node, Set<Node>) - Method in class edu.cmu.tetrad.search.utils.DagSepsets
-
Returns true just in case msep(a, b | c) in the DAG.
- isIndependent(Node, Node, Set<Node>) - Method in interface edu.cmu.tetrad.search.utils.SepsetProducer
- isIndependent(Node, Node, Set<Node>) - Method in class edu.cmu.tetrad.search.utils.SepsetsConservative
- isIndependent(Node, Node, Set<Node>) - Method in class edu.cmu.tetrad.search.utils.SepsetsGreedy
- isIndependent(Node, Node, Set<Node>) - Method in class edu.cmu.tetrad.search.utils.SepsetsPossibleMsep
- isIndependent(Node, Node, Set<Node>) - Method in class edu.cmu.tetrad.search.utils.SepsetsSet
- isIndependentPooled(ResolveSepsets.Method, List<IndependenceTest>, Node, Node, Set<Node>) - Static method in class edu.cmu.tetrad.search.utils.ResolveSepsets
-
Tests for independence using one of the pooled methods
- isIndependentPooled(ResolveSepsetsDci.Method, List<IndependenceTest>, Node, Node, Set<Node>) - Static method in class edu.cmu.tetrad.search.work_in_progress.ResolveSepsetsDci
-
Tests for independence using one of the pooled methods
- isIndependentPooledAverage(List<IndependenceTest>, Node, Node, Set<Node>) - Static method in class edu.cmu.tetrad.search.utils.ResolveSepsets
-
Checks independence from pooled samples by taking the average p value
- isIndependentPooledAverage(List<IndependenceTest>, Node, Node, Set<Node>) - Static method in class edu.cmu.tetrad.search.work_in_progress.ResolveSepsetsDci
-
Checks independence from pooled samples by taking the average p value
- isIndependentPooledAverageTest(List<IndependenceTest>, Node, Node, Set<Node>) - Static method in class edu.cmu.tetrad.search.utils.ResolveSepsets
-
Checks independence from pooled samples by taking the average test statistic CURRENTLY ONLY WORKS FOR CHISQUARE TEST
- isIndependentPooledAverageTest(List<IndependenceTest>, Node, Node, Set<Node>) - Static method in class edu.cmu.tetrad.search.work_in_progress.ResolveSepsetsDci
-
Checks independence from pooled samples by taking the average test statistic CURRENTLY ONLY WORKS FOR CHISQUARE TEST
- isIndependentPooledFisher(List<IndependenceTest>, Node, Node, Set<Node>) - Static method in class edu.cmu.tetrad.search.utils.ResolveSepsets
-
Checks independence from pooled samples using Fisher's method.
- isIndependentPooledFisher(List<IndependenceTest>, Node, Node, Set<Node>) - Static method in class edu.cmu.tetrad.search.work_in_progress.ResolveSepsetsDci
-
Checks independence from pooled samples using Fisher's method.
- isIndependentPooledFisher2(List<IndependenceTest>, Node, Node, Set<Node>) - Static method in class edu.cmu.tetrad.search.utils.ResolveSepsets
-
Eliminates from considerations independence tests that cannot be evaluated (due to missing variables mainly).
- isIndependentPooledFisher2(List<IndependenceTest>, Node, Node, Set<Node>) - Static method in class edu.cmu.tetrad.search.work_in_progress.ResolveSepsetsDci
-
Eliminates from considerations independence tests that cannot be evaluated (due to missing variables mainly).
- isIndependentPooledMudholkerGeorge(List<IndependenceTest>, Node, Node, Set<Node>) - Static method in class edu.cmu.tetrad.search.utils.ResolveSepsets
-
Checks independence from pooled samples using Mudholker and George's method
- isIndependentPooledMudholkerGeorge(List<IndependenceTest>, Node, Node, Set<Node>) - Static method in class edu.cmu.tetrad.search.work_in_progress.ResolveSepsetsDci
-
Checks independence from pooled samples using Mudholker and George's method
- isIndependentPooledMudholkerGeorge2(List<IndependenceTest>, Node, Node, Set<Node>) - Static method in class edu.cmu.tetrad.search.utils.ResolveSepsets
-
The same as isIndepenentPooledMudholkerGeoerge, except that only available independence tests are used.
- isIndependentPooledMudholkerGeorge2(List<IndependenceTest>, Node, Node, Set<Node>) - Static method in class edu.cmu.tetrad.search.work_in_progress.ResolveSepsetsDci
-
The same as isIndepenentPooledMudholkerGeoerge, except that only available independence tests are used.
- isIndependentPooledRandom(List<IndependenceTest>, Node, Node, Set<Node>) - Static method in class edu.cmu.tetrad.search.utils.ResolveSepsets
-
Checks independence from pooled samples by randomly selecting a p value
- isIndependentPooledRandom(List<IndependenceTest>, Node, Node, Set<Node>) - Static method in class edu.cmu.tetrad.search.work_in_progress.ResolveSepsetsDci
-
Checks independence from pooled samples by randomly selecting a p value
- isIndependentPooledStouffer(List<IndependenceTest>, Node, Node, Set<Node>) - Static method in class edu.cmu.tetrad.search.utils.ResolveSepsets
-
Checks independence from pooled samples using Stouffer et al.'s method
- isIndependentPooledStouffer(List<IndependenceTest>, Node, Node, Set<Node>) - Static method in class edu.cmu.tetrad.search.work_in_progress.ResolveSepsetsDci
-
Checks independence from pooled samples using Stouffer et al.'s method
- isIndependentPooledTippett(List<IndependenceTest>, Node, Node, Set<Node>) - Static method in class edu.cmu.tetrad.search.utils.ResolveSepsets
-
Checks independence from pooled samples using Tippett's method
- isIndependentPooledTippett(List<IndependenceTest>, Node, Node, Set<Node>) - Static method in class edu.cmu.tetrad.search.work_in_progress.ResolveSepsetsDci
-
Checks independence from pooled samples using Tippett's method
- isIndependentPooledWilkinson(List<IndependenceTest>, Node, Node, Set<Node>, int) - Static method in class edu.cmu.tetrad.search.utils.ResolveSepsets
-
Checks independence from pooled samples using Wilkinson's method
- isIndependentPooledWilkinson(List<IndependenceTest>, Node, Node, Set<Node>, int) - Static method in class edu.cmu.tetrad.search.work_in_progress.ResolveSepsetsDci
-
Checks independence from pooled samples using Wilkinson's method
- isIndependentPooledWorsleyFriston(List<IndependenceTest>, Node, Node, Set<Node>) - Static method in class edu.cmu.tetrad.search.utils.ResolveSepsets
-
Checks independence from pooled samples using Worsley and Friston's method
- isIndependentPooledWorsleyFriston(List<IndependenceTest>, Node, Node, Set<Node>) - Static method in class edu.cmu.tetrad.search.work_in_progress.ResolveSepsetsDci
-
Checks independence from pooled samples using Worsley and Friston's method
- isInitializedRandomly() - Method in class edu.cmu.tetrad.sem.Parameter
- isInitSync() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.simulation.MeasurementSimulator
-
Returns 'true' if cells in the simulation will be synchronized, 'false' if not.
- isInitSync() - Method in class edu.cmu.tetrad.study.gene.tetradapp.model.MeasurementSimulatorParams
- isInWhichTier(Node) - Method in class edu.cmu.tetrad.data.Knowledge
-
Returns the index of the tier of node if it's in a tier, otherwise -1.
- isIpen() - Method in class edu.cmu.tetrad.search.work_in_progress.Glasso
- isIs() - Method in class edu.cmu.tetrad.search.work_in_progress.Glasso
- isItr() - Method in class edu.cmu.tetrad.search.work_in_progress.Glasso
- isJointMarginalSupported() - Method in class edu.cmu.tetrad.bayes.ApproximateUpdater
- isJointMarginalSupported() - Method in interface edu.cmu.tetrad.bayes.BayesUpdater
-
Returns the joint marginal probability of the given variables taking the given values, given the evidence.
- isJointMarginalSupported() - Method in class edu.cmu.tetrad.bayes.CptInvariantUpdater
- isJointMarginalSupported() - Method in class edu.cmu.tetrad.bayes.Identifiability
- isJointMarginalSupported() - Method in class edu.cmu.tetrad.bayes.JunctionTreeUpdater
- isJointMarginalSupported() - Method in class edu.cmu.tetrad.bayes.RowSummingExactUpdater
- isLegalFirstEdge(Node, Node) - Method in interface edu.cmu.tetrad.search.utils.LegalPairs
- isLegalMag() - Method in class edu.cmu.tetrad.search.utils.GraphSearchUtils.LegalMagRet
- isLegalName(String) - Static method in class edu.cmu.tetrad.util.NamingProtocol
- isLegalPag() - Method in class edu.cmu.tetrad.search.utils.GraphSearchUtils.LegalPagRet
- isLegalPag(Graph) - Static method in class edu.cmu.tetrad.search.utils.GraphSearchUtils
- isLegalPair(Node, Node, Node, List<Node>, List<Node>) - Method in interface edu.cmu.tetrad.search.utils.LegalPairs
- isLog() - Method in class edu.cmu.tetrad.search.utils.FgesOrienter
-
True iff log output should be produced.
- isLogging() - Method in class edu.cmu.tetrad.util.TetradLogger
-
States whether the logger is turned on or not.
- isManipulated(int) - Method in class edu.cmu.tetrad.bayes.Evidence
- isManipulated(int) - Method in class edu.cmu.tetrad.bayes.Manipulation
- isManipulated(int) - Method in class edu.cmu.tetrad.sem.SemEvidence
- isManipulated(int) - Method in class edu.cmu.tetrad.sem.SemManipulation
- isMConnectedTo(Node, Node, Set<Node>) - Method in class edu.cmu.tetrad.graph.Paths
-
Detemrmines whether x and y are d-connected given z.
- isMConnectedTo(Node, Node, Set<Node>, Map<Node, Set<Node>>) - Method in class edu.cmu.tetrad.graph.Paths
-
Detemrmines whether x and y are d-connected given z.
- isMConnectedTo(Set<Node>, Set<Node>, Set<Node>) - Method in class edu.cmu.tetrad.graph.Paths
- isMConnectedTo(Set<Node>, Set<Node>, Set<Node>, Map<Node, Set<Node>>) - Method in class edu.cmu.tetrad.graph.Paths
-
Checks to see if x and y are d-connected given z.
- isMeasuredDataSaved() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.simulation.MeasurementSimulator
-
Returns 'true' if measured data is being saved out for the getModel simulation, 'false' if not.
- isMeekPreventCycles() - Method in class edu.cmu.tetrad.search.Pcd
- isMeekPreventCycles() - Method in class edu.cmu.tetrad.search.utils.PcCommon
- isMeekPreventCycles() - Method in class edu.cmu.tetrad.search.work_in_progress.Kpc
- isMeekPreventCycles() - Method in class edu.cmu.tetrad.search.work_in_progress.SampleVcpc
- isMeekPreventCycles() - Method in class edu.cmu.tetrad.search.work_in_progress.SampleVcpcFast
- isMeekPreventCycles() - Method in class edu.cmu.tetrad.search.work_in_progress.VcPc
- isMeekPreventCycles() - Method in class edu.cmu.tetrad.search.work_in_progress.VcPcAlt
- isMeekPreventCycles() - Method in class edu.cmu.tetrad.search.work_in_progress.VcPcFast
- isMissingValue(Object) - Method in class edu.cmu.tetrad.data.AbstractVariable
-
Tests whether the given value is the missing data marker.
- isMissingValue(Object) - Method in class edu.cmu.tetrad.data.ContinuousVariable
-
Determines whether the argument is equal to the missing value marker.
- isMissingValue(Object) - Method in class edu.cmu.tetrad.data.DiscreteVariable
-
Determines whether the given value is the missing value marker.
- isMissingValue(Object) - Method in interface edu.cmu.tetrad.data.Variable
-
Tests whether the given value is the missing data marker.
- isMixed() - Method in class edu.cmu.tetrad.data.BoxDataSet
- isMixed() - Method in class edu.cmu.tetrad.data.CorrelationMatrixOnTheFly
- isMixed() - Method in class edu.cmu.tetrad.data.CovarianceMatrix
- isMixed() - Method in class edu.cmu.tetrad.data.CovarianceMatrixOnTheFly
- isMixed() - Method in interface edu.cmu.tetrad.data.DataModel
- isMixed() - Method in class edu.cmu.tetrad.data.DataModelList
- isMixed() - Method in interface edu.cmu.tetrad.data.DataSet
- isMixed() - Method in class edu.cmu.tetrad.data.IndependenceFacts
- isMixed() - Method in class edu.cmu.tetrad.data.NumberObjectDataSet
- isMixed() - Method in class edu.cmu.tetrad.data.TimeSeriesData
- isMSeparated(Node, Node, Set<Node>) - Method in class edu.cmu.tetrad.search.test.MsepTest
-
Auxiliary method to calculate msep(x, y | z) directly from nodes instead of from variables.
- isMSeparatedFrom(Node, Node, Set<Node>) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
-
Determines whether x and y are d-separated given z.
- isMSeparatedFrom(Node, Node, Set<Node>) - Method in class edu.cmu.tetrad.graph.Paths
-
Determines whether one n ode is d-separated from another.
- isMSeparatedFrom(Set<Node>, Set<Node>, Set<Node>) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
-
Determines whether two nodes are d-separated given z.
- isMSeparatedFrom(Set<Node>, Set<Node>, Set<Node>, Map<Node, Set<Node>>) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
-
Determines whether two nodes are d-separated given z.
- isNewSession() - Method in class edu.cmu.tetrad.session.Session
- isNoData() - Method in class edu.cmu.tetrad.study.performance.ComparisonParameters
- isNondirectedEdge(Edge) - Static method in class edu.cmu.tetrad.graph.Edges
- isNull() - Method in class edu.cmu.tetrad.graph.Edge
- isOneEdgeFaithfulnessAssumed() - Method in class edu.cmu.tetrad.study.performance.ComparisonParameters
- isOnlyCanCauseNextTier(int) - Method in class edu.cmu.tetrad.data.Knowledge
- isParallelized() - Method in class edu.cmu.tetrad.algcomparison.TimeoutComparison
- isParameterBoundsEnforced() - Method in interface edu.cmu.tetrad.sem.ISemIm
- isParameterBoundsEnforced() - Method in class edu.cmu.tetrad.sem.SemIm
- isParameterizable(Node) - Method in class edu.cmu.tetrad.graph.Dag
- isParameterizable(Node) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
- isParameterizable(Node) - Method in interface edu.cmu.tetrad.graph.Graph
- isParameterizable(Node) - Method in class edu.cmu.tetrad.graph.LagGraph
- isParameterizable(Node) - Method in class edu.cmu.tetrad.graph.SemGraph
- isParameterizable(Node) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- isParent(int, int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.biolingua.BiolinguaDigraph
-
Returns true if node p is parent of node c.
- isParentOf(Node, Node) - Method in class edu.cmu.tetrad.graph.Dag
- isParentOf(Node, Node) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
-
Determines whether one node is a parent of another.
- isParentOf(Node, Node) - Method in interface edu.cmu.tetrad.graph.Graph
-
Determines whether node1 is a parent of node2.
- isParentOf(Node, Node) - Method in class edu.cmu.tetrad.graph.LagGraph
- isParentOf(Node, Node) - Method in class edu.cmu.tetrad.graph.SemGraph
- isParentOf(Node, Node) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- isPartiallyOrientedEdge(Edge) - Static method in class edu.cmu.tetrad.graph.Edges
- isPermissibleCombination(int[]) - Method in class edu.cmu.tetrad.bayes.Proposition
- isPositiveDefinite(Matrix) - Static method in class edu.cmu.tetrad.util.MatrixUtils
-
Return true if the given matrix is symmetric positive definite--that is, if it would make a valid covariance matrix.
- isPossibleMsepSearchDone() - Method in class edu.cmu.tetrad.search.Cfci
- isRawDataSaved() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.simulation.MeasurementSimulator
-
Returns true if raw data is being saved in the getModel simulation, false if not.
- isRawDataSaved() - Method in class edu.cmu.tetrad.study.gene.tetradapp.model.MeasurementSimulatorParams
- isRequired(Node) - Method in class edu.cmu.tetrad.search.utils.GrowShrinkTree
- isRequired(String, String) - Method in class edu.cmu.tetrad.data.Knowledge
-
Determines whether the edge var1 --> var2 is required.
- isRequiredByGroups(String, String) - Method in class edu.cmu.tetrad.data.Knowledge
-
Legacy.
- isSatisfyBackDoorCriterion(Graph, Node, Node, Set<Node>) - Method in class edu.cmu.tetrad.graph.Paths
-
Check to see if a set of variables Z satisfies the back-door criterion relative to node x and node y.
- isSaveCPDAGs() - Method in class edu.cmu.tetrad.algcomparison.Comparison
- isSaveCPDAGs() - Method in class edu.cmu.tetrad.algcomparison.TimeoutComparison
- isSaveData() - Method in class edu.cmu.tetrad.algcomparison.Comparison
- isSaveGraphs() - Method in class edu.cmu.tetrad.algcomparison.Comparison
- isSaveGraphs() - Method in class edu.cmu.tetrad.algcomparison.TimeoutComparison
- isSavePags() - Method in class edu.cmu.tetrad.algcomparison.Comparison
- isSavePags() - Method in class edu.cmu.tetrad.algcomparison.TimeoutComparison
- isSelected(Node) - Method in class edu.cmu.tetrad.data.BoxDataSet
- isSelected(Node) - Method in class edu.cmu.tetrad.data.CorrelationMatrixOnTheFly
- isSelected(Node) - Method in class edu.cmu.tetrad.data.CovarianceMatrix
- isSelected(Node) - Method in class edu.cmu.tetrad.data.CovarianceMatrixOnTheFly
- isSelected(Node) - Method in interface edu.cmu.tetrad.data.DataSet
- isSelected(Node) - Method in interface edu.cmu.tetrad.data.ICovarianceMatrix
- isSelected(Node) - Method in class edu.cmu.tetrad.data.NumberObjectDataSet
- isSessionChanged() - Method in class edu.cmu.tetrad.session.Session
- isShowAlgorithmIndices() - Method in class edu.cmu.tetrad.algcomparison.Comparison
- isShowAlgorithmIndices() - Method in class edu.cmu.tetrad.algcomparison.TimeoutComparison
- isShowErrorTerms() - Method in class edu.cmu.tetrad.graph.SemGraph
- isShowSimulationIndices() - Method in class edu.cmu.tetrad.algcomparison.Comparison
- isShowSimulationIndices() - Method in class edu.cmu.tetrad.algcomparison.TimeoutComparison
- isShowUtilities() - Method in class edu.cmu.tetrad.algcomparison.Comparison
- isShowUtilities() - Method in class edu.cmu.tetrad.algcomparison.TimeoutComparison
- isSimulatedPositiveDataOnly() - Method in interface edu.cmu.tetrad.sem.ISemIm
- isSimulatedPositiveDataOnly() - Method in class edu.cmu.tetrad.sem.SemIm
- isSingular() - Method in class edu.cmu.tetrad.data.CovarianceMatrix
- isSortByUtility() - Method in class edu.cmu.tetrad.algcomparison.Comparison
- isSortByUtility() - Method in class edu.cmu.tetrad.algcomparison.TimeoutComparison
- isSquare() - Method in class edu.cmu.tetrad.util.Matrix
- isSquare() - Method in class edu.cmu.tetrad.util.Matrix2
- isSquare(double[][]) - Static method in class edu.cmu.tetrad.util.MatrixUtils
- isStable(Matrix) - Static method in class edu.cmu.tetrad.search.IcaLingD
-
Whether the BHat matrix represents a stable model.
- isStructurallyIdentical(SessionNode) - Method in class edu.cmu.tetrad.session.SessionNode
-
Tests whether two session nodes that are not necessarily object identical are nevertheless identical in structure.
- isSubtrek(List<Node>, List<Node>) - Method in class edu.cmu.tetrad.search.work_in_progress.Dci
-
Determines whether one trek is a subtrek of another trek
- isSupportConnected() - Method in class edu.cmu.tetrad.sem.EmpiricalCdf
- isSupportLowerBoundInclusive() - Method in class edu.cmu.tetrad.sem.EmpiricalCdf
-
Deprecated.
- isSupportUpperBoundInclusive() - Method in class edu.cmu.tetrad.sem.EmpiricalCdf
-
Deprecated.
- isSymmetric(double) - Method in class edu.cmu.tetrad.util.Matrix
- isSymmetric(double) - Method in class edu.cmu.tetrad.util.Matrix2
- isSymmetric(double[][], double) - Static method in class edu.cmu.tetrad.util.MatrixUtils
- isTabDelimitedTables() - Method in class edu.cmu.tetrad.algcomparison.Comparison
- isTabDelimitedTables() - Method in class edu.cmu.tetrad.algcomparison.TimeoutComparison
- isTierForbiddenWithin(int) - Method in class edu.cmu.tetrad.data.Knowledge
-
Checks whether it is the case that any variable is forbidden by any other variable within a given tier.
- isTimeLagModel() - Method in class edu.cmu.tetrad.graph.Dag
- isTimeLagModel() - Method in class edu.cmu.tetrad.graph.EdgeListGraph
- isTimeLagModel() - Method in interface edu.cmu.tetrad.graph.Graph
- isTimeLagModel() - Method in class edu.cmu.tetrad.graph.LagGraph
- isTimeLagModel() - Method in class edu.cmu.tetrad.graph.SemGraph
- isTimeLagModel() - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- isTruthAdj() - Method in class edu.cmu.tetrad.algcomparison.statistic.utils.ArrowConfusion
-
Returns true if the truth graph is used to determine adjacency for arrowhead FP's.
- isUnderlineTriple(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.Dag
-
States whether r-s-r is an underline triple or not.
- isUnderlineTriple(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
-
States whether r-s-r is an underline triple or not.
- isUnderlineTriple(Node, Node, Node) - Method in interface edu.cmu.tetrad.graph.Graph
-
States whether r-s-r is an underline triple or not.
- isUnderlineTriple(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.LagGraph
-
States whether r-s-r is an underline triple or not.
- isUnderlineTriple(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.SemGraph
-
States whether r-s-r is an underline triple or not.
- isUnderlineTriple(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
-
States whether r-s-r is an underline triple or not.
- isUnderlineTriple(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.Underlines
-
States whether r-s-r is an underline triple or not.
- isUndirectedEdge(Edge) - Static method in class edu.cmu.tetrad.graph.Edges
- isUndirectedFromTo(Node, Node) - Method in class edu.cmu.tetrad.graph.Paths
- isUnshieldedCollider(Node, Node, Node) - Method in class edu.cmu.tetrad.search.utils.DagSepsets
-
True iff i*-*j*-*k is an unshielded collider.
- isUnshieldedCollider(Node, Node, Node) - Method in interface edu.cmu.tetrad.search.utils.SepsetProducer
- isUnshieldedCollider(Node, Node, Node) - Method in class edu.cmu.tetrad.search.utils.SepsetsConservative
- isUnshieldedCollider(Node, Node, Node) - Method in class edu.cmu.tetrad.search.utils.SepsetsGreedy
- isUnshieldedCollider(Node, Node, Node) - Method in class edu.cmu.tetrad.search.utils.SepsetsPossibleMsep
- isUnshieldedCollider(Node, Node, Node) - Method in class edu.cmu.tetrad.search.utils.SepsetsSet
- isVariableListEqual(int[]) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.PolynomialTerm
-
Returns true iff the given variable list is equal to the variable list of this term.
- isVerbose() - Method in class edu.cmu.tetrad.cluster.KMeans
- isVerbose() - Method in class edu.cmu.tetrad.data.CorrelationMatrixOnTheFly
- isVerbose() - Method in class edu.cmu.tetrad.data.CovarianceMatrixOnTheFly
- isVerbose() - Method in class edu.cmu.tetrad.search.Cfci
-
Whether verbose output (about independencies) is output.
- isVerbose() - Method in class edu.cmu.tetrad.search.Fasd
- isVerbose() - Method in interface edu.cmu.tetrad.search.IndependenceTest
-
Returns true if the test prints verbose output.
- isVerbose() - Method in class edu.cmu.tetrad.search.IndTestIod
-
Returns true if the test is verbose.
- isVerbose() - Method in class edu.cmu.tetrad.search.Pcd
- isVerbose() - Method in class edu.cmu.tetrad.search.Rfci
-
Returns whether verbose output should be printed.
- isVerbose() - Method in class edu.cmu.tetrad.search.score.GicScores
- isVerbose() - Method in class edu.cmu.tetrad.search.score.IndTestScore
- isVerbose() - Method in class edu.cmu.tetrad.search.score.SemBicScore
- isVerbose() - Method in class edu.cmu.tetrad.search.SvarFci
-
Returns whether verbose output is to be printed.
- isVerbose() - Method in class edu.cmu.tetrad.search.test.IndTestChiSquare
-
Returns true if verbose output should be printed.
- isVerbose() - Method in class edu.cmu.tetrad.search.test.IndTestConditionalCorrelation
-
Returns true if verbose output should be printed.
- isVerbose() - Method in class edu.cmu.tetrad.search.test.IndTestConditionalGaussianLrt
-
Returns true iff verbose output should be printed.
- isVerbose() - Method in class edu.cmu.tetrad.search.test.IndTestDegenerateGaussianLrt
-
Returns true iff verbose output should be printed.
- isVerbose() - Method in class edu.cmu.tetrad.search.test.IndTestFisherZ
-
Returns true iff verbose output should be printed.
- isVerbose() - Method in class edu.cmu.tetrad.search.test.IndTestFisherZConcatenateResiduals
-
Return True if verbose output should be printed.
- isVerbose() - Method in class edu.cmu.tetrad.search.test.IndTestFisherZFisherPValue
-
Returns True if verbose output should be printed.
- isVerbose() - Method in class edu.cmu.tetrad.search.test.IndTestGSquare
-
Returns True if verbose output is printed.
- isVerbose() - Method in class edu.cmu.tetrad.search.test.IndTestHsic
- isVerbose() - Method in class edu.cmu.tetrad.search.test.IndTestIndependenceFacts
-
Returns whether verbose output is to be printed.
- isVerbose() - Method in class edu.cmu.tetrad.search.test.IndTestMulti
-
Returns true if the test prints verbose output.
- isVerbose() - Method in class edu.cmu.tetrad.search.test.IndTestMvpLrt
-
Returns true if verbose output is printed.
- isVerbose() - Method in class edu.cmu.tetrad.search.test.IndTestProbabilistic
- isVerbose() - Method in class edu.cmu.tetrad.search.test.IndTestRegression
- isVerbose() - Method in class edu.cmu.tetrad.search.test.IndTestTrekSep
-
Returns true if verbose output should be printed.
- isVerbose() - Method in class edu.cmu.tetrad.search.test.Kci
-
Returns true if verbose output is printed.
- isVerbose() - Method in class edu.cmu.tetrad.search.test.MsepTest
-
Returns True just in case verbose output should be printed.
- isVerbose() - Method in class edu.cmu.tetrad.search.test.ScoreIndTest
-
Returns true if verbose ouput should be printed.
- isVerbose() - Method in class edu.cmu.tetrad.search.utils.SepsetsGreedy
- isVerbose() - Method in class edu.cmu.tetrad.search.utils.SepsetsPossibleMsep
- isVerbose() - Method in class edu.cmu.tetrad.search.utils.SepsetsSet
- isVerbose() - Method in class edu.cmu.tetrad.search.utils.SvarFciOrient
-
True iff verbose output should be printed.
- isVerbose() - Method in class edu.cmu.tetrad.search.utils.TsDagToPag
-
True iff verbose output should be printed.
- isVerbose() - Method in class edu.cmu.tetrad.search.work_in_progress.Fas2
- isVerbose() - Method in class edu.cmu.tetrad.search.work_in_progress.GraspTol
- isVerbose() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestCramerT
- isVerbose() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestFisherZGeneralizedInverse
-
Returns True just in case verbose output should be printed.
- isVerbose() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestFisherZPercentIndependent
- isVerbose() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestFisherZRecursive
- isVerbose() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestMixedMultipleTTest
-
Returns whether verbose output should be printed.
- isVerbose() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestMnlrLr
-
Returns whether verbose output should be printed.
- isVerbose() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestMultinomialLogisticRegression
- isVerbose() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestPositiveCorr
- isVerbose() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestSepsetDci
- isVerbose() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestUniformScatter
- isVerbose() - Method in class edu.cmu.tetrad.search.work_in_progress.OtherPermAlgs
- isVerbose() - Method in class edu.cmu.tetrad.search.work_in_progress.ProbabilisticMapIndependence
- isVerbose() - Method in class edu.cmu.tetrad.search.work_in_progress.SemBicScoreDeterministic
- isVerbose() - Method in class edu.cmu.tetrad.search.work_in_progress.VcFas
- isVerbose() - Method in class edu.cmu.tetrad.sem.LargeScaleSimulation
- isVerbose() - Method in class edu.pitt.csb.mgm.IndTestMultinomialLogisticRegressionWald
- isViolatedBy(Graph) - Method in class edu.cmu.tetrad.data.Knowledge
- isWithoutReplacements() - Method in class edu.cmu.tetrad.data.BootstrapSampler
- iterate() - Method in class edu.cmu.tetrad.bayes.FactoredBayesStructuralEM
-
This iterate2 method also uses BdeMetricCache but it uses the factorScoreMD method which can handle missing data and latent variables.
- iterations() - Method in class edu.cmu.tetrad.cluster.KMeans
- iterator() - Method in class edu.pitt.isp.sverchkov.data.DataTableImpl
- ItkPredictorSearch - Class in edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.ideker
-
This class contains methods which implement the algorithm described in the paper " " by Ideker, Thorsen and Karp.
- ItkPredictorSearch(int, int[][], String[]) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.ideker.ItkPredictorSearch
- ItkPredictorSearch.Gene - Class in edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.ideker
- ITR - Static variable in class edu.cmu.tetrad.util.Params
J
- jgpml - package jgpml
- jgpml.covariancefunctions - package jgpml.covariancefunctions
- jointEntropy(int[], int[]) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.reveal.RevealEvaluator
-
This method computes the joint entropy of two arrays.
- jointEntropy(int[], int[]) - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.LTestReveal
- jointEntropy(int[], int[]) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.RevealEvaluator
-
This method computes the joint entropy of two arrays.
- jointEntropy(int[], int[][]) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.reveal.RevealEvaluator
- jointEntropy(int[], int[][]) - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.LTestReveal
- jointEntropy(int[], int[][]) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.RevealEvaluator
- JOptionUtils - Class in edu.cmu.tetrad.util
-
Stores some utility items for displaying JOptionPane messages.
- JOptionUtils() - Constructor for class edu.cmu.tetrad.util.JOptionUtils
- JsonUtils - Class in edu.cmu.tetrad.util
-
Dec 9, 2016 5:43:47 PM
- JsonUtils() - Constructor for class edu.cmu.tetrad.util.JsonUtils
- JunctionTreeAlgorithm - Class in edu.cmu.tetrad.bayes
-
Junction Tree Algorithm.
- JunctionTreeAlgorithm(BayesIm) - Constructor for class edu.cmu.tetrad.bayes.JunctionTreeAlgorithm
- JunctionTreeAlgorithm(Graph, DataModel) - Constructor for class edu.cmu.tetrad.bayes.JunctionTreeAlgorithm
- JunctionTreeUpdater - Class in edu.cmu.tetrad.bayes
-
Jan 21, 2020 11:03:09 AM
- JunctionTreeUpdater(BayesIm) - Constructor for class edu.cmu.tetrad.bayes.JunctionTreeUpdater
- JunctionTreeUpdater(BayesIm, Evidence) - Constructor for class edu.cmu.tetrad.bayes.JunctionTreeUpdater
- JUSTIFIED - Enum constant in enum class edu.cmu.tetrad.util.TextTable.Delimiter
K
- kamadaKawaiLayout(Graph, boolean, double, double, double) - Static method in class edu.cmu.tetrad.graph.LayoutUtil
- KamadaKawaiLayout(Graph) - Constructor for class edu.cmu.tetrad.graph.LayoutUtil.KamadaKawaiLayout
- Kci - Class in edu.cmu.tetrad.algcomparison.independence
-
Wrapper for KCI test.
- Kci - Class in edu.cmu.tetrad.search.test
-
Gives an implementation of the Kernal Independence Test (KCI) by Kun Zhang, which is a general test of conditional independence.
- Kci() - Constructor for class edu.cmu.tetrad.algcomparison.independence.Kci
- Kci(DataSet, double) - Constructor for class edu.cmu.tetrad.search.test.Kci
-
Constructor.
- KCI_ALPHA - Static variable in class edu.cmu.tetrad.util.Params
- KCI_CUTOFF - Static variable in class edu.cmu.tetrad.util.Params
- KCI_EPSILON - Static variable in class edu.cmu.tetrad.util.Params
- KCI_NUM_BOOTSTRAPS - Static variable in class edu.cmu.tetrad.util.Params
- KCI_USE_APPROMATION - Static variable in class edu.cmu.tetrad.util.Params
- kendallsTau(double[], double[]) - Static method in class edu.cmu.tetrad.util.StatUtils
- kernel(double) - Method in class edu.cmu.tetrad.search.Lofs
- Kernel - Interface in edu.cmu.tetrad.search.utils
-
Gives an implemented that is implemented by classes that evaluate scalar valued kernels
- KERNEL_MULTIPLIER - Static variable in class edu.cmu.tetrad.util.Params
- KERNEL_REGRESSION_SAMPLE_SIZE - Static variable in class edu.cmu.tetrad.util.Params
- KERNEL_TYPE - Static variable in class edu.cmu.tetrad.util.Params
- KERNEL_WIDTH - Static variable in class edu.cmu.tetrad.util.Params
- kernel1(double) - Method in class edu.cmu.tetrad.search.Lofs
- kernel2(double) - Method in class edu.cmu.tetrad.search.Lofs
- kernel3(double) - Method in class edu.cmu.tetrad.search.Lofs
- kernel4(double) - Method in class edu.cmu.tetrad.search.Lofs
- kernel5(double) - Method in class edu.cmu.tetrad.search.Lofs
- kernel6(double) - Method in class edu.cmu.tetrad.search.Lofs
- kernel7(double) - Method in class edu.cmu.tetrad.search.Lofs
- kernel8(double) - Method in class edu.cmu.tetrad.search.Lofs
- KernelGaussian - Class in edu.cmu.tetrad.search.utils
-
Soces the Gaussian kernel for a given bandwidth.
- KernelGaussian(double) - Constructor for class edu.cmu.tetrad.search.utils.KernelGaussian
-
Creates a new Gaussian kernel with the given bandwidth
- KernelGaussian(DataSet, Node) - Constructor for class edu.cmu.tetrad.search.utils.KernelGaussian
-
Creates a new Gaussian kernel using the median distance between points to set the bandwidth
- KernelUtils - Class in edu.cmu.tetrad.search.utils
-
Provides various kernel utilities.
- KernelUtils() - Constructor for class edu.cmu.tetrad.search.utils.KernelUtils
- KMeans - Class in edu.cmu.tetrad.cluster
-
Implements the "batch" version of the K Means clustering algorithm-- that is, in one sweep, assign each point to its nearest center, and then in a second sweep, reset each center to the mean of the cluster for that center, repeating until convergence.
- Knowledge - Class in edu.cmu.tetrad.data
-
Stores information about required and forbidden edges and common causes for use in algorithm.
- Knowledge() - Constructor for class edu.cmu.tetrad.data.Knowledge
- Knowledge(Knowledge) - Constructor for class edu.cmu.tetrad.data.Knowledge
- Knowledge(Collection<String>) - Constructor for class edu.cmu.tetrad.data.Knowledge
- KnowledgeBoxInput - Interface in edu.cmu.tetrad.data
-
Tags classes that can yield graphs as input to knowledge.
- KnowledgeEdge - Class in edu.cmu.tetrad.data
-
Implements a knowledge edge X-->Y as a simple ordered pair of strings.
- KnowledgeEdge(String, String) - Constructor for class edu.cmu.tetrad.data.KnowledgeEdge
-
Constructs a knowledge edge for from-->to.
- KnowledgeGroup - Class in edu.cmu.tetrad.data
-
Represents a "Other Group" in Knowledge, which can be understood as: Group1 -> Group2 where there are edges between all members of Group1 to Group2.
- KnowledgeGroup(int) - Constructor for class edu.cmu.tetrad.data.KnowledgeGroup
-
Constructs an empty instance of a knowledge group.
- KnowledgeGroup(int, Set<String>, Set<String>) - Constructor for class edu.cmu.tetrad.data.KnowledgeGroup
-
Constructs a group given the type.
- KnowledgeTransferable - Interface in edu.cmu.tetrad.data
-
Interface implemented by classes that are capable of participating in the transfer of knowledge objects.
- Kpc - Class in edu.cmu.tetrad.search.work_in_progress
-
Kernelized PC algorithm.
- Kpc(DataSet, double) - Constructor for class edu.cmu.tetrad.search.work_in_progress.Kpc
-
Constructs a new PC search using for the given dataset.
- kurtosis - Enum constant in enum class edu.cmu.tetrad.search.Lofs.Score
- kurtosis(double[]) - Static method in class edu.cmu.tetrad.util.StatUtils
- kurtosis(double[], int) - Static method in class edu.cmu.tetrad.util.StatUtils
- kurtosis(long[]) - Static method in class edu.cmu.tetrad.util.StatUtils
- kurtosis(long[], int) - Static method in class edu.cmu.tetrad.util.StatUtils
L
- L - Variable in class jgpml.GaussianProcess
-
Cholesky decomposition of the input
- LAG - Static variable in interface edu.cmu.tetrad.graph.Node
- LaggedEdge - Class in edu.cmu.tetrad.study.gene.tetrad.gene.history
-
wrapper class for passing factor+edge via a propertyChange event
- LaggedEdge(String, LaggedFactor) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.history.LaggedEdge
-
Creates new LaggedEdge
- LaggedFactor - Class in edu.cmu.tetrad.study.gene.tetrad.gene.history
-
Identifies a particular factor (by name) at a particular lag (integer).
- LaggedFactor(LaggedFactor) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.history.LaggedFactor
-
Copy constructor- creates a new object with the same properties as the original
- LaggedFactor(String, int) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.history.LaggedFactor
-
Constructs a new lagged factor with a given name and time lag.
- LagGraph - Class in edu.cmu.tetrad.graph
-
Implements a graph allowing nodes in the getModel time lag to have parents taken from previous time lags.
- LagGraph - Interface in edu.cmu.tetrad.study.gene.tetrad.gene.history
-
Lag graph.
- LagGraph() - Constructor for class edu.cmu.tetrad.graph.LagGraph
- LagGraphParams - Class in edu.cmu.tetrad.study.gene.tetrad.gene.graph
- LagGraphParams(Parameters) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.graph.LagGraphParams
- LAMBDA1 - Static variable in class edu.cmu.tetrad.util.Params
- LargeScaleSimulation - Class in edu.cmu.tetrad.sem
-
Stores a SEM model, pared down, for purposes of simulating data sets with large numbers of variables and sample sizes.
- LargeScaleSimulation(Graph) - Constructor for class edu.cmu.tetrad.sem.LargeScaleSimulation
- LargeScaleSimulation(Graph, List<Node>, int[]) - Constructor for class edu.cmu.tetrad.sem.LargeScaleSimulation
- LAST_ID - Static variable in class edu.cmu.tetrad.data.AbstractVariable
-
The last ID assigned to a variable.
- LATENT - Static variable in class edu.cmu.tetrad.graph.NodeType
- LATENT_MEASURED_IMPURE_PARENTS - Static variable in class edu.cmu.tetrad.util.Params
- LATENT_PREFIX - Static variable in class edu.cmu.tetrad.search.utils.ClusterUtils
- LatentCommonAncestorFalseNegativeBidirected - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- LatentCommonAncestorFalseNegativeBidirected() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.LatentCommonAncestorFalseNegativeBidirected
- LatentCommonAncestorFalsePositiveBidirected - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- LatentCommonAncestorFalsePositiveBidirected() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.LatentCommonAncestorFalsePositiveBidirected
- LatentCommonAncestorRecallBidirected - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- LatentCommonAncestorRecallBidirected() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.LatentCommonAncestorRecallBidirected
- LatentCommonAncestorTruePositiveBidirected - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- LatentCommonAncestorTruePositiveBidirected() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.LatentCommonAncestorTruePositiveBidirected
- latentStructToEdgeListGraph(DMSearch.LatentStructure) - Method in class edu.cmu.tetrad.search.work_in_progress.DMSearch.LatentStructure
- LatentStructure() - Constructor for class edu.cmu.tetrad.search.work_in_progress.DMSearch.LatentStructure
- layoutByCausalOrder(Graph) - Static method in class edu.cmu.tetrad.graph.LayoutUtil
- LayoutUtil - Class in edu.cmu.tetrad.graph
- LayoutUtil() - Constructor for class edu.cmu.tetrad.graph.LayoutUtil
- LayoutUtil.FruchtermanReingoldLayout - Class in edu.cmu.tetrad.graph
-
Lays out a graph by linearly summing repulsive force between all nodes and attractive force between adjacent nodes.
- LayoutUtil.KamadaKawaiLayout - Class in edu.cmu.tetrad.graph
-
Lays out a graph by placing springs between the nodes and letting the system settle (one node at a time).
- learn(double, int) - Method in class edu.pitt.csb.mgm.Mgm
-
Learn MGM traditional way with objective function tolerance.
- learnBackTrack(ConvexProximal, DoubleMatrix1D, double, int) - Method in class edu.pitt.csb.mgm.ProximalGradient
- learnBNRFCI(DataSet, int, Graph) - Method in class edu.cmu.tetrad.calibration.DataForCalibrationRfci
- learnEdges(int) - Method in class edu.pitt.csb.mgm.Mgm
-
Learn MGM using edge convergence using default 3 iterations of no edge changes.
- learnEdges(int, int) - Method in class edu.pitt.csb.mgm.Mgm
-
Learn MGM using edge convergence using edgeChangeTol (see ProximalGradient for documentation).
- LEE_AND_HASTIE - Static variable in class edu.cmu.tetrad.algcomparison.simulation.SimulationTypes
- LeeHastieSimulation - Class in edu.cmu.tetrad.algcomparison.simulation
-
A version of the Lee and Hastic simulation which is guaranteed ot generate a discrete data set.
- LeeHastieSimulation(RandomGraph) - Constructor for class edu.cmu.tetrad.algcomparison.simulation.LeeHastieSimulation
- LEFT_JUSTIFIED - Static variable in class edu.cmu.tetrad.util.TextTable
-
Set
justificationto this if the columns should be left justified. - leftRight(double[], double[]) - Method in class edu.cmu.tetrad.search.Fask
-
A left/right judgment for double[] arrays (data) as input.
- LegalMagRet(boolean, String) - Constructor for class edu.cmu.tetrad.search.utils.GraphSearchUtils.LegalMagRet
- LegalPag - Class in edu.cmu.tetrad.algcomparison.statistic
-
Legal PAG
- LegalPag() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.LegalPag
- LegalPagRet(boolean, String) - Constructor for class edu.cmu.tetrad.search.utils.GraphSearchUtils.LegalPagRet
- LegalPairs - Interface in edu.cmu.tetrad.search.utils
-
Determines whether nodes indexed as (n1, center, n2) form a legal pair of edges in a graph for purposes of some algorithm that uses this information.
- like() - Method in class edu.cmu.tetrad.data.BoxDataSet
- like() - Method in class edu.cmu.tetrad.data.ByteDataBox
- like() - Method in interface edu.cmu.tetrad.data.DataBox
- like() - Method in interface edu.cmu.tetrad.data.DataSet
- like() - Method in class edu.cmu.tetrad.data.DoubleDataBox
- like() - Method in class edu.cmu.tetrad.data.FloatDataBox
- like() - Method in class edu.cmu.tetrad.data.IntDataBox
- like() - Method in class edu.cmu.tetrad.data.LongDataBox
- like() - Method in class edu.cmu.tetrad.data.MixedDataBox
- like() - Method in class edu.cmu.tetrad.data.NumberObjectDataSet
- like() - Method in class edu.cmu.tetrad.data.ShortDataBox
- like() - Method in class edu.cmu.tetrad.data.VerticalDoubleDataBox
- like() - Method in class edu.cmu.tetrad.data.VerticalIntDataBox
- like() - Method in class edu.cmu.tetrad.util.Matrix
- like() - Method in class edu.cmu.tetrad.util.Matrix2
- like() - Method in class edu.cmu.tetrad.util.Vector
- like(String) - Method in class edu.cmu.tetrad.data.AbstractVariable
- like(String) - Method in class edu.cmu.tetrad.data.ContinuousVariable
- like(String) - Method in class edu.cmu.tetrad.data.DiscreteVariable
- like(String) - Method in class edu.cmu.tetrad.graph.GraphNode
- like(String) - Method in interface edu.cmu.tetrad.graph.Node
-
Creates a new node of the same type as this one with the given name.
- like(String) - Method in class edu.cmu.tetrad.session.SessionNode
- LikelihoodRet() - Constructor for class edu.cmu.tetrad.bayes.BayesProperties.LikelihoodRet
- LINEAR_FISHER_MODEL - Static variable in class edu.cmu.tetrad.algcomparison.simulation.SimulationTypes
- LinearFisherModel - Class in edu.cmu.tetrad.algcomparison.simulation
-
Linear Fisher Model.
- LinearFisherModel(RandomGraph) - Constructor for class edu.cmu.tetrad.algcomparison.simulation.LinearFisherModel
- LinearFisherModel(RandomGraph, List<DataModel>) - Constructor for class edu.cmu.tetrad.algcomparison.simulation.LinearFisherModel
- LinearFunction - Class in edu.cmu.tetrad.study.gene.tetrad.gene.history
-
Implements a linear update function, Gi.0 = L(Parents(G0.0)) + ei, where P is a polynomial function and ei is a random noise term.
- LinearFunction(LagGraph) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.history.LinearFunction
-
Constructs a polyomial function where each factor is given a zero polynomial.
- LinearGaussian - Annotation Interface in edu.cmu.tetrad.annotation
-
Data with Gaussian variables that have linear relationships.
- LinearSimExp1 - Class in edu.cmu.tetrad.study.gene.tetrad.gene.simexp
-
Implements a particular simulation for experimental purposes.
- LinearSimExp1(String) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.simexp.LinearSimExp1
- LinearSineSimulation - Class in edu.cmu.tetrad.algcomparison.simulation
-
A simulation method based on the mixed variable polynomial assumption.
- LinearSineSimulation(RandomGraph) - Constructor for class edu.cmu.tetrad.algcomparison.simulation.LinearSineSimulation
- LingamStudy - Class in edu.cmu.tetrad.study.examples.conditions
-
An example script to simulate data and run a comparison analysis on it.
- LingamStudy() - Constructor for class edu.cmu.tetrad.study.examples.conditions.LingamStudy
- listColliderTriples(Graph) - Static method in class edu.cmu.tetrad.graph.GraphUtils
- listUnmeasuredLatents() - Method in interface edu.cmu.tetrad.sem.ISemIm
- listUnmeasuredLatents() - Method in class edu.cmu.tetrad.sem.SemIm
- lngamma(double) - Static method in class edu.cmu.tetrad.util.ProbUtils
-
This is a more literal (that is, exact) copy of the log gamma method from Numerical Recipes than the following one.
- lnXpluslnY(double, double) - Method in class edu.pitt.dbmi.algo.bayesian.constraint.inference.BCInference
-
Takes ln(x) and ln(y) as input, and returns ln(x + y)
- lnXplusY(double, double) - Method in class edu.cmu.tetrad.study.RBExperiments
- load(String, int, int) - Static method in class jgpml.CsvtoMatrix
-
Load data
- loadContinuousData(File, String, char, String, boolean, Delimiter, boolean) - Static method in class edu.cmu.tetrad.data.SimpleDataLoader
-
Loads a continuous dataset from a file.
- LoadContinuousDataAndGraphs - Class in edu.cmu.tetrad.data.simulation
-
Load data sets and graphs from a directory.
- LoadContinuousDataAndGraphs(String) - Constructor for class edu.cmu.tetrad.data.simulation.LoadContinuousDataAndGraphs
- LoadContinuousDataAndSingleGraph - Class in edu.cmu.tetrad.data.simulation
-
Load data sets and graphs from a directory.
- LoadContinuousDataAndSingleGraph(String) - Constructor for class edu.cmu.tetrad.data.simulation.LoadContinuousDataAndSingleGraph
- LoadContinuousDataSmithSim - Class in edu.cmu.tetrad.data.simulation
-
Load data sets and graphs from a directory.
- LoadContinuousDataSmithSim(String) - Constructor for class edu.cmu.tetrad.data.simulation.LoadContinuousDataSmithSim
- loadCovarianceMatrix(char[], String, DelimiterType, char, String) - Static method in class edu.cmu.tetrad.data.SimpleDataLoader
-
Parses a covariance matrix from a char[] array.
- loadCovarianceMatrix(File, String, DelimiterType, char, String) - Static method in class edu.cmu.tetrad.data.SimpleDataLoader
-
Parses the given files for a tabular data set, returning a RectangularDataSet if successful.
- loadData(String, String) - Static method in class edu.pitt.csb.mgm.MixedUtils
- LoadDataAndGraphs - Class in edu.cmu.tetrad.data.simulation
-
Load data sets and graphs from a directory.
- LoadDataAndGraphs(String) - Constructor for class edu.cmu.tetrad.data.simulation.LoadDataAndGraphs
- LoadDataFromFileWithoutGraph - Class in edu.cmu.tetrad.data.simulation
-
Load data sets and graphs from a directory.
- LoadDataFromFileWithoutGraph(String) - Constructor for class edu.cmu.tetrad.data.simulation.LoadDataFromFileWithoutGraph
- loadDataSet(String, String) - Static method in class edu.pitt.csb.mgm.MixedUtils
- loadDelim(String, String) - Static method in class edu.pitt.csb.mgm.MixedUtils
- loadDiscreteData(File, String, char, String, boolean, Delimiter, boolean) - Static method in class edu.cmu.tetrad.data.SimpleDataLoader
-
Loads a discrete dataset from a file.
- LOADED_FROM_FILES - Static variable in class edu.cmu.tetrad.algcomparison.simulation.SimulationTypes
- loadGraph(File) - Static method in class edu.cmu.tetrad.graph.GraphSaveLoadUtils
- loadGraphBNTPcMatrix(List<Node>, DataSet) - Static method in class edu.cmu.tetrad.graph.GraphSaveLoadUtils
- loadGraphJson(File) - Static method in class edu.cmu.tetrad.graph.GraphSaveLoadUtils
- loadGraphPcalg(File) - Static method in class edu.cmu.tetrad.graph.GraphSaveLoadUtils
- loadGraphPcAlgMatrix(DataSet) - Static method in class edu.cmu.tetrad.algcomparison.algorithm.external.ExternalAlgorithmPcalgPc
- loadGraphRMatrix(Graph) - Static method in class edu.cmu.tetrad.graph.GraphSaveLoadUtils
- loadGraphRuben(File) - Static method in class edu.cmu.tetrad.graph.GraphSaveLoadUtils
- loadGraphTxt(File) - Static method in class edu.cmu.tetrad.graph.GraphSaveLoadUtils
- loadKnowledge(File, DelimiterType, String) - Static method in class edu.cmu.tetrad.data.SimpleDataLoader
-
Loads knowledge from a file.
- loadMixedData(File, String, char, String, boolean, int, Delimiter, boolean) - Static method in class edu.cmu.tetrad.data.SimpleDataLoader
-
Loads a mixed dataset from a file.
- loadRSpecial(File) - Static method in class edu.cmu.tetrad.graph.GraphSaveLoadUtils
- localScore() - Method in class edu.cmu.tetrad.search.utils.GrowShrinkTree
- localScore(int) - Method in class edu.cmu.tetrad.search.score.GraphScore
- localScore(int) - Method in class edu.cmu.tetrad.search.score.ImagesScore
-
Returns the (aggregate) local node score, which is obtained by averaging the local scores obtained from each individual score provided in the constructor, excluding scores that are returned as undefined (which are left out of the average).
- localScore(int) - Method in class edu.cmu.tetrad.search.score.IndTestScore
- localScore(int) - Method in interface edu.cmu.tetrad.search.score.Score
-
Returns the local score of the gien node in the graph.
- localScore(int[]) - Method in class edu.cmu.tetrad.search.utils.GrowShrinkTree
- localScore(int, int) - Method in class edu.cmu.tetrad.search.score.GraphScore
- localScore(int, int) - Method in class edu.cmu.tetrad.search.score.ImagesScore
-
Returns the (aggregate) local score for a variable given one of its parents, which is obtained by averaging the local such scores obtained from each individual score provided in the constructor, excluding scores that are returned as undefined (which are left out of the average).
- localScore(int, int) - Method in class edu.cmu.tetrad.search.score.IndTestScore
-
Specialized scoring method for a single parent.
- localScore(int, int) - Method in interface edu.cmu.tetrad.search.score.Score
-
Returns the local score of the graph.
- localScore(int, int[]) - Method in class edu.cmu.tetrad.search.score.BdeScore
-
Returns the score for the given parent given its parents, where these are specified as column indices into the dataset.
- localScore(int, int[]) - Method in class edu.cmu.tetrad.search.score.BdeuScore
-
Calculates the BDeu score of a node given its parents.
- localScore(int, int...) - Method in class edu.cmu.tetrad.search.score.ConditionalGaussianScore
-
Calculates the sample likelihood and BIC score for i given its parents in a simple SEM model.
- localScore(int, int...) - Method in class edu.cmu.tetrad.search.score.DegenerateGaussianScore
-
Calculates the sample likelihood and BIC score for i given its parents in a simple SEM model.
- localScore(int, int[]) - Method in class edu.cmu.tetrad.search.score.DiscreteBicScore
-
Returns the score of the given nodes given its parents.
- localScore(int, int...) - Method in class edu.cmu.tetrad.search.score.EbicScore
-
Returns the score of the node i given its parents.
- localScore(int, int...) - Method in class edu.cmu.tetrad.search.score.GicScores
- localScore(int, int[]) - Method in class edu.cmu.tetrad.search.score.GraphScore
-
Calculates the sample likelihood and BIC score for y given its z in a simple SEM model.
- localScore(int, int[]) - Method in class edu.cmu.tetrad.search.score.ImagesScore
-
Returns the (aggregate) local score for a variable given its parents, which is obtained by averaging the local such scores obtained from each individual score provided in the constructor, excluding scores that are returned as undefined (which are left out of the average).
- localScore(int, int[]) - Method in class edu.cmu.tetrad.search.score.IndTestScore
-
Calculates the sample likelihood and BIC score for i, given its parents in a simple SEM model
- localScore(int, int...) - Method in class edu.cmu.tetrad.search.score.MvpScore
-
The local score of the child given its parents.
- localScore(int, int...) - Method in class edu.cmu.tetrad.search.score.PoissonPriorScore
- localScore(int, int...) - Method in interface edu.cmu.tetrad.search.score.Score
-
The score of a node given its parents.
- localScore(int, int...) - Method in class edu.cmu.tetrad.search.score.SemBicScore
- localScore(int, int...) - Method in class edu.cmu.tetrad.search.score.ZsbScore
-
Returns the score for the child given the parents.
- localScore(int, int...) - Method in class edu.cmu.tetrad.search.work_in_progress.MagSemBicScore
-
Return the BIC score for a node given its parents.
- localScore(int, int...) - Method in class edu.cmu.tetrad.search.work_in_progress.MnlrScore
-
The local score of the child given its parents.
- localScore(int, int...) - Method in class edu.cmu.tetrad.search.work_in_progress.SemBicScoreDeterministic
-
Calculates the sample likelihood and BIC score for i given its parents in a simple SEM model
- localScore(int, int[], int) - Method in class edu.cmu.tetrad.search.score.ImagesScore
- localScoreDiff(int, int) - Method in class edu.cmu.tetrad.search.score.GraphScore
-
The "unconditional difference."
- localScoreDiff(int, int) - Method in interface edu.cmu.tetrad.search.score.Score
-
Returns the local score difference of the graph.
- localScoreDiff(int, int, int[]) - Method in class edu.cmu.tetrad.search.score.BdeScore
-
Returns the different between localScore(y | z, x) and localScore(y | z)
- localScoreDiff(int, int, int[]) - Method in class edu.cmu.tetrad.search.score.BdeuScore
-
Calculates localScore(y | z, x) - localScore(y | z).
- localScoreDiff(int, int, int[]) - Method in class edu.cmu.tetrad.search.score.ConditionalGaussianScore
-
Calculates localScore(y | z, x) - localScore(z).
- localScoreDiff(int, int, int[]) - Method in class edu.cmu.tetrad.search.score.DegenerateGaussianScore
- localScoreDiff(int, int, int[]) - Method in class edu.cmu.tetrad.search.score.DiscreteBicScore
-
Returns localScore(y | z, x) - localScore(y | z).
- localScoreDiff(int, int, int[]) - Method in class edu.cmu.tetrad.search.score.EbicScore
- localScoreDiff(int, int, int[]) - Method in class edu.cmu.tetrad.search.score.GicScores
- localScoreDiff(int, int, int[]) - Method in class edu.cmu.tetrad.search.score.GraphScore
-
Returns a "score difference", which amounts to a conditional local scoring criterion results
- localScoreDiff(int, int, int[]) - Method in class edu.cmu.tetrad.search.score.ImagesScore
-
Returns the average of the individual scores returned from each component score from their localScoreDiff methods.
- localScoreDiff(int, int, int[]) - Method in class edu.cmu.tetrad.search.score.IndTestScore
- localScoreDiff(int, int, int[]) - Method in class edu.cmu.tetrad.search.score.MvpScore
-
localScore(y | z, x) - localScore(y | z).
- localScoreDiff(int, int, int[]) - Method in class edu.cmu.tetrad.search.score.PoissonPriorScore
- localScoreDiff(int, int, int[]) - Method in interface edu.cmu.tetrad.search.score.Score
-
Returns the score difference of the graph.
- localScoreDiff(int, int, int[]) - Method in class edu.cmu.tetrad.search.score.SemBicScore
- localScoreDiff(int, int, int[]) - Method in class edu.cmu.tetrad.search.score.ZsbScore
-
Returns localScore(y | z, x) - localScore(y | z).
- localScoreDiff(int, int, int[]) - Method in class edu.cmu.tetrad.search.work_in_progress.MagSemBicScore
- localScoreDiff(int, int, int[]) - Method in class edu.cmu.tetrad.search.work_in_progress.MnlrScore
-
localScore(y | z, x) - localScore(y | z).
- localScoreDiff(int, int, int[]) - Method in class edu.cmu.tetrad.search.work_in_progress.SemBicScoreDeterministic
- LOCK - Static variable in class edu.cmu.tetrad.graph.NodeType
- Lofs - Class in edu.cmu.tetrad.search
-
Implements a number of methods which take a fixed graph as input and use linear, non-Gaussian methods to orient the edges in the graph.
- Lofs(Graph, List<DataSet>) - Constructor for class edu.cmu.tetrad.search.Lofs
-
Constructor.
- Lofs.Rule - Enum Class in edu.cmu.tetrad.search
-
Give a list of options for rules for doing the non-Gaussian orientations.
- Lofs.Score - Enum Class in edu.cmu.tetrad.search
-
Gives a list of options for non-Gaussian transformations that can be used for some scores.
- log(String, String) - Method in class edu.cmu.tetrad.util.TetradLogger
-
Logs the given message with a newline associated with the given event.
- logbeta(double, double) - Static method in class edu.cmu.tetrad.util.ProbUtils
-
Calculates the log beta function of p and q.
- logChoose(int, int) - Static method in class edu.cmu.tetrad.util.MathUtils
- logClusters(Set<Set<Integer>>, List<Node>) - Static method in class edu.cmu.tetrad.search.utils.ClusterUtils
- logCombinations(int, int) - Static method in class edu.cmu.tetrad.util.ChoiceGenerator
- logcosh - Enum constant in enum class edu.cmu.tetrad.search.Lofs.Score
- LOGCOSH - Static variable in class edu.cmu.tetrad.search.FastIca
-
One of the function types that can be used to approximate negative entropy.
- logCoshExp() - Static method in class edu.cmu.tetrad.util.StatUtils
- logCoshScore(double[]) - Static method in class edu.cmu.tetrad.util.StatUtils
- logData(DataSet, double, boolean, int) - Static method in class edu.cmu.tetrad.data.DataTransforms
-
Log or unlog data
- logDataModelList(String, DataModelList) - Static method in class edu.cmu.tetrad.data.LogDataUtils
- LogDataUtils - Class in edu.cmu.tetrad.data
-
Sundry methods for logging data.
- LogDataUtils() - Constructor for class edu.cmu.tetrad.data.LogDataUtils
- logFactorial(int) - Static method in class edu.cmu.tetrad.util.MathUtils
- logistic(double) - Static method in class edu.cmu.tetrad.util.MathUtils
- LogisticRegression - Class in edu.cmu.tetrad.regression
-
Implements a logistic regression algorithm based on a Javascript implementation by John Pezzullo.
- LogisticRegression(DataSet) - Constructor for class edu.cmu.tetrad.regression.LogisticRegression
-
A mixed data set.
- LogisticRegression.Result - Class in edu.cmu.tetrad.regression
- LogNormal - Class in edu.cmu.tetrad.util.dist
-
Represents a lognormal distribution for purposes of sampling.
- LogNormal(double) - Constructor for class edu.cmu.tetrad.util.dist.LogNormal
- logsum(List<Double>) - Static method in class edu.cmu.tetrad.util.StatUtils
- logtheta - Variable in class jgpml.GaussianProcess
-
hyperparameters
- LogUtils - Class in edu.cmu.tetrad.util
-
Sets up streams for logging via the Java logging API.
- LogUtilsSearch - Class in edu.cmu.tetrad.search.utils
-
Contains utilities for logging search steps.
- LogUtilsSearch() - Constructor for class edu.cmu.tetrad.search.utils.LogUtilsSearch
- LongDataBox - Class in edu.cmu.tetrad.data
-
Stores a 2D array of long data.
- LongDataBox(long[][]) - Constructor for class edu.cmu.tetrad.data.LongDataBox
-
Constructs a new data box using the given 2D long data array as data.
- LOWER_BOUND - Static variable in class edu.cmu.tetrad.util.Params
- LPAREN - Enum constant in enum class edu.cmu.tetrad.calculator.parser.Token
- LT - Static variable in class edu.cmu.tetrad.sem.ParamConstraintType
-
A "less than" constraint.
- LTestBoolSearch - Class in edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.akutsu
-
This is merely a main program used to read a binarized measurement data set and to instantiate a BoolSearch and run one or more search methods of that instance.
- LTestBoolSearch - Class in edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin
-
This is merely a main program used to read a binarized measurement data set and to instantiate a BoolSearch and run one or more search methods of that instance.
- LTestBoolSearch() - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.akutsu.LTestBoolSearch
- LTestBoolSearch() - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.LTestBoolSearch
- LTester - Class in edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.biolingua
-
Class that makes some very simple tests on the classes LtMatrix, Graph, and Biolingua
- LTester() - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.biolingua.LTester
- LTestPredictorSearch - Class in edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.ideker
- LTestPredictorSearch() - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.ideker.LTestPredictorSearch
- LTestQnet3 - Class in edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.akutsu
- LTestQnet3() - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.akutsu.LTestQnet3
- LTestReveal - Class in edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin
- LTestReveal() - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.LTestReveal
- LTestRevealSearch - Class in edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.reveal
-
This is merely a main program used to read a binarized measurement data set and to instantiate a RevealSearch and run one or more search methods of that instance.
- LTestRevealSearch - Class in edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin
-
This is merely a main program used to read a binarized measurement data set and to instantiate a RevealSearch and run one or more search methods of that instance.
- LTestRevealSearch() - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.reveal.LTestRevealSearch
- LTestRevealSearch() - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.LTestRevealSearch
- LTestSsys1 - Class in edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.akutsu
- LTestSsys1() - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.akutsu.LTestSsys1
- LTMatrix - Class in edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util
-
Implements a space-efficient Lower Triangular Matrix of elements of type
short - LTMatrix(String) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.LTMatrix
-
Creates a lower triangular matrix reading it from file
fname. - LTMatrix(String, int) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.LTMatrix
-
Creates a lower triangular matrix with
nrowsrows. - LTMatrixF - Class in edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util
-
Implements a space-efficient Lower Triangular Matrix of elements of type
float - LTMatrixF(String) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.LTMatrixF
-
Creates a lower triangular matrix reading it from file
fname. - LTMatrixF(String, int) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.LTMatrixF
-
Creates a lower triangular matrix with
nrowsrows.
M
- m - Variable in class edu.pitt.isp.sverchkov.data.AdTree
-
The number of attributes.
- MagSemBicScore - Class in edu.cmu.tetrad.algcomparison.score
-
Wrapper for linear, Gaussian SEM BIC score.
- MagSemBicScore - Class in edu.cmu.tetrad.search.work_in_progress
-
Gives a BIC score for a linear, Gaussian MAG (Mixed Ancestral Graph).
- MagSemBicScore() - Constructor for class edu.cmu.tetrad.algcomparison.score.MagSemBicScore
- MagSemBicScore(DataSet, boolean) - Constructor for class edu.cmu.tetrad.search.work_in_progress.MagSemBicScore
-
Constructor.
- MagSemBicScore(ICovarianceMatrix) - Constructor for class edu.cmu.tetrad.search.work_in_progress.MagSemBicScore
-
Constructor.
- MagSemBicTest - Class in edu.cmu.tetrad.algcomparison.independence
-
Wrapper for Fisher Z test.
- MagSemBicTest() - Constructor for class edu.cmu.tetrad.algcomparison.independence.MagSemBicTest
- main(String...) - Static method in class edu.cmu.tetrad.algcomparison.examples.CompareExternalAlgorithms
- main(String...) - Static method in class edu.cmu.tetrad.algcomparison.examples.ExampleCompareFromFiles
- main(String...) - Static method in class edu.cmu.tetrad.algcomparison.examples.ExampleCompareSimulation
- main(String...) - Static method in class edu.cmu.tetrad.algcomparison.examples.ExampleCompareSimulation2
- main(String...) - Static method in class edu.cmu.tetrad.algcomparison.examples.ExampleCompareSimulationTimeSeries
- main(String...) - Static method in class edu.cmu.tetrad.algcomparison.examples.ExampleNonlinearSave
- main(String...) - Static method in class edu.cmu.tetrad.algcomparison.examples.ExampleSave
- main(String...) - Static method in class edu.cmu.tetrad.algcomparison.examples.MVPCompareFromFiles
- main(String...) - Static method in class edu.cmu.tetrad.algcomparison.examples.RunConfig
- main(String...) - Static method in class edu.cmu.tetrad.algcomparison.examples.RunKemmeren
- main(String...) - Static method in class edu.cmu.tetrad.algcomparison.examples.Save
- main(String...) - Static method in class edu.cmu.tetrad.algcomparison.examples.SaveDGSimulations
- main(String...) - Static method in class edu.cmu.tetrad.algcomparison.examples.TestBoss
- main(String...) - Static method in class edu.cmu.tetrad.algcomparison.examples.TestDegenerateGaussian
- main(String[]) - Static method in class edu.cmu.tetrad.calibration.DataForCalibrationRfci
- main(String[]) - Static method in class edu.cmu.tetrad.classify.ClassifierMbDiscrete
-
Runs MbClassify using moves-line arguments.
- main(String[]) - Static method in class edu.cmu.tetrad.graph.Paths.AllCliquesAlgorithm
- main(String...) - Static method in class edu.cmu.tetrad.search.utils.GraphoidAxioms
-
The main methods.
- main(String[]) - Static method in class edu.cmu.tetrad.search.utils.HungarianAlgorithm
- main(String...) - Static method in class edu.cmu.tetrad.search.work_in_progress.IndTestUniformScatter
- main(String...) - Static method in class edu.cmu.tetrad.simulation.GdistanceApply
- main(String...) - Static method in class edu.cmu.tetrad.simulation.GdistanceRandomApply
- main(String...) - Static method in class edu.cmu.tetrad.simulation.GdistanceTest
- main(String...) - Static method in class edu.cmu.tetrad.simulation.HsimCompareRepeat
- main(String[]) - Static method in class edu.cmu.tetrad.simulation.HsimEvalFromData
- main(String[]) - Static method in class edu.cmu.tetrad.simulation.HsimRepeatAuto
- main(String[]) - Static method in class edu.cmu.tetrad.simulation.HsimSchedule
- main(String[]) - Static method in class edu.cmu.tetrad.simulation.HsimStudy
- main(String[]) - Static method in class edu.cmu.tetrad.simulation.HsimStudyAuto
- main(String...) - Static method in class edu.cmu.tetrad.study.examples.conditions.BryanSensitivityStudy
- main(String...) - Static method in class edu.cmu.tetrad.study.examples.conditions.Condition1
- main(String...) - Static method in class edu.cmu.tetrad.study.examples.conditions.Condition2
- main(String...) - Static method in class edu.cmu.tetrad.study.examples.conditions.ExampleCompareFromFiles
- main(String...) - Static method in class edu.cmu.tetrad.study.examples.conditions.ExampleCompareSimulation
- main(String...) - Static method in class edu.cmu.tetrad.study.examples.conditions.ExampleCompareSimulationDiscrete
- main(String...) - Static method in class edu.cmu.tetrad.study.examples.conditions.ExampleFirstInflection
- main(String...) - Static method in class edu.cmu.tetrad.study.examples.conditions.ExampleSave
- main(String...) - Static method in class edu.cmu.tetrad.study.examples.conditions.ExampleStars
- main(String...) - Static method in class edu.cmu.tetrad.study.examples.conditions.LingamStudy
- main(String[]) - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.akutsu.LTestBoolSearch
- main(String[]) - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.akutsu.LTestQnet3
- main(String[]) - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.akutsu.LTestSsys1
- main(String[]) - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.biolingua.BiolinguaRunner
- main(String[]) - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.biolingua.LTester
- main(String[]) - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.ideker.LTestPredictorSearch
- main(String[]) - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.ideker.ReadControl
- main(String[]) - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.ideker.ReadIdeker
- main(String[]) - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.reveal.LTestRevealSearch
- main(String[]) - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.LTestBoolSearch
- main(String[]) - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.LTestReveal
- main(String[]) - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.LTestRevealSearch
- main(String[]) - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.SimulateNetwork
- main(String[]) - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.SimulateNetworkMain
- main(String[]) - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.simexp.LinearSimExp1
- main(String[]) - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.util.HandleyConvert
-
Converts the graph file from the moves line.
- main(String...) - Static method in class edu.cmu.tetrad.study.performance.ComparisonScript
- main(String...) - Static method in class edu.cmu.tetrad.study.performance.ExploreComparison
- main(String...) - Static method in class edu.cmu.tetrad.study.performance.PerformanceTests
- main(String...) - Static method in class edu.cmu.tetrad.study.performance.PerformanceTestsDan
- main(String[]) - Static method in class edu.cmu.tetrad.study.RBExperiments
- main(String[]) - Static method in class edu.cmu.tetrad.util.RandomUtil
- main(String[]) - Static method in class edu.cmu.tetrad.util.UniformityTest
- main(String[]) - Static method in class edu.pitt.csb.mgm.ExampleMixedSearch
- main(String[]) - Static method in class edu.pitt.csb.mgm.ExploreIndepTests
- main(String[]) - Static method in class edu.pitt.csb.mgm.Mgm
- main(String[]) - Static method in class edu.pitt.csb.mgm.MixedUtils
- main(String[]) - Static method in class edu.pitt.csb.stability.StabilityUtils
- main(String[]) - Static method in class edu.pitt.dbmi.algo.bayesian.constraint.inference.BayesianConstraintInference
-
Main method.
- main(String[]) - Static method in class edu.pitt.dbmi.algo.bayesian.constraint.inference.BayesianConstraintInferenceTest
-
Main method.
- main(String[]) - Static method in class edu.pitt.isp.sverchkov.data.AdTreeTest
-
Test the AD tree
- main(String[]) - Static method in class jgpml.covariancefunctions.CovLINard
- main(String[]) - Static method in class jgpml.covariancefunctions.CovLINone
- main(String[]) - Static method in class jgpml.covariancefunctions.CovNNone
- main(String[]) - Static method in class jgpml.covariancefunctions.CovNNoneNoise
- main(String[]) - Static method in class jgpml.covariancefunctions.CovSEiso
- main(String[]) - Static method in class jgpml.CsvtoMatrix
-
Simple example of how to use this class.
- main(String[]) - Static method in class jgpml.GaussianProcess
-
A simple test
- majority - Enum constant in enum class edu.cmu.tetrad.search.utils.ResolveSepsets.Method
- majority - Enum constant in enum class edu.cmu.tetrad.search.work_in_progress.ResolveSepsetsDci.Method
- Majority - Enum constant in enum class edu.pitt.dbmi.algo.resampling.ResamplingEdgeEnsemble
- makeContinuousData(DataSet) - Static method in class edu.pitt.csb.mgm.MixedUtils
- makeDAG(int, double, int) - Method in class edu.cmu.tetrad.calibration.DataForCalibrationRfci
- makeGraph(Matrix, List<Node>) - Static method in class edu.cmu.tetrad.search.IcaLingD
-
Returns a graph given a coefficient matrix and a list of variables.
- makeGraph(List<Cstar.Record>) - Method in class edu.cmu.tetrad.search.Cstar
-
Makes a graph of the estimated predictors to the effect.
- makeLatexTable(String[][]) - Static method in class edu.cmu.tetrad.simulation.HsimUtils
- makeMixedData(DataSet, Map<String, Integer>) - Static method in class edu.pitt.csb.mgm.MixedUtils
- makeMixedData(DataSet, Map<String, String>, int) - Static method in class edu.pitt.csb.mgm.MixedUtils
- makeMixedGraph(Graph, Map<String, Integer>) - Static method in class edu.pitt.csb.mgm.MixedUtils
- makeTable(LinkedList<Cstar.Record>) - Method in class edu.cmu.tetrad.search.Cstar
-
Returns a text table from the given records
- makeValidOrder(List<Node>) - Method in class edu.cmu.tetrad.graph.Paths
- makeVertIntBox(DataSet) - Static method in class edu.cmu.tetrad.simulation.HsimUtils
- ManipulatingBayesUpdater - Interface in edu.cmu.tetrad.bayes
-
Interface for a Bayes updating algorithm that's capable of doing manipulation.
- Manipulation - Class in edu.cmu.tetrad.bayes
-
Stores information for a variable source about evidence we have for each variable as well as whether each variable has been manipulated.
- Manipulation(Manipulation) - Constructor for class edu.cmu.tetrad.bayes.Manipulation
-
Copy constructor.
- Manipulation(VariableSource) - Constructor for class edu.cmu.tetrad.bayes.Manipulation
-
Constructs a container for evidence for the given Bayes IM.
- MANUAL - Enum constant in enum class edu.cmu.tetrad.search.score.GicScores.RuleType
- MANUAL - Static variable in class edu.cmu.tetrad.bayes.MlBayesIm
-
Inidicates that new rows in this BayesIm should be initialized as unknowns, forcing them to be specified manually.
- ManualActiveLagGraph - Class in edu.cmu.tetrad.study.gene.tetrad.gene.graph
-
Constructs as a (manual) update graph.
- ManualActiveLagGraph() - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ManualActiveLagGraph
-
Using the given parameters, constructs an BasicLagGraph.
- ManualLagGraph - Class in edu.cmu.tetrad.study.gene.tetrad.gene.graph
-
Constructs as a (manual) update graph.
- ManualLagGraph(ManualLagGraphParams) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ManualLagGraph
-
Using the given parameters, constructs an BasicLagGraph.
- ManualLagGraphParams - Class in edu.cmu.tetrad.study.gene.tetrad.gene.graph
-
Stores the parameters needed to generate a new lag graph, whether randomized or manually constructed.
- ManualLagGraphParams() - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ManualLagGraphParams
-
Constructs a new parameters object.
- Mapping - Class in edu.cmu.tetrad.sem
-
Maps a parameter to the matrix element where its value is stored in the model.
- Mapping(ISemIm, Parameter, Matrix, int, int) - Constructor for class edu.cmu.tetrad.sem.Mapping
-
Constructs matrix new mapping using the given freeParameters.
- MARKOV_BLANKET - Enum constant in enum class edu.cmu.tetrad.search.MarkovCheck.ConditioningSetType
- MARKOV_BLANKET_GRAPH - Enum constant in enum class edu.cmu.tetrad.search.FgesMb.TrimmingStyle
- MarkovAdequacyScore - Class in edu.cmu.tetrad.algcomparison.statistic
-
Tests whether the p-values under the null distribution are distributed as Uniform, and if so, returns the proportion of judgements of dependence under the Alternative Hypothesis.
- MarkovAdequacyScore() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.MarkovAdequacyScore
- markovBlanket(Node, Graph) - Static method in class edu.cmu.tetrad.graph.GraphUtils
-
Returns a Markov blanket of a node for a DAG, CPDAG, MAG, or PAG.
- markovBlanketSubgraph(Node, Graph) - Static method in class edu.cmu.tetrad.graph.GraphUtils
-
Calculates the subgraph over the Markov blanket of a target node in a given DAG, CPDAG, MAG, or PAG.
- MarkovCheck - Class in edu.cmu.tetrad.search
-
Checks whether a graph is locally Markov or locally Faithful given a data set.
- MarkovCheck(Graph, IndependenceTest, MarkovCheck.ConditioningSetType) - Constructor for class edu.cmu.tetrad.search.MarkovCheck
-
Constructor.
- MarkovCheck.AllSubsetsIndependenceFacts - Class in edu.cmu.tetrad.search
- MarkovCheck.ConditioningSetType - Enum Class in edu.cmu.tetrad.search
-
The type of conditioning set to use for the Markov check.
- MathewsCorrAdj - Class in edu.cmu.tetrad.algcomparison.statistic
-
Calculates the Matthew's correlation coefficient for adjacencies.
- MathewsCorrAdj() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.MathewsCorrAdj
- MathewsCorrArrow - Class in edu.cmu.tetrad.algcomparison.statistic
-
Calculates the Matthew's correlation coefficient for adjacencies.
- MathewsCorrArrow() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.MathewsCorrArrow
- MathUtils - Class in edu.cmu.tetrad.util
-
Some extra mathematical functions not contained in org.apache.commons.math3.util.FastMath.
- MathUtils() - Constructor for class edu.cmu.tetrad.util.MathUtils
- Matrix - Class in edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util
-
Implements a Matrix of elements of type
short - Matrix - Class in edu.cmu.tetrad.util
-
Wraps the Apache math3 linear algebra library for most uses in Tetrad.
- Matrix(double[][]) - Constructor for class edu.cmu.tetrad.util.Matrix
- Matrix(int, int) - Constructor for class edu.cmu.tetrad.util.Matrix
- Matrix(Matrix) - Constructor for class edu.cmu.tetrad.util.Matrix
- Matrix(String) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.Matrix
-
Creates a matrix reading it from a file
fname. - Matrix(String, int) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.Matrix
-
Creates a matrix with name
mname, andnrowsrows. - Matrix(RealMatrix) - Constructor for class edu.cmu.tetrad.util.Matrix
- Matrix2 - Class in edu.cmu.tetrad.util
-
Wraps the Apache math3 linear algebra library for most uses in Tetrad.
- Matrix2(double[][]) - Constructor for class edu.cmu.tetrad.util.Matrix2
- Matrix2(int, int) - Constructor for class edu.cmu.tetrad.util.Matrix2
- Matrix2(Matrix2) - Constructor for class edu.cmu.tetrad.util.Matrix2
- Matrix2(RealMatrix) - Constructor for class edu.cmu.tetrad.util.Matrix2
- MatrixF - Class in edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util
-
Implements a Matrix of elements of type
float - MatrixF(String) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.MatrixF
-
Creates a matrix reading it from a file
fname. - MatrixF(String, int) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.MatrixF
-
Creates a matrix with name
mname, andnrowsrows. - MatrixOperations - Class in jgpml.covariancefunctions
-
Some useful operations defined over Matrices
- MatrixOperations() - Constructor for class jgpml.covariancefunctions.MatrixOperations
- MatrixUtils - Class in edu.cmu.tetrad.util
-
Class Matrix includes several public static functions performing matrix operations.
- MatrixUtils() - Constructor for class edu.cmu.tetrad.util.MatrixUtils
- max(double[]) - Static method in class edu.cmu.tetrad.util.StatUtils
- max(double[], int) - Static method in class edu.cmu.tetrad.util.StatUtils
- max(long[]) - Static method in class edu.cmu.tetrad.util.StatUtils
- max(long[], int) - Static method in class edu.cmu.tetrad.util.StatUtils
- MAX - Static variable in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.LagGraphParams
- MAX - Static variable in class edu.cmu.tetrad.study.gene.tetrad.gene.history.SimpleRandomizer
-
Indicates maximum indegree.
- MAX_CATEGORIES - Static variable in class edu.cmu.tetrad.util.Params
- MAX_DEGREE - Static variable in class edu.cmu.tetrad.util.Params
- MAX_DISTINCT_VALUES_DISCRETE - Static variable in class edu.cmu.tetrad.util.Params
- MAX_FLOAT - Static variable in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.BasicMatrix
-
Maximum float value
- MAX_INDEGREE - Static variable in class edu.cmu.tetrad.util.Params
- MAX_INT - Static variable in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.BasicMatrix
-
Maximum int value
- MAX_ITERATIONS - Static variable in class edu.cmu.tetrad.util.Params
- MAX_OUTDEGREE - Static variable in class edu.cmu.tetrad.util.Params
- MAX_P - Enum constant in enum class edu.cmu.tetrad.search.utils.PcCommon.ColliderDiscovery
- MAX_PATH_LENGTH - Static variable in class edu.cmu.tetrad.util.Params
- MAX_SHORT - Static variable in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.BasicMatrix
-
Maximum short value
- maxCliques() - Method in class edu.cmu.tetrad.graph.Paths
- maxEntApprox(double[]) - Static method in class edu.cmu.tetrad.util.StatUtils
- maximalCliques(Graph, List<Node>) - Static method in class edu.cmu.tetrad.graph.GraphUtils
- MaximalityCondition - Class in edu.cmu.tetrad.algcomparison.statistic
-
MaximalMag statistic.
- MaximalityCondition() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.MaximalityCondition
- maximization(double) - Method in class edu.cmu.tetrad.bayes.EmBayesEstimator
-
This method iteratively estimates the parameters of the Bayes net using the dataset until the parameters don't change.
- maximization(double) - Method in class edu.cmu.tetrad.bayes.FactoredBayesStructuralEM
-
This method allows specification of the tolerance parameter used in Bayes EM estimation.
- MAXIT - Static variable in class edu.cmu.tetrad.util.Params
- MaxP - Class in edu.cmu.tetrad.search.utils
-
Performs a Max-P orientation of unshielded triples in a graph.
- MaxP(IndependenceTest) - Constructor for class edu.cmu.tetrad.search.utils.MaxP
-
Constructor.
- MAY_NOT_CONTAIN - Enum constant in enum class edu.cmu.tetrad.calculator.parser.ExpressionParser.RestrictionType
- MAY_ONLY_CONTAIN - Enum constant in enum class edu.cmu.tetrad.calculator.parser.ExpressionParser.RestrictionType
- MB - Static variable in class edu.cmu.tetrad.util.Params
- MbUtils - Class in edu.cmu.tetrad.search.utils
-
Provides some useful utilities for dealing with Markov blankets and Markov blanket DAGs.
- MbUtils() - Constructor for class edu.cmu.tetrad.search.utils.MbUtils
- mconn - Variable in class edu.cmu.tetrad.search.MarkovCheck.AllSubsetsIndependenceFacts
- mean(double[]) - Static method in class edu.cmu.tetrad.util.StatUtils
- mean(double[], int) - Static method in class edu.cmu.tetrad.util.StatUtils
- mean(long[]) - Static method in class edu.cmu.tetrad.util.StatUtils
- mean(long[], int) - Static method in class edu.cmu.tetrad.util.StatUtils
- mean(Matrix) - Static method in class edu.cmu.tetrad.data.DataUtils
- mean(Vector, int) - Static method in class edu.cmu.tetrad.util.StatUtils
- mean(Matrix) - Static method in class jgpml.covariancefunctions.MatrixOperations
- MEAN - Static variable in class edu.cmu.tetrad.sem.ParamType
-
A mean parameter.
- MEAN - Static variable in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.LagGraphParams
- MEAN - Static variable in class edu.cmu.tetrad.study.gene.tetrad.gene.history.SimpleRandomizer
-
Indicates mean indegree.
- MEAN_HIGH - Static variable in class edu.cmu.tetrad.util.Params
- MEAN_LOW - Static variable in class edu.cmu.tetrad.util.Params
- meanAbsolute(double[]) - Static method in class edu.cmu.tetrad.util.StatUtils
- MeanInterpolator - Class in edu.cmu.tetrad.data
-
Returns a data set in which missing values in each column are filled using the mean of that column.
- MeanInterpolator() - Constructor for class edu.cmu.tetrad.data.MeanInterpolator
- means() - Method in class edu.cmu.tetrad.sem.StandardizedSemIm
- means(double[][]) - Static method in class edu.cmu.tetrad.data.DataUtils
-
Column major data.
- means(Matrix) - Static method in class edu.cmu.tetrad.data.DataUtils
- MEASURED - Static variable in class edu.cmu.tetrad.graph.NodeType
- MEASURED_MEASURED_IMPURE_ASSOCIATIONS - Static variable in class edu.cmu.tetrad.util.Params
- MEASURED_MEASURED_IMPURE_PARENTS - Static variable in class edu.cmu.tetrad.util.Params
- MEASUREMENT_MODEL_DEGREE - Static variable in class edu.cmu.tetrad.util.Params
- MEASUREMENT_VARIANCE - Static variable in class edu.cmu.tetrad.util.Params
- MeasurementSimulator - Class in edu.cmu.tetrad.study.gene.tetrad.gene.simulation
-
Simulates measurement genetic data using an underlying GeneHistory object to generate individual cell data.
- MeasurementSimulator(Parameters) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.simulation.MeasurementSimulator
-
Constructs a measurement simulator using the given history.
- MeasurementSimulatorParams - Class in edu.cmu.tetrad.study.gene.tetradapp.model
-
Wraps MeasurementSimulator so that it may be used as a parameter object.
- MeasurementSimulatorParams(Parameters) - Constructor for class edu.cmu.tetrad.study.gene.tetradapp.model.MeasurementSimulatorParams
-
Constructs a measurement simulator using the given history.
- median(double[]) - Static method in class edu.cmu.tetrad.util.StatUtils
- median(double[], int) - Static method in class edu.cmu.tetrad.util.StatUtils
- median(long[]) - Static method in class edu.cmu.tetrad.util.StatUtils
- median(long[], int) - Static method in class edu.cmu.tetrad.util.StatUtils
- MEEK_PREVENT_CYCLES - Static variable in class edu.cmu.tetrad.util.Params
- MEEK_VERBOSE - Static variable in class edu.cmu.tetrad.util.Params
- meekPreventCycles(boolean) - Method in class edu.cmu.tetrad.search.Cpc
-
Sets to true just in case edges will not be added if they would create cycles.
- MeekRules - Class in edu.cmu.tetrad.search.utils
-
Implements Meek's complete orientation rule set for PC (Chris Meek (1995), "Causal inference and causal explanation with background knowledge"), modified for Conservative PC to check noncolliders against recorded noncolliders before orienting.
- MeekRules() - Constructor for class edu.cmu.tetrad.search.utils.MeekRules
-
Constructs the
MeekRuleswith no logging. - Memorable - Interface in edu.cmu.tetrad.util
-
Tags a session node as "memorable", so that it won't be forgotten when a model is destroyed.
- Mgm - Class in edu.cmu.tetrad.algcomparison.algorithm.mixed
-
MGM.
- Mgm - Class in edu.pitt.csb.mgm
-
Implementation of Lee and Hastie's (2012) pseudolikelihood method for learning Mixed Gaussian-Categorical Graphical Models Created by ajsedgewick on 7/15/15.
- Mgm() - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.mixed.Mgm
- Mgm(DoubleMatrix2D, DoubleMatrix2D, List<Node>, int[], double[]) - Constructor for class edu.pitt.csb.mgm.Mgm
- Mgm(DataSet, double[]) - Constructor for class edu.pitt.csb.mgm.Mgm
- MGM_PARAM1 - Static variable in class edu.cmu.tetrad.util.Params
- MGM_PARAM2 - Static variable in class edu.cmu.tetrad.util.Params
- MGM_PARAM3 - Static variable in class edu.cmu.tetrad.util.Params
- Mgm.MGMParams - Class in edu.pitt.csb.mgm
- MGMParams() - Constructor for class edu.pitt.csb.mgm.Mgm.MGMParams
- MGMParams(DoubleMatrix1D, int, int) - Constructor for class edu.pitt.csb.mgm.Mgm.MGMParams
- MGMParams(DoubleMatrix2D, DoubleMatrix1D, DoubleMatrix2D, DoubleMatrix2D, DoubleMatrix1D, DoubleMatrix1D) - Constructor for class edu.pitt.csb.mgm.Mgm.MGMParams
- MGMParams(Mgm.MGMParams) - Constructor for class edu.pitt.csb.mgm.Mgm.MGMParams
- MGMWrapper(double...) - Constructor for class edu.pitt.csb.stability.SearchWrappers.MGMWrapper
- MillisecondTimes - Class in edu.cmu.tetrad.util
-
Reports elapsed time in wall time, user time, and CPU time in milliseconds.
- MillisecondTimes() - Constructor for class edu.cmu.tetrad.util.MillisecondTimes
- MillisecondTimes.Type - Enum Class in edu.cmu.tetrad.util
- Mimbuild - Class in edu.cmu.tetrad.search
-
Provides an implementation of Mimbuild, an algorithm that takes a clustering of variables, each of which is explained by a single latent, then forms the implied covariance matrix over the latent variables, then runs a CPDAG search to in the structure over the latent themselves.
- Mimbuild() - Constructor for class edu.cmu.tetrad.search.Mimbuild
- MimbuildTrek - Class in edu.cmu.tetrad.search
-
Implements Mimbuild using the theory of treks and ranks.
- MimbuildTrek() - Constructor for class edu.cmu.tetrad.search.MimbuildTrek
- mimClusters(Graph) - Static method in class edu.cmu.tetrad.search.utils.ClusterUtils
- MimUtils - Class in edu.cmu.tetrad.search.utils
-
Provides some utility methods for Purify, Build Clusters, and Mimbuild.
- MimUtils() - Constructor for class edu.cmu.tetrad.search.utils.MimUtils
- min(double[]) - Static method in class edu.cmu.tetrad.util.StatUtils
- min(double[], int) - Static method in class edu.cmu.tetrad.util.StatUtils
- min(long[]) - Static method in class edu.cmu.tetrad.util.StatUtils
- min(long[], int) - Static method in class edu.cmu.tetrad.util.StatUtils
- MIN_CATEGORIES - Static variable in class edu.cmu.tetrad.util.Params
- MIN_FLOAT - Static variable in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.BasicMatrix
-
Minimum float value
- MIN_INT - Static variable in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.BasicMatrix
-
Minimum int value
- MIN_SHORT - Static variable in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.BasicMatrix
-
Minimum short getValue
- minCoveringSet(SortedSet[][]) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.ideker.ItkPredictorSearch
- minus(Matrix) - Method in class edu.cmu.tetrad.util.Matrix
- minus(Matrix2) - Method in class edu.cmu.tetrad.util.Matrix2
- minus(Vector) - Method in class edu.cmu.tetrad.util.Vector
- MisclassificationUtils - Class in edu.cmu.tetrad.graph
-
Some utilities for generating misclassification tables for graphs.
- MisclassificationUtils() - Constructor for class edu.cmu.tetrad.graph.MisclassificationUtils
- MISCLASSIFICATTONS - Enum constant in enum class edu.cmu.tetrad.algcomparison.comparegraphs.CompareTwoGraphs.ComparisonType
- MISSING_VALUE - Static variable in class edu.cmu.tetrad.data.DiscreteVariable
-
This is the index in the data which represents missing data internally for this variable.
- Mixed - Enum constant in enum class edu.cmu.tetrad.data.DataType
- Mixed - Annotation Interface in edu.cmu.tetrad.annotation
-
Data with variables that have linear relationship.
- MixedDataBox - Class in edu.cmu.tetrad.data
-
Stores a 2D array of double continuousData.
- MixedDataBox(List<Node>, int) - Constructor for class edu.cmu.tetrad.data.MixedDataBox
-
The variables here are used only to determine which columns are discrete and which are continuous; bounds checking is not done.
- MixedDataBox(List<Node>, int, double[][], int[][]) - Constructor for class edu.cmu.tetrad.data.MixedDataBox
-
This constructor allows other data readers to populate the fields directly.
- MixedUtils - Class in edu.pitt.csb.mgm
-
Created by ajsedgewick on 7/29/15.
- MixedUtils() - Constructor for class edu.pitt.csb.mgm.MixedUtils
- MixtureOfGaussians - Class in edu.cmu.tetrad.util.dist
-
Wraps a chi square distribution for purposes of drawing random samples.
- MixtureOfGaussians(double, double, double, double, double) - Constructor for class edu.cmu.tetrad.util.dist.MixtureOfGaussians
- mkRandSEMDAG(int, int) - Static method in class edu.cmu.tetrad.simulation.HsimUtils
- MlBayesEstimator - Class in edu.cmu.tetrad.bayes
-
Estimates parameters of the given Bayes net from the given data using maximum likelihood method.
- MlBayesEstimator() - Constructor for class edu.cmu.tetrad.bayes.MlBayesEstimator
- MlBayesIm - Class in edu.cmu.tetrad.bayes
-
Stores a table of probabilities for a Bayes net and, together with BayesPm and Dag, provides methods to manipulate this table.
- MlBayesIm(BayesIm) - Constructor for class edu.cmu.tetrad.bayes.MlBayesIm
-
Copy constructor.
- MlBayesIm(BayesPm) - Constructor for class edu.cmu.tetrad.bayes.MlBayesIm
-
Constructs a new BayesIm from the given BayesPm, initializing all values as Double.NaN ("?").
- MlBayesIm(BayesPm, int) - Constructor for class edu.cmu.tetrad.bayes.MlBayesIm
-
Constructs a new BayesIm from the given BayesPm, initializing values either as MANUAL or RANDOM.
- MlBayesIm(BayesPm, BayesIm, int) - Constructor for class edu.cmu.tetrad.bayes.MlBayesIm
-
Constructs a new BayesIm from the given BayesPm, initializing values either as MANUAL or RANDOM, but using values from the old BayesIm provided where posssible.
- MlBayesImObs - Class in edu.cmu.tetrad.bayes
-
Stores a table of probabilities for a Bayes net and, together with BayesPm and Dag, provides methods to manipulate this table.
- MlBayesImObs(BayesIm) - Constructor for class edu.cmu.tetrad.bayes.MlBayesImObs
- MlBayesImObs(BayesPm) - Constructor for class edu.cmu.tetrad.bayes.MlBayesImObs
-
Constructs a new BayesIm from the given BayesPm, initializing all values as Double.NaN ("?").
- MlBayesImObs(BayesPm, int) - Constructor for class edu.cmu.tetrad.bayes.MlBayesImObs
-
Constructs a new BayesIm from the given BayesPm, initializing values either as MANUAL or RANDOM.
- MlBayesImObs(BayesPm, BayesIm, int) - Constructor for class edu.cmu.tetrad.bayes.MlBayesImObs
-
Constructs a new BayesIm from the given BayesPm, initializing values either as MANUAL or RANDOM, but using values from the old BayesIm provided where posssible.
- Mmhc - Class in edu.cmu.tetrad.search.work_in_progress
-
Implements the MMHC algorithm.
- Mmhc(IndependenceTest, DataSet) - Constructor for class edu.cmu.tetrad.search.work_in_progress.Mmhc
- Mmmb - Class in edu.cmu.tetrad.search.work_in_progress
-
Implements the Min-Max Markov Blanks (MMMB) algorithm as defined in Tsamardinos, Aliferis, and Statnikov, Time and Sample Efficient Discovery of Markov Blankets and Direct Causal Relations (KDD 2003).
- Mmmb(IndependenceTest, int, boolean) - Constructor for class edu.cmu.tetrad.search.work_in_progress.Mmmb
-
Constructs.
- MnlrLikelihood - Class in edu.cmu.tetrad.search.work_in_progress
-
Calculates Mixed Variables Polynomial likelihood.
- MnlrLikelihood(DataSet, double, int) - Constructor for class edu.cmu.tetrad.search.work_in_progress.MnlrLikelihood
-
Constructor.
- Mnlrlrt - Class in edu.cmu.tetrad.algcomparison.independence
-
Wrapper for Fisher Z test.
- Mnlrlrt() - Constructor for class edu.cmu.tetrad.algcomparison.independence.Mnlrlrt
- MnlrScore - Class in edu.cmu.tetrad.search.work_in_progress
-
Implements a mixed variable polynomial BIC score for fGES.
- MnlrScore(DataSet, double, int) - Constructor for class edu.cmu.tetrad.search.work_in_progress.MnlrScore
-
Constructor.
- ModeInterpolator - Class in edu.cmu.tetrad.bayes
-
Creates a data set in which missing values in each column are filled using the mode of that column.
- ModeInterpolator() - Constructor for class edu.cmu.tetrad.bayes.ModeInterpolator
- MODEL_CREATED - Static variable in class edu.cmu.tetrad.session.SessionEvent
- MODEL_DESTROYED - Static variable in class edu.cmu.tetrad.session.SessionEvent
- MODEL_UNCLEAR - Static variable in class edu.cmu.tetrad.session.SessionEvent
- modelCreated(SessionEvent) - Method in class edu.cmu.tetrad.session.SessionAdapter
-
Indicates that a model has been created for a node.
- modelCreated(SessionEvent) - Method in interface edu.cmu.tetrad.session.SessionListener
-
Indicates that a model has been created for a node.
- modelDestroyed(SessionEvent) - Method in class edu.cmu.tetrad.session.SessionAdapter
-
Indicates that a model has been destroyed for a node.
- modelDestroyed(SessionEvent) - Method in interface edu.cmu.tetrad.session.SessionListener
-
Indicates that a model has been destroyed for a node.
- ModelGenerator - Class in edu.cmu.tetrad.bayes
-
Provides static methods for generating variants of an input graph.
- ModelGenerator() - Constructor for class edu.cmu.tetrad.bayes.ModelGenerator
- modelHasChanged(SessionNode) - Static method in class edu.cmu.tetrad.session.ModificationRegistery
- modelUnclear(SessionEvent) - Method in class edu.cmu.tetrad.session.SessionAdapter
-
Indicates that the createModel method has been called but there is more than one model consistent with the parents, so a choice has to be made.
- modelUnclear(SessionEvent) - Method in interface edu.cmu.tetrad.session.SessionListener
-
Indicates that the createModel method has been called but there is more than one model consistent with the parents, so a choice has to be made.
- ModificationRegistery - Class in edu.cmu.tetrad.session
-
Allows editors launched for session nodes to register that relevant changes have been made that will require models downstream to be reconstructed.
- ModificationRegistery() - Constructor for class edu.cmu.tetrad.session.ModificationRegistery
- moralize(Graph) - Static method in class edu.cmu.tetrad.bayes.GraphTools
-
Create a moral graph.
- Move(Edge, Edge, HbsmsBeam.Move.Type) - Constructor for class edu.cmu.tetrad.search.work_in_progress.HbsmsBeam.Move
- Move(Edge, HbsmsBeam.Move.Type) - Constructor for class edu.cmu.tetrad.search.work_in_progress.HbsmsBeam.Move
- moveTo(Node, int) - Method in class edu.cmu.tetrad.search.utils.TeyssierScorer
-
Moves v to a new index.
- moveToEnd() - Method in interface edu.cmu.tetrad.util.TetradLogger.LogDisplayOutputStream
-
Should move the log to the end of the stream.
- msep - Variable in class edu.cmu.tetrad.search.MarkovCheck.AllSubsetsIndependenceFacts
- MSeparationScore - Class in edu.cmu.tetrad.algcomparison.score
-
Wrapper for Fisher Z test.
- MSeparationScore() - Constructor for class edu.cmu.tetrad.algcomparison.score.MSeparationScore
-
Use this empty constructor to satisfy the java reflection
- MSeparationScore(Graph) - Constructor for class edu.cmu.tetrad.algcomparison.score.MSeparationScore
- MSeparationTest - Class in edu.cmu.tetrad.algcomparison.independence
-
Wrapper for M-separation test.
- MSeparationTest() - Constructor for class edu.cmu.tetrad.algcomparison.independence.MSeparationTest
-
Use this empty constructor to satisfy the java reflection
- MSeparationTest(Graph) - Constructor for class edu.cmu.tetrad.algcomparison.independence.MSeparationTest
- MsepTest - Class in edu.cmu.tetrad.search.test
-
Checks independence facts for variables associated with the nodes in a given graph by checking m-separation facts on the underlying nodes.
- MsepTest(IndependenceFacts) - Constructor for class edu.cmu.tetrad.search.test.MsepTest
-
Constructor.
- MsepTest(IndependenceFacts, boolean) - Constructor for class edu.cmu.tetrad.search.test.MsepTest
-
Constructor.
- MsepTest(IndependenceFacts, List<Node>) - Constructor for class edu.cmu.tetrad.search.test.MsepTest
-
Constructor.
- MsepTest(Graph) - Constructor for class edu.cmu.tetrad.search.test.MsepTest
-
Constructor.
- MsepTest(Graph, boolean) - Constructor for class edu.cmu.tetrad.search.test.MsepTest
-
Constructor.
- mu(double[]) - Static method in class edu.cmu.tetrad.util.StatUtils
- mu(double[], int) - Static method in class edu.cmu.tetrad.util.StatUtils
- mu(long[]) - Static method in class edu.cmu.tetrad.util.StatUtils
- mu(long[], int) - Static method in class edu.cmu.tetrad.util.StatUtils
- mudholkergeorge - Enum constant in enum class edu.cmu.tetrad.search.utils.ResolveSepsets.Method
- mudholkergeorge - Enum constant in enum class edu.cmu.tetrad.search.work_in_progress.ResolveSepsetsDci.Method
- mudholkergeorge2 - Enum constant in enum class edu.cmu.tetrad.search.utils.ResolveSepsets.Method
- mudholkergeorge2 - Enum constant in enum class edu.cmu.tetrad.search.work_in_progress.ResolveSepsetsDci.Method
- muHat(double[]) - Static method in class edu.cmu.tetrad.util.StatUtils
- muHat(double[], int) - Static method in class edu.cmu.tetrad.util.StatUtils
- muHat(long[]) - Static method in class edu.cmu.tetrad.util.StatUtils
- muHat(long[], int) - Static method in class edu.cmu.tetrad.util.StatUtils
- MultiDataSetAlgorithm - Interface in edu.cmu.tetrad.algcomparison.algorithm
-
Implements an algorithm that takes multiple data sets as input.
- MultidataUtils - Class in edu.cmu.tetrad.util
-
Aug 7, 2018 10:21:59 AM
- MultiDimIntTable - Class in edu.cmu.tetrad.util
-
Stores a table of cells with int values of arbitrary dimension.
- MultiDimIntTable(int[]) - Constructor for class edu.cmu.tetrad.util.MultiDimIntTable
-
Constructs a new multidimensional table of integer cells, with the given (fixed) dimensions.
- MultiGeneralAndersonDarlingTest - Class in edu.cmu.tetrad.data
-
Implements the Anderson-Darling test against the given CDF, with P values calculated as in R's ad.test method (in package nortest).
- MultiGeneralAndersonDarlingTest(List<List<Double>>, List<RealDistribution>) - Constructor for class edu.cmu.tetrad.data.MultiGeneralAndersonDarlingTest
-
Constructs an Anderson-Darling test for the given column of data.
- MultinomialLogisticRegressionWald - Class in edu.cmu.tetrad.algcomparison.independence
-
Wrapper for Fisher Z test.
- MultinomialLogisticRegressionWald() - Constructor for class edu.cmu.tetrad.algcomparison.independence.MultinomialLogisticRegressionWald
- multinormalProb(double[], double[], double[][]) - Static method in class edu.cmu.tetrad.util.ProbUtils
-
Compute the probability over a rectangular region with correlation matrix c.
- multOuter(Vector, Vector) - Static method in class edu.cmu.tetrad.util.TetradAlgebra
- mutualInformation(int, int[], int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.reveal.RevealEvaluator
-
This method computes the mutual information between a gene and a set of presumptive causes (other genes).
- mutualInformation(int, int[], int) - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.LTestReveal
- mutualInformation(int, int[], int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.RevealEvaluator
-
This method computes the mutual information between a gene and a set of presumptive causes (other genes).
- mutualInformation(int, int[], int[]) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.RevealEvaluator
-
This method computes the mutual information between a gene and a set of presumptive causes (other genes).
- MVPBicScore - Class in edu.cmu.tetrad.algcomparison.score
-
Wrapper for MVP BIC Score.
- MVPBicScore() - Constructor for class edu.cmu.tetrad.algcomparison.score.MVPBicScore
- MVPCompareFromFiles - Class in edu.cmu.tetrad.algcomparison.examples
-
An example script to load in data sets and graphs from files and analyze them.
- MVPCompareFromFiles() - Constructor for class edu.cmu.tetrad.algcomparison.examples.MVPCompareFromFiles
- MvpLikelihood - Class in edu.cmu.tetrad.search.score
-
Calculates Mixed Variables Polynomial likelihood.
- MvpLikelihood(DataSet, double, int, boolean) - Constructor for class edu.cmu.tetrad.search.score.MvpLikelihood
- Mvplrt - Class in edu.cmu.tetrad.algcomparison.independence
-
Wrapper for Fisher Z test.
- Mvplrt() - Constructor for class edu.cmu.tetrad.algcomparison.independence.Mvplrt
- MvpScore - Class in edu.cmu.tetrad.search.score
-
Implements a mixed variable polynomial BIC score.
- MvpScore(DataSet, double, int, boolean) - Constructor for class edu.cmu.tetrad.search.score.MvpScore
-
Constructor.
- MyContext() - Constructor for class edu.cmu.tetrad.sem.GeneralizedSemEstimator.MyContext
N
- n - Variable in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.BasicMatrix
-
Number of rows ( == # columns) of this matrix
- N(double[]) - Static method in class edu.cmu.tetrad.util.StatUtils
- N(long[]) - Static method in class edu.cmu.tetrad.util.StatUtils
- name - Variable in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.BasicMatrix
-
Name of the matrix
- name() - Element in annotation interface edu.cmu.tetrad.annotation.Algorithm
-
Name of the algorithm.
- name() - Element in annotation interface edu.cmu.tetrad.annotation.Score
- name() - Element in annotation interface edu.cmu.tetrad.annotation.TestOfIndependence
- NamingProtocol - Class in edu.cmu.tetrad.util
-
Specifies the protocol used in Tetrad for variable names.
- NamingProtocol() - Constructor for class edu.cmu.tetrad.util.NamingProtocol
- NANDY - Enum constant in enum class edu.cmu.tetrad.search.score.GicScores.RuleType
- NANDY - Enum constant in enum class edu.cmu.tetrad.search.score.SemBicScore.RuleType
- nandyBic(int, int, int[]) - Method in class edu.cmu.tetrad.search.score.SemBicScore
- NbComponent - Interface in edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin
- NbFunction - Class in edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin
- NbFunction(double, double, NbComponent[], int[], String) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.NbFunction
- NbFunctionAnd - Class in edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin
- NbFunctionAnd(double, double, NbComponent[], int[], String) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.NbFunctionAnd
- NbFunctionOr - Class in edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin
- NbFunctionOr(double, double, NbComponent[], int[], String) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.NbFunctionOr
- NbFunctionSum - Class in edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin
- NbFunctionSum(double, double, NbComponent[], int[], String) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.NbFunctionSum
- NbFunctionSV - Class in edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin
- NbFunctionSV(double, double, NbComponent[], int[], String) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.NbFunctionSV
- NbGene - Class in edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin
- NbGene(double, double, NbComponent[], int[], String) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.NbGene
- NbGeneAnd - Class in edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin
- NbGeneAnd(double, double, NbComponent[], int[], String, double) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.NbGeneAnd
- NbGeneOr - Class in edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin
- NbGeneOr(double, double, NbComponent[], int[], String, double) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.NbGeneOr
- NC - Static variable in class edu.cmu.tetrad.sem.ParamComparison
-
Indicates that the two freeParameters are not compared.
- nEdges - Variable in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.BasicGraph
-
Total number of edges in the graph
- negativeInfinity() - Static method in class edu.cmu.tetrad.search.work_in_progress.HbsmsBeam.Score
- negativeLogLikelihood(Matrix, Matrix, Matrix, Matrix) - Method in class jgpml.GaussianProcess
-
Computes minus the log likelihood and its partial derivatives with respect to the hyperparameters; this mode is used to fit the hyperparameters.
- NEITHER - Enum constant in enum class edu.cmu.tetrad.calculator.expression.ExpressionDescriptor.Position
- NetBuilderModel - Class in edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin
- NetBuilderModel(double[], int) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.NetBuilderModel
- newExecution() - Method in interface edu.cmu.tetrad.session.ExecutionRestarter
-
Specifies a procedure that should be followed when a new execution has been initiated.
- NEWLINE - Static variable in class edu.pitt.isp.sverchkov.data.DataTools
- next() - Method in class edu.cmu.tetrad.search.utils.DagInCpcagIterator
-
Successive calls to this method return successive DAGs in the CPDAG, in a more or less natural enumeration of them in which an arbitrary undirected edge is picked, oriented one way, Meek rules applied, then a remaining unoriented edge is picked, oriented one way, and so on, until a DAG is obtained, and then by backtracking the other orientation of each chosen edge is tried.
- next() - Method in class edu.cmu.tetrad.search.utils.DagIterator
-
Successive calls to this method return successive DAGs in the CPDAG, in a more or less natural enumeration of them in which an arbitrary undirected edge is picked, oriented one way, Meek rules applied, then a remaining unoriented edge is picked, oriented one way, and so on, until a DAG is obtained, and then by backtracking the other orientation of each chosen edge is tried.
- next() - Method in class edu.cmu.tetrad.util.ChoiceGenerator
- next() - Method in class edu.cmu.tetrad.util.CombinationGenerator
- next() - Method in class edu.cmu.tetrad.util.CombinationIterator
- next() - Method in class edu.cmu.tetrad.util.PermutationGenerator
- next() - Method in class edu.cmu.tetrad.util.SelectionGenerator
- next() - Method in class edu.cmu.tetrad.util.SublistGenerator
- nextBeta(double, double) - Method in class edu.cmu.tetrad.util.RandomUtil
- nextChiSquare(double) - Method in class edu.cmu.tetrad.util.RandomUtil
- nextDouble() - Method in class edu.cmu.tetrad.util.RandomUtil
- nextExponential(double) - Method in class edu.cmu.tetrad.util.RandomUtil
- nextGamma(double, double) - Method in class edu.cmu.tetrad.util.RandomUtil
- nextGumbel(double, double) - Method in class edu.cmu.tetrad.util.RandomUtil
- nextIncrementalRelease() - Method in class edu.cmu.tetrad.util.Version
- nextInt(int) - Method in class edu.cmu.tetrad.util.RandomUtil
- nextLong() - Method in class edu.cmu.tetrad.util.RandomUtil
- nextMajorVersion() - Method in class edu.cmu.tetrad.util.Version
- nextMinorSubversion() - Method in class edu.cmu.tetrad.util.Version
- nextMinorVersion() - Method in class edu.cmu.tetrad.util.Version
- nextNormal(double, double) - Method in class edu.cmu.tetrad.util.RandomUtil
- nextParameterName(String) - Method in class edu.cmu.tetrad.sem.GeneralizedSemPm
-
Given base b (a String), returns the first name in the sequence "b1", "b2", "b3", etc., which is not already the name of a node in the workbench.
- nextPoisson(double) - Method in class edu.cmu.tetrad.util.RandomUtil
- nextRandom() - Method in interface edu.cmu.tetrad.study.gene.tetrad.gene.history.RandomDistribution
-
Draws a new noise value from the underlying distribution.
- nextRandom() - Method in class edu.cmu.tetrad.util.dist.Beta
-
Returns the next random.
- nextRandom() - Method in class edu.cmu.tetrad.util.dist.ChiSquare
- nextRandom() - Method in class edu.cmu.tetrad.util.dist.Discrete
- nextRandom() - Method in interface edu.cmu.tetrad.util.dist.Distribution
-
Returns the next random number from the distribution.
- nextRandom() - Method in class edu.cmu.tetrad.util.dist.Exponential
- nextRandom() - Method in class edu.cmu.tetrad.util.dist.Gamma
- nextRandom() - Method in class edu.cmu.tetrad.util.dist.GaussianPower
- nextRandom() - Method in class edu.cmu.tetrad.util.dist.Indicator
- nextRandom() - Method in class edu.cmu.tetrad.util.dist.LogNormal
- nextRandom() - Method in class edu.cmu.tetrad.util.dist.MixtureOfGaussians
- nextRandom() - Method in class edu.cmu.tetrad.util.dist.Normal
- nextRandom() - Method in class edu.cmu.tetrad.util.dist.Poisson
- nextRandom() - Method in class edu.cmu.tetrad.util.dist.SingleValue
- nextRandom() - Method in class edu.cmu.tetrad.util.dist.Split
- nextRandom() - Method in class edu.cmu.tetrad.util.dist.TruncatedNormal
- nextRandom() - Method in class edu.cmu.tetrad.util.dist.Uniform
- nextT(double) - Method in class edu.cmu.tetrad.util.RandomUtil
- nextToken() - Method in class edu.cmu.tetrad.calculator.parser.ExpressionLexer
- nextToken() - Method in class edu.cmu.tetrad.data.RegexTokenizer
- nextTokenIncludingWhitespace() - Method in class edu.cmu.tetrad.calculator.parser.ExpressionLexer
- nextTruncatedNormal(double, double, double, double) - Method in class edu.cmu.tetrad.util.RandomUtil
- nextUniform(double, double) - Method in class edu.cmu.tetrad.util.RandomUtil
- nil - Enum constant in enum class edu.cmu.tetrad.graph.EdgeTypeProbability.EdgeType
- nl - Enum constant in enum class edu.cmu.tetrad.graph.Edge.Property
- NLSemSimulation - Class in edu.cmu.tetrad.algcomparison.simulation
-
NL SEM simulation.
- NLSemSimulation(RandomGraph) - Constructor for class edu.cmu.tetrad.algcomparison.simulation.NLSemSimulation
- nNodes - Variable in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.BasicGraph
-
Number of nodes
- NO_RANDOMLY_DETERMINED_INDEPENDENCE - Static variable in class edu.cmu.tetrad.util.Params
- NO_TYPE - Static variable in class edu.cmu.tetrad.graph.NodeType
- NoAlmostCyclicPathsCondition - Class in edu.cmu.tetrad.algcomparison.statistic
-
No almost cyclic paths condition.
- NoAlmostCyclicPathsCondition() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.NoAlmostCyclicPathsCondition
- NoAlmostCyclicPathsInMagCondition - Class in edu.cmu.tetrad.algcomparison.statistic
-
No almost cyclic paths condition in MAG.
- NoAlmostCyclicPathsInMagCondition() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.NoAlmostCyclicPathsInMagCondition
- NoCyclicPathsCondition - Class in edu.cmu.tetrad.algcomparison.statistic
-
No cyclic paths condition.
- NoCyclicPathsCondition() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.NoCyclicPathsCondition
- NoCyclicPathsInMagCondition - Class in edu.cmu.tetrad.algcomparison.statistic
-
No cyclic paths condition.
- NoCyclicPathsInMagCondition() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.NoCyclicPathsInMagCondition
- Node - Interface in edu.cmu.tetrad.graph
-
Represents an object with a name, node type, and position that can serve as a node in a graph.
- NODE_ADDED - Static variable in class edu.cmu.tetrad.session.SessionEvent
- NODE_REMOVED - Static variable in class edu.cmu.tetrad.session.SessionEvent
- nodeAdded(SessionEvent) - Method in class edu.cmu.tetrad.session.SessionAdapter
-
Indicates that a node has been added.
- nodeAdded(SessionEvent) - Method in interface edu.cmu.tetrad.session.SessionListener
-
Indicates that a node has been added.
- NodeId(String, int) - Constructor for class edu.cmu.tetrad.graph.TimeLagGraph.NodeId
- nodeNames - Variable in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.BasicGraph
-
Node names
- NodePair - Class in edu.cmu.tetrad.graph
-
An unordered pair of nodes.
- NodePair(Node, Node) - Constructor for class edu.cmu.tetrad.graph.NodePair
- nodeRemoved(SessionEvent) - Method in class edu.cmu.tetrad.session.SessionAdapter
-
Indicates that a node has been removed.
- nodeRemoved(SessionEvent) - Method in interface edu.cmu.tetrad.session.SessionListener
-
Indicates that a node has been removed.
- NodesInCyclesPrecision - Class in edu.cmu.tetrad.algcomparison.statistic
-
The adjacency precision.
- NodesInCyclesPrecision() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.NodesInCyclesPrecision
- NodesInCyclesRecall - Class in edu.cmu.tetrad.algcomparison.statistic
-
The adjacency precision.
- NodesInCyclesRecall() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.NodesInCyclesRecall
- NodeType - Class in edu.cmu.tetrad.graph
-
A typesafe enum of the types of the types of nodes in a graph (MEASURED, LATENT, ERROR).
- NodeVariableType - Enum Class in edu.cmu.tetrad.graph
-
Node variable type.
- noEdgeRequired(String, String) - Method in class edu.cmu.tetrad.data.Knowledge
- NOMINAL - Static variable in class edu.cmu.tetrad.data.DiscreteVariableType
- NON_LINEAR_STRUCTURAL_EQUATION_MODEL - Static variable in class edu.cmu.tetrad.algcomparison.simulation.SimulationTypes
- NonancestorPrecision - Class in edu.cmu.tetrad.algcomparison.statistic
-
Number of NOT X~~>Y in true graph for which also NOT X~~>Y in estimated graph.
- NonancestorPrecision() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.NonancestorPrecision
- NonancestorRecall - Class in edu.cmu.tetrad.algcomparison.statistic
-
Number of NOT X~~>Y in true graph for which also NOT X~~>Y in estimated graph.
- NonancestorRecall() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.NonancestorRecall
- NONCOLLIDER - Enum constant in enum class edu.cmu.tetrad.search.utils.GraphSearchUtils.CpcTripleType
- NONCOLLIDER - Enum constant in enum class edu.cmu.tetrad.search.work_in_progress.VcPc.CpcTripleType
- NONCOLLIDER - Enum constant in enum class edu.cmu.tetrad.search.work_in_progress.VcPcFast.CpcTripleType
- nondirectedEdge(Node, Node) - Static method in class edu.cmu.tetrad.graph.Edges
-
Constructs a new nondirected edge from nodeA to nodeB (o-o).
- None - Enum constant in enum class edu.cmu.tetrad.search.utils.ClusterSignificance.CheckType
- NONE - Enum constant in enum class edu.cmu.tetrad.calculator.parser.ExpressionParser.RestrictionType
- NONE - Enum constant in enum class edu.cmu.tetrad.search.Fask.AdjacencyMethod
- NONE - Enum constant in enum class edu.cmu.tetrad.search.FgesMb.TrimmingStyle
- NONE - Enum constant in enum class edu.cmu.tetrad.search.utils.BpcTestType
- NONE - Enum constant in enum class edu.cmu.tetrad.search.utils.PcCommon.PcHeuristicType
- NONE - Static variable in class edu.cmu.tetrad.data.ContinuousDiscretizationSpec
- NONE - Static variable in class edu.cmu.tetrad.sem.ParamConstraintType
-
No constraint.
- Nonexecutable - Annotation Interface in edu.cmu.tetrad.annotation
-
Indicates an algorithm is nonexecutable.
- nonSmooth(double, DoubleMatrix1D, DoubleMatrix1D) - Method in class edu.pitt.csb.mgm.ConvexProximal
-
Calculate value of h(X) and proxOperator of h(X) at the same time for efficiency reasons.
- nonSmooth(double, DoubleMatrix1D, DoubleMatrix1D) - Method in class edu.pitt.csb.mgm.Mgm
-
Calculates penalty term and proximal operator at the same time for speed
- nonSmoothValue(DoubleMatrix1D) - Method in class edu.pitt.csb.mgm.Mgm
-
Calculates penalty term of objective function
- norm1() - Method in class edu.cmu.tetrad.util.Matrix
- norm1() - Method in class edu.cmu.tetrad.util.Matrix2
- norm2(DoubleMatrix1D) - Static method in class edu.pitt.csb.mgm.ProximalGradient
- Normal - Class in edu.cmu.tetrad.util.dist
-
A normal distribution that allows its parameters to be set and allows random sampling.
- Normal(double, double) - Constructor for class edu.cmu.tetrad.util.dist.Normal
- normalCdf(double) - Static method in class edu.cmu.tetrad.util.ProbUtils
-
Normal cumulative distribution function (the value which results by integrating the normal distribution function from negative infinity up to y).
- normalCdf(double, double, double) - Method in class edu.cmu.tetrad.util.RandomUtil
- normalizeAll() - Method in interface edu.cmu.tetrad.bayes.BayesIm
-
Normalizes all rows in the tables associated with each of node in turn.
- normalizeAll() - Method in class edu.cmu.tetrad.bayes.DirichletBayesIm
-
Normalizes all rows in the tables associated with each of node in turn.
- normalizeAll() - Method in class edu.cmu.tetrad.bayes.MlBayesIm
-
Normalizes all rows in the tables associated with each of node in turn.
- normalizeAll() - Method in class edu.cmu.tetrad.bayes.MlBayesImObs
-
Normalizes all rows in the tables associated with each of node in turn.
- normalizeAll() - Method in class edu.cmu.tetrad.bayes.UpdatedBayesIm
- normalizeNode(int) - Method in interface edu.cmu.tetrad.bayes.BayesIm
-
Normalizes all rows in the table associated with a given node.
- normalizeNode(int) - Method in class edu.cmu.tetrad.bayes.DirichletBayesIm
-
Normalizes all rows in the table associated with a given node.
- normalizeNode(int) - Method in class edu.cmu.tetrad.bayes.MlBayesIm
-
Normalizes all rows in the table associated with a given node.
- normalizeNode(int) - Method in class edu.cmu.tetrad.bayes.MlBayesImObs
-
Normalizes all rows in the table associated with a given node.
- normalizeNode(int) - Method in class edu.cmu.tetrad.bayes.UpdatedBayesIm
- normalizeRow(int, int) - Method in interface edu.cmu.tetrad.bayes.BayesIm
-
Normalizes the given row.
- normalizeRow(int, int) - Method in class edu.cmu.tetrad.bayes.DirichletBayesIm
-
Normalizes the given row.
- normalizeRow(int, int) - Method in class edu.cmu.tetrad.bayes.MlBayesIm
-
Normalizes the given row.
- normalizeRow(int, int) - Method in class edu.cmu.tetrad.bayes.MlBayesImObs
-
Normalizes the given row.
- normalizeRow(int, int) - Method in class edu.cmu.tetrad.bayes.UpdatedBayesIm
- normalPdf(double) - Static method in class edu.cmu.tetrad.util.ProbUtils
- normalPdf(double, double, double) - Method in class edu.cmu.tetrad.util.RandomUtil
- normalQuantile(double) - Static method in class edu.cmu.tetrad.util.ProbUtils
- normalRand() - Static method in class edu.cmu.tetrad.util.ProbUtils
-
Normal random generator
- NoSemidirectedF1 - Class in edu.cmu.tetrad.algcomparison.statistic
-
Calculates the F1 statistic for adjacencies.
- NoSemidirectedF1() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.NoSemidirectedF1
- NoSemidirectedPrecision - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- NoSemidirectedPrecision() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.NoSemidirectedPrecision
- NoSemidirectedRecall - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- NoSemidirectedRecall() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.NoSemidirectedRecall
- nRooks(boolean[][]) - Static method in class edu.cmu.tetrad.search.utils.NRooks
-
Solves the N-Rooks problem for the given board or allowable positions.
- NRooks - Class in edu.cmu.tetrad.search.utils
-
Returns row positions for placing rooks for an n x n matrix so the rooks cannot attach each other, with a given boolean[][] specification of where rooks are allowed to be placed.
- NRooks() - Constructor for class edu.cmu.tetrad.search.utils.NRooks
- NULL - Enum constant in enum class edu.cmu.tetrad.graph.Endpoint
- NUM_BASIS_FUNCTIONS - Static variable in class edu.cmu.tetrad.util.Params
- NUM_BSC_BOOTSTRAP_SAMPLES - Static variable in class edu.cmu.tetrad.util.Params
- NUM_CATEGORIES - Static variable in class edu.cmu.tetrad.util.Params
- NUM_CATEGORIES_TO_DISCRETIZE - Static variable in class edu.cmu.tetrad.util.Params
- NUM_LAGS - Static variable in class edu.cmu.tetrad.util.Params
- NUM_LATENTS - Static variable in class edu.cmu.tetrad.util.Params
- NUM_MEASURES - Static variable in class edu.cmu.tetrad.util.Params
- NUM_RANDOMIZED_SEARCH_MODELS - Static variable in class edu.cmu.tetrad.util.Params
- NUM_ROUNDS - Static variable in class edu.cmu.tetrad.util.Params
- NUM_RUNS - Static variable in class edu.cmu.tetrad.util.Params
- NUM_STARTS - Static variable in class edu.cmu.tetrad.util.Params
- NUM_STRUCTURAL_EDGES - Static variable in class edu.cmu.tetrad.util.Params
- NUM_STRUCTURAL_NODES - Static variable in class edu.cmu.tetrad.util.Params
- NUM_SUBSAMPLES - Static variable in class edu.cmu.tetrad.util.Params
- NUM_THREADS - Static variable in class edu.cmu.tetrad.util.Params
- NumAmbiguousTriples - Class in edu.cmu.tetrad.algcomparison.statistic
-
The adjacency precision.
- NumAmbiguousTriples() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.NumAmbiguousTriples
- NUMBER - Enum constant in enum class edu.cmu.tetrad.calculator.parser.Token
- NUMBER_OF_EXPANSIONS - Static variable in class edu.cmu.tetrad.util.Params
- NUMBER_RESAMPLING - Static variable in class edu.cmu.tetrad.util.Params
- NumberFormatUtil - Class in edu.cmu.tetrad.util
-
Provides an application-wide "memory" of the number format to be used.
- NumberObjectDataSet - Class in edu.cmu.tetrad.data
-
Wraps a 2D array of Number objects in such a way that mixed data sets can be stored.
- NumberObjectDataSet(Number[][], List<Node>) - Constructor for class edu.cmu.tetrad.data.NumberObjectDataSet
- NumberOfEdgesEst - Class in edu.cmu.tetrad.algcomparison.statistic
-
Prints the number of edges in the estimated graph.
- NumberOfEdgesEst() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.NumberOfEdgesEst
- NumberOfEdgesTrue - Class in edu.cmu.tetrad.algcomparison.statistic
-
Prints the number of edges in the true graph.
- NumberOfEdgesTrue() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.NumberOfEdgesTrue
- NumBidirectedBothNonancestorAncestor - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected edge precision.
- NumBidirectedBothNonancestorAncestor() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.NumBidirectedBothNonancestorAncestor
- NumBidirectedEdgesEst - Class in edu.cmu.tetrad.algcomparison.statistic
-
The adjacency precision.
- NumBidirectedEdgesEst() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.NumBidirectedEdgesEst
- NumBidirectedEdgesTrue - Class in edu.cmu.tetrad.algcomparison.statistic
-
The adjacency precision.
- NumBidirectedEdgesTrue() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.NumBidirectedEdgesTrue
- NumColoredDD - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- NumColoredDD() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.NumColoredDD
- NumColoredNL - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- NumColoredNL() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.NumColoredNL
- NumColoredPD - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- NumColoredPD() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.NumColoredPD
- NumColoredPL - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- NumColoredPL() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.NumColoredPL
- numCols() - Method in class edu.cmu.tetrad.data.ByteDataBox
- numCols() - Method in interface edu.cmu.tetrad.data.DataBox
- numCols() - Method in class edu.cmu.tetrad.data.DoubleDataBox
- numCols() - Method in class edu.cmu.tetrad.data.FloatDataBox
- numCols() - Method in class edu.cmu.tetrad.data.IntDataBox
- numCols() - Method in class edu.cmu.tetrad.data.LongDataBox
- numCols() - Method in class edu.cmu.tetrad.data.MixedDataBox
- numCols() - Method in class edu.cmu.tetrad.data.ShortDataBox
- numCols() - Method in class edu.cmu.tetrad.data.VerticalDoubleDataBox
- numCols() - Method in class edu.cmu.tetrad.data.VerticalIntDataBox
- NumCommonMeasuredAncestorBidirected - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- NumCommonMeasuredAncestorBidirected() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.NumCommonMeasuredAncestorBidirected
- NumCompatibleDefiniteDirectedEdgeAncestors - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- NumCompatibleDefiniteDirectedEdgeAncestors() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.NumCompatibleDefiniteDirectedEdgeAncestors
- NumCompatibleDirectedEdgeConfounded - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- NumCompatibleDirectedEdgeConfounded() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.NumCompatibleDirectedEdgeConfounded
- NumCompatibleDirectedEdgeNonAncestors - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- NumCompatibleDirectedEdgeNonAncestors() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.NumCompatibleDirectedEdgeNonAncestors
- NumCompatibleEdges - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- NumCompatibleEdges() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.NumCompatibleEdges
- NumCompatiblePossiblyDirectedEdgeAncestors - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- NumCompatiblePossiblyDirectedEdgeAncestors() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.NumCompatiblePossiblyDirectedEdgeAncestors
- NumCompatiblePossiblyDirectedEdgeNonAncestors - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- NumCompatiblePossiblyDirectedEdgeNonAncestors() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.NumCompatiblePossiblyDirectedEdgeNonAncestors
- NumCompatibleVisibleAncestors - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- NumCompatibleVisibleAncestors() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.NumCompatibleVisibleAncestors
- NumCompatibleVisibleNonancestors - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- NumCompatibleVisibleNonancestors() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.NumCompatibleVisibleNonancestors
- NumCorrectDDAncestors - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- NumCorrectDDAncestors() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.NumCorrectDDAncestors
- NumCorrectPDAncestors - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- NumCorrectPDAncestors() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.NumCorrectPDAncestors
- NumCorrectVisibleAncestors - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- NumCorrectVisibleAncestors() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.NumCorrectVisibleAncestors
- NumDefinitelyDirected - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- NumDefinitelyDirected() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.NumDefinitelyDirected
- NumDefinitelyNotDirectedPaths - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- NumDefinitelyNotDirectedPaths() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.NumDefinitelyNotDirectedPaths
- NumDirectedEdgeAncestors - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- NumDirectedEdgeAncestors() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.NumDirectedEdgeAncestors
- NumDirectedEdgeBnaMeasuredCounfounded - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- NumDirectedEdgeBnaMeasuredCounfounded() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.NumDirectedEdgeBnaMeasuredCounfounded
- NumDirectedEdgeNoMeasureAncestors - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- NumDirectedEdgeNoMeasureAncestors() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.NumDirectedEdgeNoMeasureAncestors
- NumDirectedEdgeNotAncNotRev - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- NumDirectedEdgeNotAncNotRev() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.NumDirectedEdgeNotAncNotRev
- NumDirectedEdgeReversed - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- NumDirectedEdgeReversed() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.NumDirectedEdgeReversed
- NumDirectedEdges - Class in edu.cmu.tetrad.algcomparison.statistic
-
Number of X-->Y in est.
- NumDirectedEdges() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.NumDirectedEdges
- NumDirectedEdgeVisible - Class in edu.cmu.tetrad.algcomparison.statistic
-
Number of X-->Y for which X-->Y visible in true PAG.
- NumDirectedEdgeVisible() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.NumDirectedEdgeVisible
- NumDirectedPathsEst - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- NumDirectedPathsEst() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.NumDirectedPathsEst
- NumDirectedPathsTrue - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- NumDirectedPathsTrue() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.NumDirectedPathsTrue
- NumDirectedShouldBePartiallyDirected - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- NumDirectedShouldBePartiallyDirected() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.NumDirectedShouldBePartiallyDirected
- NumIncorrectDDAncestors - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- NumIncorrectDDAncestors() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.NumIncorrectDDAncestors
- NumIncorrectPDAncestors - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- NumIncorrectPDAncestors() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.NumIncorrectPDAncestors
- NumIncorrectVisibleAncestors - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- NumIncorrectVisibleAncestors() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.NumIncorrectVisibleAncestors
- NumLatentCommonAncestorBidirected - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- NumLatentCommonAncestorBidirected() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.NumLatentCommonAncestorBidirected
- NumNondirectedEdges - Class in edu.cmu.tetrad.algcomparison.statistic
-
Number of X---Y in est.
- NumNondirectedEdges() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.NumNondirectedEdges
- numParameters() - Method in interface jgpml.covariancefunctions.CovarianceFunction
-
Returns the number of hyperparameters of this
CovarianceFunction - numParameters() - Method in class jgpml.covariancefunctions.CovLINard
-
Returns the number of hyperparameters of this
CovarianceFunction - numParameters() - Method in class jgpml.covariancefunctions.CovLINone
-
Returns the number of hyperparameters of this
CovarianceFunction - numParameters() - Method in class jgpml.covariancefunctions.CovNNone
-
Returns the number of hyperparameters of this
CovarianceFunction - numParameters() - Method in class jgpml.covariancefunctions.CovNNoneNoise
-
Returns the number of hyperparameters of this
CovarianceFunction - numParameters() - Method in class jgpml.covariancefunctions.CovNoise
-
Returns the number of hyperparameters of
CovSEard - numParameters() - Method in class jgpml.covariancefunctions.CovSEard
-
Returns the number of hyperparameters of
CovSEard - numParameters() - Method in class jgpml.covariancefunctions.CovSEiso
-
Returns the number of hyperparameters of this
CovarianceFunction - numParameters() - Method in class jgpml.covariancefunctions.CovSum
-
Returns the number of hyperparameters of this
CovarianceFunction - NumPartiallyOrientedEdges - Class in edu.cmu.tetrad.algcomparison.statistic
-
Number of Xo->Y in est.
- NumPartiallyOrientedEdges() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.NumPartiallyOrientedEdges
- NumPossiblyDirected - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- NumPossiblyDirected() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.NumPossiblyDirected
- numRows() - Method in class edu.cmu.tetrad.data.ByteDataBox
- numRows() - Method in interface edu.cmu.tetrad.data.DataBox
- numRows() - Method in class edu.cmu.tetrad.data.DoubleDataBox
- numRows() - Method in class edu.cmu.tetrad.data.FloatDataBox
- numRows() - Method in class edu.cmu.tetrad.data.IntDataBox
- numRows() - Method in class edu.cmu.tetrad.data.LongDataBox
- numRows() - Method in class edu.cmu.tetrad.data.MixedDataBox
- numRows() - Method in class edu.cmu.tetrad.data.ShortDataBox
- numRows() - Method in class edu.cmu.tetrad.data.VerticalDoubleDataBox
- numRows() - Method in class edu.cmu.tetrad.data.VerticalIntDataBox
- NumUndirectedEdges - Class in edu.cmu.tetrad.algcomparison.statistic
-
Number of X---Y in est.
- NumUndirectedEdges() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.NumUndirectedEdges
- numVals(DoubleMatrix1D) - Static method in class edu.pitt.csb.mgm.MixedUtils
- NumVisibleEst - Class in edu.cmu.tetrad.algcomparison.statistic
-
Number of X-->Y visible in est.
- NumVisibleEst() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.NumVisibleEst
O
- oneFactorTest(int, int, int, int) - Method in interface edu.cmu.tetrad.search.utils.TetradTest
- oneFactorTest(int, int, int, int) - Method in class edu.cmu.tetrad.search.utils.TetradTestContinuous
- oneFactorTest(int, int, int, int) - Method in class edu.cmu.tetrad.search.utils.TetradTestDiscrete
- oneFactorTest(int, int, int, int) - Method in class edu.cmu.tetrad.search.utils.TetradTestPopulation
- oneFactorTest(int, int, int, int, int) - Method in interface edu.cmu.tetrad.search.utils.TetradTest
- oneFactorTest(int, int, int, int, int) - Method in class edu.cmu.tetrad.search.utils.TetradTestContinuous
- oneFactorTest(int, int, int, int, int) - Method in class edu.cmu.tetrad.search.utils.TetradTestDiscrete
- oneFactorTest(int, int, int, int, int) - Method in class edu.cmu.tetrad.search.utils.TetradTestPopulation
- OPERATOR - Enum constant in enum class edu.cmu.tetrad.calculator.parser.Token
- optimize(SemIm) - Method in interface edu.cmu.tetrad.sem.SemOptimizer
-
Optimizes the fitting function of a Sem by adjusting its parameter values.
- optimize(SemIm) - Method in class edu.cmu.tetrad.sem.SemOptimizerEm
- optimize(SemIm) - Method in class edu.cmu.tetrad.sem.SemOptimizerPowell
- optimize(SemIm) - Method in class edu.cmu.tetrad.sem.SemOptimizerRegression
-
Fit the freeParameters by doing local regressions.
- optimize(SemIm) - Method in class edu.cmu.tetrad.sem.SemOptimizerRicf
-
Optimizes the fitting function of the given Sem using the Powell method from Numerical Recipes by adjusting the freeParameters of the Sem.
- optimize(SemIm) - Method in class edu.cmu.tetrad.sem.SemOptimizerScattershot
-
Optimizes the fitting function of the given Sem using the Powell method from Numerical Recipes by adjusting the freeParameters of the Sem.
- OrderedPair<E> - Class in edu.cmu.tetrad.graph
-
An ordered pair of objects.
- OrderedPair(E, E) - Constructor for class edu.cmu.tetrad.graph.OrderedPair
- orient() - Method in class edu.cmu.tetrad.search.Lofs
-
Orients the graph and returns the oriented graph.
- orient(Graph) - Method in class edu.cmu.tetrad.search.utils.FciOrient
-
Performs final FCI orientation on the given graph.
- orient(Graph) - Method in class edu.cmu.tetrad.search.utils.FgesOrienter
- orient(Graph) - Method in class edu.cmu.tetrad.search.utils.MaxP
-
Adds colliders to the given graph using the max P rule.
- orient(Graph) - Method in class edu.cmu.tetrad.search.utils.SvarFciOrient
- ORIENT_BIDIRECTED - Enum constant in enum class edu.cmu.tetrad.search.utils.PcCommon.ConflictRule
- orient_pairwise - Enum constant in enum class edu.cmu.tetrad.annotation.AlgType
-
If algorithm orients edges pairwise.
- ORIENT_TOWARD_DCONNECTIONS - Static variable in class edu.cmu.tetrad.util.Params
- ORIENT_VISIBLE_FEEDBACK_LOOPS - Static variable in class edu.cmu.tetrad.util.Params
- ORIENTATION_ALPHA - Static variable in class edu.cmu.tetrad.util.Params
- OrientationConfusion - Class in edu.cmu.tetrad.algcomparison.statistic.utils
-
A confusion matrix for orientations:
- OrientationConfusion(Graph, Graph) - Constructor for class edu.cmu.tetrad.algcomparison.statistic.utils.OrientationConfusion
- OrientationPrecision - Class in edu.cmu.tetrad.algcomparison.statistic
-
The orientation precision.
- OrientationPrecision() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.OrientationPrecision
- OrientationRecall - Class in edu.cmu.tetrad.algcomparison.statistic
-
The orientation recall.
- OrientationRecall() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.OrientationRecall
- orientCollider(Node, Node, Node, PcCommon.ConflictRule, Graph) - Static method in class edu.cmu.tetrad.search.utils.PcCommon
-
Orient a single unshielded triple, x*-*y*-*z, in a graph.
- orientCollidersUsingSepsets(SepsetMap, Knowledge, Graph, boolean, boolean) - Static method in class edu.cmu.tetrad.search.utils.GraphSearchUtils
-
Step C of PC; orients colliders using specified sepset.
- orientImplied(Graph) - Method in class edu.cmu.tetrad.search.utils.MeekRules
-
Uses the Meek rules to do as many orientations in the given graph as possible.
- orientTailPath(List<Node>, Graph) - Method in class edu.cmu.tetrad.search.utils.FciOrient
-
Orients every edge on a path as undirected (i.e.
- other - Enum constant in enum class edu.cmu.tetrad.search.Lofs.Score
- OTHER_PERM_METHOD - Static variable in class edu.cmu.tetrad.util.Params
- OtherPermAlgs - Class in edu.cmu.tetrad.search.work_in_progress
-
Implements various permutation algorithms, including BOSS and GASP.
- OtherPermAlgs(IndependenceTest) - Constructor for class edu.cmu.tetrad.search.work_in_progress.OtherPermAlgs
- OtherPermAlgs(IndependenceTest, Score) - Constructor for class edu.cmu.tetrad.search.work_in_progress.OtherPermAlgs
- OtherPermAlgs(Score) - Constructor for class edu.cmu.tetrad.search.work_in_progress.OtherPermAlgs
- OtherPermAlgs.Method - Enum Class in edu.cmu.tetrad.search.work_in_progress
- outerProduct(double[], double[]) - Static method in class edu.cmu.tetrad.util.MatrixUtils
- OUTPUT_CPDAG - Static variable in class edu.cmu.tetrad.util.Params
- OUTPUT_RBD - Static variable in class edu.cmu.tetrad.util.Params
- OutputGraph - Interface in edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util
-
Represents a graph that's output by a genetic search algorithm.
- OVERWRITE_EXISTING - Enum constant in enum class edu.cmu.tetrad.search.utils.PcCommon.ConflictRule
P
- p - Variable in class edu.cmu.tetrad.bayes.BayesProperties.LikelihoodRet
- PAG - Enum constant in enum class edu.cmu.tetrad.algcomparison.comparegraphs.CompareTwoGraphs.CompareToType
- PAG - Enum constant in enum class edu.cmu.tetrad.study.performance.ComparisonParameters.ResultType
- PAG_of_the_true_DAG - Enum constant in enum class edu.cmu.tetrad.algcomparison.Comparison.ComparisonGraph
- PAG_of_the_true_DAG - Enum constant in enum class edu.cmu.tetrad.algcomparison.TimeoutComparison.ComparisonGraph
- PAG_SAMPLING_RFCI_PARAMETERS - Static variable in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.PagSampleRfci
- PagAdjacencyPrecision - Class in edu.cmu.tetrad.algcomparison.statistic
-
The adjacency precision.
- PagAdjacencyPrecision() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.PagAdjacencyPrecision
- PagAdjacencyRecall - Class in edu.cmu.tetrad.algcomparison.statistic
-
The adjacency recall.
- PagAdjacencyRecall() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.PagAdjacencyRecall
- PagSampleRfci - Class in edu.cmu.tetrad.algcomparison.algorithm.oracle.pag
-
Jan 29, 2023 3:45:09 PM
- PagSampleRfci() - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.PagSampleRfci
- PagSamplingRfci - Class in edu.pitt.dbmi.algo.bayesian.constraint.search
-
Jan 29, 2023 4:10:52 PM
- PagSamplingRfci(DataSet) - Constructor for class edu.pitt.dbmi.algo.bayesian.constraint.search.PagSamplingRfci
- pagToMag(Graph) - Static method in class edu.cmu.tetrad.graph.GraphTransforms
- PARALLEL - Static variable in class edu.cmu.tetrad.search.FastIca
-
The algorithm type where all components are extracted simultaneously.
- PARALLELIZED - Static variable in class edu.cmu.tetrad.util.Params
- ParamComparison - Class in edu.cmu.tetrad.sem
-
A typesafe enum of the types of the various comparisons parameter may have with respect to one another for SEM estimation.
- ParamConstraint - Class in edu.cmu.tetrad.sem
-
A class for implementing constraints on the values of the freeParameters of of instances of the SemIm class.
- ParamConstraint(SemIm, Parameter, ParamConstraintType, double) - Constructor for class edu.cmu.tetrad.sem.ParamConstraint
-
The first constructor specifies the parameter and a number and the type of relation imposed by the constraint.
- ParamConstraintType - Class in edu.cmu.tetrad.sem
-
A typesafe enum of the types of the types of constraints on freeParameters for SEM models (LT, GT, EQ).
- ParamDescription - Class in edu.cmu.tetrad.util
-
Describes a parameter.
- ParamDescription(String, String, String, Serializable) - Constructor for class edu.cmu.tetrad.util.ParamDescription
- ParamDescription(String, String, String, Serializable, double, double) - Constructor for class edu.cmu.tetrad.util.ParamDescription
- ParamDescription(String, String, String, Serializable, int, int) - Constructor for class edu.cmu.tetrad.util.ParamDescription
- ParamDescriptions - Class in edu.cmu.tetrad.util
-
Stores descriptions of the parameters for the simulation box.
- Parameter - Class in edu.cmu.tetrad.sem
-
Stores information about the identity of a SEM parameter--its name, its type (COEF, COVAR), and the node(s) it is associated with.
- Parameter(String, ParamType, Node, Node) - Constructor for class edu.cmu.tetrad.sem.Parameter
- PARAMETER - Enum constant in enum class edu.cmu.tetrad.calculator.parser.Token
- ParameterColumn - Class in edu.cmu.tetrad.algcomparison.statistic
-
Adds a column to the output table in which values for the given parameter are listed.
- ParameterColumn(String) - Constructor for class edu.cmu.tetrad.algcomparison.statistic.ParameterColumn
- ParameterPair - Class in edu.cmu.tetrad.sem
-
Implements an ordered pair of objects (a, b) suitable for storing in HashSets.
- ParameterPair(Parameter, Parameter) - Constructor for class edu.cmu.tetrad.sem.ParameterPair
-
Constructs a new ordered pair (a, b).
- ParameterRange(Edge, double, double, double) - Constructor for class edu.cmu.tetrad.sem.StandardizedSemIm.ParameterRange
- Parameters - Class in edu.cmu.tetrad.util
-
Stores a list of named parameters with their values.
- Parameters() - Constructor for class edu.cmu.tetrad.util.Parameters
- Parameters(Parameters) - Constructor for class edu.cmu.tetrad.util.Parameters
- ParameterUtils - Class in edu.cmu.tetrad.util
-
A utility to create/modify parameters.
- parameterValues() - Method in interface edu.cmu.tetrad.algcomparison.utils.ParameterValues
- parameterValues() - Method in class edu.cmu.tetrad.data.simulation.LoadDataFromFileWithoutGraph
- ParameterValues - Interface in edu.cmu.tetrad.algcomparison.utils
-
Tags a class that can return values for parameters.
- Params - Class in edu.cmu.tetrad.util
-
May 7, 2019 2:53:27 PM
- ParamsResettable - Interface in edu.cmu.tetrad.session
-
Tags models whose parameters can be reset.
- ParamType - Class in edu.cmu.tetrad.sem
-
A typesafe enum of the types of the types of freeParameters for SEM models (COEF, MEAN, VAR, COVAR).
- parent(Node, Node) - Method in class edu.cmu.tetrad.search.utils.TeyssierScorer
- PARENT_ADDED - Static variable in class edu.cmu.tetrad.session.SessionEvent
- PARENT_REMOVED - Static variable in class edu.cmu.tetrad.session.SessionEvent
- parentAdded(SessionEvent) - Method in class edu.cmu.tetrad.session.SessionAdapter
-
Indicates that a parent has been added to a node.
- parentAdded(SessionEvent) - Method in interface edu.cmu.tetrad.session.SessionListener
-
Indicates that a parent has been added to a node.
- parentRemoved(SessionEvent) - Method in class edu.cmu.tetrad.session.SessionAdapter
-
Indicates that a parent has been removed from a node.
- parentRemoved(SessionEvent) - Method in interface edu.cmu.tetrad.session.SessionListener
-
Indicates that a parent has been removed from a node.
- PARENTS - Enum constant in enum class edu.cmu.tetrad.search.MarkovCheck.ConditioningSetType
- parseEquation(String) - Method in class edu.cmu.tetrad.calculator.parser.ExpressionParser
-
Parses an equation of the form Variable = Expression.
- parseExpression(String) - Method in class edu.cmu.tetrad.calculator.parser.ExpressionParser
-
Parses the given expression, or throws an exception if its not possible.
- parseGraphXml(Element, Map<String, Node>) - Static method in class edu.cmu.tetrad.graph.GraphSaveLoadUtils
- parseJSONArrayToTetradEdges(Graph, JSONArray) - Static method in class edu.cmu.tetrad.util.JsonUtils
- parseJSONArrayToTetradNodes(JSONArray) - Static method in class edu.cmu.tetrad.util.JsonUtils
- parseJSONArrayToTetradTriple(JSONObject) - Static method in class edu.cmu.tetrad.util.JsonUtils
- parseJSONArrayToTetradTriples(JSONArray) - Static method in class edu.cmu.tetrad.util.JsonUtils
- parseJSONObjectToEdgeProperty(String) - Static method in class edu.cmu.tetrad.util.JsonUtils
- parseJSONObjectToEdgeTypeProperty(JSONObject) - Static method in class edu.cmu.tetrad.util.JsonUtils
- parseJSONObjectToTetradEdge(Graph, JSONObject) - Static method in class edu.cmu.tetrad.util.JsonUtils
- parseJSONObjectToTetradGraph(String) - Static method in class edu.cmu.tetrad.util.JsonUtils
- parseJSONObjectToTetradGraph(JSONObject) - Static method in class edu.cmu.tetrad.util.JsonUtils
- parseJSONObjectToTetradNode(JSONObject) - Static method in class edu.cmu.tetrad.util.JsonUtils
- partialCorrelation(Matrix) - Static method in class edu.cmu.tetrad.util.StatUtils
-
Assumes that the given covariance matrix was extracted in such a way that the order of the variables (in either direction) is X, Y, Z1, ..., Zn, where the partial correlation one wants is correlation(X, Y | Z1,...,Zn).
- partialCorrelation(Matrix, int, int, int...) - Static method in class edu.cmu.tetrad.util.StatUtils
- PartialCorrelation - Class in edu.cmu.tetrad.search.utils
-
Calculates partial correlation using the recursive method.
- PartialCorrelation(ICovarianceMatrix) - Constructor for class edu.cmu.tetrad.search.utils.PartialCorrelation
-
Constructor
- PartialCorrelation(List<Node>, Matrix, int) - Constructor for class edu.cmu.tetrad.search.utils.PartialCorrelation
-
Constructor.
- PartialCorrelationPdf - Class in edu.cmu.tetrad.util
-
Frequency function of partial correlation r(12|34...k), assuming that the true partial correlation is equal to zero.
- PartialCorrelationPdf(int, int) - Constructor for class edu.cmu.tetrad.util.PartialCorrelationPdf
-
Constructs a new zero partial correlation distribution function with the given values for n and k.
- partialCorrelationPrecisionMatrix(Matrix) - Static method in class edu.cmu.tetrad.util.StatUtils
- partialCovarianceWhittaker(Matrix) - Static method in class edu.cmu.tetrad.util.StatUtils
-
Assumes that the given covariance matrix was extracted in such a way that the order of the variables (in either direction) is X, Y, Z1, ..., Zn, where the partial covariance one wants is covariance(X, Y | Z1,...,Zn).
- partialCovarianceWhittaker(Matrix, int, int, int...) - Static method in class edu.cmu.tetrad.util.StatUtils
- partiallyOrientedEdge(Node, Node) - Static method in class edu.cmu.tetrad.graph.Edges
-
Constructs a new partially oriented edge from nodeA to nodeB (o->).
- partialStandardDeviation(Matrix, int, int...) - Static method in class edu.cmu.tetrad.util.StatUtils
- partialVariance(Matrix, int, int...) - Static method in class edu.cmu.tetrad.util.StatUtils
- partitionToClusters(List<List<Node>>) - Static method in class edu.cmu.tetrad.search.utils.ClusterUtils
- Patel - Enum constant in enum class edu.cmu.tetrad.search.Lofs.Rule
- Patel25 - Enum constant in enum class edu.cmu.tetrad.search.Lofs.Rule
- Patel50 - Enum constant in enum class edu.cmu.tetrad.search.Lofs.Rule
- Patel75 - Enum constant in enum class edu.cmu.tetrad.search.Lofs.Rule
- Patel90 - Enum constant in enum class edu.cmu.tetrad.search.Lofs.Rule
- path - Variable in class edu.cmu.tetrad.algcomparison.algorithm.ExternalAlgorithm
- paths() - Method in class edu.cmu.tetrad.graph.Dag
- paths() - Method in class edu.cmu.tetrad.graph.EdgeListGraph
- paths() - Method in interface edu.cmu.tetrad.graph.Graph
- paths() - Method in class edu.cmu.tetrad.graph.LagGraph
- paths() - Method in class edu.cmu.tetrad.graph.SemGraph
- paths() - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- Paths - Class in edu.cmu.tetrad.graph
- Paths(Graph) - Constructor for class edu.cmu.tetrad.graph.Paths
- Paths.AllCliquesAlgorithm - Class in edu.cmu.tetrad.graph
- pathString(Graph, Node...) - Static method in class edu.cmu.tetrad.graph.GraphUtils
- pathString(Graph, Node, Node, Node) - Static method in class edu.cmu.tetrad.graph.Triple
- pathString(Graph, List<Node>) - Static method in class edu.cmu.tetrad.graph.GraphUtils
- Pc - Class in edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag
-
Peter/Clark algorithm (PC).
- Pc - Class in edu.cmu.tetrad.search
-
Implements the Peter/Clark (PC) algorithm, which uses conditional independence testing as an oracle to first of all remove extraneous edges from a complete graph, then to orient the unshielded colliders in the graph, and finally to make any additional orientations that are capable of avoiding additional unshielded colliders in the graph.
- Pc() - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Pc
- Pc(IndependenceWrapper) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Pc
- Pc(IndependenceTest) - Constructor for class edu.cmu.tetrad.search.Pc
-
Constructs a new PC search using the given independence test as oracle.
- PC - Enum constant in enum class edu.cmu.tetrad.study.performance.ComparisonParameters.Algorithm
- PC_STABLE - Enum constant in enum class edu.cmu.tetrad.search.Cstar.CpdagAlgorithm
- PcCommon - Class in edu.cmu.tetrad.search.utils
-
Prodies some common implementation pieces of variaous PC-like algorithms, with options for collider discovery type, FAS type, and conflict rule.
- PcCommon(IndependenceTest) - Constructor for class edu.cmu.tetrad.search.utils.PcCommon
-
Constructs a CPC algorithm that uses the given independence test as oracle.
- PcCommon.ColliderDiscovery - Enum Class in edu.cmu.tetrad.search.utils
-
Give the options for the collider discovery algroithm to use--FAS with sepsets reasoning, FAS with conservative reasoning, or FAS with Max P reasoning.
- PcCommon.ConflictRule - Enum Class in edu.cmu.tetrad.search.utils
-
Gives the type of conflict to be used, priority (when there is a conflict, keep the orientation that has already been made), bidirected (when there is a conflict, orient a bidirected edge), or overwrite (when there is a conflict, use the new orientation).
- PcCommon.FasType - Enum Class in edu.cmu.tetrad.search.utils
-
Gives the type of FAS used, regular or stable.
- PcCommon.PcHeuristicType - Enum Class in edu.cmu.tetrad.search.utils
-
NONE = no heuristic, PC-1 = sort nodes alphabetically; PC-1 = sort edges by p-value; PC-3 = additionally sort edges in reverse order using p-values of associated independence facts.
- Pcd - Class in edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag
-
PC.
- Pcd - Class in edu.cmu.tetrad.search
-
Modifies the PC algorithm to handle the deterministic case.
- Pcd() - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Pcd
- Pcd(IndependenceTest) - Constructor for class edu.cmu.tetrad.search.Pcd
-
Constructs a new PC search using the given independence test as oracle.
- pcdOrientC(IndependenceTest, Knowledge, Graph) - Static method in class edu.cmu.tetrad.search.utils.GraphSearchUtils
-
Performs step C of the algorithm, as indicated on page xxx of CPS, with the modification that X--W--Y is oriented as X-->W<--Y if W is *determined by* the sepset of (X, Y), rather than W just being *in* the sepset of (X, Y).
- PcLingam - Class in edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag
-
Peter/Clark algorithm (PC).
- PcLingam - Class in edu.cmu.tetrad.search
-
Implements the PC-LiNGAM algorithm which first finds a CPDAG for the variables and then uses a non-Gaussian orientation method to orient the undirected edges.
- PcLingam() - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.PcLingam
- PcLingam(ScoreWrapper) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.PcLingam
- PcLingam(Graph, DataSet) - Constructor for class edu.cmu.tetrad.search.PcLingam
-
Constructor.
- PcMb - Class in edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag
-
PC.
- PcMb - Class in edu.cmu.tetrad.search
-
Searches for a CPDAG representing all the Markov blankets for a given target T consistent with the given independence information.
- PcMb() - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.PcMb
- PcMb(IndependenceWrapper) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.PcMb
- PcMb(IndependenceTest, int) - Constructor for class edu.cmu.tetrad.search.PcMb
-
Constructs a new search.
- pcOrientbk(Knowledge, Graph, List<Node>) - Static method in class edu.cmu.tetrad.search.utils.GraphSearchUtils
-
Orients according to background knowledge.
- PcStableWrapper(double...) - Constructor for class edu.pitt.csb.stability.SearchWrappers.PcStableWrapper
- pd - Enum constant in enum class edu.cmu.tetrad.graph.Edge.Property
- PENALTY_DISCOUNT - Static variable in class edu.cmu.tetrad.util.Params
- PENALTY_DISCOUNT_ZS - Static variable in class edu.cmu.tetrad.util.Params
- PERCENT_DISCRETE - Static variable in class edu.cmu.tetrad.util.Params
- PERCENT_RESAMPLE_SIZE - Static variable in class edu.cmu.tetrad.util.Params
- PercentAmbiguous - Class in edu.cmu.tetrad.algcomparison.statistic
-
The adjacency precision.
- PercentAmbiguous() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.PercentAmbiguous
- PercentBidirectedEdges - Class in edu.cmu.tetrad.algcomparison.statistic
-
The adjacency precision.
- PercentBidirectedEdges() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.PercentBidirectedEdges
- PerformanceTests - Class in edu.cmu.tetrad.study.performance
-
Runs some basic performance tests of various algorithm.
- PerformanceTests() - Constructor for class edu.cmu.tetrad.study.performance.PerformanceTests
- PerformanceTestsDan - Class in edu.cmu.tetrad.study.performance
-
Contains some tests for Dan Malinsky, that might be of interest to others.
- PerformanceTestsDan() - Constructor for class edu.cmu.tetrad.study.performance.PerformanceTestsDan
- PermutationGenerator - Class in edu.cmu.tetrad.util
-
Generates all of the permutations of [0,..., numObjects - 1], where numObjects is numObjects nonnegative integer.
- PermutationGenerator(int) - Constructor for class edu.cmu.tetrad.util.PermutationGenerator
-
Constructs numObjects new choice generator for numObjects choose b.
- PermutationMatrixPair - Class in edu.cmu.tetrad.search.utils
-
Stores a matrix together with a row and column permutation.
- PermutationMatrixPair(Matrix, int[], int[]) - Constructor for class edu.cmu.tetrad.search.utils.PermutationMatrixPair
-
Constructs with a given matrix M and a row and column permutation (which may be null).
- PermutationSearch - Class in edu.cmu.tetrad.search
-
Implements common elements of a permutation search.
- PermutationSearch(SuborderSearch) - Constructor for class edu.cmu.tetrad.search.PermutationSearch
-
Constructs a new PermutationSearch using the given SuborderSearch.
- permuteRows() - Method in class edu.cmu.tetrad.data.BoxDataSet
-
Randomly permutes the rows of the dataset.
- permuteRows() - Method in interface edu.cmu.tetrad.data.DataSet
-
Randomizes the rows of the data set.
- permuteRows() - Method in class edu.cmu.tetrad.data.NumberObjectDataSet
-
Randomly permutes the rows of the dataset.
- PI - Static variable in class edu.cmu.tetrad.calculator.expression.ConstantExpression
-
Constant expression for PI.
- PI_THR - Static variable in class edu.cmu.tetrad.util.Params
- pl - Enum constant in enum class edu.cmu.tetrad.graph.Edge.Property
- plus(Matrix) - Method in class edu.cmu.tetrad.util.Matrix
- plus(Matrix2) - Method in class edu.cmu.tetrad.util.Matrix2
- plus(Vector) - Method in class edu.cmu.tetrad.util.Vector
- Pm - Interface in edu.cmu.tetrad.util
-
Tagging interface for parametric models.
- Point - Class in edu.cmu.tetrad.util
-
Implements an n-dimensional point.
- Point(Vector) - Constructor for class edu.cmu.tetrad.util.Point
-
Constructs a point with coordinates as in the given vector.
- pointsTowards(Node) - Method in class edu.cmu.tetrad.graph.Edge
- PointXy - Class in edu.cmu.tetrad.util
-
Stores a (x, y) point without having to use awt classes.
- PointXy(int, int) - Constructor for class edu.cmu.tetrad.util.PointXy
-
Constructs a new point with the given coordinates.
- PointXy(PointXy) - Constructor for class edu.cmu.tetrad.util.PointXy
-
Copy constructor.
- poisson(double, double, boolean) - Static method in class edu.cmu.tetrad.util.StatUtils
-
Calculates the Poisson Distribution for mean x and k events for doubles.
- Poisson - Class in edu.cmu.tetrad.util.dist
-
Wraps a chi square distribution for purposes of drawing random samples.
- POISSON_LAMBDA - Static variable in class edu.cmu.tetrad.util.Params
- poissonCdf(int, double) - Static method in class edu.cmu.tetrad.util.ProbUtils
- poissonPmf(int, double) - Static method in class edu.cmu.tetrad.util.ProbUtils
- PoissonPriorScore - Class in edu.cmu.tetrad.algcomparison.score
-
Wrapper for the Poisson prior score (Bryan)
- PoissonPriorScore - Class in edu.cmu.tetrad.search.score
-
Implements Poisson prior score, a novel (unpubished) score that replaces the penalty term in BIC by the log of the Poisson distribution.
- PoissonPriorScore() - Constructor for class edu.cmu.tetrad.algcomparison.score.PoissonPriorScore
- PoissonPriorScore(DataSet, boolean) - Constructor for class edu.cmu.tetrad.search.score.PoissonPriorScore
-
Constructs the score using a covariance matrix.
- PoissonPriorScore(ICovarianceMatrix) - Constructor for class edu.cmu.tetrad.search.score.PoissonPriorScore
-
Constructs the score using a covariance matrix.
- poissonQuantile(double, double) - Static method in class edu.cmu.tetrad.util.ProbUtils
- poissonRand(double) - Static method in class edu.cmu.tetrad.util.ProbUtils
-
Poisson random generator from Numerical Recipes
- PoissonScoreTest - Class in edu.cmu.tetrad.algcomparison.independence
-
Wrapper for Fisher Z test.
- PoissonScoreTest() - Constructor for class edu.cmu.tetrad.algcomparison.independence.PoissonScoreTest
- Polynomial - Class in edu.cmu.tetrad.study.gene.tetrad.gene.history
-
Implements a polynomial as a sum of a list of terms whose variables are identified as integers in the set {0, 1, 2, ...}.
- Polynomial - Enum constant in enum class edu.cmu.tetrad.search.test.ConditionalCorrelationIndependence.Basis
- Polynomial(List<PolynomialTerm>) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.history.Polynomial
-
Constructs a polynomial from a list of terms.
- PolynomialFunction - Class in edu.cmu.tetrad.study.gene.tetrad.gene.history
-
Implements a polynomial update function, Gi.0 = P(Parents(G0.0)) + ei, where P is a polynomial function and ei is a random noise term.
- PolynomialFunction(LagGraph) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.history.PolynomialFunction
-
Constructs a polyomial function where each factor is given a zero polynomial.
- PolynomialTerm - Class in edu.cmu.tetrad.study.gene.tetrad.gene.history
-
Implements a term in a polymonial whose variables are mapped to indices in in the set {0, 1, 2, ...}.
- PolynomialTerm(double, int[]) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.history.PolynomialTerm
-
Constructs a term.
- POPULATION - Enum constant in enum class edu.cmu.tetrad.search.utils.BpcTestType
- PositiveCorr - Class in edu.cmu.tetrad.algcomparison.independence
-
Wrapper for Fisher Z test.
- PositiveCorr() - Constructor for class edu.cmu.tetrad.algcomparison.independence.PositiveCorr
- PositiveCorrScore - Class in edu.cmu.tetrad.algcomparison.score
-
Wrapper for Fisher Z test.
- PositiveCorrScore() - Constructor for class edu.cmu.tetrad.algcomparison.score.PositiveCorrScore
- POSSIBLE_MSEP_DONE - Static variable in class edu.cmu.tetrad.util.Params
- possibleAncestor(Node, Node) - Method in class edu.cmu.tetrad.graph.Paths
- PossibleMConnectingPath - Class in edu.cmu.tetrad.search.utils
-
Finds possible d-connecting undirectedPaths for the IonSearch.
- possibleMsep(Node, Node, int) - Method in class edu.cmu.tetrad.graph.Paths
- PossibleMsepFci - Class in edu.cmu.tetrad.search.utils
-
Implements the Possible-M-Sep search step of Spirtes, et al's (1993) FCI algorithm (pp 144-145).
- PossibleMsepFci(Graph, IndependenceTest) - Constructor for class edu.cmu.tetrad.search.utils.PossibleMsepFci
-
Creates a new SepSet and assumes that none of the variables have yet been checked.
- pow() - Static method in class edu.cmu.tetrad.util.StatUtils
- powerSet(List<Node>) - Static method in class edu.cmu.tetrad.search.utils.GraphSearchUtils
- PRAOerrors - Class in edu.cmu.tetrad.simulation
-
Created by Erich on 8/21/2016.
- PRAOerrors(double[], String) - Constructor for class edu.cmu.tetrad.simulation.PRAOerrors
- PRAOerrors(List<PRAOerrors>, String) - Constructor for class edu.cmu.tetrad.simulation.PRAOerrors
- PRECOMPUTE_COVARIANCES - Static variable in class edu.cmu.tetrad.util.Params
- predict(Matrix) - Method in class jgpml.GaussianProcess
-
Computes Gaussian predictions, whose mean and variance are returned.
- predictMean(Matrix) - Method in class jgpml.GaussianProcess
-
Computes Gaussian predictions, whose mean is returned.
- predictor(int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.ideker.ItkPredictorSearch
- PREFIX - Enum constant in enum class edu.cmu.tetrad.calculator.expression.ExpressionDescriptor.Position
- Preserved - Enum constant in enum class edu.pitt.dbmi.algo.resampling.ResamplingEdgeEnsemble
- PreviousStepOnly - Class in edu.cmu.tetrad.study.gene.tetrad.gene.history
-
Initializes a graph by adding the previous time step only of each variable.
- PreviousStepOnly() - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.history.PreviousStepOnly
- PRINT_STREAM - Static variable in class edu.cmu.tetrad.util.Params
- printClusterPValues(Set<List<Integer>>) - Method in class edu.cmu.tetrad.search.utils.ClusterSignificance
- printEdges() - Method in class edu.cmu.tetrad.graph.RandomGraph.UniformGraphGenerator
- printGraphDegrees() - Method in class edu.cmu.tetrad.study.performance.PerformanceTests
- printStuffForKlea() - Method in class edu.cmu.tetrad.study.performance.PerformanceTests
- PRIOR_EQUIVALENT_SAMPLE_SIZE - Static variable in class edu.cmu.tetrad.util.Params
- PRIORITIZE_EXISTING - Enum constant in enum class edu.cmu.tetrad.search.utils.PcCommon.ConflictRule
- PROB_CYCLE - Static variable in class edu.cmu.tetrad.util.Params
- PROB_REMOVE_COLUMN - Static variable in class edu.cmu.tetrad.util.Params
- PROB_TWO_CYCLE - Static variable in class edu.cmu.tetrad.util.Params
- PROBABILISTIC_TEST_PARAMETERS - Static variable in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.PagSampleRfci
- ProbabilisticMapIndependence - Class in edu.cmu.tetrad.search.work_in_progress
-
Uses BCInference by Cooper and Bui to calculate probabilistic conditional independence judgments.
- ProbabilisticMapIndependence(DataSet) - Constructor for class edu.cmu.tetrad.search.work_in_progress.ProbabilisticMapIndependence
-
Initializes the test using a discrete data sets.
- ProbabilisticTest - Class in edu.cmu.tetrad.algcomparison.independence
-
Dec 17, 2018 3:44:46 PM
- ProbabilisticTest() - Constructor for class edu.cmu.tetrad.algcomparison.independence.ProbabilisticTest
- probability(double) - Method in class edu.cmu.tetrad.sem.EmpiricalCdf
- PROBABILITY_OF_EDGE - Static variable in class edu.cmu.tetrad.util.Params
- probConstraint(BCCausalInference.OP, int, int, int[]) - Method in class edu.pitt.dbmi.algo.bayesian.constraint.inference.BCCausalInference
-
This function takes a constraint, which has a value of either OP.dependent or OP.independent, of the form "X independent Y given Z" or "X dependent Y given Z" and returns a probability for that constraint given the data in cases and assumed prior probability for that constraint given the data in cases and assumed prior probabilities.
- probConstraint(BCInference.OP, int, int, int[]) - Method in class edu.pitt.dbmi.algo.bayesian.constraint.inference.BCInference
-
This function takes a constraint, which has a value of either OP.dependent or OP.independent, of the form "X independent Y given Z" or "X dependent Y given Z" and returns a probability for that constraint given the data in cases and assumed prior probability for that constraint given the data in cases and assumed prior probabilities.
- probConstraint(BCInference.OP, Node, Node, Node[]) - Method in class edu.cmu.tetrad.search.work_in_progress.ProbabilisticMapIndependence
- probConstraint(BCInference, BCInference.OP, Node, Node, Node[], Map<Node, Integer>) - Method in class edu.cmu.tetrad.search.test.IndTestProbabilistic
- ProbUtils - Class in edu.cmu.tetrad.util
-
Implements a number of important functions from probability and statistics.> 0
- ProbUtils() - Constructor for class edu.cmu.tetrad.util.ProbUtils
- produce_undirected_graphs - Enum constant in enum class edu.cmu.tetrad.annotation.AlgType
-
If an algorithm produces undirected graphs.
- product(double[][], double[]) - Static method in class edu.cmu.tetrad.util.MatrixUtils
- product(double[][], double[][]) - Static method in class edu.cmu.tetrad.util.MatrixUtils
- product(double[], double[][]) - Static method in class edu.cmu.tetrad.util.MatrixUtils
- product(Vector, Matrix) - Static method in class edu.cmu.tetrad.util.MatrixUtils
- ProportionSemidirectedPathsNotReversedEst - Class in edu.cmu.tetrad.algcomparison.statistic
-
Proportion of semi(X, Y) in estimated graph for which there is no semi(Y, X) in true graph.
- ProportionSemidirectedPathsNotReversedEst() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.ProportionSemidirectedPathsNotReversedEst
- ProportionSemidirectedPathsNotReversedTrue - Class in edu.cmu.tetrad.algcomparison.statistic
-
Proportion of semi(X, Y) in true graph for which there is no semi(Y, Z) in estimated graph.
- ProportionSemidirectedPathsNotReversedTrue() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.ProportionSemidirectedPathsNotReversedTrue
- Proposition - Class in edu.cmu.tetrad.bayes
-
Represents propositions over the variables of a particular BayesIm describing an event of a fairly general sort--namely, conjunctions of propositions that particular variables take on values from a particular disjunctive list of categories.
- Proposition(Proposition) - Constructor for class edu.cmu.tetrad.bayes.Proposition
-
Copies the info out of the old proposition into a new proposition for the new BayesIm.
- Proposition(VariableSource, Proposition) - Constructor for class edu.cmu.tetrad.bayes.Proposition
-
Copies the info out of the old proposition into a new proposition for the new BayesIm.
- ProximalGradient - Class in edu.pitt.csb.mgm
-
Implementation of Nesterov's 83 method as described in Beck and Teboulle, 2009 aka Fast Iterative Shrinkage Thresholding Algorithm
- ProximalGradient() - Constructor for class edu.pitt.csb.mgm.ProximalGradient
-
Constructor using defaults from Becker et al 2011.
- ProximalGradient(double, double, boolean) - Constructor for class edu.pitt.csb.mgm.ProximalGradient
-
Constructor, set parameters for a proximal gradient run
- proximalOperator(double, DoubleMatrix1D) - Method in class edu.pitt.csb.mgm.Mgm
-
A proximal operator for the MGM
- pseudoInverse(double[][]) - Static method in class edu.cmu.tetrad.util.MatrixUtils
- purify(List<List<Node>>) - Method in interface edu.cmu.tetrad.search.utils.IPurify
- purify(List<List<Node>>) - Method in class edu.cmu.tetrad.search.utils.PurifyScoreBased
- purify(List<List<Node>>) - Method in class edu.cmu.tetrad.search.utils.PurifyTetradBased
- purify(List<List<Integer>>) - Method in class edu.cmu.tetrad.search.utils.PurifySextadBased
- Purify - Class in edu.cmu.tetrad.search.utils
-
Implements the Purify algorithm, which is a implementation of the automated purification methods described on CPS and the report "Learning Measurement Models" CMU-CALD-03-100.
- Purify(CorrelationMatrix, double, BpcTestType, Clusters) - Constructor for class edu.cmu.tetrad.search.utils.Purify
-
INITIALIZATION o
- Purify(DataSet, double, BpcTestType, Clusters) - Constructor for class edu.cmu.tetrad.search.utils.Purify
- Purify(TetradTest, Clusters) - Constructor for class edu.cmu.tetrad.search.utils.Purify
- PurifyScoreBased - Class in edu.cmu.tetrad.search.utils
-
Implements a score-based Purify method.
- PurifyScoreBased(TetradTest, List<Set<String>>) - Constructor for class edu.cmu.tetrad.search.utils.PurifyScoreBased
- PurifySextadBased - Class in edu.cmu.tetrad.search.utils
-
Implments a sextad-based Purify method.
- PurifySextadBased(DeltaSextadTest, double) - Constructor for class edu.cmu.tetrad.search.utils.PurifySextadBased
- PurifyTetradBased - Class in edu.cmu.tetrad.search.utils
-
Implements a tetrad-based purify method.
- PurifyTetradBased(TetradTest) - Constructor for class edu.cmu.tetrad.search.utils.PurifyTetradBased
- put(String, ParamDescription) - Method in class edu.cmu.tetrad.util.ParamDescriptions
- putAll(Parameters) - Method in class edu.cmu.tetrad.util.Parameters
- putParam(Class, Parameters) - Method in class edu.cmu.tetrad.session.SessionNode
-
Sets the parameter object for the given model class to the given object.
- putParameterValue(String, double) - Method in class edu.cmu.tetrad.sem.GeneralizedSemEstimator.MyContext
- putVariableValue(String, double) - Method in class edu.cmu.tetrad.sem.GeneralizedSemEstimator.MyContext
- PvalueDistanceToAlpha - Class in edu.cmu.tetrad.algcomparison.statistic
-
Estimates whether the p-values under the null are Uniform usign the Markov Checker.
- PvalueDistanceToAlpha(double) - Constructor for class edu.cmu.tetrad.algcomparison.statistic.PvalueDistanceToAlpha
- PvalueUniformityUnderNull - Class in edu.cmu.tetrad.algcomparison.statistic
-
Estimates whether the p-values under the null are Uniform usign the Markov Checker.
- PvalueUniformityUnderNull(double) - Constructor for class edu.cmu.tetrad.algcomparison.statistic.PvalueUniformityUnderNull
Q
- quartile(double[], int) - Static method in class edu.cmu.tetrad.util.StatUtils
- quartile(double[], int, int) - Static method in class edu.cmu.tetrad.util.StatUtils
- quartile(long[], int) - Static method in class edu.cmu.tetrad.util.StatUtils
- quartile(long[], int, int) - Static method in class edu.cmu.tetrad.util.StatUtils
R
- R1 - Class in edu.cmu.tetrad.algcomparison.algorithm.pairwise
-
R1.
- R1 - Enum constant in enum class edu.cmu.tetrad.search.Lofs.Rule
- R1() - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.pairwise.R1
- R1(Algorithm) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.pairwise.R1
- R1TimeLag - Enum constant in enum class edu.cmu.tetrad.search.Lofs.Rule
- R2 - Class in edu.cmu.tetrad.algcomparison.algorithm.pairwise
-
R2.
- R2 - Enum constant in enum class edu.cmu.tetrad.search.Lofs.Rule
- R2() - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.pairwise.R2
- R2(Algorithm) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.pairwise.R2
- R3 - Class in edu.cmu.tetrad.algcomparison.algorithm.pairwise
-
R3.
- R3 - Enum constant in enum class edu.cmu.tetrad.search.Lofs.Rule
- R3() - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.pairwise.R3
- R3(Algorithm) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.pairwise.R3
- random - Enum constant in enum class edu.cmu.tetrad.search.utils.ResolveSepsets.Method
- random - Enum constant in enum class edu.cmu.tetrad.search.work_in_progress.ResolveSepsetsDci.Method
- RANDOM - Static variable in class edu.cmu.tetrad.bayes.MlBayesIm
-
Indicates that new rows in this BayesIm should be initialized randomly.
- RANDOM_FOWARD_DAG - Static variable in class edu.cmu.tetrad.algcomparison.graph.GraphTypes
- RANDOM_ONE_FACTOR_MIM - Static variable in class edu.cmu.tetrad.algcomparison.graph.GraphTypes
- RANDOM_SELECTION_SIZE - Static variable in class edu.cmu.tetrad.util.Params
- RANDOM_TWO_FACTOR_MIM - Static variable in class edu.cmu.tetrad.algcomparison.graph.GraphTypes
- RandomActiveLagGraph - Class in edu.cmu.tetrad.study.gene.tetrad.gene.graph
-
Constructs as a randomized update workbench.
- RandomActiveLagGraph(LagGraphParams) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.graph.RandomActiveLagGraph
-
Using the given parameters, constructs an BasicLagGraph that is randomized upon construction.
- randomBifactorModel(int, int, int, int, int, int) - Static method in class edu.cmu.tetrad.data.DataGraphUtils
-
First a random single factor model is created with the specified number of latent nodes and latent edges, and impurity structure.
- randomClusters(int) - Static method in class edu.cmu.tetrad.cluster.KMeans
-
Constructs a new KMeansBatch, initializing the algorithm by randomly assigning each point in the data to one of the numCenters clusters, then calculating the centroid of each cluster.
- randomCyclicGraph2(int, int, int) - Static method in class edu.cmu.tetrad.graph.RandomGraph
-
Makes a cyclic graph by repeatedly adding cycles of length of 3, 4, or 5 to the graph, then finally adding two cycles.
- randomCyclicGraph3(int, int, int, double, double) - Static method in class edu.cmu.tetrad.graph.RandomGraph
-
Makes a cyclic graph by repeatedly adding cycles of length of 3, 4, or 5 to the graph, then finally adding two cycles.
- randomDag(int, int, int, int, int, int, boolean) - Static method in class edu.cmu.tetrad.graph.RandomGraph
- randomDag(List<Node>, int, int, int, int, int, boolean) - Static method in class edu.cmu.tetrad.graph.RandomGraph
- RandomDistribution - Interface in edu.cmu.tetrad.study.gene.tetrad.gene.history
-
A distribution from which noise values are drawn.
- RandomForward - Class in edu.cmu.tetrad.algcomparison.graph
-
Creates a random graph by adding forward edges.
- RandomForward() - Constructor for class edu.cmu.tetrad.algcomparison.graph.RandomForward
- randomGraph(int, int, int, int, int, int, boolean) - Static method in class edu.cmu.tetrad.graph.RandomGraph
- randomGraph(List<Node>, int, int, int, int, int, boolean) - Static method in class edu.cmu.tetrad.graph.RandomGraph
-
Defaults to random forward graphs.
- RandomGraph - Class in edu.cmu.tetrad.graph
- RandomGraph - Interface in edu.cmu.tetrad.algcomparison.graph
-
An interface to represent a random graph of some sort.
- RandomGraph() - Constructor for class edu.cmu.tetrad.graph.RandomGraph
- RandomGraph.UniformGraphGenerator - Class in edu.cmu.tetrad.graph
-
Generates random DAGs uniformly with certain classes of DAGs using variants of Markov chain algorithm by Malancon, Dutour, and Philippe.
- randomGraphRandomForwardEdges(int, int, int, int, int, int, boolean) - Static method in class edu.cmu.tetrad.graph.RandomGraph
- randomGraphRandomForwardEdges(List<Node>, int, int, int, int, int, boolean) - Static method in class edu.cmu.tetrad.graph.RandomGraph
- randomGraphRandomForwardEdges(List<Node>, int, int, int, int, int, boolean, boolean) - Static method in class edu.cmu.tetrad.graph.RandomGraph
- randomGraphUniform(List<Node>, int, int, int, int, int, boolean, int) - Static method in class edu.cmu.tetrad.graph.RandomGraph
- randomize() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.BooleanFunction
-
Chooses a random function by flipping a coin for each value in table.
- RANDOMIZE - Static variable in class edu.cmu.tetrad.graph.NodeType
- RANDOMIZE_COLUMNS - Static variable in class edu.cmu.tetrad.util.Params
- randomizeGraph(LagGraph) - Method in interface edu.cmu.tetrad.study.gene.tetrad.gene.history.GraphRandomizer
-
Randomizes the given lag graph--in other words, chooses random edges for the graph according to a particlar scheme (see instantiations).
- randomizeIncompleteRows(int) - Method in interface edu.cmu.tetrad.bayes.BayesIm
-
Randomizes any row in the table for the given node index that has a Double.NaN value in it.
- randomizeIncompleteRows(int) - Method in class edu.cmu.tetrad.bayes.DirichletBayesIm
-
Randomizes any row in the table for the given node index that has a Double.NaN value in it.
- randomizeIncompleteRows(int) - Method in class edu.cmu.tetrad.bayes.MlBayesIm
-
Randomizes any row in the table for the given node index that has a Double.NaN value in it.
- randomizeIncompleteRows(int) - Method in class edu.cmu.tetrad.bayes.MlBayesImObs
-
Randomizes any row in the table for the given node index that has a Double.NaN value in it.
- randomizeIncompleteRows(int) - Method in class edu.cmu.tetrad.bayes.UpdatedBayesIm
- randomizeRow(int, int) - Method in interface edu.cmu.tetrad.bayes.BayesIm
-
Assigns random probability values to the child values of this row that add to 1.
- randomizeRow(int, int) - Method in class edu.cmu.tetrad.bayes.DirichletBayesIm
-
Assigns random probability values to the child values of this row that add to 1.
- randomizeRow(int, int) - Method in class edu.cmu.tetrad.bayes.MlBayesIm
-
Assigns random probability values to the child values of this row that add to 1.
- randomizeRow(int, int) - Method in class edu.cmu.tetrad.bayes.MlBayesImObs
-
Assigns random probability values to the child values of this row that add to 1.
- randomizeRow(int, int) - Method in class edu.cmu.tetrad.bayes.UpdatedBayesIm
- randomizeTable(int) - Method in interface edu.cmu.tetrad.bayes.BayesIm
-
Randomizes every row in the table for the given node index.
- randomizeTable(int) - Method in class edu.cmu.tetrad.bayes.DirichletBayesIm
-
Randomizes every row in the table for the given node index.
- randomizeTable(int) - Method in class edu.cmu.tetrad.bayes.MlBayesIm
-
Randomizes every row in the table for the given node index.
- randomizeTable(int) - Method in class edu.cmu.tetrad.bayes.MlBayesImObs
-
Randomizes every row in the table for the given node index.
- randomizeTable(int) - Method in class edu.cmu.tetrad.bayes.UpdatedBayesIm
- randomMim(Graph, int, int, int, int, boolean) - Static method in class edu.cmu.tetrad.data.DataGraphUtils
- randomPoints(int) - Static method in class edu.cmu.tetrad.cluster.KMeans
-
Constructs a new KMeansBatch, initializing the algorithm by picking
numCeneterscenters randomly from the data itself. - RandomSampler - Class in edu.cmu.tetrad.data
-
Provides a static method for sampling without replacement from a dataset to create a new dataset with a sample size supplied by the user.
- RandomSampler() - Constructor for class edu.cmu.tetrad.data.RandomSampler
- randomScaleFreeGraph(int, int, double, double, double, double) - Static method in class edu.cmu.tetrad.graph.RandomGraph
- randomSimulation(int) - Method in class edu.cmu.tetrad.simulation.GdistanceRandom
- RandomSingleFactorMim - Class in edu.cmu.tetrad.algcomparison.graph
-
Creates a random graph by adding forward edges.
- RandomSingleFactorMim() - Constructor for class edu.cmu.tetrad.algcomparison.graph.RandomSingleFactorMim
- randomSingleFactorModel(int, int, int, int, int, int) - Static method in class edu.cmu.tetrad.data.DataGraphUtils
- RandomTwoFactorMim - Class in edu.cmu.tetrad.algcomparison.graph
-
Creates a random graph by adding forward edges.
- RandomTwoFactorMim() - Constructor for class edu.cmu.tetrad.algcomparison.graph.RandomTwoFactorMim
- RandomUtil - Class in edu.cmu.tetrad.util
-
Provides a common random number generator to be used throughout Tetrad, to avoid problems that happen when random number generators are created more often than once per millisecond.
- range(double[]) - Static method in class edu.cmu.tetrad.util.StatUtils
- range(double[], int) - Static method in class edu.cmu.tetrad.util.StatUtils
- range(long[]) - Static method in class edu.cmu.tetrad.util.StatUtils
- range(long[], int) - Static method in class edu.cmu.tetrad.util.StatUtils
- rank() - Method in class edu.cmu.tetrad.util.Matrix
- rank() - Method in class edu.cmu.tetrad.util.Matrix2
- rankCorrelation(double[], double[]) - Static method in class edu.cmu.tetrad.util.StatUtils
- ranks(double[]) - Static method in class edu.cmu.tetrad.data.DataUtils
- RBExperiments - Class in edu.cmu.tetrad.study
- RBExperiments() - Constructor for class edu.cmu.tetrad.study.RBExperiments
- RC - Enum constant in enum class edu.cmu.tetrad.search.Lofs.Rule
- rcg(TeyssierScorer) - Method in class edu.cmu.tetrad.search.work_in_progress.OtherPermAlgs
- RCG - Enum constant in enum class edu.cmu.tetrad.search.work_in_progress.OtherPermAlgs.Method
- RCIT_NUM_FEATURES - Static variable in class edu.cmu.tetrad.util.Params
- ReadControl - Class in edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.ideker
- ReadControl() - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.ideker.ReadControl
- readerToGraphJson(Reader) - Static method in class edu.cmu.tetrad.graph.GraphSaveLoadUtils
- readerToGraphRuben(Reader) - Static method in class edu.cmu.tetrad.graph.GraphSaveLoadUtils
- readerToGraphTxt(Reader) - Static method in class edu.cmu.tetrad.graph.GraphSaveLoadUtils
- readerToGraphTxt(String) - Static method in class edu.cmu.tetrad.graph.GraphSaveLoadUtils
- readGraph(File) - Method in class edu.cmu.tetrad.data.simulation.LoadContinuousDataSmithSim
- ReadIdeker - Class in edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.ideker
- ReadIdeker() - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.ideker.ReadIdeker
- RealCovariance - Interface in edu.cmu.tetrad.stat.correlation
-
Jan 27, 2016 4:46:07 PM
- RealCovarianceMatrix - Class in edu.cmu.tetrad.stat.correlation
-
Jan 27, 2016 5:35:01 PM
- RealCovarianceMatrix(double[][]) - Constructor for class edu.cmu.tetrad.stat.correlation.RealCovarianceMatrix
- RealCovarianceMatrixForkJoin - Class in edu.cmu.tetrad.stat.correlation
-
Jan 27, 2016 5:37:40 PM
- RealCovarianceMatrixForkJoin(double[][], int) - Constructor for class edu.cmu.tetrad.stat.correlation.RealCovarianceMatrixForkJoin
- RealVariance - Interface in edu.cmu.tetrad.stat
-
Feb 9, 2016 3:13:19 PM
- RealVarianceVector - Class in edu.cmu.tetrad.stat
-
Feb 9, 2016 3:14:08 PM
- RealVarianceVector(double[][]) - Constructor for class edu.cmu.tetrad.stat.RealVarianceVector
- RealVarianceVectorForkJoin - Class in edu.cmu.tetrad.stat
-
Feb 9, 2016 3:15:29 PM
- RealVarianceVectorForkJoin(double[][], int) - Constructor for class edu.cmu.tetrad.stat.RealVarianceVectorForkJoin
- REDIRECT - Enum constant in enum class edu.cmu.tetrad.search.work_in_progress.HbsmsBeam.Move.Type
- RegexTokenizer - Class in edu.cmu.tetrad.data
-
Tokenizes the given input character sequence using the type of delimiter specified bythe given CPDAG.
- RegexTokenizer(CharSequence, Pattern, char) - Constructor for class edu.cmu.tetrad.data.RegexTokenizer
-
Constructs a tokenizer for the given input line, using the given Pattern as delimiter.
- registerEditor(SessionNode, JComponent) - Static method in class edu.cmu.tetrad.session.ModificationRegistery
-
Registers an editor which could modify model.
- regress(double[], double[][]) - Static method in class edu.cmu.tetrad.regression.RegressionDataset
- regress(DiscreteVariable, List<Node>) - Method in class edu.cmu.tetrad.regression.LogisticRegression
-
x must be binary; regressors must be continuous or binary.
- regress(Node, Node...) - Method in interface edu.cmu.tetrad.regression.Regression
-
Regresses
targeton theregressors, yielding a regression plane. - regress(Node, Node...) - Method in class edu.cmu.tetrad.regression.RegressionCovariance
- regress(Node, Node...) - Method in class edu.cmu.tetrad.regression.RegressionDataset
- regress(Node, List<Node>) - Method in interface edu.cmu.tetrad.regression.Regression
-
Regresses
targeton theregressors, yielding a regression plane. - regress(Node, List<Node>) - Method in class edu.cmu.tetrad.regression.RegressionCovariance
-
Regresses the given target on the given regressors, yielding a regression plane, in which coefficients are given for each regressor plus the constant (if means have been specified, that is, for the last), and se, t, and p values are given for each regressor.
- regress(Node, List<Node>) - Method in class edu.cmu.tetrad.regression.RegressionDataset
-
Regresses the target on the given regressors.
- Regression - Interface in edu.cmu.tetrad.regression
-
Implements a multiple regression model, allowing data to be specified either as a tabular data set or as a covariance matrix plus list of means.
- RegressionCovariance - Class in edu.cmu.tetrad.regression
-
Implements a regression model from correlations--that is, from a correlation matrix, a list of standard deviations, and a list of means.
- RegressionCovariance(ICovarianceMatrix) - Constructor for class edu.cmu.tetrad.regression.RegressionCovariance
-
Constructs a covariance-based regression model using the given covariance matrix, assuming that no means are specified.
- RegressionDataset - Class in edu.cmu.tetrad.regression
-
Implements a regression model from tabular continuous data.
- RegressionDataset(DataSet) - Constructor for class edu.cmu.tetrad.regression.RegressionDataset
-
Constructs a linear regression model for the given tabular data set.
- RegressionDataset(Matrix, List<Node>) - Constructor for class edu.cmu.tetrad.regression.RegressionDataset
- RegressionResult - Class in edu.cmu.tetrad.regression
-
Stores the various components of a regression result so they can be passed around together more easily.
- RegressionResult(boolean, String[], int, double[], double[], double[], double[], double, double, double, Vector) - Constructor for class edu.cmu.tetrad.regression.RegressionResult
-
A result for a variety of regression algorithm.
- RegressionUtils - Class in edu.cmu.tetrad.regression
-
Sundry utilities for regression.
- RegressionUtils() - Constructor for class edu.cmu.tetrad.regression.RegressionUtils
- REGULAR - Enum constant in enum class edu.cmu.tetrad.search.utils.PcCommon.FasType
- ReidentifyVariables - Class in edu.cmu.tetrad.sem
-
Utility for reidentifying variables for multiple indicator structure searches.
- ReidentifyVariables() - Constructor for class edu.cmu.tetrad.sem.ReidentifyVariables
- reidentifyVariables1(List<List<Node>>, Graph) - Static method in class edu.cmu.tetrad.sem.ReidentifyVariables
- reidentifyVariables2(List<List<Node>>, Graph, DataSet) - Static method in class edu.cmu.tetrad.sem.ReidentifyVariables
- remove() - Method in class edu.cmu.tetrad.util.CombinationIterator
- remove(int) - Method in class edu.cmu.tetrad.data.DataModelList
-
Removes the DataModel at the given index.
- remove(IndependenceFact) - Method in class edu.cmu.tetrad.data.IndependenceFacts
- REMOVE - Enum constant in enum class edu.cmu.tetrad.search.work_in_progress.HbsmsBeam.Move.Type
- REMOVE_COLLIDER - Enum constant in enum class edu.cmu.tetrad.search.work_in_progress.HbsmsBeam.Move.Type
- REMOVE_EFFECT_NODES - Static variable in class edu.cmu.tetrad.util.Params
- removeAmbiguousTriple(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.Dag
- removeAmbiguousTriple(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
- removeAmbiguousTriple(Node, Node, Node) - Method in interface edu.cmu.tetrad.graph.Graph
- removeAmbiguousTriple(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.LagGraph
- removeAmbiguousTriple(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.SemGraph
- removeAmbiguousTriple(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- removeAmbiguousTriple(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.Underlines
- removeAttribute(String) - Method in class edu.cmu.tetrad.data.ContinuousVariable
- removeAttribute(String) - Method in class edu.cmu.tetrad.data.DiscreteVariable
- removeAttribute(String) - Method in class edu.cmu.tetrad.graph.Dag
- removeAttribute(String) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
- removeAttribute(String) - Method in interface edu.cmu.tetrad.graph.Graph
- removeAttribute(String) - Method in class edu.cmu.tetrad.graph.GraphNode
- removeAttribute(String) - Method in class edu.cmu.tetrad.graph.LagGraph
- removeAttribute(String) - Method in interface edu.cmu.tetrad.graph.Node
- removeAttribute(String) - Method in class edu.cmu.tetrad.graph.SemGraph
- removeAttribute(String) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- removeAttribute(String) - Method in class edu.cmu.tetrad.session.SessionNode
- removeBidirectedOrientations(Graph) - Static method in class edu.cmu.tetrad.graph.GraphUtils
- removeByPossibleMsep(IndependenceTest, SepsetMap) - Method in class edu.cmu.tetrad.graph.Paths
-
Remove edges by the possible m-separation rule.
- removeCategory(int, int) - Method in class edu.cmu.tetrad.bayes.Proposition
- removeChild(SessionNode) - Method in class edu.cmu.tetrad.session.SessionNode
-
Removes a child from the node.
- removeCols(int[]) - Method in class edu.cmu.tetrad.data.BoxDataSet
-
Removes the given columns from the data set.
- removeCols(int[]) - Method in interface edu.cmu.tetrad.data.DataSet
-
Removes the given columns from the data set.
- removeCols(int[]) - Method in class edu.cmu.tetrad.data.NumberObjectDataSet
-
Removes the given columns from the data set.
- removeColumn(int) - Method in class edu.cmu.tetrad.data.BoxDataSet
-
Removes the column for the variable at the given index, reducing the number of columns by one.
- removeColumn(int) - Method in interface edu.cmu.tetrad.data.DataSet
-
Removes the variable (and data) at the given index.
- removeColumn(int) - Method in class edu.cmu.tetrad.data.NumberObjectDataSet
-
Removes the column for the variable at the given index, reducing the number of columns by one.
- removeColumn(Node) - Method in class edu.cmu.tetrad.data.BoxDataSet
-
Removes the columns for the given variable from the dataset, reducing the number of columns by one.
- removeColumn(Node) - Method in interface edu.cmu.tetrad.data.DataSet
-
Removes the given variable, along with all of its data.
- removeColumn(Node) - Method in class edu.cmu.tetrad.data.NumberObjectDataSet
-
Removes the columns for the given variable from the dataset, reducing the number of columns by one.
- removeConditioningVariable(String) - Method in class edu.cmu.tetrad.data.Histogram
-
Removes a conditioning variable.
- removeConstantColumns(DataSet) - Static method in class edu.cmu.tetrad.data.DataTransforms
- removeDottedUnderlineTriple(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.Dag
- removeDottedUnderlineTriple(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
- removeDottedUnderlineTriple(Node, Node, Node) - Method in interface edu.cmu.tetrad.graph.Graph
- removeDottedUnderlineTriple(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.LagGraph
- removeDottedUnderlineTriple(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.SemGraph
- removeDottedUnderlineTriple(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- removeDottedUnderlineTriple(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.Underlines
- removeEdge(Edge) - Method in class edu.cmu.tetrad.graph.Dag
- removeEdge(Edge) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
-
Removes an edge from the graph.
- removeEdge(Edge) - Method in interface edu.cmu.tetrad.graph.Graph
-
Removes the given edge from the graph.
- removeEdge(Edge) - Method in class edu.cmu.tetrad.graph.LagGraph
- removeEdge(Edge) - Method in class edu.cmu.tetrad.graph.SemGraph
- removeEdge(Edge) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- removeEdge(Node, Node) - Method in class edu.cmu.tetrad.graph.Dag
- removeEdge(Node, Node) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
-
Removes the edge connecting the two given nodes.
- removeEdge(Node, Node) - Method in interface edu.cmu.tetrad.graph.Graph
-
Removes the edge connecting the two given nodes, provided there is exactly one such edge.
- removeEdge(Node, Node) - Method in class edu.cmu.tetrad.graph.LagGraph
- removeEdge(Node, Node) - Method in class edu.cmu.tetrad.graph.SemGraph
- removeEdge(Node, Node) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- removeEdge(String, LaggedFactor) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ActiveLagGraph
-
Attempts to remove an edge from the graph.
- removeEdge(String, LaggedFactor) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ManualLagGraph
- removeEdge(String, LaggedFactor) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.BasicLagGraph
-
Removes the lagged factor from the list of lagged factors associated with the given factor.
- removeEdge(String, LaggedFactor) - Method in interface edu.cmu.tetrad.study.gene.tetrad.gene.history.LagGraph
-
Removes the lagged factor from the list of lagged factors associated with the given factor.
- removeEdges(Node, Node) - Method in class edu.cmu.tetrad.graph.Dag
- removeEdges(Node, Node) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
-
Removes all edges connecting node A to node B.
- removeEdges(Node, Node) - Method in interface edu.cmu.tetrad.graph.Graph
-
Removes all edges connecting node A to node B.
- removeEdges(Node, Node) - Method in class edu.cmu.tetrad.graph.LagGraph
- removeEdges(Node, Node) - Method in class edu.cmu.tetrad.graph.SemGraph
- removeEdges(Node, Node) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- removeEdges(Collection<Edge>) - Method in class edu.cmu.tetrad.graph.Dag
- removeEdges(Collection<Edge>) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
-
Removes any relevant edge objects found in this collection.
- removeEdges(Collection<Edge>) - Method in interface edu.cmu.tetrad.graph.Graph
-
Iterates through the list and removes any permissible edges found.
- removeEdges(Collection<Edge>) - Method in class edu.cmu.tetrad.graph.LagGraph
- removeEdges(Collection<Edge>) - Method in class edu.cmu.tetrad.graph.SemGraph
- removeEdges(Collection<Edge>) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- removeFactor(String) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ActiveLagGraph
-
Attempts to remove a factor from the graph.
- removeFactor(String) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ManualLagGraph
- removeFactor(String) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.BasicLagGraph
-
Removes a factor from the graph.
- removeFactor(String) - Method in interface edu.cmu.tetrad.study.gene.tetrad.gene.history.LagGraph
-
Removes a factor from the graph.
- removeForbidden(String, String) - Method in class edu.cmu.tetrad.data.Knowledge
-
Marks the edge var1 --> var2 as not forbid.
- removeFromClusters(String) - Method in class edu.cmu.tetrad.data.Clusters
-
Removes the given variable from the clusters.
- removeFromTiers(String) - Method in class edu.cmu.tetrad.data.Knowledge
-
Removes the given variable by name or search string from all tiers.
- removeHighLagEdges(int) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- removeKnowledgeGroup(int) - Method in class edu.cmu.tetrad.data.Knowledge
-
Removes the knowledge group at the given index.
- removeLatent(Node) - Method in class edu.cmu.tetrad.search.work_in_progress.DMSearch.LatentStructure
- removeNaN(double[]) - Static method in class edu.cmu.tetrad.util.StatUtils
- removeNextOutputStream() - Method in class edu.cmu.tetrad.util.TetradLogger
- removeNode(Node) - Method in class edu.cmu.tetrad.graph.Dag
- removeNode(Node) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
-
Removes a node from the graph.
- removeNode(Node) - Method in interface edu.cmu.tetrad.graph.Graph
-
Removes a node from the graph.
- removeNode(Node) - Method in class edu.cmu.tetrad.graph.LagGraph
- removeNode(Node) - Method in class edu.cmu.tetrad.graph.SemGraph
- removeNode(Node) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- removeNode(SessionNode) - Method in class edu.cmu.tetrad.session.Session
-
Removes the given node from the session, removing any connectivity the node might have to other objects.> 0
- removeNodes(List<Node>) - Method in class edu.cmu.tetrad.graph.Dag
- removeNodes(List<Node>) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
-
Removes any relevant node objects found in this collection.
- removeNodes(List<Node>) - Method in interface edu.cmu.tetrad.graph.Graph
-
Iterates through the list and removes any permissible nodes found.
- removeNodes(List<Node>) - Method in class edu.cmu.tetrad.graph.LagGraph
- removeNodes(List<Node>) - Method in class edu.cmu.tetrad.graph.SemGraph
- removeNodes(List<Node>) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- removeNonSkeletonEdges(Graph, Knowledge) - Static method in class edu.cmu.tetrad.graph.GraphUtils
- removeOutputStream(OutputStream) - Method in class edu.cmu.tetrad.util.TetradLogger
-
Removes the given stream from the logger.
- removeParam(Class) - Method in class edu.cmu.tetrad.session.SessionNode
-
Removes the parameter object for the given model class.
- removeParent(SessionNode) - Method in class edu.cmu.tetrad.session.SessionNode
-
Removes a parent from the node.
- removeProperty(Edge.Property) - Method in class edu.cmu.tetrad.graph.EdgeTypeProbability
- removePropertyChangeListener(PropertyChangeListener) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ActiveLagGraph
-
Unregisters a listener for events concerning the lag graph.
- removeRandomColumns(DataSet, double) - Static method in class edu.cmu.tetrad.data.DataTransforms
- removeRequired(String, String) - Method in class edu.cmu.tetrad.data.Knowledge
-
Marks the edge var1 --> var2 as not required.
- removeRows(int[]) - Method in class edu.cmu.tetrad.data.BoxDataSet
-
Removes the given rows from the data set.
- removeRows(int[]) - Method in interface edu.cmu.tetrad.data.DataSet
-
Removes the given rows from the data set.
- removeRows(int[]) - Method in class edu.cmu.tetrad.data.NumberObjectDataSet
-
Removes the given rows from the data set.
- removeSessionListener(SessionListener) - Method in class edu.cmu.tetrad.session.Session
-
Removes a session listener.
- removeSessionListener(SessionListener) - Method in class edu.cmu.tetrad.session.SessionNode
-
Removes a session listener.
- removeSessionListener(SessionListener) - Method in class edu.cmu.tetrad.session.SessionSupport
-
Removes a listener for SessionEvents.
- removeSimilarEdges(Node, Node) - Method in class edu.cmu.tetrad.search.SvarFges
- removeTetradLoggerListener(TetradLoggerListener) - Method in class edu.cmu.tetrad.util.TetradLogger
-
Removes the given listener from the logger.
- removeTriplesNotInGraph() - Method in class edu.cmu.tetrad.graph.Dag
- removeTriplesNotInGraph() - Method in class edu.cmu.tetrad.graph.EdgeListGraph
- removeTriplesNotInGraph() - Method in interface edu.cmu.tetrad.graph.Graph
- removeTriplesNotInGraph() - Method in class edu.cmu.tetrad.graph.LagGraph
- removeTriplesNotInGraph() - Method in class edu.cmu.tetrad.graph.SemGraph
- removeTriplesNotInGraph() - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- removeTriplesNotInGraph() - Method in class edu.cmu.tetrad.graph.Underlines
- removeUnderlineTriple(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.Dag
- removeUnderlineTriple(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
- removeUnderlineTriple(Node, Node, Node) - Method in interface edu.cmu.tetrad.graph.Graph
- removeUnderlineTriple(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.LagGraph
- removeUnderlineTriple(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.SemGraph
- removeUnderlineTriple(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- removeUnderlineTriple(Node, Node, Node) - Method in class edu.cmu.tetrad.graph.Underlines
- removeVariables(List<String>) - Method in class edu.cmu.tetrad.data.CorrelationMatrixOnTheFly
- removeVariables(List<String>) - Method in class edu.cmu.tetrad.data.CovarianceMatrix
- removeVariables(List<String>) - Method in class edu.cmu.tetrad.data.CovarianceMatrixOnTheFly
- removeVariables(List<String>) - Method in interface edu.cmu.tetrad.data.ICovarianceMatrix
- removeZeroEdges(Graph) - Method in class edu.cmu.tetrad.search.work_in_progress.HbsmsBeam
- renameFactor(String, String) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ActiveLagGraph
-
Attempts to rename a factor.
- renameFactor(String, String) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ManualLagGraph
- renameFactor(String, String) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.BasicLagGraph
-
Renames a factor, changing all occurances of the old name to the new one
- renameFactor(String, String) - Method in interface edu.cmu.tetrad.study.gene.tetrad.gene.history.LagGraph
-
Renames a factor, changing all occurances of the old name to the new one
- reorientAllWith(Endpoint) - Method in class edu.cmu.tetrad.graph.Dag
- reorientAllWith(Endpoint) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
- reorientAllWith(Endpoint) - Method in interface edu.cmu.tetrad.graph.Graph
-
Reorients all edges in the graph with the given endpoint.
- reorientAllWith(Endpoint) - Method in class edu.cmu.tetrad.graph.LagGraph
- reorientAllWith(Endpoint) - Method in class edu.cmu.tetrad.graph.SemGraph
- reorientAllWith(Endpoint) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- REPETITION_CHANGED - Static variable in class edu.cmu.tetrad.session.SessionEvent
- repetitionChanged(SessionEvent) - Method in class edu.cmu.tetrad.session.SessionAdapter
-
Indicates that the repetition of some node has changed.
- repetitionChanged(SessionEvent) - Method in interface edu.cmu.tetrad.session.SessionListener
-
Indicates that the repetition of some node has changed.
- replaceMissingWithRandom(DataSet) - Static method in class edu.cmu.tetrad.data.DataTransforms
- replaceNodes(Graph, List<Node>) - Static method in class edu.cmu.tetrad.graph.GraphUtils
-
Converts the given graph,
originalGraph, to use the new variables (with the same names as the old). - replaceNodes(List<Node>, Graph) - Static method in class edu.cmu.tetrad.graph.GraphUtils
-
Converts the given list of nodes,
originalNodes, to use the replacement nodes for them by the same name in the givengraph. - replaceNodes(List<Node>, List<Node>) - Static method in class edu.cmu.tetrad.graph.GraphUtils
-
Converts the given list of nodes,
originalNodes, to use the new variables (with the same names as the old). - repmat(double[][], int) - Static method in class edu.cmu.tetrad.util.MatrixUtils
-
Make a n repeat copy of the rows and columns of the matrix mat.
- repmat(double[][], int, int) - Static method in class edu.cmu.tetrad.util.MatrixUtils
-
Make a repeat copy of matrix mat.
- REQUIRED - Static variable in class edu.cmu.tetrad.data.KnowledgeGroup
-
The types of groups (Can an enum be used instead?)
- requiredEdgesIterator() - Method in class edu.cmu.tetrad.data.Knowledge
-
Iterator over the KnowledgeEdge's representing required edges.
- requiresIndependenceTest(Class) - Method in class edu.cmu.tetrad.annotation.AlgorithmAnnotations
-
Checks if the algorithm requires independence test.
- requiresScore(Class) - Method in class edu.cmu.tetrad.annotation.AlgorithmAnnotations
-
Checks if the algorithm requires a score.
- RESAMPLING_ENSEMBLE - Static variable in class edu.cmu.tetrad.util.Params
- RESAMPLING_WITH_REPLACEMENT - Static variable in class edu.cmu.tetrad.util.Params
- ResamplingEdgeEnsemble - Enum Class in edu.pitt.dbmi.algo.resampling
-
Sep 12, 2018 4:07:46 PM
- reseedRandomGenerator(long) - Method in class edu.cmu.tetrad.sem.EmpiricalCdf
- reset() - Method in class edu.cmu.tetrad.search.utils.GrowShrinkTree
- reset() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.GeneHistory
-
Resets the history initialization array to that a new data set can be generated.
- reset() - Method in class edu.cmu.tetrad.util.TetradLogger
-
Resets the logger by removing any configuration info set with
setTetradLoggerConfig. - reset(int[]) - Method in class edu.cmu.tetrad.util.MultiDimIntTable
-
Resets the table, allowing a different dimensionality.
- resetCache() - Method in class edu.cmu.tetrad.search.utils.TetradTestDiscrete
- resetErrorPositions() - Method in class edu.cmu.tetrad.graph.SemGraph
- resetMag() - Method in class edu.cmu.tetrad.search.work_in_progress.MagSemBicScore
-
Sets the MAG to null.
- resetOrder() - Method in class edu.cmu.tetrad.search.work_in_progress.MagSemBicScore
-
Sets the order ot null.
- resetParams(Object) - Method in interface edu.cmu.tetrad.session.ParamsResettable
-
In some cases (for instance, algorithm runners), cloned session models need to have the object-identically same parameter objects as before cloning.
- resetToFreshlyCreated() - Method in class edu.cmu.tetrad.session.SessionNode
-
Resets this sesion node to the state it was in when first constructed.
- residuals(DataSet, Graph) - Static method in class edu.cmu.tetrad.regression.RegressionUtils
- residuals(Node, List<Node>, List<Integer>) - Method in class edu.cmu.tetrad.search.test.ConditionalCorrelationIndependence
-
Calculates the residuals of x regressed nonparametrically onto z.
- resolveSepsets(List<SepsetMapDci>, List<IndependenceTest>, ResolveSepsetsDci.Method, SepsetMapDci, SepsetMapDci) - Static method in class edu.cmu.tetrad.search.work_in_progress.ResolveSepsetsDci
-
Resolves all inconsistencies between sepsets using a paricular method.
- ResolveSepsets - Class in edu.cmu.tetrad.search.utils
-
Provides some utilities for resolving inconsistencies that arise between sepsets learned for overlapping datasets.
- ResolveSepsets() - Constructor for class edu.cmu.tetrad.search.utils.ResolveSepsets
- ResolveSepsets.Method - Enum Class in edu.cmu.tetrad.search.utils
-
Gives the method to be used to resolve sepsets when they conflict.
- ResolveSepsetsDci - Class in edu.cmu.tetrad.search.work_in_progress
-
Utilities for resolving inconsistencies that arise between sepsets learned for overlapping datasets.
- ResolveSepsetsDci() - Constructor for class edu.cmu.tetrad.search.work_in_progress.ResolveSepsetsDci
- ResolveSepsetsDci.Method - Enum Class in edu.cmu.tetrad.search.work_in_progress
- restoreOriginalModel() - Method in class edu.cmu.tetrad.session.SessionNode
- restrictConnectionsToList(List) - Method in class edu.cmu.tetrad.session.SessionNode
-
Removes any parents or children of the node that are not in the given list.
- RESTRICTED_BOSS - Enum constant in enum class edu.cmu.tetrad.search.Cstar.CpdagAlgorithm
- RestrictedBoss - Class in edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag
-
BOSS-DC (Best Order Score Search Divide and Conquer)
- RestrictedBoss() - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.RestrictedBoss
- RestrictedBoss(ScoreWrapper) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.RestrictedBoss
- restrictListenersToSessionNodes() - Method in class edu.cmu.tetrad.session.SessionNode
-
Removes any listeners that are not SessionNodes.
- restrictToMeasured(DataSet) - Static method in class edu.cmu.tetrad.data.DataTransforms
- restrictToMeasured(Graph) - Static method in class edu.cmu.tetrad.graph.GraphUtils
- restrictToProposition(Proposition) - Method in class edu.cmu.tetrad.bayes.Proposition
-
Restricts this proposition to the categories for each variable that are true in the given proposition.
- Result(double, double, int, boolean) - Constructor for class edu.cmu.tetrad.search.test.ChiSquareTest.Result
-
Constructs a new g square result using the given parameters.
- Result(double, double, int, boolean) - Constructor for class edu.cmu.tetrad.search.test.GSquareTest.Result
-
Constructs a new g square result using the given parameters.
- Result(Matrix) - Constructor for class edu.cmu.tetrad.search.work_in_progress.Glasso.Result
- Result(String, List<String>, double[], double[], int, int, int, double[], double[], double[], double, double, double, double) - Constructor for class edu.cmu.tetrad.regression.LogisticRegression.Result
-
Constructs a new LinRegrResult.
- resultGraph() - Method in class edu.cmu.tetrad.search.PcMb
-
Returns the result graph.
- retainValues(SemIm, SemGraph) - Static method in class edu.cmu.tetrad.sem.SemIm
-
Constructs a new SEM IM with the given graph, retaining parameter values from
semImfor nodes of the same name and edges connecting nodes of the same names. - ReturnsBootstrapGraphs - Interface in edu.cmu.tetrad.algcomparison.algorithm
- RevealEvaluator - Class in edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.reveal
-
Provides the methods for computing mutual information between expression levels between genes and, for a given gene, between points in time determined by a lag value.
- RevealEvaluator - Class in edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin
-
Provides the methods for computing mutual information between expression levels between genes and, for a given gene, between points in time determined by a lag value.
- RevealEvaluator(int[][]) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.reveal.RevealEvaluator
- RevealEvaluator(int[][]) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.RevealEvaluator
- RevealOutputGraph - Class in edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.akutsu
- RevealOutputGraph - Class in edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.reveal
- RevealOutputGraph - Class in edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin
- RevealOutputGraph(int, int[][], int[][], String[], String) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.akutsu.RevealOutputGraph
- RevealOutputGraph(int, int[][], int[][], String[], String) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.reveal.RevealOutputGraph
- RevealOutputGraph(int, int[][], int[][], String[], String) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.RevealOutputGraph
- RevealSearch - Class in edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.reveal
-
This class contains as a member variable (cases) the time series data stored in an int array of microarray measurements.
- RevealSearch - Class in edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin
-
This class contains as a member variable (cases) the time series data stored in an int array of microarray measurements.
- RevealSearch(int[][], String[]) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.reveal.RevealSearch
- RevealSearch(int[][], String[]) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.RevealSearch
- reverse() - Method in class edu.cmu.tetrad.graph.Edge
- revertSeed(long) - Method in class edu.cmu.tetrad.util.RandomUtil
- Rfci - Class in edu.cmu.tetrad.algcomparison.algorithm.oracle.pag
-
RFCI.
- Rfci - Class in edu.cmu.tetrad.search
-
Implements the Really Fast Causal Inference (RFCI) algorithm, which aims to do a correct inference of inferrable causal structure under the assumption that unmeasured common causes of variables in the data may exist.
- Rfci() - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Rfci
- Rfci(IndependenceWrapper) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Rfci
- Rfci(IndependenceTest) - Constructor for class edu.cmu.tetrad.search.Rfci
-
Constructs a new RFCI search for the given independence test and background knowledge.
- Rfci(IndependenceTest, List<Node>) - Constructor for class edu.cmu.tetrad.search.Rfci
-
Constructs a new RFCI search for the given independence test and background knowledge and a list of variables to search over.
- RFCI_PARAMETERS - Static variable in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.PagSampleRfci
- RfciBsc - Class in edu.cmu.tetrad.algcomparison.algorithm.oracle.pag
-
Jan 4, 2019 4:32:05 PM
- RfciBsc - Class in edu.pitt.dbmi.algo.bayesian.constraint.search
-
Dec 17, 2018 3:28:15 PM
- RfciBsc() - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.RfciBsc
- RfciBsc(Rfci) - Constructor for class edu.pitt.dbmi.algo.bayesian.constraint.search.RfciBsc
- RIC - Enum constant in enum class edu.cmu.tetrad.search.score.GicScores.RuleType
- RICc - Enum constant in enum class edu.cmu.tetrad.search.score.GicScores.RuleType
- ricf(SemGraph, ICovarianceMatrix, double) - Method in class edu.cmu.tetrad.sem.Ricf
- Ricf - Class in edu.cmu.tetrad.sem
-
Implements ICF as specified in Drton and Richardson (2003), Iterative Conditional Fitting for Gaussian Ancestral Graph Models, using hints from previous implementations by Drton in the ggm package in R and by Silva in the Purify class.
- Ricf() - Constructor for class edu.cmu.tetrad.sem.Ricf
- Ricf.FitConGraphResult - Class in edu.cmu.tetrad.sem
- Ricf.RicfResult - Class in edu.cmu.tetrad.sem
- ricf2(Graph, ICovarianceMatrix, double) - Method in class edu.cmu.tetrad.sem.Ricf
-
same as above but takes a Graph instead of a SemGraph
- RicfResult(DoubleMatrix2D, DoubleMatrix2D, DoubleMatrix2D, DoubleMatrix2D, int, double, ICovarianceMatrix) - Constructor for class edu.cmu.tetrad.sem.Ricf.RicfResult
- RIGHT_JUSTIFIED - Static variable in class edu.cmu.tetrad.util.TextTable
-
Set
justificationto this if the columns should be right justified. - robustSkew(double[], double[], boolean) - Static method in class edu.cmu.tetrad.search.Fask
- RocCalculator - Class in edu.cmu.tetrad.util
-
Calculates a ROC curve and AUC (area under curve) for a list of scored cases whose inclusion in category C is known.
- RocCalculator(double[], boolean[], int) - Constructor for class edu.cmu.tetrad.util.RocCalculator
-
Constructs a calculator using the parameter information below.
- rowCount() - Method in interface edu.pitt.isp.sverchkov.data.DataTable
- rowCount() - Method in class edu.pitt.isp.sverchkov.data.DataTableImpl
- RowSummingExactUpdater - Class in edu.cmu.tetrad.bayes
-
Performs updating operations on a BayesIm by summing over cells in the joint probability table for the BayesIm.
- RowSummingExactUpdater(BayesIm) - Constructor for class edu.cmu.tetrad.bayes.RowSummingExactUpdater
-
Constructs a new updater for the given Bayes net.
- RowSummingExactUpdater(BayesIm, Evidence) - Constructor for class edu.cmu.tetrad.bayes.RowSummingExactUpdater
-
Constructs a new updater for the given Bayes net.
- RPAREN - Enum constant in enum class edu.cmu.tetrad.calculator.parser.Token
- Rskew - Class in edu.cmu.tetrad.algcomparison.algorithm.pairwise
-
RSkew.
- Rskew() - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.pairwise.Rskew
- Rskew(Algorithm) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.pairwise.Rskew
- RSkew - Enum constant in enum class edu.cmu.tetrad.search.Lofs.Rule
- RSKEW - Enum constant in enum class edu.cmu.tetrad.search.Fask.LeftRight
- RskewE - Class in edu.cmu.tetrad.algcomparison.algorithm.pairwise
-
RSkewE.
- RskewE() - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.pairwise.RskewE
- RskewE(Algorithm) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.pairwise.RskewE
- RSkewE - Enum constant in enum class edu.cmu.tetrad.search.Lofs.Rule
- ruleR0(Graph) - Method in class edu.cmu.tetrad.search.utils.FciOrient
-
Orients colliders in the graph.
- ruleR0(Graph) - Method in class edu.cmu.tetrad.search.utils.SvarFciOrient
-
Orients colliders in the graph.
- ruleR1(Node, Node, Node, Graph) - Method in class edu.cmu.tetrad.search.utils.FciOrient
- ruleR10(Node, Node, Graph) - Method in class edu.cmu.tetrad.search.utils.FciOrient
-
Tries to apply Zhang's rule R10 to a pair of nodes A and C which are assumed to be such that Ao->C.
- ruleR2(Node, Node, Node, Graph) - Method in class edu.cmu.tetrad.search.utils.FciOrient
- ruleR3(Graph) - Method in class edu.cmu.tetrad.search.utils.FciOrient
-
Implements the double-triangle orientation rule, which states that if D*-oB, A*->B<-*C and A*-oDo-*C, and !adj(a, c), D*-oB, then D*->B.
- ruleR3(Graph) - Method in class edu.cmu.tetrad.search.utils.SvarFciOrient
-
Implements the double-triangle orientation rule, which states that if D*-oB, A*->B<-*C and A*-oDo-*C, then D*->B.
- ruleR4B(Graph) - Method in class edu.cmu.tetrad.search.utils.FciOrient
-
The triangles that must be oriented this way (won't be done by another rule) all look like the ones below, where the dots are a collider path from L to A with each node on the path (except L) a parent of C.
- ruleR4B(Graph) - Method in class edu.cmu.tetrad.search.utils.SvarFciOrient
-
The triangles that must be oriented this way (won't be done by another rule) all look like the ones below, where the dots are a collider path from L to A with each node on the path (except L) a parent of C.
- ruleR5(Graph) - Method in class edu.cmu.tetrad.search.utils.FciOrient
-
Implements Zhang's rule R5, orient circle undirectedPaths: for any Ao-oB, if there is an uncovered circle path u = [A,C,...,D,B] such that A,D nonadjacent and B,C nonadjacent, then A---B and orient every edge on u undirected.
- ruleR5(Graph) - Method in class edu.cmu.tetrad.search.utils.SvarFciOrient
-
Implements Zhang's rule R5, orient circle undirectedPaths: for any Ao-oB, if there is an uncovered circle path u = [A,C,...,D,B] such that A,D nonadjacent and B,C nonadjacent, then A---B and orient every edge on u undirected.
- ruleR6R7(Graph) - Method in class edu.cmu.tetrad.search.utils.FciOrient
-
Implements Zhang's rules R6 and R7, applies them over the graph once.
- ruleR6R7(Graph) - Method in class edu.cmu.tetrad.search.utils.SvarFciOrient
-
Implements Zhang's rules R6 and R7, applies them over the graph once.
- ruleR8(Node, Node, Graph) - Method in class edu.cmu.tetrad.search.utils.FciOrient
-
Tries to apply Zhang's rule R8 to a pair of nodes A and C which are assumed to be such that Ao->C.
- ruleR9(Node, Node, Graph) - Method in class edu.cmu.tetrad.search.utils.FciOrient
-
Tries to apply Zhang's rule R9 to a pair of nodes A and C which are assumed to be such that Ao->C.
- rulesR1R2cycle(Graph) - Method in class edu.cmu.tetrad.search.utils.FciOrient
- rulesR1R2cycle(Graph) - Method in class edu.cmu.tetrad.search.utils.SvarFciOrient
- rulesR8R9R10(Graph) - Method in class edu.cmu.tetrad.search.utils.FciOrient
-
Implements Zhang's rules R8, R9, R10, applies them over the graph once.
- rulesR8R9R10(Graph) - Method in class edu.cmu.tetrad.search.utils.SvarFciOrient
-
Implements Zhang's rules R8, R9, R10, applies them over the graph once.
- run(int) - Method in class edu.cmu.tetrad.simulation.HsimAutoC
- run(int) - Method in class edu.cmu.tetrad.simulation.HsimAutoRun
- run(int, double, int, double, int, int, boolean) - Static method in class edu.cmu.tetrad.simulation.HsimRobustCompare
- run(int, int) - Method in class edu.cmu.tetrad.simulation.HsimRepeatAC
- run(int, int) - Method in class edu.cmu.tetrad.simulation.HsimRepeatAutoRun
- run(String, String, char, String[], boolean) - Static method in class edu.cmu.tetrad.simulation.HsimRun
- runCallables(List<Callable<Boolean>>, boolean) - Static method in class edu.cmu.tetrad.util.ConcurrencyUtils
- RunConfig - Class in edu.cmu.tetrad.algcomparison.examples
-
An example script to save out data files and graphs from a simulation.
- RunConfig() - Constructor for class edu.cmu.tetrad.algcomparison.examples.RunConfig
- RunKemmeren - Class in edu.cmu.tetrad.algcomparison.examples
- RunKemmeren() - Constructor for class edu.cmu.tetrad.algcomparison.examples.RunKemmeren
S
- SAG - Enum constant in enum class edu.cmu.tetrad.search.Fofc.Algorithm
- SAG - Enum constant in enum class edu.cmu.tetrad.search.Ftfc.Algorithm
- SAG - Enum constant in enum class edu.cmu.tetrad.search.utils.BpcTestType
- sample() - Method in class edu.cmu.tetrad.sem.EmpiricalCdf
- sample(int) - Method in class edu.cmu.tetrad.sem.EmpiricalCdf
- sample(DataSet, int) - Method in class edu.cmu.tetrad.data.BootstrapSampler
-
This method takes a dataset and a sample size and creates a new dataset containing that number of samples by drawing with replacement from the original dataset.
- sample(DataSet, int) - Static method in class edu.cmu.tetrad.data.RandomSampler
-
This method takes a dataset and a sample size and creates a new dataset containing that number of samples by drawing with replacement from the original dataset.
- SAMPLE_SIZE - Static variable in class edu.cmu.tetrad.util.Params
- SAMPLE_STYLE - Static variable in class edu.cmu.tetrad.util.Params
- SampleVcpc - Class in edu.cmu.tetrad.search.work_in_progress
-
Implements a conservative version of PC, in which the Markov condition is assumed but faithfulness is tested locally.
- SampleVcpc(IndependenceTest) - Constructor for class edu.cmu.tetrad.search.work_in_progress.SampleVcpc
-
Constructs a CPC algorithm that uses the given independence test as oracle.
- SampleVcpcFast - Class in edu.cmu.tetrad.search.work_in_progress
-
Implements a conservative version of PC, in which the Markov condition is assumed but faithfulness is tested locally.
- SampleVcpcFast(IndependenceTest) - Constructor for class edu.cmu.tetrad.search.work_in_progress.SampleVcpcFast
-
Constructs a CPC algorithm that uses the given independence test as oracle.
- Save - Class in edu.cmu.tetrad.algcomparison.examples
-
An example script to save out data files and graphs from a simulation.
- Save() - Constructor for class edu.cmu.tetrad.algcomparison.examples.Save
- SAVE_BOOTSTRAP_GRAPHS - Static variable in class edu.cmu.tetrad.util.Params
- SAVE_LATENT_VARS - Static variable in class edu.cmu.tetrad.util.Params
- saveCSV(DataTable<Attribute, Value>, File, boolean) - Static method in class edu.pitt.isp.sverchkov.data.DataTools
- SaveDGSimulations - Class in edu.cmu.tetrad.algcomparison.examples
-
An example script to save out data files and graphs from a simulation.
- SaveDGSimulations() - Constructor for class edu.cmu.tetrad.algcomparison.examples.SaveDGSimulations
- saveGraph(Graph, File, boolean) - Static method in class edu.cmu.tetrad.graph.GraphSaveLoadUtils
- saveKnowledge(Knowledge, Writer) - Static method in class edu.cmu.tetrad.data.DataWriter
- saveToFiles(String, Simulation, Parameters) - Method in class edu.cmu.tetrad.algcomparison.Comparison
-
Saves simulationWrapper data.
- saveToFiles(String, Simulation, Parameters) - Method in class edu.cmu.tetrad.algcomparison.TimeoutComparison
-
Saves simulationWrapper data.
- saveToFilesSingleSimulation(String, Simulation, Parameters) - Method in class edu.cmu.tetrad.algcomparison.Comparison
-
Saves simulationWrapper data.
- scalarMult(double) - Method in class edu.cmu.tetrad.util.Matrix
- scalarMult(double) - Method in class edu.cmu.tetrad.util.Matrix2
- scalarMult(double) - Method in class edu.cmu.tetrad.util.Vector
- scalarProduct(double, double[]) - Static method in class edu.cmu.tetrad.util.MatrixUtils
- scalarProduct(double, double[][]) - Static method in class edu.cmu.tetrad.util.MatrixUtils
-
Multiplies the given matrix through by the given scalar.
- scale(Matrix) - Static method in class edu.cmu.tetrad.search.IcaLingD
-
Scales the given matrix M by diving each entry (i, j) by M(j, j)
- SCALE_FREE_ALPHA - Static variable in class edu.cmu.tetrad.util.Params
- SCALE_FREE_BETA - Static variable in class edu.cmu.tetrad.util.Params
- SCALE_FREE_DAG - Static variable in class edu.cmu.tetrad.algcomparison.graph.GraphTypes
- SCALE_FREE_DELTA_IN - Static variable in class edu.cmu.tetrad.util.Params
- SCALE_FREE_DELTA_OUT - Static variable in class edu.cmu.tetrad.util.Params
- ScaleFree - Class in edu.cmu.tetrad.algcomparison.graph
-
Returns a scale free graph.
- ScaleFree() - Constructor for class edu.cmu.tetrad.algcomparison.graph.ScaleFree
- score() - Method in class edu.cmu.tetrad.search.utils.TeyssierScorer
- score(Graph) - Method in class edu.cmu.tetrad.sem.DagScorer
-
Runs the estimator on the data and SemPm passed in through the constructor.
- score(Graph) - Method in interface edu.cmu.tetrad.sem.Scorer
- score(List<Node>) - Method in class edu.cmu.tetrad.search.utils.TeyssierScorer
-
Scores the given permutation.
- Score - Interface in edu.cmu.tetrad.search.score
-
Interface for a score.
- Score - Annotation Interface in edu.cmu.tetrad.annotation
-
Sep 1, 2017 10:51:13 AM
- Score(Scorer) - Constructor for class edu.cmu.tetrad.search.work_in_progress.HbsmsBeam.Score
- Score(Scorer) - Constructor for class edu.cmu.tetrad.search.work_in_progress.HbsmsGes.Score
- ScoreAnnotations - Class in edu.cmu.tetrad.annotation
-
Sep 26, 2017 1:14:01 AM
- scoreDag(Graph) - Method in class edu.cmu.tetrad.search.Fges
- scoreDag(Graph) - Method in class edu.cmu.tetrad.search.FgesMb
- scoreDag(Graph) - Method in class edu.cmu.tetrad.search.SvarFges
-
Scores the given DAG, up to a constant.
- scoreDag(Graph) - Method in interface edu.cmu.tetrad.search.utils.DagScorer
- scoreDag(Graph) - Method in class edu.cmu.tetrad.search.utils.FgesOrienter
-
Scores the given DAG, up to a constant.
- scoreDag(Graph) - Method in class edu.cmu.tetrad.search.work_in_progress.HbsmsGes
- scoreDag(Graph, DataModel, boolean) - Static method in class edu.cmu.tetrad.search.score.SemBicScorer
-
Scores the given DAG using the given data model, usimg a BIC score.
- scoreDag(Graph, DataModel, double, boolean) - Static method in class edu.cmu.tetrad.search.score.SemBicScorer
-
Scores the given DAG using the given data model, usimg a BIC score.
- ScoreDescriptions - Class in edu.cmu.tetrad.util
-
May 14, 2019 11:23:54 AM
- ScoredGraph - Class in edu.cmu.tetrad.search.score
-
Stores a graph with a score for the graph.
- ScoredGraph(Graph, Double) - Constructor for class edu.cmu.tetrad.search.score.ScoredGraph
- scoreGraph(Graph) - Method in class edu.cmu.tetrad.search.work_in_progress.HbsmsBeam
- scoreGraph(Graph) - Method in class edu.cmu.tetrad.search.work_in_progress.HbsmsGes
- ScoreIndTest - Class in edu.cmu.tetrad.search.test
-
Gives a way of interpreting a score as an independence test.
- ScoreIndTest(Score) - Constructor for class edu.cmu.tetrad.search.test.ScoreIndTest
- ScoreIndTest(Score, DataModel) - Constructor for class edu.cmu.tetrad.search.test.ScoreIndTest
- scoreLnGam(Node, Set<Node>, BayesPm, BayesIm) - Method in class edu.cmu.tetrad.bayes.BdeMetricCache
-
Computes the BDe score, using the logarithm of the gamma function, relative to the data, of the factor determined by a node and its parents.
- Scorer - Interface in edu.cmu.tetrad.sem
-
Interface for a class that represents a scoring of a SEM model.
- scoreRow(int, Matrix, List<List<Integer>>, List<List<Double>>) - Method in class edu.cmu.tetrad.search.Lofs
- scoreTest() - Method in class edu.cmu.tetrad.bayes.FactoredBayesStructuralEM
- ScoreType - Enum Class in edu.cmu.tetrad.sem
-
Author : Jeremy Espino MD Created 1/12/18 2:05 PM
- ScoreWrapper - Interface in edu.cmu.tetrad.algcomparison.score
-
Interface that algorithm must implement.
- sd(double[]) - Static method in class edu.cmu.tetrad.util.StatUtils
- sd(double[], int) - Static method in class edu.cmu.tetrad.util.StatUtils
- sd(long[]) - Static method in class edu.cmu.tetrad.util.StatUtils
- sd(long[], int) - Static method in class edu.cmu.tetrad.util.StatUtils
- search() - Method in class edu.cmu.tetrad.search.BFci
-
Does the search and returns a PAG.
- search() - Method in class edu.cmu.tetrad.search.Bpc
-
Runs the search and returns the graph, or null if there is no model.
- search() - Method in class edu.cmu.tetrad.search.Ccd
-
The search method assumes that the IndependenceTest provided to the constructor is a conditional independence oracle for the SEM (or Bayes network) which describes the causal structure of the population.
- search() - Method in class edu.cmu.tetrad.search.Cfci
-
Performs the search and returns the PAG.
- search() - Method in class edu.cmu.tetrad.search.Cpc
-
Runs CPC starting with a fully connected graph over all the variables in the domain of the independence test.
- search() - Method in class edu.cmu.tetrad.search.Dagma
-
NEEDS DOCUMENTATION
- search() - Method in class edu.cmu.tetrad.search.DirectLingam
-
NEEDS DOCUMENTATION
- search() - Method in class edu.cmu.tetrad.search.Fas
-
Runs the search and returns the resulting (undirected) graph.
- search() - Method in class edu.cmu.tetrad.search.Fasd
-
Discovers all adjacencies in data.
- search() - Method in class edu.cmu.tetrad.search.Fask
-
Runs the search on the concatenated data, returning a graph, possibly cyclic, possibly with two-cycles.
- search() - Method in class edu.cmu.tetrad.search.Fci
- search() - Method in class edu.cmu.tetrad.search.FciMax
-
Performs the search and returns the PAG.
- search() - Method in class edu.cmu.tetrad.search.Fges
-
Greedy equivalence search: Start from the empty graph, add edges till the model is significant.
- search() - Method in class edu.cmu.tetrad.search.Fofc
-
Runs the search and returns a graph of clusters with the ir respective latent parents.
- search() - Method in class edu.cmu.tetrad.search.Ftfc
-
Runs the search and returns a graph of clusters, each of which has two common latent parents.
- search() - Method in class edu.cmu.tetrad.search.GFci
-
Runs the graph and returns the search PAG.
- search() - Method in class edu.cmu.tetrad.search.GraspFci
-
Run the search and return s a PAG.
- search() - Method in interface edu.cmu.tetrad.search.IGraphSearch
-
Runs the search and returns a graph.
- search() - Method in class edu.cmu.tetrad.search.Pc
-
Runs PC starting with a complete graph over all nodes of the given conditional independence test, using the given independence test and knowledge and returns the resultant graph.
- search() - Method in class edu.cmu.tetrad.search.Pcd
-
Runs PC starting with a complete graph over all nodes of the given conditional independence test, using the given independence test and knowledge and returns the resultant graph.
- search() - Method in class edu.cmu.tetrad.search.PcLingam
-
Runs the search and returns the result graph.
- search() - Method in class edu.cmu.tetrad.search.PcMb
-
Does the search.
- search() - Method in class edu.cmu.tetrad.search.PermutationSearch
-
Performe the search and return a CPDAG.
- search() - Method in class edu.cmu.tetrad.search.Rfci
-
Runs the search and returns the RFCI PAG.
- search() - Method in class edu.cmu.tetrad.search.SpFci
-
Runs the search and returns the discovered PAG.
- search() - Method in class edu.cmu.tetrad.search.SvarFas
-
Discovers all adjacencies in data.
- search() - Method in class edu.cmu.tetrad.search.SvarFci
-
Runs the search and returns the PAG.
- search() - Method in class edu.cmu.tetrad.search.SvarFges
-
Greedy equivalence search: Start from the empty graph, add edges till the model is significant.
- search() - Method in class edu.cmu.tetrad.search.SvarGfci
-
Runs the search and returns a PAG.
- search() - Method in class edu.cmu.tetrad.search.utils.FgesOrienter
-
Greedy equivalence search: Start from the empty graph, add edges till model is significant.
- search() - Method in class edu.cmu.tetrad.search.utils.PcCommon
-
Runs the search and returns the search graph.
- search() - Method in class edu.cmu.tetrad.search.utils.PossibleMsepFci
-
Performs pairwise comparisons of each variable in the graph with the variables that have not already been checked.
- search() - Method in class edu.cmu.tetrad.search.utils.Purify
-
****************************************************** SEARCH INTERFACE *******************************************************
- search() - Method in class edu.cmu.tetrad.search.utils.ShiftSearch
- search() - Method in class edu.cmu.tetrad.search.work_in_progress.BpcTetradPurifyWashdown
-
Runs the search and returns a graph.
- search() - Method in class edu.cmu.tetrad.search.work_in_progress.Dci
-
Begins the DCI search procedure, described at each step
- search() - Method in class edu.cmu.tetrad.search.work_in_progress.DMSearch
- search() - Method in class edu.cmu.tetrad.search.work_in_progress.Fas2
-
Discovers all adjacencies in data.
- search() - Method in class edu.cmu.tetrad.search.work_in_progress.Fas3
-
Runs the search and returns the resulting (undirected) graph.
- search() - Method in class edu.cmu.tetrad.search.work_in_progress.FasDci
-
Discovers all adjacencies in data.
- search() - Method in class edu.cmu.tetrad.search.work_in_progress.FasFdr
-
Discovers all adjacencies in data.
- search() - Method in class edu.cmu.tetrad.search.work_in_progress.FasLofs
-
Runs the search on the concatenated data, returning a graph, possibly cyclic, possibly with two-cycles.
- search() - Method in class edu.cmu.tetrad.search.work_in_progress.Glasso
- search() - Method in interface edu.cmu.tetrad.search.work_in_progress.Hbsms
- search() - Method in class edu.cmu.tetrad.search.work_in_progress.HbsmsBeam
- search() - Method in class edu.cmu.tetrad.search.work_in_progress.HbsmsGes
- search() - Method in class edu.cmu.tetrad.search.work_in_progress.InverseCorrelation
- search() - Method in class edu.cmu.tetrad.search.work_in_progress.Ion
-
Runs the ION search and returns a list of compatible graphs.
- search() - Method in class edu.cmu.tetrad.search.work_in_progress.Kpc
-
Runs PC starting with a complete graph over all nodes of the given conditional independence test, using the given independence test and knowledge and returns the resultant graph.
- search() - Method in class edu.cmu.tetrad.search.work_in_progress.Mmhc
-
Runs PC starting with a fully connected graph over all of the variables in the domain of the independence test.
- search() - Method in class edu.cmu.tetrad.search.work_in_progress.SampleVcpc
- search() - Method in class edu.cmu.tetrad.search.work_in_progress.SampleVcpcFast
- search() - Method in class edu.cmu.tetrad.search.work_in_progress.VcFas
-
Discovers all adjacencies in data.
- search() - Method in class edu.cmu.tetrad.search.work_in_progress.VcPc
- search() - Method in class edu.cmu.tetrad.search.work_in_progress.VcPcAlt
- search() - Method in class edu.cmu.tetrad.search.work_in_progress.VcPcFast
- search() - Method in class edu.cmu.tetrad.search.work_in_progress.Washdown
-
Runs the Washdown algorithm and return a graph.
- search() - Method in class edu.pitt.csb.mgm.Mgm
-
Simple search command for GraphSearch implementation.
- search() - Method in class edu.pitt.dbmi.algo.bayesian.constraint.search.PagSamplingRfci
- search() - Method in class edu.pitt.dbmi.algo.bayesian.constraint.search.RfciBsc
- search() - Method in class edu.pitt.dbmi.algo.resampling.GeneralResamplingSearch
- search() - Method in class edu.pitt.dbmi.algo.resampling.GeneralResamplingTest
- search(DataModel, Parameters) - Method in interface edu.cmu.tetrad.algcomparison.algorithm.Algorithm
-
Runs the search.
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.cluster.Bpc
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.cluster.Fofc
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.cluster.Ftfc
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.continuous.dag.Dagma
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.continuous.dag.DirectLingam
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.continuous.dag.IcaLingam
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.continuous.dag.IcaLingD
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.external.ExternalAlgorithmBnlearnMmhc
-
Reads in the relevant graph from the file (see above) and returns it.
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.external.ExternalAlgorithmBNTPc
-
Reads in the relevant graph from the file (see above) and returns it.
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.external.ExternalAlgorithmIntersection
-
Reads in the relevant graph from the file (see above) and returns it.
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.external.ExternalAlgorithmPcalgGes
-
Reads in the relevant graph from the file (see above) and returns it.
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.external.ExternalAlgorithmPcalgPc
-
Reads in the relevant graph from the file (see above) and returns it.
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.external.ExternalAlgorithmTetrad
-
Reads in the relevant graph from the file and returns it.
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.FirstInflection
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.mixed.Mgm
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.Fask
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FaskConcatenated
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FaskLofsConcatenated
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FaskVote
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FasLofs
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FciIod
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FgesConcatenated
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.Images
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Boss
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Cpc
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Fas
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Fges
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.FgesMb
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.FgesMeasurement
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.GesMe
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Grasp
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Pc
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Pcd
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.PcLingam
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.PcMb
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.RestrictedBoss
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.SingleGraphAlg
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Sp
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Bfci
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Ccd
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Cfci
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Fci
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.FciMax
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Gfci
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.GraspFci
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.PagSampleRfci
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Rfci
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.RfciBsc
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.SpFci
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.SvarFci
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.SvarGfci
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pattern.Cstar
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.other.FactorAnalysis
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.other.Glasso
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.Eb
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.FaskPw
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.R1
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.R2
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.R3
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.Rskew
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.RskewE
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.Skew
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.SkewE
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.Tanh
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.StabilitySelection
- search(DataModel, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.StARS
- search(DataSet) - Method in class edu.pitt.csb.stability.DataGraphSearch
- search(DataSet) - Method in class edu.pitt.csb.stability.SearchWrappers.FgesWrapper
- search(DataSet) - Method in class edu.pitt.csb.stability.SearchWrappers.MGMWrapper
- search(DataSet) - Method in class edu.pitt.csb.stability.SearchWrappers.PcStableWrapper
- search(IFas) - Method in class edu.cmu.tetrad.search.SvarFci
-
Runs the search using a particular implementation of FAS.
- search(IFas, List<Node>) - Method in class edu.cmu.tetrad.search.Pcd
- search(IFas, List<Node>) - Method in class edu.cmu.tetrad.search.Rfci
-
Runs the search and returns the RFCI PAG.
- search(IFas, Set<Node>) - Method in class edu.cmu.tetrad.search.Pc
-
Runs the search using a particular implementation of the fast adjacency search (FAS), over the given sublist of nodes.
- search(Parameters) - Method in class edu.cmu.tetrad.search.work_in_progress.FaskVote
-
Does the search.
- search(List<DataModel>, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FaskConcatenated
- search(List<DataModel>, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FaskLofsConcatenated
- search(List<DataModel>, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FaskVote
- search(List<DataModel>, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FciIod
- search(List<DataModel>, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FgesConcatenated
- search(List<DataModel>, Parameters) - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.Images
- search(List<DataModel>, Parameters) - Method in interface edu.cmu.tetrad.algcomparison.algorithm.MultiDataSetAlgorithm
-
Runs the search.
- search(List<Node>) - Method in class edu.cmu.tetrad.search.Fas
-
Discovers all adjacencies in data.
- search(List<Node>) - Method in class edu.cmu.tetrad.search.FgesMb
-
Greedy equivalence search: Start from the empty graph, add edges till the model is significant.
- search(List<Node>) - Method in class edu.cmu.tetrad.search.Pcd
-
Runs PC starting with a complete graph over the given list of nodes, using the given independence test and knowledge and returns the resultant graph.
- search(List<Node>) - Method in class edu.cmu.tetrad.search.PcMb
-
Searches for the MB CPDAG for the given targets.
- search(List<Node>) - Method in class edu.cmu.tetrad.search.Rfci
-
Searches of a specific sublist of nodes.
- search(List<Node>) - Method in class edu.cmu.tetrad.search.utils.PcCommon
-
Runs the search over the given list of nodes only, returning the serach graph.
- search(List<Node>) - Method in class edu.cmu.tetrad.search.work_in_progress.Fas2
- search(List<Node>) - Method in class edu.cmu.tetrad.search.work_in_progress.Fas3
-
Discovers all adjacencies in data.
- search(List<Node>) - Method in class edu.cmu.tetrad.search.work_in_progress.Kpc
-
Runs PC starting with a commplete graph over the given list of nodes, using the given independence test and knowledge and returns the resultant graph.
- search(List<List<Node>>, List<String>, ICovarianceMatrix) - Method in class edu.cmu.tetrad.search.Mimbuild
-
Does a Mimbuild search.
- search(List<List<Node>>, List<String>, ICovarianceMatrix) - Method in class edu.cmu.tetrad.search.MimbuildTrek
-
Does the search and returns the graph.
- search(Set<Node>) - Method in class edu.cmu.tetrad.search.Pc
-
Runs PC starting with a complete graph over the given list of nodes, using the given independence test and knowledge and returns the resultant graph.
- search_for_Markov_blankets - Enum constant in enum class edu.cmu.tetrad.annotation.AlgType
-
If an algorithm searches for Markov blanekts.
- search_for_structure_over_latents - Enum constant in enum class edu.cmu.tetrad.annotation.AlgType
-
If an algorithm searches for structure over latents.
- searchParams - Variable in class edu.pitt.csb.stability.DataGraphSearch
- searchSuborder(List<Node>, List<Node>, Map<Node, GrowShrinkTree>) - Method in class edu.cmu.tetrad.search.Boss
- searchSuborder(List<Node>, List<Node>, Map<Node, GrowShrinkTree>) - Method in class edu.cmu.tetrad.search.Sp
-
This is the method called by PermutationSearch per tier.
- searchSuborder(List<Node>, List<Node>, Map<Node, GrowShrinkTree>) - Method in interface edu.cmu.tetrad.search.SuborderSearch
-
Searches the suborder.
- SearchWrappers - Class in edu.pitt.csb.stability
-
Created by ajsedgewick on 9/4/15.
- SearchWrappers() - Constructor for class edu.pitt.csb.stability.SearchWrappers
- SearchWrappers.FgesWrapper - Class in edu.pitt.csb.stability
- SearchWrappers.MGMWrapper - Class in edu.pitt.csb.stability
- SearchWrappers.PcStableWrapper - Class in edu.pitt.csb.stability
- SEED - Static variable in class edu.cmu.tetrad.util.Params
- select(Node) - Method in class edu.cmu.tetrad.data.CorrelationMatrixOnTheFly
- select(Node) - Method in class edu.cmu.tetrad.data.CovarianceMatrix
- select(Node) - Method in class edu.cmu.tetrad.data.CovarianceMatrixOnTheFly
- select(Node) - Method in interface edu.cmu.tetrad.data.ICovarianceMatrix
- SELECTION_MIN_EFFECT - Static variable in class edu.cmu.tetrad.util.Params
- SelectionGenerator - Class in edu.cmu.tetrad.util
-
Generates (nonrecursively) all of the selections from a items, where a is a nonnegative integer.
- SelectionGenerator(int) - Constructor for class edu.cmu.tetrad.util.SelectionGenerator
-
Constructs a new selection generator for a items.
- SELF_LOOP_COEF - Static variable in class edu.cmu.tetrad.util.Params
- SEM_BIC_RULE - Static variable in class edu.cmu.tetrad.util.Params
- SEM_BIC_STRUCTURE_PRIOR - Static variable in class edu.cmu.tetrad.util.Params
- SEM_GIC_RULE - Static variable in class edu.cmu.tetrad.util.Params
- SemBic - Enum constant in enum class edu.cmu.tetrad.sem.ScoreType
- SemBicDTest - Class in edu.cmu.tetrad.algcomparison.independence
-
Wrapper for Fisher Z test.
- SemBicDTest() - Constructor for class edu.cmu.tetrad.algcomparison.independence.SemBicDTest
- SemBicScore - Class in edu.cmu.tetrad.algcomparison.score
-
Wrapper for linear, Gaussian SEM BIC score.
- SemBicScore - Class in edu.cmu.tetrad.search.score
-
Implements the linear, Gaussian BIC score, with a 'penalty discount' multiplier on the BIC penalty.
- SemBicScore() - Constructor for class edu.cmu.tetrad.algcomparison.score.SemBicScore
- SemBicScore(DataSet, boolean) - Constructor for class edu.cmu.tetrad.search.score.SemBicScore
-
Constructs the score using a covariance matrix.
- SemBicScore(ICovarianceMatrix) - Constructor for class edu.cmu.tetrad.search.score.SemBicScore
-
Constructs the score using a covariance matrix.
- SemBicScore.RuleType - Enum Class in edu.cmu.tetrad.search.score
-
Gives two options for calculating the BIC score, one describe by Chickering and the other due to Nandy et al.
- SemBicScoreDeterministic - Class in edu.cmu.tetrad.algcomparison.score
-
Wrapper for Fisher Z test.
- SemBicScoreDeterministic - Class in edu.cmu.tetrad.search.work_in_progress
-
Implements the continuous BIC score for FGES.
- SemBicScoreDeterministic() - Constructor for class edu.cmu.tetrad.algcomparison.score.SemBicScoreDeterministic
- SemBicScoreDeterministic(ICovarianceMatrix) - Constructor for class edu.cmu.tetrad.search.work_in_progress.SemBicScoreDeterministic
-
Constructs the score using a covariance matrix.
- SemBicScorer - Class in edu.cmu.tetrad.search.score
-
Scores an entire DAG using the SemBicScore.
- SemBicScorer() - Constructor for class edu.cmu.tetrad.search.score.SemBicScorer
- SemBicTest - Class in edu.cmu.tetrad.algcomparison.independence
-
Wrapper for Fisher Z test.
- SemBicTest() - Constructor for class edu.cmu.tetrad.algcomparison.independence.SemBicTest
- SemEstimator - Class in edu.cmu.tetrad.sem
-
Estimates a SemIm given a CovarianceMatrix and a SemPm.
- SemEstimator(DataSet, SemPm) - Constructor for class edu.cmu.tetrad.sem.SemEstimator
-
Constructs a Sem Estimator that does default estimation.
- SemEstimator(DataSet, SemPm, SemOptimizer) - Constructor for class edu.cmu.tetrad.sem.SemEstimator
-
Constructs a new SemEstimator that uses the specified optimizer.
- SemEstimator(ICovarianceMatrix, SemPm) - Constructor for class edu.cmu.tetrad.sem.SemEstimator
-
Constructs a SEM estimator that does default estimation.
- SemEstimator(ICovarianceMatrix, SemPm, SemOptimizer) - Constructor for class edu.cmu.tetrad.sem.SemEstimator
-
Constructs a new SemEstimator that uses the specified optimizer.
- SemEstimatorGibbs - Class in edu.cmu.tetrad.sem
-
Implements the Gibbs sampler apporach to obtain samples of arbitrary size from the posterior distribution over the freeParameters of a SEM given a continuous dataset and a SemPm.
- SemEstimatorGibbs(int, double, double, double, double, SemPm, SemIm, boolean) - Constructor for class edu.cmu.tetrad.sem.SemEstimatorGibbs
- SemEstimatorGibbs(SemPm, SemIm, double[][], boolean, double, int) - Constructor for class edu.cmu.tetrad.sem.SemEstimatorGibbs
- SemEstimatorGibbsParams - Class in edu.cmu.tetrad.sem
-
Stores the freeParameters for an instance of a SemEstimatorGibbs.
- SemEvidence - Class in edu.cmu.tetrad.sem
-
Stores information for a SemIm about evidence we have for each variable as well as whether each variable has been manipulated.
- SemEvidence(SemEvidence) - Constructor for class edu.cmu.tetrad.sem.SemEvidence
- SemEvidence(SemIm) - Constructor for class edu.cmu.tetrad.sem.SemEvidence
-
Constructs a container for evidence for the given Bayes IM.
- SemGraph - Class in edu.cmu.tetrad.graph
-
Represents the graphical structure of a structural equation model.
- SemGraph() - Constructor for class edu.cmu.tetrad.graph.SemGraph
-
Constructs a new, empty SemGraph.
- SemGraph(Graph) - Constructor for class edu.cmu.tetrad.graph.SemGraph
-
Constructs a new SemGraph from the nodes and edges of the given graph.
- SemGraph(SemGraph) - Constructor for class edu.cmu.tetrad.graph.SemGraph
-
Copy constructor.
- SEMIDIRECTED_PATHS_TO_TARGETS - Enum constant in enum class edu.cmu.tetrad.search.FgesMb.TrimmingStyle
- SemidirectedPathF1 - Class in edu.cmu.tetrad.algcomparison.statistic
-
Calculates the F1 statistic for adjacencies.
- SemidirectedPathF1() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.SemidirectedPathF1
- semidirectedPathsFromTo(Node, Node, int) - Method in class edu.cmu.tetrad.graph.Paths
- SemidirectedPrecision - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- SemidirectedPrecision() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.SemidirectedPrecision
- SemidirectedRecall - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- SemidirectedRecall() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.SemidirectedRecall
- semigraphoid() - Method in class edu.cmu.tetrad.search.utils.GraphoidAxioms
-
Checked whether the IM is a semigraphoid.
- SemIm - Class in edu.cmu.tetrad.sem
-
Stores an instantiated structural equation model (SEM), with error covariance terms, possibly cyclic, suitable for estimation and simulation.
- SemIm(SemIm) - Constructor for class edu.cmu.tetrad.sem.SemIm
-
Copy constructor.
- SemIm(SemPm) - Constructor for class edu.cmu.tetrad.sem.SemIm
-
Constructs a new SEM IM from a SEM PM.
- SemIm(SemPm, ICovarianceMatrix) - Constructor for class edu.cmu.tetrad.sem.SemIm
-
Constructs a SEM model using the given SEM PM and sample covariance matrix.
- SemIm(SemPm, SemIm, Parameters) - Constructor for class edu.cmu.tetrad.sem.SemIm
-
Constructs a new SEM IM from the given SEM PM, using the old SEM IM and params object to guide the choice of parameter values.
- SemIm(SemPm, Parameters) - Constructor for class edu.cmu.tetrad.sem.SemIm
-
Constructs a new SEM IM from the given SEM PM, using the given params object to guide the choice of parameter values.
- SemIm(SemPm, List<Node>, List<Node>, Matrix, double[]) - Constructor for class edu.cmu.tetrad.sem.SemIm
- SemManipulation - Class in edu.cmu.tetrad.sem
-
Stores information for a BayesIm about evidence we have for each variable as well as whether each variable has been manipulated.
- SemManipulation(SemIm) - Constructor for class edu.cmu.tetrad.sem.SemManipulation
-
Constructs a container for evidence for the given Bayes IM.
- SemManipulation(SemManipulation) - Constructor for class edu.cmu.tetrad.sem.SemManipulation
- SemOptimizer - Interface in edu.cmu.tetrad.sem
-
Interface for algorithm that optimize the fitting function of a SemIm model by adjusting its freeParameters in search of a global maximum.
- SemOptimizerEm - Class in edu.cmu.tetrad.sem
-
Optimizes a DAG SEM with hidden variables using expectation-maximization.
- SemOptimizerEm() - Constructor for class edu.cmu.tetrad.sem.SemOptimizerEm
- SemOptimizerPowell - Class in edu.cmu.tetrad.sem
-
Optimizes a SEM using Powell's method from the Apache library.
- SemOptimizerPowell() - Constructor for class edu.cmu.tetrad.sem.SemOptimizerPowell
-
Blank constructor.
- SemOptimizerRegression - Class in edu.cmu.tetrad.sem
-
Optimizes a DAG SEM by regressing each varaible onto its parents using a linear regression.
- SemOptimizerRegression() - Constructor for class edu.cmu.tetrad.sem.SemOptimizerRegression
-
Blank constructor.
- SemOptimizerRicf - Class in edu.cmu.tetrad.sem
-
Optimizes a SEM using RICF (see that class).
- SemOptimizerRicf() - Constructor for class edu.cmu.tetrad.sem.SemOptimizerRicf
-
Blank constructor.
- SemOptimizerScattershot - Class in edu.cmu.tetrad.sem
-
Optimizes a SEM by randomly selecting points in cubes of decreasing size about a given point.
- SemOptimizerScattershot() - Constructor for class edu.cmu.tetrad.sem.SemOptimizerScattershot
-
Blank constructor.
- SemPm - Class in edu.cmu.tetrad.sem
-
Parametric model for Structural Equation Models.
- SemPm(Graph) - Constructor for class edu.cmu.tetrad.sem.SemPm
-
Constructs a BayesPm from the given Graph, which must be convertible first into a ProtoSemGraph and then into a SemGraph.
- SemPm(SemGraph) - Constructor for class edu.cmu.tetrad.sem.SemPm
-
Constructs a new SemPm from the given SemGraph.
- SemPm(SemPm) - Constructor for class edu.cmu.tetrad.sem.SemPm
-
Copy constructor.
- SemProposition - Class in edu.cmu.tetrad.sem
-
Represents propositions over the variables of a particular BayesIm describing and event of a fairly general sort--namely, conjunctions of propositions that particular variables take on values from a particular disjunctive list of categories.
- SemProposition(SemIm) - Constructor for class edu.cmu.tetrad.sem.SemProposition
-
Creates a new Proposition which allows all values.
- SemProposition(SemProposition) - Constructor for class edu.cmu.tetrad.sem.SemProposition
- SemSimulation - Class in edu.cmu.tetrad.algcomparison.simulation
-
SEM simulation.
- SemSimulation(RandomGraph) - Constructor for class edu.cmu.tetrad.algcomparison.simulation.SemSimulation
- SemSimulation(SemIm) - Constructor for class edu.cmu.tetrad.algcomparison.simulation.SemSimulation
- SemSimulation(SemPm) - Constructor for class edu.cmu.tetrad.algcomparison.simulation.SemSimulation
- SemStdErrorEstimator - Class in edu.cmu.tetrad.sem
-
Includes methods for estimating the standard errors of the freeParameters of an estimated SEM.
- SemStdErrorEstimator() - Constructor for class edu.cmu.tetrad.sem.SemStdErrorEstimator
-
Blank constructor.
- SemThenDiscretize - Class in edu.cmu.tetrad.algcomparison.simulation
-
SEM the discretize.
- SemThenDiscretize(RandomGraph) - Constructor for class edu.cmu.tetrad.algcomparison.simulation.SemThenDiscretize
- SemThenDiscretize(RandomGraph, DataType) - Constructor for class edu.cmu.tetrad.algcomparison.simulation.SemThenDiscretize
- SemUpdater - Class in edu.cmu.tetrad.sem
-
Calculates updated structural equation models given evidence of the form X1=x1',...,The main task of such and algorithm is to calculate P(X = x' | evidence), where evidence takes the form of a Proposition over the variables in the Bayes net, possibly with additional information about which variables in the Bayes net have been manipulated.
- SemUpdater(SemIm) - Constructor for class edu.cmu.tetrad.sem.SemUpdater
- SemXmlParser - Class in edu.cmu.tetrad.sem
-
This class takes an xml element representing a SEM im and converts it to a SemIM
- SemXmlParser() - Constructor for class edu.cmu.tetrad.sem.SemXmlParser
- SemXmlRenderer - Class in edu.cmu.tetrad.sem
-
This class converts a SemIm into xml.
- SemXmlRenderer() - Constructor for class edu.cmu.tetrad.sem.SemXmlRenderer
- SepsetMap - Class in edu.cmu.tetrad.search.utils
-
Stores a map from pairs of nodes to separating sets--that is, for each unordered pair of nodes {node1, node2} in a graph, stores a set of nodes conditional on which node1 and node2 are independent (where the nodes are considered as variables) or stores null if the pair was not judged to be independent.
- SepsetMap() - Constructor for class edu.cmu.tetrad.search.utils.SepsetMap
-
Constructor.
- SepsetMap(SepsetMap) - Constructor for class edu.cmu.tetrad.search.utils.SepsetMap
-
Copy constructor.
- SepsetMapDci - Class in edu.cmu.tetrad.search.work_in_progress
-
This is the same as the usual SepsetMap described below, but also keeps up with the individual sets of conditioning nodes for d-separation relations for use with the Distributed Causal Inference (DCI) algorithm.
- SepsetMapDci() - Constructor for class edu.cmu.tetrad.search.work_in_progress.SepsetMapDci
- SepsetMapDci(SepsetMapDci) - Constructor for class edu.cmu.tetrad.search.work_in_progress.SepsetMapDci
- SepsetProducer - Interface in edu.cmu.tetrad.search.utils
-
Provides a covenience interface for classes that can generate and keep track of sepsets.
- SepsetsConservative - Class in edu.cmu.tetrad.search.utils
-
Provides a SepsetProcuder that selects the first sepset it comes to from among the extra sepsets or the adjacents of i or k, or null if none is found.
- SepsetsConservative(Graph, IndependenceTest, SepsetMap, int) - Constructor for class edu.cmu.tetrad.search.utils.SepsetsConservative
- SepsetsGreedy - Class in edu.cmu.tetrad.search.utils
-
Provides a SepsetProcuder that selects the first sepset it comes to from among the extra sepsets or the adjacents of i or k, or null if none is found.
- SepsetsGreedy(Graph, IndependenceTest, SepsetMap, int, Knowledge) - Constructor for class edu.cmu.tetrad.search.utils.SepsetsGreedy
- SepsetsPossibleMsep - Class in edu.cmu.tetrad.search.utils
-
Provides a sepset producer using conditional independence tests to generate the Sepset map, for the case where possible msep sets are required.
- SepsetsPossibleMsep(Graph, IndependenceTest, Knowledge, int, int) - Constructor for class edu.cmu.tetrad.search.utils.SepsetsPossibleMsep
- SepsetsSet - Class in edu.cmu.tetrad.search.utils
-
Provides a sepset producer using conditional independence tests to generate the Sepset map.
- SepsetsSet(SepsetMap, IndependenceTest) - Constructor for class edu.cmu.tetrad.search.utils.SepsetsSet
- serializableInstance() - Static method in class edu.cmu.tetrad.bayes.ApproximateUpdater
-
Returns a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.bayes.BayesImProbs
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.bayes.BayesPm
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.bayes.CptInvariantMarginalCalculator
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.bayes.CptInvariantUpdater
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.bayes.DirichletBayesIm
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.bayes.Evidence
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.bayes.Identifiability
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.bayes.Manipulation
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.bayes.MlBayesIm
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.bayes.MlBayesImObs
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.bayes.Proposition
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.bayes.RowSummingExactUpdater
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.bayes.StoredCellProbs
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.bayes.StoredCellProbsObs
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.bayes.UpdatedBayesIm
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.calculator.expression.ConstantExpression
- serializableInstance() - Static method in class edu.cmu.tetrad.calculator.expression.EvaluationExpression
- serializableInstance() - Static method in enum class edu.cmu.tetrad.calculator.expression.ExpressionDescriptor.Position
- serializableInstance() - Static method in class edu.cmu.tetrad.calculator.expression.VariableExpression
- serializableInstance() - Static method in class edu.cmu.tetrad.classify.ClassifierBayesUpdaterDiscrete
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.data.BoxDataSet
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.data.ByteDataBox
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.data.Clusters
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.data.ContinuousDiscretizationSpec
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.data.ContinuousVariable
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.data.CorrelationMatrix
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.data.CorrelationMatrixOnTheFly
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.data.CovarianceMatrix
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.data.CovarianceMatrixOnTheFly
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.data.DataModelList
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.data.DelimiterType
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.data.DiscreteDiscretizationSpec
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.data.DiscreteVariable
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.data.DiscreteVariableType
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.data.DoubleDataBox
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.data.FloatDataBox
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.data.IndependenceFacts
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.data.IntDataBox
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.data.Knowledge
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.data.KnowledgeEdge
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.data.KnowledgeGroup
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.data.LongDataBox
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.data.MixedDataBox
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.data.NumberObjectDataSet
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.data.ShortDataBox
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.data.SplitCasesSpec
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.data.TimeSeriesData
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.data.VerticalDoubleDataBox
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.data.VerticalIntDataBox
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.graph.Dag
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.graph.Edge
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.graph.EdgeListGraph
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.graph.GraphNode
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.graph.IndependenceFact
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.graph.LagGraph
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.graph.NodeType
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.graph.SemGraph
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.graph.TimeLagGraph
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.graph.Triple
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.regression.LogisticRegression.Result
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.regression.LogisticRegression
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.regression.RegressionResult
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.search.score.ScoredGraph
- serializableInstance() - Static method in class edu.cmu.tetrad.search.test.IndependenceResult
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in enum class edu.cmu.tetrad.search.utils.BpcAlgorithmType
- serializableInstance() - Static method in enum class edu.cmu.tetrad.search.utils.BpcTestType
- serializableInstance() - Static method in class edu.cmu.tetrad.search.utils.DeltaSextadTest
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.search.utils.SepsetMap
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.search.utils.Sextad
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.search.work_in_progress.SepsetMapDci
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.search.work_in_progress.Sextad
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.sem.DagScorer
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.sem.GeneralizedSemIm
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.sem.GeneralizedSemPm
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.sem.Mapping
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.sem.ParamConstraint
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.sem.ParamConstraintType
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.sem.Parameter
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.sem.ParameterPair
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.sem.ParamType
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.sem.SemEstimator
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.sem.SemEstimatorGibbsParams
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.sem.SemEvidence
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.sem.SemIm
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.sem.SemManipulation
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.sem.SemOptimizerEm
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.sem.SemOptimizerPowell
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.sem.SemOptimizerRegression
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.sem.SemOptimizerRicf
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.sem.SemOptimizerScattershot
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.sem.SemPm
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.sem.SemProposition
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.sem.SemUpdater
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.sem.StandardizedSemIm.ParameterRange
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.sem.StandardizedSemIm
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.session.Session
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.session.SessionNode
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.session.Type1
- serializableInstance() - Static method in class edu.cmu.tetrad.session.Type10
- serializableInstance() - Static method in class edu.cmu.tetrad.session.Type11
- serializableInstance() - Static method in class edu.cmu.tetrad.session.Type12
- serializableInstance() - Static method in class edu.cmu.tetrad.session.Type2
- serializableInstance() - Static method in class edu.cmu.tetrad.session.Type3
- serializableInstance() - Static method in class edu.cmu.tetrad.session.Type4
- serializableInstance() - Static method in class edu.cmu.tetrad.session.Type5
- serializableInstance() - Static method in class edu.cmu.tetrad.session.Type6
- serializableInstance() - Static method in class edu.cmu.tetrad.session.Type7
- serializableInstance() - Static method in class edu.cmu.tetrad.session.Type8
- serializableInstance() - Static method in class edu.cmu.tetrad.session.Type9
- serializableInstance() - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ActiveLagGraph
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.LagGraphParams
- serializableInstance() - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ManualActiveLagGraph
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ManualLagGraph
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ManualLagGraphParams
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.RandomActiveLagGraph
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.StoredLagGraphParams
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.BasalInitializer
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.BasicLagGraph
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.BooleanFunction
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.BooleanGlassFunction
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.DishModel
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.GeneHistory
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.IndexedConnectivity
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.IndexedLagGraph
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.IndexedParent
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.LaggedEdge
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.LaggedFactor
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.LinearFunction
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.Polynomial
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.PolynomialFunction
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.PolynomialTerm
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.simulation.MeasurementSimulator
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.study.gene.tetradapp.model.BooleanGlassGeneIm
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.study.gene.tetradapp.model.BooleanGlassGenePm
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.study.gene.tetradapp.model.MeasurementSimulatorParams
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.util.DefaultTetradLoggerConfig.DefaultEvent
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.util.DefaultTetradLoggerConfig
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.util.dist.Beta
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.util.dist.ChiSquare
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.util.dist.Discrete
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.util.dist.Exponential
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.util.dist.Gamma
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.util.dist.GaussianPower
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.util.dist.Indicator
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.util.dist.LogNormal
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.util.dist.MixtureOfGaussians
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.util.dist.Normal
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.util.dist.Poisson
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.util.dist.SingleValue
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.util.dist.Split
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.util.dist.TruncatedNormal
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.util.dist.Uniform
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.util.Matrix
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.util.Matrix2
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.util.Parameters
- serializableInstance() - Static method in class edu.cmu.tetrad.util.PartialCorrelationPdf
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.util.PointXy
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.util.TetradLogger.EmptyConfig
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.util.Vector
-
Generates a simple exemplar of this class to test serialization.
- serializableInstance() - Static method in class edu.cmu.tetrad.util.Version
-
Generates a simple exemplar of this class to test serialization.
- serializeCurrentDirectory() - Method in class edu.cmu.tetrad.util.TetradSerializableUtils
-
Finds all classes inside the stated scope that implement TetradSerializable and serializes them out to the getCurrentDirectory() directory.
- serialVersionUID - Static variable in interface edu.cmu.tetrad.algcomparison.graph.RandomGraph
- serialVersionUID - Static variable in interface edu.cmu.tetrad.algcomparison.independence.IndependenceWrapper
- serialVersionUID - Static variable in interface edu.cmu.tetrad.algcomparison.score.ScoreWrapper
- serialVersionUID - Static variable in interface edu.cmu.tetrad.algcomparison.simulation.Simulation
- serialVersionUID - Static variable in interface edu.cmu.tetrad.algcomparison.statistic.Statistic
- serialVersionUID - Static variable in interface edu.cmu.tetrad.bayes.BayesUpdater
- serialVersionUID - Static variable in interface edu.cmu.tetrad.bayes.ManipulatingBayesUpdater
- serialVersionUID - Static variable in interface edu.cmu.tetrad.calculator.expression.Expression
- serialVersionUID - Static variable in interface edu.cmu.tetrad.calculator.expression.ExpressionDescriptor
- serialVersionUID - Static variable in interface edu.cmu.tetrad.calculator.expression.ExpressionSignature
- serialVersionUID - Static variable in interface edu.cmu.tetrad.data.Covariances
- serialVersionUID - Static variable in interface edu.cmu.tetrad.data.DataBox
- serialVersionUID - Static variable in interface edu.cmu.tetrad.data.DataModel
- serialVersionUID - Static variable in interface edu.cmu.tetrad.data.DataSet
- serialVersionUID - Static variable in interface edu.cmu.tetrad.data.KnowledgeBoxInput
- serialVersionUID - Static variable in interface edu.cmu.tetrad.data.KnowledgeTransferable
- serialVersionUID - Static variable in interface edu.cmu.tetrad.data.Simulator
- serialVersionUID - Static variable in interface edu.cmu.tetrad.data.Variable
-
Required serial version UID for serialization.
- serialVersionUID - Static variable in interface edu.cmu.tetrad.data.VariableSource
- serialVersionUID - Static variable in interface edu.cmu.tetrad.graph.Graph
- serialVersionUID - Static variable in interface edu.cmu.tetrad.graph.Node
- serialVersionUID - Static variable in interface edu.cmu.tetrad.sem.ISemIm
- serialVersionUID - Static variable in interface edu.cmu.tetrad.sem.SemOptimizer
- serialVersionUID - Static variable in interface edu.cmu.tetrad.session.Executable
- serialVersionUID - Static variable in interface edu.cmu.tetrad.session.ExecutionRestarter
- serialVersionUID - Static variable in interface edu.cmu.tetrad.session.ParamsResettable
- serialVersionUID - Static variable in interface edu.cmu.tetrad.session.SessionModel
- serialVersionUID - Static variable in interface edu.cmu.tetrad.study.gene.tetrad.gene.history.GraphRandomizer
- serialVersionUID - Static variable in interface edu.cmu.tetrad.study.gene.tetrad.gene.history.Initializer
- serialVersionUID - Static variable in interface edu.cmu.tetrad.study.gene.tetrad.gene.history.RandomDistribution
- serialVersionUID - Static variable in interface edu.cmu.tetrad.study.gene.tetrad.gene.history.UpdateFunction
- serialVersionUID - Static variable in interface edu.cmu.tetrad.util.dist.Distribution
- serialVersionUID - Static variable in interface edu.cmu.tetrad.util.Im
- Session - Class in edu.cmu.tetrad.session
-
Stores a directed graph over models of specific types, where the possible parent relationships between the models are given in the constructors of the model classes themselves.
- Session(String) - Constructor for class edu.cmu.tetrad.session.Session
-
Constructs a new session with the given name.
- SESSION - Static variable in class edu.cmu.tetrad.graph.NodeType
- SessionAdapter - Class in edu.cmu.tetrad.session
-
Basic implementation of SessionListener with empty methods.
- SessionAdapter() - Constructor for class edu.cmu.tetrad.session.SessionAdapter
- SessionEvent - Class in edu.cmu.tetrad.session
-
Notifies a listener that some change has occurred in the session--a node has been added or removed, an edge has been added or removed, a model has been created or destroyed.
- SessionEvent(Object, int) - Constructor for class edu.cmu.tetrad.session.SessionEvent
-
Constructs an event where one session node is involved--session node added or removed, model created or destroyed.
- SessionEvent(Object, SessionEvent) - Constructor for class edu.cmu.tetrad.session.SessionEvent
-
Creates a new SessionEvent with the same information as the given event but with a new source.
- SessionEvent(Object, SessionNode, int) - Constructor for class edu.cmu.tetrad.session.SessionEvent
-
Constructs an event where one session node is involved--session node added or removed, model created or destroyed.
- SessionEvent(Object, SessionNode, SessionNode, int) - Constructor for class edu.cmu.tetrad.session.SessionEvent
-
Constructs an event where two session nodes are involved--parent added or removed.
- SessionListener - Interface in edu.cmu.tetrad.session
-
Listens for SessionEvents on a Session--nodes being added or removed, parents being added or removed, models being created or destroyed.
- SessionModel - Interface in edu.cmu.tetrad.session
-
Interface implemented by all session models in Tetrad.
- SessionNode - Class in edu.cmu.tetrad.session
-
Represents a node in a session for a model in a particular class.
- SessionNode(Class) - Constructor for class edu.cmu.tetrad.session.SessionNode
-
Creates a new session node capable of implementing the given model class.
- SessionNode(Class[]) - Constructor for class edu.cmu.tetrad.session.SessionNode
-
Creates a new session node with the given name capable of implementing the given model classes.
- SessionNode(String, String, Class) - Constructor for class edu.cmu.tetrad.session.SessionNode
-
Creates a new session node with the given name, capable of implementing the given model class.
- SessionNode(String, String, Class[]) - Constructor for class edu.cmu.tetrad.session.SessionNode
-
Creates a new session node with the given name capable of implementing the given model classes.
- SessionSupport - Class in edu.cmu.tetrad.session
-
Handles firing of SessionSupport events to listeners.
- SessionSupport(Object) - Constructor for class edu.cmu.tetrad.session.SessionSupport
-
Constructs a new session support object for the given source object.
- set(int, double) - Method in class edu.cmu.tetrad.util.Vector
- set(int, int, double) - Method in class edu.cmu.tetrad.util.Matrix
- set(int, int, double) - Method in class edu.cmu.tetrad.util.Matrix2
- set(int, int, Number) - Method in class edu.cmu.tetrad.data.ByteDataBox
-
Sets the value at the given row/column to the given Number value.
- set(int, int, Number) - Method in interface edu.cmu.tetrad.data.DataBox
-
Sets the value at the given row and column to the given Number.
- set(int, int, Number) - Method in class edu.cmu.tetrad.data.DoubleDataBox
-
Sets the value at the given row/column to the given Number value.
- set(int, int, Number) - Method in class edu.cmu.tetrad.data.FloatDataBox
-
Sets the value at the given row/column to the given Number value.
- set(int, int, Number) - Method in class edu.cmu.tetrad.data.IntDataBox
-
Sets the value at the given row/column to the given Number value.
- set(int, int, Number) - Method in class edu.cmu.tetrad.data.LongDataBox
-
Sets the value at the given row/column to the given Number value.
- set(int, int, Number) - Method in class edu.cmu.tetrad.data.MixedDataBox
-
Sets the value at the given row/column to the given Number value.
- set(int, int, Number) - Method in class edu.cmu.tetrad.data.ShortDataBox
-
Sets the value at the given row/column to the given Number value.
- set(int, int, Number) - Method in class edu.cmu.tetrad.data.VerticalDoubleDataBox
-
Sets the value at the given row/column to the given Number value.
- set(int, int, Number) - Method in class edu.cmu.tetrad.data.VerticalIntDataBox
-
Sets the value at the given row/column to the given Number value.
- set(Node, Node, Set<Node>) - Method in class edu.cmu.tetrad.search.utils.SepsetMap
-
Sets the sepset for {x, y} to be z.
- set(Node, Node, Set<Node>) - Method in class edu.cmu.tetrad.search.work_in_progress.SepsetMapDci
-
Sets the sepset for {x, y} to be z.
- set(Node, LinkedHashSet<Node>) - Method in class edu.cmu.tetrad.search.utils.SepsetMap
-
Sets the parents of x to the (ordered) set z.
- set(Node, LinkedHashSet<Node>) - Method in class edu.cmu.tetrad.search.work_in_progress.SepsetMapDci
- set(String, Object) - Method in class edu.cmu.tetrad.util.Parameters
-
Sets the given parameter to the given value.
- set(String, Object...) - Method in class edu.cmu.tetrad.util.Parameters
-
Sets the value(s) of the given parameter to a list of strings.
- set(String, String) - Method in class edu.cmu.tetrad.util.Parameters
-
Sets the given parameter to the given value.
- set(String, String...) - Method in class edu.cmu.tetrad.util.Parameters
-
Sets the value(s) of the given parameter to a list of values.
- setAcyclicityGuaranteed(boolean) - Method in class edu.cmu.tetrad.search.IcaLingam
-
Whether the ICA-LiNGAM algorithm is guaranteed to produce an acyclic graph.
- setAddOriginalDataset(boolean) - Method in class edu.pitt.dbmi.algo.resampling.GeneralResamplingSearch
- setAdjacencies(Graph) - Method in class edu.cmu.tetrad.search.SvarFges
-
Sets the set of preset adjacencies for the algorithm; edges not in this adjacencies graph will not be added.
- setAdjacencies(Graph) - Method in class edu.cmu.tetrad.search.utils.FgesOrienter
-
Sets the set of preset adjacenies for the algorithm; edges not in this adjacencies graph will not be added.
- setAdjacencyMethod(Fask.AdjacencyMethod) - Method in class edu.cmu.tetrad.search.Fask
-
Sets the adjacency method used.
- setAlgorithm(Algorithm) - Method in class edu.pitt.dbmi.algo.resampling.GeneralResamplingSearch
- setAlgorithm(ComparisonParameters.Algorithm) - Method in class edu.cmu.tetrad.study.performance.ComparisonParameters
- setAlgorithmType(int) - Method in class edu.cmu.tetrad.search.FastIca
-
If algorithmType == PARALLEL, the components are extracted simultaneously (the default).
- setAllowInternalRandomness(boolean) - Method in class edu.cmu.tetrad.search.Grasp
-
Sets whether to allow internal randomness in the algorithm.
- setAllowRandomnessInsideAlgorithm(boolean) - Method in class edu.cmu.tetrad.search.work_in_progress.GraspTol
- setAllParamSettings(Map<String, String>) - Method in interface edu.cmu.tetrad.session.SimulationParamsSource
- setAllValuesToZero() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.BasicMatrix
-
Assign zero to all elements in the matrix
- setAllValuesToZero() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.LTMatrix
-
Assign zero to all elements in the matrix
- setAllValuesToZero() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.LTMatrixF
-
Assign zero to all elements in the matrix
- setAllValuesToZero() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.Matrix
-
Assign zero to all elements in the matrix
- setAllValuesToZero() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.MatrixF
-
Assign zero to all elements in the matrix
- setAlpha(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.FractionDependentUnderAlternative
- setAlpha(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.FractionDependentUnderNull
- setAlpha(double) - Method in class edu.cmu.tetrad.algcomparison.statistic.MarkovAdequacyScore
- setAlpha(double) - Method in class edu.cmu.tetrad.regression.LogisticRegression
-
Sets the alpha level.
- setAlpha(double) - Method in interface edu.cmu.tetrad.regression.Regression
-
Sets the significance level at which coefficients are judged to be significant.
- setAlpha(double) - Method in class edu.cmu.tetrad.regression.RegressionCovariance
-
Sets the cutoff for significance.
- setAlpha(double) - Method in class edu.cmu.tetrad.regression.RegressionDataset
-
Sets the alpha level for deciding which regressors are significant based on their p values.
- setAlpha(double) - Method in class edu.cmu.tetrad.search.FastIca
-
Sets the FastICA alpha constant in range [1, 2] used in approximation to neg-entropy when 'fun == "logcosh"'
- setAlpha(double) - Method in interface edu.cmu.tetrad.search.IndependenceTest
-
Sets the significance level.
- setAlpha(double) - Method in class edu.cmu.tetrad.search.IndTestIod
-
Sets the alpha level for this test.
- setAlpha(double) - Method in class edu.cmu.tetrad.search.Lofs
-
Sets the alpha to use, where applicable.
- setAlpha(double) - Method in class edu.cmu.tetrad.search.MimbuildTrek
-
The alpha to use.
- setAlpha(double) - Method in class edu.cmu.tetrad.search.PcLingam
-
Sets the alpha level for the search.
- setAlpha(double) - Method in class edu.cmu.tetrad.search.test.ChiSquareTest
-
Sets the significance level to be used for tests.
- setAlpha(double) - Method in class edu.cmu.tetrad.search.test.ConditionalCorrelationIndependence
-
Sets the alpha cutoff.
- setAlpha(double) - Method in class edu.cmu.tetrad.search.test.GSquareTest
-
Sets the significance level to be used for tests.
- setAlpha(double) - Method in class edu.cmu.tetrad.search.test.IndTestChiSquare
-
Sets the significance level at which independence judgments should be made.
- setAlpha(double) - Method in class edu.cmu.tetrad.search.test.IndTestConditionalCorrelation
-
Sets the significance level at which independence judgments should be made.
- setAlpha(double) - Method in class edu.cmu.tetrad.search.test.IndTestConditionalGaussianLrt
-
Sets the significance level.
- setAlpha(double) - Method in class edu.cmu.tetrad.search.test.IndTestDegenerateGaussianLrt
-
Sets the significance level.
- setAlpha(double) - Method in class edu.cmu.tetrad.search.test.IndTestFisherZ
-
Sets the significance level at which independence judgments should be made.
- setAlpha(double) - Method in class edu.cmu.tetrad.search.test.IndTestFisherZConcatenateResiduals
-
Sets the significance level at which independence judgments should be made.
- setAlpha(double) - Method in class edu.cmu.tetrad.search.test.IndTestFisherZFisherPValue
-
Sets the significance level at which independence judgments should be made.
- setAlpha(double) - Method in class edu.cmu.tetrad.search.test.IndTestGSquare
-
Sets the significance level at which independence judgments should be made.
- setAlpha(double) - Method in class edu.cmu.tetrad.search.test.IndTestHsic
-
Sets the significance level at which independence judgments should be made.
- setAlpha(double) - Method in class edu.cmu.tetrad.search.test.IndTestIndependenceFacts
- setAlpha(double) - Method in class edu.cmu.tetrad.search.test.IndTestMulti
- setAlpha(double) - Method in class edu.cmu.tetrad.search.test.IndTestMvpLrt
-
Sets the significance level.
- setAlpha(double) - Method in class edu.cmu.tetrad.search.test.IndTestProbabilistic
- setAlpha(double) - Method in class edu.cmu.tetrad.search.test.IndTestRegression
-
Sets the significance level at which independence judgments should be made.
- setAlpha(double) - Method in class edu.cmu.tetrad.search.test.IndTestTrekSep
-
Sets the significance level at which independence judgments should be made.
- setAlpha(double) - Method in class edu.cmu.tetrad.search.test.Kci
-
Sets the significance level.
- setAlpha(double) - Method in class edu.cmu.tetrad.search.test.MsepTest
- setAlpha(double) - Method in class edu.cmu.tetrad.search.test.ScoreIndTest
-
Sets the significance level.
- setAlpha(double) - Method in interface edu.cmu.tetrad.search.work_in_progress.Hbsms
- setAlpha(double) - Method in class edu.cmu.tetrad.search.work_in_progress.HbsmsBeam
- setAlpha(double) - Method in class edu.cmu.tetrad.search.work_in_progress.HbsmsGes
- setAlpha(double) - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestCramerT
-
Sets the significance level for future tests.
- setAlpha(double) - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestFisherZGeneralizedInverse
-
Sets the significance level at which independence judgments should be made.
- setAlpha(double) - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestFisherZPercentIndependent
-
Sets the significance level at which independence judgments should be made.
- setAlpha(double) - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestFisherZRecursive
-
Sets the significance level at which independence judgments should be made.
- setAlpha(double) - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestMixedMultipleTTest
-
Sets the significance level.
- setAlpha(double) - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestMnlrLr
-
Sets the significance level.
- setAlpha(double) - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestMultinomialLogisticRegression
-
Sets the significance level.
- setAlpha(double) - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestPositiveCorr
-
Sets the significance level at which independence judgments should be made.
- setAlpha(double) - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestSepsetDci
- setAlpha(double) - Method in class edu.cmu.tetrad.search.work_in_progress.Kpc
-
Sets the significance level at which independence judgments should be made.
- setAlpha(double) - Method in class edu.cmu.tetrad.search.work_in_progress.ProbabilisticMapIndependence
- setAlpha(double) - Method in class edu.cmu.tetrad.study.performance.ComparisonParameters
- setAlpha(double) - Method in class edu.pitt.csb.mgm.IndTestMultinomialLogisticRegressionWald
-
Sets the significance level.
- setAlpha1(DoubleMatrix1D) - Method in class edu.pitt.csb.mgm.Mgm.MGMParams
- setAlpha2(DoubleMatrix1D) - Method in class edu.pitt.csb.mgm.Mgm.MGMParams
- setAlphaPC(double) - Method in class edu.cmu.tetrad.search.work_in_progress.DMSearch
- setAlphaSober(double) - Method in class edu.cmu.tetrad.search.work_in_progress.DMSearch
- setAmbiguousTriples(Set<Triple>) - Method in class edu.cmu.tetrad.graph.Dag
- setAmbiguousTriples(Set<Triple>) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
- setAmbiguousTriples(Set<Triple>) - Method in interface edu.cmu.tetrad.graph.Graph
- setAmbiguousTriples(Set<Triple>) - Method in class edu.cmu.tetrad.graph.LagGraph
- setAmbiguousTriples(Set<Triple>) - Method in class edu.cmu.tetrad.graph.SemGraph
- setAmbiguousTriples(Set<Triple>) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- setAmbiguousTriples(Set<Triple>) - Method in class edu.cmu.tetrad.graph.Underlines
- setAntilogCalculated(boolean) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.simulation.MeasurementSimulator
-
Sets whether the antilog of each expression level should be calculated.
- setAntilogCalculated(boolean) - Method in class edu.cmu.tetrad.study.gene.tetradapp.model.MeasurementSimulatorParams
- setApplyR1(boolean) - Method in class edu.cmu.tetrad.search.Ccd
-
Sets whether the R1 rule should be applied.
- setApproximate(boolean) - Method in class edu.cmu.tetrad.search.test.Kci
-
Sets whether the approximate algorithm should be used.
- setAutomaticLogDisplayEnabled(boolean) - Method in class edu.cmu.tetrad.util.TetradLogger
-
States whether log displays should be automatically displayed or not.
- setBasalExpression(double) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.BooleanGlassFunction
-
Sets the basalExpression.
- setBasis(ConditionalCorrelationIndependence.Basis) - Method in class edu.cmu.tetrad.search.test.ConditionalCorrelationIndependence
-
Sets the basis.
- setBasis(ConditionalCorrelationIndependence.Basis) - Method in class edu.cmu.tetrad.search.test.IndTestConditionalCorrelation
-
Sets the basis used for the calculation.
- setBeamWidth(int) - Method in interface edu.cmu.tetrad.search.work_in_progress.Hbsms
- setBeamWidth(int) - Method in class edu.cmu.tetrad.search.work_in_progress.HbsmsBeam
- setBeamWidth(int) - Method in class edu.cmu.tetrad.search.work_in_progress.HbsmsGes
- setBeta(DoubleMatrix2D) - Method in class edu.pitt.csb.mgm.Mgm.MGMParams
- setBetad(DoubleMatrix1D) - Method in class edu.pitt.csb.mgm.Mgm.MGMParams
- setBetaHigh(double) - Method in class edu.cmu.tetrad.algcomparison.simulation.LinearSineSimulation
- setBetaLow(double) - Method in class edu.cmu.tetrad.algcomparison.simulation.LinearSineSimulation
- setBollenTest(DeltaTetradTest) - Method in class edu.cmu.tetrad.search.utils.TetradTestContinuous
- setBooleanInfluenceRate(double) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.BooleanGlassFunction
-
Sets the rate at which the output of the Glass function influences the change in expression level of a gene.
- setBossUseBes(boolean) - Method in class edu.cmu.tetrad.search.BFci
- setBoundGraph(Graph) - Method in class edu.cmu.tetrad.search.Fges
-
If non-null, edges not adjacent in this graph will not be added.
- setBoundGraph(Graph) - Method in class edu.cmu.tetrad.search.FgesMb
-
If non-null, edges not adjacent in this graph will not be added.
- setBoundsEnforced(boolean) - Method in class edu.cmu.tetrad.bayes.DirichletDataSetProbs
-
True iff bounds checking is performed on variable values indices.
- setBoxType(String) - Method in class edu.cmu.tetrad.session.SessionNode
-
Sets the (optional) name for this node.
- setBThreshold(double) - Method in class edu.cmu.tetrad.search.IcaLingam
-
The threshold to use for set small elements to zero in the B Hat matrices.
- setBThreshold(double) - Method in class edu.cmu.tetrad.search.IcaLingD
-
The threshold to use for set small elements to zero in the B Hat matrices.
- setC(int) - Method in class edu.cmu.tetrad.search.utils.ShiftSearch
- setCanceled(boolean) - Method in class edu.cmu.tetrad.util.TaskManager
- setCategories(Node, List<String>) - Method in class edu.cmu.tetrad.bayes.BayesPm
-
Sets the number of values for the given node to the given number.
- setCategory(int, int) - Method in class edu.cmu.tetrad.bayes.Proposition
-
Sets the given value to true and all other values to false for the given variable.
- setCategoryNamesDisplayed(boolean) - Method in class edu.cmu.tetrad.data.DiscreteVariable
-
Sets whether categories for this variable should be displayed.
- setCellProbability(int[], double) - Method in class edu.cmu.tetrad.bayes.StoredCellProbsObs
- setCenter(int, int) - Method in class edu.cmu.tetrad.data.ContinuousVariable
-
Sets the (x, y) coordinates of the center of this node.
- setCenter(int, int) - Method in class edu.cmu.tetrad.data.DiscreteVariable
-
Sets the (x, y) coordinates of the center of this node.
- setCenter(int, int) - Method in class edu.cmu.tetrad.graph.GraphNode
-
Sets the (x, y) coordinates of the center of this node.
- setCenter(int, int) - Method in interface edu.cmu.tetrad.graph.Node
-
Sets the (x, y) coordinates of the center of this node.
- setCenter(int, int) - Method in class edu.cmu.tetrad.session.SessionNode
- setCenteringComp(JComponent) - Static method in class edu.cmu.tetrad.util.JOptionUtils
-
Sets the centering component used throughout.
- setCenterX(int) - Method in class edu.cmu.tetrad.data.ContinuousVariable
-
Sets the x coordinate of the center of this node.
- setCenterX(int) - Method in class edu.cmu.tetrad.data.DiscreteVariable
-
Sets the x coordinate of the center of this node.
- setCenterX(int) - Method in class edu.cmu.tetrad.graph.GraphNode
-
Sets the x coordinate of the center of this node.
- setCenterX(int) - Method in interface edu.cmu.tetrad.graph.Node
-
Sets the x coordinate of the center of this node.
- setCenterX(int) - Method in class edu.cmu.tetrad.session.SessionNode
- setCenterY(int) - Method in class edu.cmu.tetrad.data.ContinuousVariable
-
Sets the y coordinate of the center of this node.
- setCenterY(int) - Method in class edu.cmu.tetrad.data.DiscreteVariable
-
Sets the y coordinate of the center of this node.
- setCenterY(int) - Method in class edu.cmu.tetrad.graph.GraphNode
-
Sets the y coordinate of the center of this node.
- setCenterY(int) - Method in interface edu.cmu.tetrad.graph.Node
-
Sets the y coordinate of the center of this node.
- setCenterY(int) - Method in class edu.cmu.tetrad.session.SessionNode
- setChangeFlag(boolean) - Method in class edu.cmu.tetrad.search.utils.FciOrient
-
Sets the change flag--marks externally that a change has been made.
- setCheckType(ClusterSignificance.CheckType) - Method in class edu.cmu.tetrad.search.Bpc
-
Sets the cluster significance type.
- setCheckType(ClusterSignificance.CheckType) - Method in class edu.cmu.tetrad.search.Fofc
-
Sets which type of cluster check should be performed.
- setCheckType(ClusterSignificance.CheckType) - Method in class edu.cmu.tetrad.search.utils.ClusterSignificance
- setChipChipVariability(double) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.simulation.MeasurementSimulator
-
Sets the chip to chip variability.
- setChipChipVariability(double) - Method in class edu.cmu.tetrad.study.gene.tetradapp.model.MeasurementSimulatorParams
- setClusterName(int, String) - Method in class edu.cmu.tetrad.data.Clusters
- setCoefficient(double) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.PolynomialTerm
-
Sets the coefficient.
- setCoefficient(int, int, double) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.LinearFunction
-
Sets the coefficient for the given parent of the given factor.
- setCoefficient(String, LaggedFactor, double) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.LinearFunction
-
Sets the intercept for the given factor.
- setCoefHigh(double) - Method in class edu.cmu.tetrad.algcomparison.simulation.ConditionalGaussianSimulation
- setCoefLow(double) - Method in class edu.cmu.tetrad.algcomparison.simulation.ConditionalGaussianSimulation
- setCoefRange(double, double) - Method in class edu.cmu.tetrad.sem.LargeScaleSimulation
- setCoefSymmetric(boolean) - Method in class edu.cmu.tetrad.algcomparison.simulation.ConditionalGaussianSimulation
- setColliderDiscovery(PcCommon.ColliderDiscovery) - Method in class edu.cmu.tetrad.search.utils.PcCommon
-
Sets the type of collider discovery to do.
- setColumnSpacing(int) - Method in class edu.cmu.tetrad.util.TextTable
-
Sets the number of spaces between columns, to some number >= 0.
- setCompareToTrue(boolean) - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FgesConcatenated
- setCompareToTrue(boolean) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.GesMe
- setCompareToType(CompareTwoGraphs.CompareToType) - Method in class edu.cmu.tetrad.algcomparison.comparegraphs.CompareTwoGraphs
- setComparisonGraph(Comparison.ComparisonGraph) - Method in class edu.cmu.tetrad.algcomparison.Comparison
-
The type of graph the results are compared to.
- setComparisonGraph(TimeoutComparison.ComparisonGraph) - Method in class edu.cmu.tetrad.algcomparison.TimeoutComparison
-
The type of graph the results are compared to.
- setComparisontype(CompareTwoGraphs.ComparisonType) - Method in class edu.cmu.tetrad.algcomparison.comparegraphs.CompareTwoGraphs
- setCompleteRuleSetUsed(boolean) - Method in class edu.cmu.tetrad.search.BFci
-
Sets whether the complete (Zhang's) rule set should be used.
- setCompleteRuleSetUsed(boolean) - Method in class edu.cmu.tetrad.search.Cfci
-
Sets whether the complete rule set should be used.
- setCompleteRuleSetUsed(boolean) - Method in class edu.cmu.tetrad.search.Fci
-
Sets whether the Zhang complete rule set should be used; false if only R1-R4 (the rule set of the original FCI) should be used.
- setCompleteRuleSetUsed(boolean) - Method in class edu.cmu.tetrad.search.FciMax
-
Sets whether Zhang's complete rule set is used in the search.
- setCompleteRuleSetUsed(boolean) - Method in class edu.cmu.tetrad.search.GFci
-
Sets whether Zhang's complete rules are used.
- setCompleteRuleSetUsed(boolean) - Method in class edu.cmu.tetrad.search.GraspFci
-
Sets whether Zhang's complete rules set is used.
- setCompleteRuleSetUsed(boolean) - Method in class edu.cmu.tetrad.search.SpFci
-
Sets whether Zhang's complete rule set is used.
- setCompleteRuleSetUsed(boolean) - Method in class edu.cmu.tetrad.search.SvarFci
-
Sets whether Zhang's complete rule set is to be used.
- setCompleteRuleSetUsed(boolean) - Method in class edu.cmu.tetrad.search.SvarGfci
-
Sets whether the complete rule set is used.
- setCompleteRuleSetUsed(boolean) - Method in class edu.cmu.tetrad.search.utils.DagToPag
- setCompleteRuleSetUsed(boolean) - Method in class edu.cmu.tetrad.search.utils.FciOrient
- setCompleteRuleSetUsed(boolean) - Method in class edu.cmu.tetrad.search.utils.SvarFciOrient
- setCompleteRuleSetUsed(boolean) - Method in class edu.cmu.tetrad.search.utils.TsDagToPag
- setConfigForClass(Class) - Method in class edu.cmu.tetrad.util.TetradLogger
-
If there is a pre-defined configuration for the given model it is set, otherwise an exception is thrown.
- setConflictRule(PcCommon.ConflictRule) - Method in class edu.cmu.tetrad.search.Cpc
-
Sets which conflict rule to use for resolving collider orientation conflicts.
- setConflictRule(PcCommon.ConflictRule) - Method in class edu.cmu.tetrad.search.Pc
-
Sets which conflict-rule to use for resolving collider orientation conflicts.
- setConflictRule(PcCommon.ConflictRule) - Method in class edu.cmu.tetrad.search.utils.MaxP
-
Sets the PC conflict rule to use for orientation.
- setConflictRule(PcCommon.ConflictRule) - Method in class edu.cmu.tetrad.search.utils.PcCommon
-
Sets the conflict rule to use.
- setCopyData(boolean) - Method in class edu.cmu.tetrad.algcomparison.TimeoutComparison
- setCorrectResult(Graph) - Method in class edu.cmu.tetrad.study.performance.ComparisonResult
- setCovariance(int, int, double) - Method in interface edu.cmu.tetrad.data.Covariances
-
Sets the covariance at (i, j) to a particular value.
- setCovMatrix(ICovarianceMatrix) - Method in class edu.cmu.tetrad.search.utils.TetradTestContinuous
- setCovMatrix(ICovarianceMatrix) - Method in class edu.cmu.tetrad.sem.SemIm
-
Sets the sample covariance matrix for this Sem as a submatrix of the given matrix.
- setCpdag(boolean) - Method in class edu.cmu.tetrad.search.Dagma
- setCpdagAlgorithm(Cstar.CpdagAlgorithm) - Method in class edu.cmu.tetrad.search.Cstar
-
The CSTaR algorithm can use any CPDAG algorithm; here you can set it.
- setCutoff(double) - Method in class edu.cmu.tetrad.search.test.IndTestProbabilistic
- setCutoff(double) - Method in class edu.pitt.dbmi.algo.bayesian.constraint.search.PagSamplingRfci
- setCutoffConstrainSearch(double) - Method in class edu.pitt.dbmi.algo.bayesian.constraint.search.RfciBsc
- setCutoffDataSearch(double) - Method in class edu.pitt.dbmi.algo.bayesian.constraint.search.RfciBsc
- setData(DataSet) - Method in class edu.cmu.tetrad.search.work_in_progress.DMSearch
- setData(DataSet) - Method in class edu.pitt.dbmi.algo.resampling.GeneralResamplingSearch
- setDataFile(String) - Method in class edu.cmu.tetrad.study.performance.ComparisonParameters
- setDataFromFile(boolean) - Method in class edu.cmu.tetrad.study.performance.ComparisonParameters
- setDataSet(DataSet) - Method in class edu.cmu.tetrad.sem.SemIm
-
Calculates the covariance matrix of the given DataSet and sets the sample covariance matrix for this model to a subset of it.
- setDataType(ComparisonParameters.DataType) - Method in class edu.cmu.tetrad.study.performance.ComparisonParameters
- setDecayRate(double) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.BooleanGlassFunction
-
Sets the rate at which expression levels tend to return to equilibrium.
- setDefaultBw(DataSet, Node) - Method in interface edu.cmu.tetrad.search.utils.Kernel
-
Sets bandwidth from data using default method
- setDefaultBw(DataSet, Node) - Method in class edu.cmu.tetrad.search.utils.KernelGaussian
-
Default setting of bandwidth based on median distance heuristic
- setDefaultToKnowledgeLayout(boolean) - Method in class edu.cmu.tetrad.data.Knowledge
- setDefaultValue(Serializable) - Method in class edu.cmu.tetrad.util.ParamDescription
- setDelimiter(char) - Method in class edu.cmu.tetrad.simulation.HsimAutoC
- setDelimiter(char) - Method in class edu.cmu.tetrad.simulation.HsimAutoRun
- setDelimiter(char) - Method in class edu.cmu.tetrad.simulation.HsimRepeatAC
- setDelimiter(char) - Method in class edu.cmu.tetrad.simulation.HsimRepeatAutoRun
- setDelimiter(DelimiterType) - Method in interface edu.cmu.tetrad.data.IDataReader
-
The delimiter between entries in a line, one of DelimiterType.WHITESPACE, DelimiterType.TAB, DelimiterType.COMMA, DelimiterType.COLON
- setDelimiter(TextTable.Delimiter) - Method in class edu.cmu.tetrad.util.TextTable
- setDelta(double) - Method in class edu.cmu.tetrad.search.Fask
-
Sets the delta to use.
- setDepth(int) - Method in class edu.cmu.tetrad.search.BFci
- setDepth(int) - Method in class edu.cmu.tetrad.search.Cfci
-
Sets the depth--i.e., the maximum number of variables conditioned on in any test.
- setDepth(int) - Method in class edu.cmu.tetrad.search.Cpc
-
Sets the maximum number of variables conditioned on in any conditional independence test.
- setDepth(int) - Method in class edu.cmu.tetrad.search.Fas
-
Sets the depth of the search, which is the maximum number of variables that ben be conditioned on in any conditional independence test.
- setDepth(int) - Method in class edu.cmu.tetrad.search.Fasd
-
Sets the maximum number of variables conditioned on in any test.
- setDepth(int) - Method in class edu.cmu.tetrad.search.Fask
- setDepth(int) - Method in class edu.cmu.tetrad.search.Fci
-
Sets the depth of search, which is the maximum number of variables conditioned on in any test.
- setDepth(int) - Method in class edu.cmu.tetrad.search.FciMax
-
Sets the maximum nubmer of variables conditioned in any test.
- setDepth(int) - Method in class edu.cmu.tetrad.search.GFci
-
Sets the depth of the search for the possible m-sep search.
- setDepth(int) - Method in class edu.cmu.tetrad.search.Grasp
-
Sets the maximum depth of the depth-first search that GRaSP performs while searching for a weakly increasing tuck sequence that improves the score.
- setDepth(int) - Method in class edu.cmu.tetrad.search.GraspFci
- setDepth(int) - Method in interface edu.cmu.tetrad.search.IFas
-
Sets the depth of the search--that is, the maximum number of variables conditioned on in the search.
- setDepth(int) - Method in class edu.cmu.tetrad.search.Pc
-
Sets the depth of the search--that is, the maximum number of conditioning nodes for any conditional independence checked.
- setDepth(int) - Method in class edu.cmu.tetrad.search.Pcd
-
Sets the depth of the search--that is, the maximum number of conditioning nodes for any conditional independence checked.
- setDepth(int) - Method in class edu.cmu.tetrad.search.PcMb
-
Sets the maximum number of conditioning variables for any conditional independence test.
- setDepth(int) - Method in class edu.cmu.tetrad.search.Rfci
-
Sets the maximum number of variables conditioned on in any test.
- setDepth(int) - Method in class edu.cmu.tetrad.search.SpFci
-
Sets the maximum number of variables conditioned on.
- setDepth(int) - Method in class edu.cmu.tetrad.search.SvarFas
-
Sets the depth--i.e., the maximum number of variables conditioned on in any test, -1 for unlimited.
- setDepth(int) - Method in class edu.cmu.tetrad.search.SvarFci
-
Sets the depth of search.
- setDepth(int) - Method in class edu.cmu.tetrad.search.utils.Bes
-
Sets the depth for the search, which is the maximum number of variables conditioned on.
- setDepth(int) - Method in class edu.cmu.tetrad.search.utils.FgesOrienter
-
-1 for unlimited depth, otherwise a number >= 0.
- setDepth(int) - Method in class edu.cmu.tetrad.search.utils.MaxP
- setDepth(int) - Method in class edu.cmu.tetrad.search.utils.PcCommon
-
Sets the maximum number of variables conditioned on in any conditional independence test.
- setDepth(int) - Method in class edu.cmu.tetrad.search.utils.PossibleMsepFci
- setDepth(int) - Method in class edu.cmu.tetrad.search.utils.SepsetsGreedy
- setDepth(int) - Method in class edu.cmu.tetrad.search.work_in_progress.Dci
- setDepth(int) - Method in class edu.cmu.tetrad.search.work_in_progress.Fas2
- setDepth(int) - Method in class edu.cmu.tetrad.search.work_in_progress.Fas3
-
Sets the depth of the search, which is the maximum number of variables that ben be conditioned on in any conditional independence test.
- setDepth(int) - Method in class edu.cmu.tetrad.search.work_in_progress.FasDci
- setDepth(int) - Method in class edu.cmu.tetrad.search.work_in_progress.FasFdr
-
Sets the depth of the search--i.e., the maximum number of variables conditioned on for any conditional independence test.
- setDepth(int) - Method in class edu.cmu.tetrad.search.work_in_progress.FasLofs
- setDepth(int) - Method in class edu.cmu.tetrad.search.work_in_progress.GraspTol
- setDepth(int) - Method in class edu.cmu.tetrad.search.work_in_progress.Kpc
-
Sets the depth of the search--that is, the maximum number of conditioning nodes for any conditional independence checked.
- setDepth(int) - Method in class edu.cmu.tetrad.search.work_in_progress.Mmhc
- setDepth(int) - Method in class edu.cmu.tetrad.search.work_in_progress.OtherPermAlgs
- setDepth(int) - Method in class edu.cmu.tetrad.search.work_in_progress.SampleVcpc
-
Sets the maximum number of variables conditioned on in any conditional independence test.
- setDepth(int) - Method in class edu.cmu.tetrad.search.work_in_progress.SampleVcpcFast
-
Sets the maximum number of variables conditioned on in any conditional independence test.
- setDepth(int) - Method in class edu.cmu.tetrad.search.work_in_progress.VcFas
- setDepth(int) - Method in class edu.cmu.tetrad.search.work_in_progress.VcPc
-
Sets the maximum number of variables conditioned on in any conditional independence test.
- setDepth(int) - Method in class edu.cmu.tetrad.search.work_in_progress.VcPcAlt
-
Sets the maximum number of variables conditioned on in any conditional independence test.
- setDepth(int) - Method in class edu.cmu.tetrad.search.work_in_progress.VcPcFast
-
Sets the maximum number of variables conditioned on in any conditional independence test.
- setDepth(int) - Method in class edu.pitt.dbmi.algo.bayesian.constraint.search.PagSamplingRfci
- setDeterminationP(double) - Method in class edu.cmu.tetrad.search.test.IndTestGSquare
-
Sets the threshold for making judgments of detemrination.
- setDeterminismThreshold(double) - Method in class edu.cmu.tetrad.search.work_in_progress.SemBicScoreDeterministic
- setDiscount(double) - Method in class edu.cmu.tetrad.search.work_in_progress.DMSearch
- setDiscreteScore(DiscreteScore) - Method in class edu.cmu.tetrad.search.utils.FgesOrienter
-
Sets the discrete scoring function to use.
- setDiscretize(boolean) - Method in class edu.cmu.tetrad.search.score.ConditionalGaussianLikelihood
-
Sets whether to discretize child variables to avoid integration.
- setDishBumpStDev(double) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.DishModel
- setDishDishVariability(double) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.simulation.MeasurementSimulator
-
Sets the standard deviation sd% (in percent) of the distribution N(100.0, sd%), from which errors will be drawn for the dish model.
- setDishDishVariability(double) - Method in class edu.cmu.tetrad.study.gene.tetradapp.model.MeasurementSimulatorParams
- setDishModel(DishModel) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.GeneHistory
-
Sets the dish model.
- setDishNumber(int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.DishModel
-
Sets the number of the getModel dish.
- setDisplayLogEnabled(boolean) - Method in class edu.cmu.tetrad.util.TetradLogger
-
Sets whether the display log should be used or not.
- setDisplayName(String) - Method in class edu.cmu.tetrad.session.SessionNode
- setDistribution(Distribution) - Method in class edu.cmu.tetrad.sem.Parameter
-
Sets the distribution that initial values should be drawn from for this parameter.
- setDmStructure(DMSearch.LatentStructure) - Method in class edu.cmu.tetrad.search.work_in_progress.DMSearch
- setDoAdjacencySearch(boolean) - Method in class edu.cmu.tetrad.search.work_in_progress.Ion
-
Sets adjacency search on or off
- setDoDiscriminatingPathColliderRule(boolean) - Method in class edu.cmu.tetrad.search.utils.FciOrient
-
Sets whether the discriminating path collider rule should be done.
- setDoDiscriminatingPathRule(boolean) - Method in class edu.cmu.tetrad.search.BFci
- setDoDiscriminatingPathRule(boolean) - Method in class edu.cmu.tetrad.search.Cfci
- setDoDiscriminatingPathRule(boolean) - Method in class edu.cmu.tetrad.search.Fci
-
Sets whether the discriminating path rule should be used.
- setDoDiscriminatingPathRule(boolean) - Method in class edu.cmu.tetrad.search.FciMax
-
Sets whether the discriminating path rule will be used in search.
- setDoDiscriminatingPathRule(boolean) - Method in class edu.cmu.tetrad.search.GFci
-
Sets whether the discriminating path rule should be used.
- setDoDiscriminatingPathRule(boolean) - Method in class edu.cmu.tetrad.search.GraspFci
- setDoDiscriminatingPathRule(boolean) - Method in class edu.cmu.tetrad.search.SpFci
-
Sets whether the discriminating path search is done.
- setDoDiscriminatingPathRule(boolean) - Method in class edu.cmu.tetrad.search.utils.DagToPag
- setDoDiscriminatingPathRule(boolean) - Method in class edu.cmu.tetrad.search.utils.TsDagToPag
- setDoDiscriminatingPathTailRule(boolean) - Method in class edu.cmu.tetrad.search.utils.FciOrient
-
Sets whether the discriminating path tail rule should be done.
- setDoPathLengthSearch(boolean) - Method in class edu.cmu.tetrad.search.work_in_progress.Ion
-
Sets path length search on or off.
- setDottedUnderLineTriples(Set<Triple>) - Method in class edu.cmu.tetrad.graph.Dag
- setDottedUnderLineTriples(Set<Triple>) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
- setDottedUnderLineTriples(Set<Triple>) - Method in interface edu.cmu.tetrad.graph.Graph
- setDottedUnderLineTriples(Set<Triple>) - Method in class edu.cmu.tetrad.graph.LagGraph
- setDottedUnderLineTriples(Set<Triple>) - Method in class edu.cmu.tetrad.graph.SemGraph
- setDottedUnderLineTriples(Set<Triple>) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- setDottedUnderLineTriples(Set<Triple>) - Method in class edu.cmu.tetrad.graph.Underlines
- setDouble(int, int, double) - Method in class edu.cmu.tetrad.data.BoxDataSet
-
Sets the value at the given (row, column) to the given double value, assuming the variable for the column is continuous.
- setDouble(int, int, double) - Method in interface edu.cmu.tetrad.data.DataSet
-
Sets the value at the given (row, column) to the given double value, assuming the variable for the column is continuous.
- setDouble(int, int, double) - Method in class edu.cmu.tetrad.data.NumberObjectDataSet
-
Sets the value at the given (row, column) to the given double value, assuming the variable for the column is continuous.
- setDoubleValue(int, int, double) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.BasicMatrix
-
Assigns double value x in matrix element (r, c).
- setDoubleValue(int, int, double) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.LTMatrix
-
Casts double x to short and assigns it to element (r,c) This method checks that x can be converted to a short without causing overflow.
- setDoubleValue(int, int, double) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.LTMatrixF
-
Casts double value x to float and assigns it to element (r,c) This method checks that x can be converted to a float without causing overflow.
- setDoubleValue(int, int, double) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.Matrix
-
Casts double value x to short and assigns it to element (r,c)
- setDoubleValue(int, int, double) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.MatrixF
-
Casts double value x to float and assigns it to element (r,c)
- setEdge(int, int, double) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.biolingua.Digraph
-
Sets a value of edge between nodes i and j
- setEdge(int, int, double) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.BasicGraph
-
Sets a value of edge between nodes i and j
- setEdgeChangeTol(int) - Method in class edu.pitt.csb.mgm.ProximalGradient
-
Positive edge change tolerance is the number of iterations with 0 edge changes needed to converge.
- setEdgeCoef(Node, Node, double) - Method in interface edu.cmu.tetrad.sem.ISemIm
- setEdgeCoef(Node, Node, double) - Method in class edu.cmu.tetrad.sem.SemIm
- setEdgeCoefficient(Node, Node, double) - Method in class edu.cmu.tetrad.sem.StandardizedSemIm
-
Sets the coefficient for the a->b edge to the given coefficient, if within range.
- setEdgeType(EdgeTypeProbability.EdgeType) - Method in class edu.cmu.tetrad.graph.EdgeTypeProbability
- setEffects(LinkedList<Double>) - Method in class edu.cmu.tetrad.search.Ida.NodeEffects
- setElapsed(long) - Method in class edu.cmu.tetrad.study.performance.ComparisonResult
- setEmpirical(boolean) - Method in class edu.cmu.tetrad.search.Fask
-
Sets whether the empirical option is selected.
- setEndpoint(Node, Node, Endpoint) - Method in class edu.cmu.tetrad.graph.Dag
- setEndpoint(Node, Node, Endpoint) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
-
If there is currently an edge from node1 to node2, sets the endpoint at node2 to the given endpoint; if there is no such edge, adds an edge --# where # is the given endpoint.
- setEndpoint(Node, Node, Endpoint) - Method in interface edu.cmu.tetrad.graph.Graph
-
Sets the endpoint type at the 'to' end of the edge from 'from' to 'to' to the given endpoint.
- setEndpoint(Node, Node, Endpoint) - Method in class edu.cmu.tetrad.graph.LagGraph
- setEndpoint(Node, Node, Endpoint) - Method in class edu.cmu.tetrad.graph.SemGraph
- setEndpoint(Node, Node, Endpoint) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- setEndpoint1(Endpoint) - Method in class edu.cmu.tetrad.graph.Edge
- setEndpoint2(Endpoint) - Method in class edu.cmu.tetrad.graph.Edge
- setEpsilon(double) - Method in class edu.cmu.tetrad.search.Lofs
- setEpsilon(double) - Method in class edu.cmu.tetrad.search.MimbuildTrek
-
Sets the parameter convergence threshold.
- setEpsilon(double) - Method in class edu.cmu.tetrad.search.test.Kci
-
Sets the epsilon.
- setErrCovar(Node, double) - Method in class edu.cmu.tetrad.sem.SemIm
- setErrCovar(Node, Node, double) - Method in class edu.cmu.tetrad.sem.SemIm
- setErrorCovariance(Node, Node, double) - Method in class edu.cmu.tetrad.sem.StandardizedSemIm
-
Sets the covariance for the a<->b edge to the given covariance, if within range.
- setErrorDistribution(int, Distribution) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.BooleanGlassFunction
-
Method setIntenalNoiseModel
- setErrorDistribution(int, Distribution) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.LinearFunction
-
Method setIntenalNoiseModel
- setErrorDistribution(int, Distribution) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.PolynomialFunction
-
Method setIntenalNoiseModel
- setErrorDistribution(int, Distribution) - Method in class edu.cmu.tetrad.study.gene.tetradapp.model.BooleanGlassGeneIm
-
Sets the error distribution for the given factor to the given distribution.
- setErrorsNormal(boolean) - Method in class edu.cmu.tetrad.sem.LargeScaleSimulation
- setErrorsTemplate(String) - Method in class edu.cmu.tetrad.sem.GeneralizedSemPm
- setErrVar(Node, double) - Method in interface edu.cmu.tetrad.sem.ISemIm
- setErrVar(Node, double) - Method in class edu.cmu.tetrad.sem.SemIm
- setEstimated(boolean) - Method in class edu.cmu.tetrad.sem.SemIm
- setEstimator(EmBayesProperties.Estimator) - Method in class edu.cmu.tetrad.bayes.EmBayesProperties
- setEventActive(String, boolean) - Method in class edu.cmu.tetrad.util.DefaultTetradLoggerConfig
- setEventActive(String, boolean) - Method in class edu.cmu.tetrad.util.TetradLogger.EmptyConfig
- setEventActive(String, boolean) - Method in interface edu.cmu.tetrad.util.TetradLoggerConfig
-
Sets whether the event associated with the given id is active or not.
- setEventsToLog(String...) - Method in class edu.cmu.tetrad.util.TetradLogger
-
This can be used to tell the logger which events to log without having to first define a
TetradLoggerConfig. - setEvidence(int, int) - Method in class edu.cmu.tetrad.bayes.JunctionTreeAlgorithm
- setEvidence(Evidence) - Method in class edu.cmu.tetrad.bayes.ApproximateUpdater
-
Sets new evidence for the next update operation.
- setEvidence(Evidence) - Method in interface edu.cmu.tetrad.bayes.BayesUpdater
-
Sets new evidence for the updater.
- setEvidence(Evidence) - Method in class edu.cmu.tetrad.bayes.CptInvariantUpdater
- setEvidence(Evidence) - Method in class edu.cmu.tetrad.bayes.Identifiability
- setEvidence(Evidence) - Method in class edu.cmu.tetrad.bayes.JunctionTreeUpdater
- setEvidence(Evidence) - Method in interface edu.cmu.tetrad.bayes.ManipulatingBayesUpdater
-
Sets new evidence for the updater.
- setEvidence(Evidence) - Method in class edu.cmu.tetrad.bayes.RowSummingExactUpdater
- setEvidence(SemEvidence) - Method in class edu.cmu.tetrad.sem.SemUpdater
-
Sets new evidence for the updater.
- setExternalGraph(Algorithm) - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.Fask
- setExternalGraph(Algorithm) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Fges
- setExternalGraph(Algorithm) - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.Eb
- setExternalGraph(Algorithm) - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.FaskPw
- setExternalGraph(Algorithm) - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.R1
- setExternalGraph(Algorithm) - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.R2
- setExternalGraph(Algorithm) - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.R3
- setExternalGraph(Algorithm) - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.Rskew
- setExternalGraph(Algorithm) - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.RskewE
- setExternalGraph(Algorithm) - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.Skew
- setExternalGraph(Algorithm) - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.SkewE
- setExternalGraph(Algorithm) - Method in class edu.cmu.tetrad.algcomparison.algorithm.pairwise.Tanh
- setExternalGraph(Algorithm) - Method in interface edu.cmu.tetrad.algcomparison.utils.TakesExternalGraph
- setExternalGraph(Graph) - Method in class edu.cmu.tetrad.search.Fasd
-
Sets the external graph.
- setExternalGraph(Graph) - Method in class edu.cmu.tetrad.search.Fask
-
Sets the external graph to use.
- setExternalGraph(Graph) - Method in class edu.cmu.tetrad.search.SvarFas
-
Sets an external graph.
- setExternalGraph(Graph) - Method in class edu.cmu.tetrad.search.SvarFges
-
Sets the initial graph.
- setExternalGraph(Graph) - Method in class edu.cmu.tetrad.search.utils.FgesOrienter
-
Sets the initial graph.
- setExternalGraph(Graph) - Method in class edu.cmu.tetrad.search.work_in_progress.VcFas
- setExternalGraph(Graph) - Method in class edu.pitt.dbmi.algo.resampling.GeneralResamplingSearch
- setExternalGraph(Graph) - Method in class edu.pitt.dbmi.algo.resampling.GeneralResamplingTest
-
Sets the initial graph.
- setExternalGraph(Graph) - Method in class edu.pitt.dbmi.algo.resampling.task.GeneralResamplingSearchRunnable
- setFactor(double) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.AbstractNbComponent
-
Sets the factor.
- setFactor(String) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.LaggedFactor
-
Sets the name of the lagged factor
- setFacts() - Method in class edu.cmu.tetrad.search.work_in_progress.SampleVcpc
- setFacts(IndependenceFacts) - Method in class edu.cmu.tetrad.search.work_in_progress.VcPc
- setFacts(IndependenceFacts) - Method in class edu.cmu.tetrad.search.work_in_progress.VcPcFast
- setFaithfulnessAssumed(boolean) - Method in class edu.cmu.tetrad.search.Fges
-
Sets whether one-edge faithfulness should be assumed.
- setFaithfulnessAssumed(boolean) - Method in class edu.cmu.tetrad.search.FgesMb
-
Sets whether one-edge faithfulness should be assumed.
- setFaithfulnessAssumed(boolean) - Method in class edu.cmu.tetrad.search.GFci
-
Sets whether one-edge faithfulness is assumed.
- setFaithfulnessAssumed(boolean) - Method in class edu.cmu.tetrad.search.SvarFges
-
Set to true if it is assumed that all path pairs with one length 1 path do not cancel.
- setFaithfulnessAssumed(boolean) - Method in class edu.cmu.tetrad.search.utils.FgesOrienter
-
Set to true if it is assumed that all path pairs with one length 1 path do not cancelAll.
- setFasType(PcCommon.FasType) - Method in class edu.cmu.tetrad.search.utils.PcCommon
- setFdr(boolean) - Method in class edu.cmu.tetrad.search.Pcd
- setFdr(boolean) - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestFisherZPercentIndependent
- setFileLoggingEnabled(boolean) - Method in class edu.cmu.tetrad.util.TetradLogger
-
Sets whether "file logging" is enabled or not, that is whether calls to
setNextOutputStreamwill be respected. - setFilename(String) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.StoredLagGraphParams
-
Sets the stored file.
- setFilenameOut(String) - Method in class edu.cmu.tetrad.simulation.HsimAutoC
- setFilenameOut(String) - Method in class edu.cmu.tetrad.simulation.HsimAutoRun
- setFilenameOut(String) - Method in class edu.cmu.tetrad.simulation.HsimRepeatAC
- setFilenameOut(String) - Method in class edu.cmu.tetrad.simulation.HsimRepeatAutoRun
- setFindMb(boolean) - Method in class edu.cmu.tetrad.search.PcMb
- setFirstStepStored(int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.simulation.MeasurementSimulator
-
Sets the index of the first step to actually be stored out.
- setFirstStepStored(int) - Method in class edu.cmu.tetrad.study.gene.tetradapp.model.MeasurementSimulatorParams
- setFixed(boolean) - Method in class edu.cmu.tetrad.sem.Parameter
-
Sets whether this parameter should be held fixed during estimation.
- setFixedParamValue(Parameter, double) - Method in interface edu.cmu.tetrad.sem.ISemIm
- setFixedParamValue(Parameter, double) - Method in class edu.cmu.tetrad.sem.SemIm
-
Sets the value of a single free parameter to the given value.
- setFlatPrior(boolean) - Method in class edu.cmu.tetrad.sem.SemEstimatorGibbsParams
- setForbidden(String, String) - Method in class edu.cmu.tetrad.data.Knowledge
-
Marks the edge var1 --> var2 as forbid.
- setForceLog(boolean) - Method in class edu.cmu.tetrad.util.TetradLogger
-
Forces the logger to log all events, useful for testing.
- setForwardSearch(boolean) - Method in class edu.cmu.tetrad.search.utils.ShiftSearch
- setFreeParamValues(double[]) - Method in interface edu.cmu.tetrad.sem.ISemIm
- setFreeParamValues(double[]) - Method in class edu.cmu.tetrad.sem.SemIm
-
Sets the values of the free freeParameters (in the order in which they appear in getFreeParameters()) to the values contained in the given array.
- setFunction(int) - Method in class edu.cmu.tetrad.search.FastIca
-
Sets the function type to be used, either LOGCOSH or EXP.
- setGamma(double) - Method in class edu.cmu.tetrad.search.score.EbicScore
-
Sets the gamma parameter for EBIC.
- setGammaHigh(double) - Method in class edu.cmu.tetrad.algcomparison.simulation.LinearSineSimulation
- setGammaLow(double) - Method in class edu.cmu.tetrad.algcomparison.simulation.LinearSineSimulation
- setGesDepth(int) - Method in class edu.cmu.tetrad.search.work_in_progress.DMSearch
- setGraph(Dag) - Method in class edu.cmu.tetrad.graph.LagGraph
- setGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.independence.MSeparationTest
- setGraph(Graph) - Method in interface edu.cmu.tetrad.algcomparison.independence.TakesGraph
- setGraph(Graph) - Method in class edu.cmu.tetrad.algcomparison.score.MSeparationScore
- setGraph(Graph) - Method in class edu.cmu.tetrad.bayes.EmBayesProperties
- setGraph(Graph) - Method in class edu.cmu.tetrad.search.work_in_progress.SampleVcpc
- setGraph(Graph) - Method in class edu.cmu.tetrad.search.work_in_progress.SampleVcpcFast
- setGraph(Graph) - Method in class edu.cmu.tetrad.search.work_in_progress.VcPc
- setGraph(Graph) - Method in class edu.cmu.tetrad.search.work_in_progress.VcPcAlt
- setGraph(Graph) - Method in class edu.cmu.tetrad.search.work_in_progress.VcPcFast
- setGraphFile(String) - Method in class edu.cmu.tetrad.study.performance.ComparisonParameters
- setGraphName(String) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.BasicGraph
-
Sets the name of the graph
- setGraphNum(int) - Method in class edu.cmu.tetrad.study.performance.ComparisonParameters
- setGuaranteeIid(boolean) - Method in class edu.cmu.tetrad.sem.GeneralizedSemIm
- setHighlighted(boolean) - Method in class edu.cmu.tetrad.graph.Edge
- setHighPValueAlpha(double) - Method in interface edu.cmu.tetrad.search.work_in_progress.Hbsms
- setHighPValueAlpha(double) - Method in class edu.cmu.tetrad.search.work_in_progress.HbsmsBeam
- setHighPValueAlpha(double) - Method in class edu.cmu.tetrad.search.work_in_progress.HbsmsGes
- setHistory(GeneHistory) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.simulation.MeasurementSimulator
-
Sets the history.
- setHistory(GeneHistory) - Method in class edu.cmu.tetrad.study.gene.tetradapp.model.MeasurementSimulatorParams
- setIa(boolean) - Method in class edu.cmu.tetrad.search.work_in_progress.Glasso
- setIdLabel(String) - Method in interface edu.cmu.tetrad.data.IDataReader
-
Deprecated.
- setIdsSupplied(boolean) - Method in interface edu.cmu.tetrad.data.IDataReader
-
Deprecated.
- setIncludeDishAndChipColumns(boolean) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.simulation.MeasurementSimulator
- setIncludeDishAndChipVariables(boolean) - Method in class edu.cmu.tetrad.study.gene.tetradapp.model.MeasurementSimulatorParams
- setIncludeNegativeCoefs(boolean) - Method in class edu.cmu.tetrad.sem.LargeScaleSimulation
- setIncludePositiveCoefs(boolean) - Method in class edu.cmu.tetrad.sem.LargeScaleSimulation
- setIncompleteCholesky(double) - Method in class edu.cmu.tetrad.search.test.IndTestHsic
-
Sets the precision for the Incomplete Choleksy factorization method for approximating Gram matrices.
- setIndegree(int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.LagGraphParams
- setIndegreeType(int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.LagGraphParams
- setIndependenceTest(ComparisonParameters.IndependenceTestType) - Method in class edu.cmu.tetrad.study.performance.ComparisonParameters
- setIndependenceWrapper(IndependenceWrapper) - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.Fask
- setIndependenceWrapper(IndependenceWrapper) - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FaskConcatenated
- setIndependenceWrapper(IndependenceWrapper) - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FaskVote
- setIndependenceWrapper(IndependenceWrapper) - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FciIod
- setIndependenceWrapper(IndependenceWrapper) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Cpc
- setIndependenceWrapper(IndependenceWrapper) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Fas
- setIndependenceWrapper(IndependenceWrapper) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Grasp
- setIndependenceWrapper(IndependenceWrapper) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Pc
- setIndependenceWrapper(IndependenceWrapper) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.PcMb
- setIndependenceWrapper(IndependenceWrapper) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Bfci
- setIndependenceWrapper(IndependenceWrapper) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Ccd
- setIndependenceWrapper(IndependenceWrapper) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Cfci
- setIndependenceWrapper(IndependenceWrapper) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Fci
- setIndependenceWrapper(IndependenceWrapper) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.FciMax
- setIndependenceWrapper(IndependenceWrapper) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Gfci
- setIndependenceWrapper(IndependenceWrapper) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.GraspFci
- setIndependenceWrapper(IndependenceWrapper) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Rfci
- setIndependenceWrapper(IndependenceWrapper) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.SpFci
- setIndependenceWrapper(IndependenceWrapper) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.SvarFci
- setIndependenceWrapper(IndependenceWrapper) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.SvarGfci
- setIndependenceWrapper(IndependenceWrapper) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pattern.Cstar
- setIndependenceWrapper(IndependenceWrapper) - Method in interface edu.cmu.tetrad.algcomparison.utils.TakesIndependenceWrapper
- setIndices(int[]) - Method in class edu.cmu.tetrad.util.IndexedMatrix
-
Sets the index array.
- setIndTestWrapper(IndependenceWrapper) - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FaskConcatenated
- setIndTestWrapper(IndependenceWrapper) - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FaskLofsConcatenated
- setIndTestWrapper(IndependenceWrapper) - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FaskVote
- setIndTestWrapper(IndependenceWrapper) - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FciIod
- setIndTestWrapper(IndependenceWrapper) - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FgesConcatenated
- setIndTestWrapper(IndependenceWrapper) - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.Images
- setIndTestWrapper(IndependenceWrapper) - Method in interface edu.cmu.tetrad.algcomparison.algorithm.MultiDataSetAlgorithm
-
Sets a test wrapper if not null.
- setIndTestWrapper(IndependenceWrapper) - Method in class edu.pitt.dbmi.algo.resampling.GeneralResamplingTest
- setInhibitExcite(int[]) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.AbstractNbComponent
-
Sets the inhibit/excite.
- setInitialGraph(Graph) - Method in class edu.cmu.tetrad.search.Fges
- setInitialGraph(Graph) - Method in class edu.cmu.tetrad.search.FgesMb
- setInitializedRandomly(boolean) - Method in class edu.cmu.tetrad.sem.Parameter
-
Set to true iff this parameter should be initialized randomly by drawing an initial value from its preset random distribution.
- setInitSync(boolean) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.GeneHistory
-
Sets whether initialization should be synchronized.
- setInitSync(boolean) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.simulation.MeasurementSimulator
-
Sets whether the expression levels of cells should be synchronized on initialization.
- setInitSync(boolean) - Method in class edu.cmu.tetrad.study.gene.tetradapp.model.MeasurementSimulatorParams
- setInputs(int[]) - Method in class edu.cmu.tetrad.search.work_in_progress.DMSearch
- setInt(int, int, int) - Method in class edu.cmu.tetrad.data.BoxDataSet
-
Sets the value at the given (row, column) to the given int value, assuming the variable for the column is discrete.
- setInt(int, int, int) - Method in interface edu.cmu.tetrad.data.DataSet
-
Sets the value at the given (row, column) to the given int value, assuming the variable for the column is discrete.
- setInt(int, int, int) - Method in class edu.cmu.tetrad.data.NumberObjectDataSet
-
Sets the value at the given (row, column) to the given int value, assuming the variable for the column is discrete.
- setIntercept(int, double) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.LinearFunction
-
Sets the intercept for the given factor.
- setIntercept(Node, double) - Method in interface edu.cmu.tetrad.sem.ISemIm
- setIntercept(Node, double) - Method in class edu.cmu.tetrad.sem.SemIm
-
Sets the intercept.
- setIntercept(String, double) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.LinearFunction
-
Sets the intercept for the given factor.
- setInterceptHigh(double) - Method in class edu.cmu.tetrad.algcomparison.simulation.LinearSineSimulation
- setInterceptLow(double) - Method in class edu.cmu.tetrad.algcomparison.simulation.LinearSineSimulation
- setInterval(int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.simulation.MeasurementSimulator
-
Returns the interval (int time steps) between time steps stored out.
- setInterval(int) - Method in class edu.cmu.tetrad.study.gene.tetradapp.model.MeasurementSimulatorParams
- setIpen(boolean) - Method in class edu.cmu.tetrad.search.work_in_progress.Glasso
- setIs(boolean) - Method in class edu.cmu.tetrad.search.work_in_progress.Glasso
- setItr(boolean) - Method in class edu.cmu.tetrad.search.work_in_progress.Glasso
- setJustification(int) - Method in class edu.cmu.tetrad.util.TextTable
-
Sets the justification, either LEFT_JUSTIFIED or RIGHT_JUSTIFIED.
- setKernel(ConditionalCorrelationIndependence.Kernel) - Method in class edu.cmu.tetrad.search.test.IndTestConditionalCorrelation
-
Sets the kernel to be used.
- setKernelMultiplier(double) - Method in class edu.cmu.tetrad.search.test.IndTestConditionalCorrelation
-
Returns the kernel multiplier.
- setKernelMultiplier(ConditionalCorrelationIndependence.Kernel) - Method in class edu.cmu.tetrad.search.test.ConditionalCorrelationIndependence
-
Sets the kernel multiplier.
- setKernelRegressionSampleSize(int) - Method in class edu.cmu.tetrad.search.test.ConditionalCorrelationIndependence
-
Sets the kernel regression sample size.
- setKernelRegressionSampleSize(int) - Method in class edu.cmu.tetrad.search.test.IndTestConditionalCorrelation
-
Sets the kernel regression sample size.
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.algcomparison.algorithm.cluster.Fofc
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.algcomparison.algorithm.cluster.Ftfc
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.Fask
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FaskConcatenated
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FaskLofsConcatenated
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FaskVote
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FasLofs
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FciIod
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FgesConcatenated
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.Images
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Boss
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Cpc
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Fas
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Fges
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.FgesMb
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.FgesMeasurement
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Grasp
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Pc
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Pcd
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.PcLingam
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.PcMb
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.SingleGraphAlg
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Sp
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Bfci
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Cfci
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Fci
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.FciMax
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Gfci
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.GraspFci
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.PagSampleRfci
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Rfci
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.RfciBsc
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.SpFci
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.SvarFci
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.SvarGfci
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.algcomparison.simulation.TimeSeriesSemSimulation
- setKnowledge(Knowledge) - Method in interface edu.cmu.tetrad.algcomparison.utils.HasKnowledge
-
Sets a knowledge object.
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.data.BoxDataSet
-
Sets knowledge to be associated with this data set.
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.data.CorrelationMatrixOnTheFly
-
Associates knowledge with this data.
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.data.CovarianceMatrix
-
Associates knowledge with this data.
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.data.CovarianceMatrixOnTheFly
-
Associates knowledge with this data.
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.data.DataModelList
- setKnowledge(Knowledge) - Method in interface edu.cmu.tetrad.data.ICovarianceMatrix
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.data.IndependenceFacts
- setKnowledge(Knowledge) - Method in interface edu.cmu.tetrad.data.KnowledgeTransferable
-
Sets knowledge to a copy of the given object.
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.data.NumberObjectDataSet
-
Sets knowledge to be associated with this data set.
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.data.TimeSeriesData
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.BFci
-
Sets the knowledge to be used for the search.
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.Boss
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.Cfci
-
Set the knowledge used in the search.
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.Cpc
-
Sets the knowledge specification used in the search.
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.Fas
-
Sets the knowledge to be used in the search.
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.Fasd
-
Sets the knowledge to be used in the search.
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.Fask
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.Fci
-
Sets background knowledge for the search.
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.FciMax
-
Sets background knowledge for the search.
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.Fges
-
Sets the background knowledge.
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.FgesMb
-
Sets the background knowledge.
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.GFci
-
Sets the knowledge to use in search.
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.Grasp
-
Sets the knowledge used in the search.
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.GraspFci
-
Sets the knowledge used in search.
- setKnowledge(Knowledge) - Method in interface edu.cmu.tetrad.search.IFas
-
Sets the knowledge for the search.
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.Lofs
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.Mimbuild
-
Sets the knowledge to be used in the search.
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.MimbuildTrek
-
The knowledge to use in the search.
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.Pc
-
Sets the knowledge specification to be used in the search.
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.Pcd
-
Sets the knowledge specification to be used in the search.
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.PcMb
-
Sets knowledge, to which the algorithm is in fact sensitive.
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.PermutationSearch
-
Sets the knowledge to be used in the search.
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.Rfci
-
Sets the knowledge used in search.
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.Sp
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.SpFci
-
Sets the knoweldge used in the search.
- setKnowledge(Knowledge) - Method in interface edu.cmu.tetrad.search.SuborderSearch
-
The knowledge being used.
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.SvarFas
-
Sets the knowledge used in the search.
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.SvarFci
-
Sets the knowledge for the search.
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.SvarFges
-
Sets the background knowledge.
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.SvarGfci
-
Sets the knowledge for the search.
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.utils.Bes
-
Sets the knowledge for the search.
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.utils.BesPermutation
-
Sets the knowledge that BES will use.
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.utils.DagToPag
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.utils.FciOrient
-
Sets the knowledge to use for the final orientation.
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.utils.FgesOrienter
-
Sets the background knowledge.
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.utils.MaxP
-
Sets the knowledge to use for orientation.
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.utils.MeekRules
-
Sets the knowledge to be used in the orientation.
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.utils.PcCommon
-
Sets the knowledge specification used in the search.
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.utils.PossibleMsepFci
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.utils.ShiftSearch
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.utils.SvarFciOrient
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.utils.TeyssierScorer
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.utils.TsDagToPag
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.work_in_progress.Fas2
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.work_in_progress.Fas3
-
Sets the knowledge to be used int the search.
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.work_in_progress.FasDci
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.work_in_progress.FasFdr
-
Sets the knowledge to be used in the search.
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.work_in_progress.FaskVote
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.work_in_progress.FasLofs
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.work_in_progress.GraspTol
- setKnowledge(Knowledge) - Method in interface edu.cmu.tetrad.search.work_in_progress.Hbsms
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.work_in_progress.HbsmsBeam
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.work_in_progress.HbsmsGes
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.work_in_progress.Ion
-
Sets the knowledge to be used for this search.
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.work_in_progress.Kpc
-
Sets the knowledge specification to be used in the search.
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.work_in_progress.Mmhc
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.work_in_progress.OtherPermAlgs
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.work_in_progress.SampleVcpc
-
Sets the knowledge specification used in the search.
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.work_in_progress.SampleVcpcFast
-
Sets the knowledge specification used in the search.
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.work_in_progress.VcFas
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.work_in_progress.VcPc
-
Sets the knowledge specification used in the search.
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.work_in_progress.VcPcAlt
-
Sets the knowledge specification used in the search.
- setKnowledge(Knowledge) - Method in class edu.cmu.tetrad.search.work_in_progress.VcPcFast
-
Sets the knowledge specification used in the search.
- setKnowledge(Knowledge) - Method in class edu.pitt.dbmi.algo.bayesian.constraint.search.PagSamplingRfci
- setKnowledge(Knowledge) - Method in class edu.pitt.dbmi.algo.resampling.GeneralResamplingSearch
-
Sets the background knowledge.
- setKnowledge(Knowledge) - Method in class edu.pitt.dbmi.algo.resampling.GeneralResamplingTest
-
Sets the background knowledge.
- setKnowledge(Knowledge) - Method in class edu.pitt.dbmi.algo.resampling.task.GeneralResamplingSearchRunnable
-
Sets the background knowledge.
- setKnowledge(List<Node>, List<Node>) - Method in class edu.cmu.tetrad.search.utils.GrowShrinkTree
- setKnowledgeGroup(int, KnowledgeGroup) - Method in class edu.cmu.tetrad.data.Knowledge
-
Legacy, do not use.
- setLambda(double) - Method in class edu.cmu.tetrad.search.score.GicScores
- setLambda(double) - Method in class edu.cmu.tetrad.search.score.PoissonPriorScore
- setLambda1(double) - Method in class edu.cmu.tetrad.search.Dagma
- setLeftRight(Fask.LeftRight) - Method in class edu.cmu.tetrad.search.Fask
-
Sets the left-right rule used
- setLevel(OutputStream, Level) - Method in class edu.cmu.tetrad.util.LogUtils
-
Sets the logging level for the given stream.
- setLinearHigh(double) - Method in class edu.cmu.tetrad.algcomparison.simulation.LinearSineSimulation
- setLinearLow(double) - Method in class edu.cmu.tetrad.algcomparison.simulation.LinearSineSimulation
- setLocation(String, PointXy) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ActiveLagGraph
- setLocation(String, PointXy) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ManualLagGraph
- setLocation(String, PointXy) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.BasicLagGraph
- setLocation(String, PointXy) - Method in interface edu.cmu.tetrad.study.gene.tetrad.gene.history.LagGraph
-
Sets the location.
- setLocationMap(DataSet) - Method in class edu.cmu.tetrad.simulation.GdistanceRandom
- setLog(boolean) - Method in class edu.cmu.tetrad.search.utils.FgesOrienter
-
Sets whether log output should be produced.
- setLogging(boolean) - Method in class edu.cmu.tetrad.util.TetradLogger
-
Sets whether the logger is on or not.
- setLoggingDirectory(String) - Method in class edu.cmu.tetrad.util.TetradLogger
-
Sets the logging directory, but first checks whether we can write to it etc.
- setLoggingFilePrefix(String) - Method in class edu.cmu.tetrad.util.TetradLogger
-
Sets the logging prefix.
- setLongDescription(String) - Method in class edu.cmu.tetrad.util.ParamDescription
- setLowerBound(double) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.BooleanGlassFunction
-
Sets the lower bound for expression levels.
- setLowerBound(double) - Method in class edu.pitt.dbmi.algo.bayesian.constraint.search.RfciBsc
- setLowerBoundDouble(double) - Method in class edu.cmu.tetrad.util.ParamDescription
- setLowerBoundInt(int) - Method in class edu.cmu.tetrad.util.ParamDescription
- setLowerBoundLong(long) - Method in class edu.cmu.tetrad.util.ParamDescription
- setMag(Graph) - Method in class edu.cmu.tetrad.search.work_in_progress.MagSemBicScore
-
Sets the MAG to wrap.
- setManipulated(int, boolean) - Method in class edu.cmu.tetrad.bayes.Evidence
- setManipulated(int, boolean) - Method in class edu.cmu.tetrad.bayes.Manipulation
- setManipulated(int, boolean) - Method in class edu.cmu.tetrad.sem.SemEvidence
- setManipulated(int, boolean) - Method in class edu.cmu.tetrad.sem.SemManipulation
- setMatrix(Matrix) - Method in class edu.cmu.tetrad.data.CorrelationMatrix
- setMatrix(Matrix) - Method in class edu.cmu.tetrad.data.CorrelationMatrixOnTheFly
- setMatrix(Matrix) - Method in class edu.cmu.tetrad.data.CovarianceMatrix
- setMatrix(Matrix) - Method in class edu.cmu.tetrad.data.CovarianceMatrixOnTheFly
- setMatrix(Matrix) - Method in interface edu.cmu.tetrad.data.ICovarianceMatrix
- setMaxDegree(int) - Method in class edu.cmu.tetrad.graph.RandomGraph.UniformGraphGenerator
-
Sets the maximum degree of any nodes in the graph.
- setMaxDegree(int) - Method in class edu.cmu.tetrad.search.Fges
-
The maximum of parents any nodes can have in the output pattern.
- setMaxDegree(int) - Method in class edu.cmu.tetrad.search.FgesMb
-
The maximum of parents any nodes can have in the output pattern.
- setMaxDegree(int) - Method in class edu.cmu.tetrad.search.GFci
-
Sets the maximum indegree of the output graph.
- setMaxDegree(int) - Method in class edu.cmu.tetrad.search.SpFci
-
Sets the max degree of the search.
- setMaxEdges(int) - Method in class edu.cmu.tetrad.graph.RandomGraph.UniformGraphGenerator
- setMaxIndegree(int) - Method in class edu.cmu.tetrad.search.SvarFges
-
The maximum of parents any nodes can have in the output pattern.
- setMaxInDegree(int) - Method in class edu.cmu.tetrad.graph.RandomGraph.UniformGraphGenerator
- setMaxit(int) - Method in class edu.cmu.tetrad.search.work_in_progress.Glasso
- setMaxIterations(int) - Method in class edu.cmu.tetrad.cluster.KMeans
-
Sets the maximum number of iterations, or -1 if the algorithm is allowed to run unconstrainted.
- setMaxIterations(int) - Method in class edu.cmu.tetrad.search.FastIca
-
Sets the maximum number of iterations to allow.
- setMaxLag(int) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- setMaxLagAllowable(int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ActiveLagGraph
-
Attemps to set the maximum allowable lag of an edge in the graph.
- setMaxLagAllowable(int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ManualLagGraph
- setMaxLagAllowable(int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.BasicLagGraph
-
Sets the maximum allowable lag.
- setMaxLagAllowable(int) - Method in interface edu.cmu.tetrad.study.gene.tetrad.gene.history.LagGraph
-
Sets the maximum allowable lag.
- setMaxNumShifts(int) - Method in class edu.cmu.tetrad.search.utils.ShiftSearch
- setMaxOutDegree(int) - Method in class edu.cmu.tetrad.graph.RandomGraph.UniformGraphGenerator
- setMaxPathLength(int) - Method in class edu.cmu.tetrad.search.BFci
-
Returns the maximum length of any discriminating path, or -1 if unlimited.
- setMaxPathLength(int) - Method in class edu.cmu.tetrad.search.Fci
-
Sets the maximum length of any discriminating path, or -1 if unlimited.
- setMaxPathLength(int) - Method in class edu.cmu.tetrad.search.FciMax
-
Sets the maximum length of any discriminating path, or -1 if unlimited.
- setMaxPathLength(int) - Method in class edu.cmu.tetrad.search.GFci
-
Sets the maximum path length for the discriminating path rule.
- setMaxPathLength(int) - Method in class edu.cmu.tetrad.search.GraspFci
-
Sets the maximum length of any discriminating path searched.
- setMaxPathLength(int) - Method in class edu.cmu.tetrad.search.Rfci
-
Sets the maximum path length for discriminating paths.
- setMaxPathLength(int) - Method in class edu.cmu.tetrad.search.SpFci
-
Sets the max path length for discriminating paths.
- setMaxPathLength(int) - Method in class edu.cmu.tetrad.search.SvarFci
-
Sets the maximum length of any discriminating path, or -1 if unlimited.
- setMaxPathLength(int) - Method in class edu.cmu.tetrad.search.SvarGfci
-
Sets the maximum length of any discriminating path.
- setMaxPathLength(int) - Method in class edu.cmu.tetrad.search.utils.DagToPag
-
Sets the maximum path length for some rules in the conversion.
- setMaxPathLength(int) - Method in class edu.cmu.tetrad.search.utils.FciOrient
- setMaxPathLength(int) - Method in class edu.cmu.tetrad.search.utils.MaxP
-
Sets the max path length to use for the max P heuristic.
- setMaxPathLength(int) - Method in class edu.cmu.tetrad.search.utils.PcCommon
- setMaxPathLength(int) - Method in class edu.cmu.tetrad.search.utils.PossibleMsepFci
- setMaxPathLength(int) - Method in class edu.cmu.tetrad.search.utils.SvarFciOrient
- setMaxPathLength(int) - Method in class edu.cmu.tetrad.search.utils.TsDagToPag
- setMaxPathLength(int) - Method in class edu.pitt.dbmi.algo.bayesian.constraint.search.PagSamplingRfci
- setMaxReachablePathLength(int) - Method in class edu.cmu.tetrad.search.Cfci
- setMaxShift(int) - Method in class edu.cmu.tetrad.search.utils.ShiftSearch
- setMean(Node, double) - Method in interface edu.cmu.tetrad.sem.ISemIm
- setMean(Node, double) - Method in class edu.cmu.tetrad.sem.SemIm
-
Sets the mean associated with the given node.
- setMeanHigh(double) - Method in class edu.cmu.tetrad.algcomparison.simulation.ConditionalGaussianSimulation
- setMeanLow(double) - Method in class edu.cmu.tetrad.algcomparison.simulation.ConditionalGaussianSimulation
- setMeanRange(double, double) - Method in class edu.cmu.tetrad.sem.LargeScaleSimulation
- setMeanStandardDeviation(Node, double) - Method in class edu.cmu.tetrad.sem.SemIm
-
Sets the mean associated with the given node.
- setMeasuredDataSaved(boolean) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.simulation.MeasurementSimulator
-
Sets whether measured data should be saved out for this simulation.
- setMedianBandwidth(DataSet, Node) - Method in class edu.cmu.tetrad.search.utils.KernelGaussian
-
Sets the bandwidth of the kernel to median distance between two points in the given vector
- setMeekPreventCycles(boolean) - Method in class edu.cmu.tetrad.search.Pc
-
Sets whether cycles should be checked.
- setMeekPreventCycles(boolean) - Method in class edu.cmu.tetrad.search.Pcd
- setMeekPreventCycles(boolean) - Method in class edu.cmu.tetrad.search.PcMb
-
Sets whether cycles should be prevented, using a cycle checker.
- setMeekPreventCycles(boolean) - Method in class edu.cmu.tetrad.search.utils.MeekRules
-
Sets whether cycles should be prevented by cycle checking.
- setMeekPreventCycles(boolean) - Method in class edu.cmu.tetrad.search.utils.PcCommon
-
Sets to true just in case edges will not be added if they would create cycles.
- setMeekPreventCycles(boolean) - Method in class edu.cmu.tetrad.search.work_in_progress.Kpc
- setMeekPreventCycles(boolean) - Method in class edu.cmu.tetrad.search.work_in_progress.SampleVcpc
-
Sets to true just in case edges will not be added if they would create cycles.
- setMeekPreventCycles(boolean) - Method in class edu.cmu.tetrad.search.work_in_progress.SampleVcpcFast
-
Sets to true just in case edges will not be added if they would create cycles.
- setMeekPreventCycles(boolean) - Method in class edu.cmu.tetrad.search.work_in_progress.VcPc
-
Sets to true just in case edges will not be added if they would create cycles.
- setMeekPreventCycles(boolean) - Method in class edu.cmu.tetrad.search.work_in_progress.VcPcAlt
-
Sets to true just in case edges will not be added if they would create cycles.
- setMeekPreventCycles(boolean) - Method in class edu.cmu.tetrad.search.work_in_progress.VcPcFast
-
Sets to true just in case edges will not be added if they would create cycles.
- setMeekVerbose(boolean) - Method in class edu.cmu.tetrad.search.Fges
-
Sets whether verbose output should be produced for the Meek rules.
- setMeekVerbose(boolean) - Method in class edu.cmu.tetrad.search.FgesMb
-
Sets whether verbose output should be produced for the Meek rules.
- setMethod(int) - Method in class edu.cmu.tetrad.data.ContinuousDiscretizationSpec
- setMethod(OtherPermAlgs.Method) - Method in class edu.cmu.tetrad.search.work_in_progress.OtherPermAlgs
- setMinClusterSize(int) - Method in class edu.cmu.tetrad.search.Mimbuild
- setMinClusterSize(int) - Method in class edu.cmu.tetrad.search.MimbuildTrek
- setMinDiscount(int) - Method in class edu.cmu.tetrad.search.work_in_progress.DMSearch
- setMissingValue(int) - Method in class edu.cmu.tetrad.data.CellTable
- setMlag(int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.LagGraphParams
- setMlag(int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ManualLagGraphParams
-
Sets the maximum lag.
- setModelClasses(Class[]) - Method in class edu.cmu.tetrad.session.SessionNode
-
Sets the model classes to the new array of model classes.
- setMultiDataSetAlgorithm(MultiDataSetAlgorithm) - Method in class edu.pitt.dbmi.algo.resampling.GeneralResamplingSearch
- setN(int) - Method in class edu.cmu.tetrad.search.work_in_progress.Glasso
- setName(String) - Method in class edu.cmu.tetrad.data.AbstractVariable
-
Sets the name of this variable.
- setName(String) - Method in class edu.cmu.tetrad.data.BoxDataSet
-
Sets the name of the data set.
- setName(String) - Method in class edu.cmu.tetrad.data.CorrelationMatrixOnTheFly
-
Sets the name of the covariance matrix.
- setName(String) - Method in class edu.cmu.tetrad.data.CovarianceMatrix
-
Sets the name of the covariance matrix.
- setName(String) - Method in class edu.cmu.tetrad.data.CovarianceMatrixOnTheFly
-
Sets the name of the covariance matrix.
- setName(String) - Method in interface edu.cmu.tetrad.data.DataModel
-
Sets the name of the data model (may be null).
- setName(String) - Method in class edu.cmu.tetrad.data.DataModelList
-
Sets the name of the data model list..
- setName(String) - Method in interface edu.cmu.tetrad.data.ICovarianceMatrix
- setName(String) - Method in class edu.cmu.tetrad.data.IndependenceFacts
- setName(String) - Method in class edu.cmu.tetrad.data.NumberObjectDataSet
-
Sets the name of the data set.
- setName(String) - Method in class edu.cmu.tetrad.data.TimeSeriesData
- setName(String) - Method in class edu.cmu.tetrad.graph.GraphNode
-
Sets the name of this variable.
- setName(String) - Method in interface edu.cmu.tetrad.graph.Node
-
Sets the name of this node.
- setName(String) - Method in class edu.cmu.tetrad.sem.Parameter
-
Sets the name for this parameter.
- setName(String) - Method in class edu.cmu.tetrad.session.Session
-
Sets the name.
- setName(String) - Method in interface edu.cmu.tetrad.session.SessionModel
-
Sets the name of the session model.
- setName(String) - Method in class edu.cmu.tetrad.session.SessionNode
- setName(String) - Method in class edu.cmu.tetrad.session.Type1
-
Sets the name of the session model.
- setName(String) - Method in class edu.cmu.tetrad.session.Type10
-
Sets the name of the session model.
- setName(String) - Method in class edu.cmu.tetrad.session.Type11
-
Sets the name of the session model.
- setName(String) - Method in class edu.cmu.tetrad.session.Type12
-
Sets the name of the session model.
- setName(String) - Method in class edu.cmu.tetrad.session.Type2
-
Sets the name of the session model.
- setName(String) - Method in class edu.cmu.tetrad.session.Type3
-
Sets the name of the session model.
- setName(String) - Method in class edu.cmu.tetrad.session.Type4
-
Sets the name of the session model.
- setName(String) - Method in class edu.cmu.tetrad.session.Type5
-
Sets the name of the session model.
- setName(String) - Method in class edu.cmu.tetrad.session.Type6
-
Sets the name of the session model.
- setName(String) - Method in class edu.cmu.tetrad.session.Type7
-
Sets the name of the session model.
- setName(String) - Method in class edu.cmu.tetrad.session.Type8
-
Sets the name of the session model.
- setName(String) - Method in class edu.cmu.tetrad.session.Type9
-
Sets the name of the session model.
- setName(String) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.AbstractNbComponent
-
Sets the name.
- setName(String) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.BasicMatrix
-
Sets the name of this matrix
- setName(String) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ManualActiveLagGraph
- setName(String) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.RandomActiveLagGraph
- setName(String) - Method in class edu.cmu.tetrad.study.gene.tetradapp.model.BooleanGlassGeneIm
- setName(String) - Method in class edu.cmu.tetrad.study.gene.tetradapp.model.BooleanGlassGenePm
- setNaturalEdgeLength(double) - Method in class edu.cmu.tetrad.graph.LayoutUtil.KamadaKawaiLayout
- setNewSession(boolean) - Method in class edu.cmu.tetrad.session.Session
- setNextEdgeAddAllowed(boolean) - Method in class edu.cmu.tetrad.session.SessionNode
-
True iff the next edge should not be added.
- setNextOutputStream() - Method in class edu.cmu.tetrad.util.TetradLogger
-
Sets the next output stream to use for logging, call
removeNextOutputStreamto remove it. - setNoData(boolean) - Method in class edu.cmu.tetrad.study.performance.ComparisonParameters
- setNodeExpression(Node, String) - Method in class edu.cmu.tetrad.sem.GeneralizedSemPm
- setNodeName(int, String) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.BasicGraph
-
Sets the name of node
iin this graph - setNodes(List<Node>) - Method in class edu.cmu.tetrad.data.IndependenceFacts
- setNodes(List<Node>) - Method in class edu.cmu.tetrad.graph.Dag
- setNodes(List<Node>) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
- setNodes(List<Node>) - Method in interface edu.cmu.tetrad.graph.Graph
- setNodes(List<Node>) - Method in class edu.cmu.tetrad.graph.LagGraph
- setNodes(List<Node>) - Method in class edu.cmu.tetrad.graph.SemGraph
- setNodes(List<Node>) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- setNodes(List<Node>) - Method in class edu.cmu.tetrad.search.Ida.NodeEffects
- setNodeType(NodeType) - Method in class edu.cmu.tetrad.data.ContinuousVariable
- setNodeType(NodeType) - Method in class edu.cmu.tetrad.data.DiscreteVariable
- setNodeType(NodeType) - Method in class edu.cmu.tetrad.graph.GraphNode
-
Sets the node type.
- setNodeType(NodeType) - Method in interface edu.cmu.tetrad.graph.Node
-
Sets the node type for this node.
- setNodeType(NodeType) - Method in class edu.cmu.tetrad.session.SessionNode
- setNodeVariableType(NodeVariableType) - Method in class edu.cmu.tetrad.data.ContinuousVariable
- setNodeVariableType(NodeVariableType) - Method in class edu.cmu.tetrad.data.DiscreteVariable
- setNodeVariableType(NodeVariableType) - Method in class edu.cmu.tetrad.graph.GraphNode
- setNodeVariableType(NodeVariableType) - Method in interface edu.cmu.tetrad.graph.Node
-
Sets the type (domain, interventional status, interventional value..) for this node variable
- setNodeVariableType(NodeVariableType) - Method in class edu.cmu.tetrad.session.SessionNode
- setNonSingularDepth(int) - Method in class edu.cmu.tetrad.search.Grasp
-
Sets the maximum depth at which singular tucks can be performed within the depth-first search of GRaSP.
- setNonSingularDepth(int) - Method in class edu.cmu.tetrad.search.GraspFci
- setNonSingularDepth(int) - Method in class edu.cmu.tetrad.search.work_in_progress.GraspTol
- setNparents(int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.AbstractNbComponent
-
Sets the number of parents.
- setNumberFormat(NumberFormat) - Method in class edu.cmu.tetrad.data.BoxDataSet
- setNumberFormat(NumberFormat) - Method in interface edu.cmu.tetrad.data.DataSet
-
The number formatter used to print out continuous values.
- setNumberFormat(NumberFormat) - Method in class edu.cmu.tetrad.data.NumberObjectDataSet
- setNumberFormat(NumberFormat) - Method in class edu.cmu.tetrad.util.NumberFormatUtil
-
Sets the number format,
nf. - setNumBins(int) - Method in class edu.cmu.tetrad.data.Histogram
-
For a continuous target, sets the number of bins for the histogram.
- setNumBootstraps(int) - Method in class edu.cmu.tetrad.search.test.Kci
-
Sets the number of bootstraps to do.
- setNumBscBootstrapSamples(int) - Method in class edu.pitt.dbmi.algo.bayesian.constraint.search.RfciBsc
- setNumCategories(Node, int) - Method in class edu.cmu.tetrad.bayes.BayesPm
-
Sets the number of values for the given node to the given number.
- setNumCategoriesToDiscretize(int) - Method in class edu.cmu.tetrad.search.score.ConditionalGaussianLikelihood
-
Sets the number of categories to use to discretize child variables to avoid integrationl
- setNumCategoriesToDiscretize(int) - Method in class edu.cmu.tetrad.search.score.ConditionalGaussianScore
-
Sets tne number of categories used to discretize, when this optimization is used.
- setNumCategoriesToDiscretize(int) - Method in class edu.cmu.tetrad.search.test.IndTestConditionalGaussianLrt
-
Sets the number of categories used to discretize variables.
- setNumCellsPerDish(int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.simulation.MeasurementSimulator
-
Sets the number of cells per dish.
- setNumCellsPerDish(int) - Method in class edu.cmu.tetrad.study.gene.tetradapp.model.MeasurementSimulatorParams
- setNumClusters(int) - Method in class edu.cmu.tetrad.data.Clusters
-
Sets the number of clusters represented, or -1 if the number is allowed to vary.
- setNumCPDAGsToStore(int) - Method in class edu.cmu.tetrad.search.SvarFges
-
Sets the number of patterns to store.
- setNumDishes(int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.simulation.MeasurementSimulator
-
Sets the number of dishes that are to be simulated.
- setNumDishes(int) - Method in class edu.cmu.tetrad.study.gene.tetradapp.model.MeasurementSimulatorParams
- setNumEdges(int) - Method in class edu.cmu.tetrad.study.performance.ComparisonParameters
- setNumEdges1(int) - Method in class edu.cmu.tetrad.simulation.GdistanceRandom
- setNumEdges2(int) - Method in class edu.cmu.tetrad.simulation.GdistanceRandom
- setNumExpansions(int) - Method in class edu.cmu.tetrad.search.FgesMb
- setNumFactors(int) - Method in class edu.cmu.tetrad.search.FactorAnalysis
-
Sets the number of factors to find.
- setNumFunctions(int) - Method in class edu.cmu.tetrad.search.test.ConditionalCorrelationIndependence
-
Sets the number of functions to use in (truncated) basis
- setNumFunctions(int) - Method in class edu.cmu.tetrad.search.test.IndTestConditionalCorrelation
-
Sets the number of orthogonal functions to use to do the calculations.
- setNumInitialLags(int) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- setNumIterations(int) - Method in class edu.cmu.tetrad.graph.RandomGraph.UniformGraphGenerator
- setNumIterations(int) - Method in class edu.cmu.tetrad.sem.SemEstimatorGibbsParams
- setNumNodes(int) - Method in class edu.cmu.tetrad.graph.RandomGraph.UniformGraphGenerator
-
Sets the number of nodes and resets all of the other parameters to default values accordingly.
- setNumRandomizedSearchModels(int) - Method in class edu.pitt.dbmi.algo.bayesian.constraint.search.PagSamplingRfci
- setNumRandomizedSearchModels(int) - Method in class edu.pitt.dbmi.algo.bayesian.constraint.search.RfciBsc
- setNumRestarts(int) - Method in class edu.cmu.tetrad.sem.SemEstimator
- setNumRestarts(int) - Method in interface edu.cmu.tetrad.sem.SemOptimizer
- setNumRestarts(int) - Method in class edu.cmu.tetrad.sem.SemOptimizerEm
- setNumRestarts(int) - Method in class edu.cmu.tetrad.sem.SemOptimizerPowell
- setNumRestarts(int) - Method in class edu.cmu.tetrad.sem.SemOptimizerRegression
- setNumRestarts(int) - Method in class edu.cmu.tetrad.sem.SemOptimizerRicf
- setNumRestarts(int) - Method in class edu.cmu.tetrad.sem.SemOptimizerScattershot
- setNumRounds(int) - Method in class edu.cmu.tetrad.search.work_in_progress.OtherPermAlgs
- setNumSamplesPerDish(int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.simulation.MeasurementSimulator
-
Sets the number of samples that will be generated in the measured data for each dish.
- setNumSamplesPerDish(int) - Method in class edu.cmu.tetrad.study.gene.tetradapp.model.MeasurementSimulatorParams
- setNumStarts(int) - Method in class edu.cmu.tetrad.search.BFci
- setNumStarts(int) - Method in class edu.cmu.tetrad.search.Boss
-
Sets the number of random starts to use.
- setNumStarts(int) - Method in class edu.cmu.tetrad.search.Grasp
-
Sets the number of times the best order algorithm should be rerun with different starting permutations in search of a best BIC scoring permutation.
- setNumStarts(int) - Method in class edu.cmu.tetrad.search.GraspFci
- setNumStarts(int) - Method in class edu.cmu.tetrad.search.work_in_progress.GraspTol
- setNumStarts(int) - Method in class edu.cmu.tetrad.search.work_in_progress.OtherPermAlgs
- setNumSubsamples(int) - Method in class edu.cmu.tetrad.search.Cstar
-
Sets the number of subsamples.
- setNumThreads(int) - Method in class edu.cmu.tetrad.search.Boss
- setNumVariables(int) - Method in class edu.cmu.tetrad.search.work_in_progress.OtherPermAlgs
- setNumVars(int) - Method in class edu.cmu.tetrad.study.performance.ComparisonParameters
- setObject(int, int, Object) - Method in class edu.cmu.tetrad.data.BoxDataSet
- setObject(int, int, Object) - Method in interface edu.cmu.tetrad.data.DataSet
-
Sets the value at the given (row, column) to the given value.
- setObject(int, int, Object) - Method in class edu.cmu.tetrad.data.NumberObjectDataSet
- setOneEdgeFaithfulnessAssumed(boolean) - Method in class edu.cmu.tetrad.study.performance.ComparisonParameters
- setOnlyCanCauseNextTier(int, boolean) - Method in class edu.cmu.tetrad.data.Knowledge
- setOrder(List<Node>) - Method in class edu.cmu.tetrad.search.PermutationSearch
- setOrder(List<Node>) - Method in class edu.cmu.tetrad.search.work_in_progress.MagSemBicScore
-
Sets the order.
- setOrdered(boolean) - Method in class edu.cmu.tetrad.search.Grasp
-
True if GRasP0 should be performed before GRaSP1 and GRaSP1 before GRaSP2.
- setOrdered(boolean) - Method in class edu.cmu.tetrad.search.GraspFci
- setOrdered(boolean) - Method in class edu.cmu.tetrad.search.work_in_progress.GraspTol
- setOrientationAlpha(double) - Method in class edu.cmu.tetrad.search.Fask
-
Sets the orientation alpha.
- setOrientStrongerDirection(boolean) - Method in class edu.cmu.tetrad.search.Lofs
-
Sets whether orientation should be done in the stronger direction, where applicable.
- setOut(OutputStream) - Method in class edu.cmu.tetrad.search.utils.ShiftSearch
- setOut(PrintStream) - Method in class edu.cmu.tetrad.search.Fas
- setOut(PrintStream) - Method in class edu.cmu.tetrad.search.Fasd
-
Sets the output to send prints to.
- setOut(PrintStream) - Method in class edu.cmu.tetrad.search.Fges
-
Sets the output stream that output (except for log output) should be sent to.
- setOut(PrintStream) - Method in class edu.cmu.tetrad.search.FgesMb
-
Sets the output stream that output (except for log output) should be sent to.
- setOut(PrintStream) - Method in class edu.cmu.tetrad.search.GFci
-
Sets the print stream used for output, default System.out.
- setOut(PrintStream) - Method in interface edu.cmu.tetrad.search.IFas
-
sets the print stream to send text to.
- setOut(PrintStream) - Method in class edu.cmu.tetrad.search.SpFci
-
Sets the output stream used to print.
- setOut(PrintStream) - Method in class edu.cmu.tetrad.search.SvarFas
-
Sets the output stream for printing, default is System.out.
- setOut(PrintStream) - Method in class edu.cmu.tetrad.search.SvarFges
-
Sets the output stream that output (except for log output) should be sent to.
- setOut(PrintStream) - Method in class edu.cmu.tetrad.search.utils.FgesOrienter
-
Sets the output stream that output (except for log output) should be sent to.
- setOut(PrintStream) - Method in class edu.cmu.tetrad.search.work_in_progress.Fas2
- setOut(PrintStream) - Method in class edu.cmu.tetrad.search.work_in_progress.Fas3
- setOut(PrintStream) - Method in class edu.cmu.tetrad.search.work_in_progress.FasFdr
- setOut(PrintStream) - Method in class edu.cmu.tetrad.sem.LargeScaleSimulation
- setOut(PrintStream) - Method in class edu.pitt.dbmi.algo.bayesian.constraint.search.RfciBsc
-
Sets the output stream that output (except for log output) should be sent to.
- setOut(PrintStream) - Method in class edu.pitt.dbmi.algo.resampling.GeneralResamplingSearch
-
Sets the output stream that output (except for log output) should be sent to.
- setOut(PrintStream) - Method in class edu.pitt.dbmi.algo.resampling.GeneralResamplingTest
-
Sets the output stream that output (except for log output) should be sent to.
- setOut(PrintStream) - Method in class edu.pitt.dbmi.algo.resampling.task.GeneralResamplingSearchRunnable
-
Sets the output stream that output (except for log output) should be sent to.
- setOut(String, int, int, int, int, String, int, double, double, String) - Method in class edu.cmu.tetrad.calibration.DataForCalibrationRfci
- setOutputDelimiter(Character) - Method in class edu.cmu.tetrad.data.BoxDataSet
-
Sets the character ('\t', ' ', ',', for instance) that is used to delimit tokens when the data set is printed out using the toString() method.
- setOutputDelimiter(Character) - Method in interface edu.cmu.tetrad.data.DataSet
-
The character used a delimiter when the dataset is output.
- setOutputDelimiter(Character) - Method in class edu.cmu.tetrad.data.NumberObjectDataSet
-
Sets the character ('\t', ' ', ',', for instance) that is used to delimit tokens when the data set is printed out using the toString() method.
- setOutputRBD(boolean) - Method in class edu.pitt.dbmi.algo.bayesian.constraint.search.RfciBsc
- setOutputs(int[]) - Method in class edu.cmu.tetrad.search.work_in_progress.DMSearch
- setParallelized(boolean) - Method in class edu.cmu.tetrad.algcomparison.Comparison
- setParallelized(boolean) - Method in class edu.cmu.tetrad.algcomparison.TimeoutComparison
- setParallelized(boolean) - Method in class edu.cmu.tetrad.search.Cstar
-
Sets whether the algorithm should be parallelized.
- setParallelized(boolean) - Method in class edu.cmu.tetrad.search.Fges
- setParallelized(boolean) - Method in class edu.cmu.tetrad.search.FgesMb
- setParallelized(boolean) - Method in class edu.cmu.tetrad.search.MarkovCheck
-
True if the checks should be parallelized.
- setParamComparison(Parameter, Parameter, ParamComparison) - Method in class edu.cmu.tetrad.sem.SemPm
-
Sets the comparison of parameter a to parameter b.
- setParameter(int, double) - Method in class edu.cmu.tetrad.util.dist.Beta
-
The order of parameters is alpha = 0, beta = 1.
- setParameter(int, double) - Method in class edu.cmu.tetrad.util.dist.ChiSquare
- setParameter(int, double) - Method in class edu.cmu.tetrad.util.dist.Discrete
- setParameter(int, double) - Method in interface edu.cmu.tetrad.util.dist.Distribution
-
Sets the index'th parameter to the given value.
- setParameter(int, double) - Method in class edu.cmu.tetrad.util.dist.Exponential
- setParameter(int, double) - Method in class edu.cmu.tetrad.util.dist.Gamma
- setParameter(int, double) - Method in class edu.cmu.tetrad.util.dist.GaussianPower
- setParameter(int, double) - Method in class edu.cmu.tetrad.util.dist.Indicator
- setParameter(int, double) - Method in class edu.cmu.tetrad.util.dist.LogNormal
- setParameter(int, double) - Method in class edu.cmu.tetrad.util.dist.MixtureOfGaussians
- setParameter(int, double) - Method in class edu.cmu.tetrad.util.dist.Normal
- setParameter(int, double) - Method in class edu.cmu.tetrad.util.dist.Poisson
- setParameter(int, double) - Method in class edu.cmu.tetrad.util.dist.SingleValue
- setParameter(int, double) - Method in class edu.cmu.tetrad.util.dist.Split
- setParameter(int, double) - Method in class edu.cmu.tetrad.util.dist.TruncatedNormal
- setParameter(int, double) - Method in class edu.cmu.tetrad.util.dist.Uniform
-
Sets the value of the i'th parameter.
- setParameterBoundsEnforced(boolean) - Method in interface edu.cmu.tetrad.sem.ISemIm
- setParameterBoundsEnforced(boolean) - Method in class edu.cmu.tetrad.sem.SemIm
- setParameterEstimationInitializationExpression(String, String) - Method in class edu.cmu.tetrad.sem.GeneralizedSemPm
- setParameterEstimationInitializationExpression(String, String, String) - Method in class edu.cmu.tetrad.sem.GeneralizedSemPm
-
Sets the expression which should be evaluated when calculating new values for the given parameter.
- setParameterExpression(String, String) - Method in class edu.cmu.tetrad.sem.GeneralizedSemPm
-
Sets the expression which should be evaluated when calculating new values for the given parameter.
- setParameterExpression(String, String, String) - Method in class edu.cmu.tetrad.sem.GeneralizedSemPm
-
Sets the expression which should be evaluated when calculating new values for the given parameter.
- setParameters(Parameters) - Method in class edu.pitt.dbmi.algo.resampling.GeneralResamplingSearch
- setParameters(Parameters) - Method in class edu.pitt.dbmi.algo.resampling.GeneralResamplingTest
- setParametersEstimationInitializationTemplate(String) - Method in class edu.cmu.tetrad.sem.GeneralizedSemPm
- setParametersTemplate(String) - Method in class edu.cmu.tetrad.sem.GeneralizedSemPm
- setParameterValue(Edge, double) - Method in class edu.cmu.tetrad.sem.StandardizedSemIm
- setParameterValue(String, double) - Method in class edu.cmu.tetrad.sem.GeneralizedSemIm
- setParamName(String) - Method in class edu.cmu.tetrad.util.ParamDescription
- setParams(Parameters) - Method in class edu.cmu.tetrad.sem.SemIm
- setParams(Mgm.MGMParams) - Method in class edu.pitt.csb.mgm.Mgm
- setParamValue(Node, Node, double) - Method in interface edu.cmu.tetrad.sem.ISemIm
- setParamValue(Node, Node, double) - Method in class edu.cmu.tetrad.sem.SemIm
-
Sets the value of a single free parameter to the given value, where the free parameter is specified by the endpoint nodes of its edge in the graph.
- setParamValue(Parameter, double) - Method in interface edu.cmu.tetrad.sem.ISemIm
- setParamValue(Parameter, double) - Method in class edu.cmu.tetrad.sem.SemIm
-
Sets the value of a single free parameter to the given value.
- setParents(NbComponent[]) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.AbstractNbComponent
-
Sets the parents.
- setPath(String) - Method in class edu.cmu.tetrad.algcomparison.algorithm.ExternalAlgorithm
- setPcHeuristicType(PcCommon.PcHeuristicType) - Method in class edu.cmu.tetrad.search.Cpc
-
Sets the PC heuristic type.
- setPcHeuristicType(PcCommon.PcHeuristicType) - Method in class edu.cmu.tetrad.search.Fas
- setPcHeuristicType(PcCommon.PcHeuristicType) - Method in class edu.cmu.tetrad.search.Fci
-
Sets which PC heuristic type should be used in the initial adjacency search.
- setPcHeuristicType(PcCommon.PcHeuristicType) - Method in class edu.cmu.tetrad.search.FciMax
-
Sets the FAS heuristic from PC used in search.
- setPcHeuristicType(PcCommon.PcHeuristicType) - Method in class edu.cmu.tetrad.search.Pc
-
Sets the PC heuristic type.
- setPcHeuristicType(PcCommon.PcHeuristicType) - Method in class edu.cmu.tetrad.search.utils.PcCommon
- setPcHeuristicType(PcCommon.PcHeuristicType) - Method in class edu.cmu.tetrad.search.work_in_progress.Fas2
- setPcHeuristicType(PcCommon.PcHeuristicType) - Method in class edu.cmu.tetrad.search.work_in_progress.Fas3
- setPenaltyDiscount(double) - Method in class edu.cmu.tetrad.search.Mimbuild
-
Sets the penalty discount of the score used to infer the structure graph.
- setPenaltyDiscount(double) - Method in class edu.cmu.tetrad.search.score.ConditionalGaussianLikelihood
-
Sets the penalty discount for this score, which is a multiplier on the panalty term of BIC.
- setPenaltyDiscount(double) - Method in class edu.cmu.tetrad.search.score.ConditionalGaussianScore
-
Sets the penalty discount for this score, which is a multiplier on the penalty discount of the BIC score.
- setPenaltyDiscount(double) - Method in class edu.cmu.tetrad.search.score.DegenerateGaussianScore
- setPenaltyDiscount(double) - Method in class edu.cmu.tetrad.search.score.DiscreteBicScore
-
Sets the penalty discount, which is a multiplier on the penalty term of BIC.
- setPenaltyDiscount(double) - Method in class edu.cmu.tetrad.search.score.GicScores
- setPenaltyDiscount(double) - Method in class edu.cmu.tetrad.search.score.SemBicScore
- setPenaltyDiscount(double) - Method in class edu.cmu.tetrad.search.SvarFges
-
Deprecated.Use the setters on the individual scores instead.
- setPenaltyDiscount(double) - Method in class edu.cmu.tetrad.search.utils.FgesOrienter
-
For BIC score, a multiplier on the penalty term.
- setPenaltyDiscount(double) - Method in interface edu.cmu.tetrad.search.utils.HasPenaltyDiscount
- setPenaltyDiscount(double) - Method in class edu.cmu.tetrad.search.work_in_progress.FasLofs
- setPenaltyDiscount(double) - Method in class edu.cmu.tetrad.search.work_in_progress.MagSemBicScore
-
Seets the penalty discount.
- setPenaltyDiscount(double) - Method in class edu.cmu.tetrad.search.work_in_progress.SemBicScoreDeterministic
- setPenaltyDiscount(double) - Method in class edu.cmu.tetrad.study.performance.ComparisonParameters
- setPercent(double) - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestFisherZPercentIndependent
- setPercentResampleSize(double) - Method in class edu.pitt.dbmi.algo.resampling.GeneralResamplingSearch
- setPercentUnregulated(double) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.LagGraphParams
- setPerms(int) - Method in class edu.cmu.tetrad.search.test.IndTestHsic
-
Set the number of bootstrap samples to use
- setPerms(int) - Method in class edu.cmu.tetrad.search.work_in_progress.Kpc
-
Set the number of bootstrap samples to use
- setPhi(DoubleMatrix2D) - Method in class edu.pitt.csb.mgm.Mgm.MGMParams
- setPixelDigitalization(double) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.simulation.MeasurementSimulator
-
Sets the pixel digitalization error.
- setPixelDigitalization(double) - Method in class edu.cmu.tetrad.study.gene.tetradapp.model.MeasurementSimulatorParams
- setPolynomial(int, Polynomial) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.PolynomialFunction
-
Sets the polynomial for the given factor.
- setPossibleMsepSearchDone(boolean) - Method in class edu.cmu.tetrad.search.Cfci
- setPossibleMsepSearchDone(boolean) - Method in class edu.cmu.tetrad.search.Fci
-
Sets whether the (time-consuming) possible msep step should be done.
- setPossibleMsepSearchDone(boolean) - Method in class edu.cmu.tetrad.search.FciMax
-
Sets whether the (time-consuming) possible msep step should be done.
- setPossibleMsepSearchDone(boolean) - Method in class edu.cmu.tetrad.search.GFci
-
Sets whether the possible m-sep search should be done.
- setPower(double) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.AbstractNbComponent
-
Sets the power.
- setPrecomputeCovariances(boolean) - Method in class edu.cmu.tetrad.algcomparison.statistic.BicDiff
- setPrecomputeCovariances(boolean) - Method in class edu.cmu.tetrad.algcomparison.statistic.BicDiffPerRecord
- setPrecomputeCovariances(boolean) - Method in class edu.cmu.tetrad.algcomparison.statistic.BicEst
- setPrecomputeCovariances(boolean) - Method in class edu.cmu.tetrad.algcomparison.statistic.BicTrue
- setPrecomputeCovariances(boolean) - Method in class edu.cmu.tetrad.calibration.DataForCalibrationRfci
- setPrecomputeCovariances(boolean) - Method in class edu.cmu.tetrad.search.utils.ShiftSearch
- setPreferLinear(boolean) - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestMixedMultipleTTest
- setPriorEqivalentSampleSize(double) - Method in class edu.pitt.dbmi.algo.bayesian.constraint.inference.BCInference
- setPriorEquivalentSampleSize(double) - Method in class edu.cmu.tetrad.search.test.IndTestProbabilistic
- setPriorEquivalentSampleSize(double) - Method in class edu.pitt.dbmi.algo.bayesian.constraint.search.PagSamplingRfci
- setProbability(double) - Method in class edu.cmu.tetrad.graph.Edge
- setProbability(double) - Method in class edu.cmu.tetrad.graph.EdgeTypeProbability
- setProbability(int, double) - Method in class edu.cmu.tetrad.bayes.MlBayesImObs
- setProbability(int, double[][]) - Method in interface edu.cmu.tetrad.bayes.BayesIm
-
Sets the probability for the given node.
- setProbability(int, double[][]) - Method in class edu.cmu.tetrad.bayes.DirichletBayesIm
-
Sets the probability for the given node.
- setProbability(int, double[][]) - Method in class edu.cmu.tetrad.bayes.MlBayesIm
-
Sets the probability for the given node.
- setProbability(int, double[][]) - Method in class edu.cmu.tetrad.bayes.MlBayesImObs
-
Sets the probability for the given node.
- setProbability(int, double[][]) - Method in class edu.cmu.tetrad.bayes.UpdatedBayesIm
- setProbability(int, int, int, double) - Method in interface edu.cmu.tetrad.bayes.BayesIm
-
Sets the probability for the given node at a given row and column in the table for that node.
- setProbability(int, int, int, double) - Method in class edu.cmu.tetrad.bayes.DirichletBayesIm
-
Sets the probability for the given node at a given row and column in the table for that node.
- setProbability(int, int, int, double) - Method in class edu.cmu.tetrad.bayes.MlBayesIm
-
Sets the probability for the given node at a given row and column in the table for that node.
- setProbability(int, int, int, double) - Method in class edu.cmu.tetrad.bayes.MlBayesImObs
-
Sets the probability for the given node at a given row and column in the table for that node.
- setProbability(int, int, int, double) - Method in class edu.cmu.tetrad.bayes.UpdatedBayesIm
- setPseudocount(int, int, int, double) - Method in class edu.cmu.tetrad.bayes.DirichletBayesIm
- setQuoteSensitive(boolean) - Method in class edu.cmu.tetrad.data.RegexTokenizer
-
True iff the parser should be aware of quotation marks and remove them from returned strings.
- setR2Orient2Cycles(boolean) - Method in class edu.cmu.tetrad.search.Lofs
-
Sets for R2 whether cycles should be oriented.
- setRandomlyInitialized(boolean) - Method in class edu.cmu.tetrad.graph.LayoutUtil.KamadaKawaiLayout
- setRawDataSaved(boolean) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.simulation.MeasurementSimulator
-
Sets whether the raw data that is generated should be saved beyond what's needed for the getModel cell being simulated.
- setRawDataSaved(boolean) - Method in class edu.cmu.tetrad.study.gene.tetradapp.model.MeasurementSimulatorParams
- setRegularizer(double) - Method in class edu.cmu.tetrad.search.test.IndTestHsic
-
Sets the regularizer.
- setRepetition(int) - Method in class edu.cmu.tetrad.session.SessionNode
- setRepetition(SessionNode, int) - Method in class edu.cmu.tetrad.session.SimulationStudy
-
Sets the number of times the given node (and all of its children) will be executed each time it is encountered in a depth first traversal of the tree.
- setRequired(String, String) - Method in class edu.cmu.tetrad.data.Knowledge
-
Marks the edge var1 --> var2 as required.
- setResamplingWithReplacement(boolean) - Method in class edu.pitt.dbmi.algo.resampling.GeneralResamplingSearch
- setResetAfterBM(boolean) - Method in class edu.cmu.tetrad.search.Boss
- setResetAfterRS(boolean) - Method in class edu.cmu.tetrad.search.Boss
- setResultGraph(Graph) - Method in class edu.cmu.tetrad.study.performance.ComparisonResult
- setResultType(ComparisonParameters.ResultType) - Method in class edu.cmu.tetrad.study.performance.ComparisonParameters
- setRevertToUnshieldedColliders(boolean) - Method in class edu.cmu.tetrad.search.utils.MeekRules
-
Sets whether orientations in the graph should be reverted to its unshielded colliders before performing any Meek rule orientations.
- setRhoAllEqual(double) - Method in class edu.cmu.tetrad.search.work_in_progress.Glasso
- setRiskBound(double) - Method in class edu.cmu.tetrad.search.score.ZsbScore
-
Sets the risk bound for the Zhang Shen Bound score.
- setRowNorm(boolean) - Method in class edu.cmu.tetrad.search.FastIca
-
A logical value indicating whether rows of the data matrix 'X' should be standardized beforehand.
- setRows(int[]) - Method in class edu.cmu.tetrad.regression.LogisticRegression
- setRows(int[]) - Method in class edu.cmu.tetrad.regression.RegressionDataset
- setRows(List<Integer>) - Method in class edu.cmu.tetrad.search.score.ConditionalGaussianLikelihood
- setRowValueAt(int, int, boolean) - Method in class edu.cmu.tetrad.study.gene.tetradapp.model.BooleanGlassGeneIm
-
Sets the value in the given row of the boolean table for the given factor to the given value (true/false).
- setRule(Lofs.Rule) - Method in class edu.cmu.tetrad.search.Lofs
-
Sets the rule to use to do the orientation.
- setRuleType(GicScores.RuleType) - Method in class edu.cmu.tetrad.search.score.GicScores
- setRuleType(SemBicScore.RuleType) - Method in class edu.cmu.tetrad.search.score.SemBicScore
- setRunParallel(boolean) - Method in class edu.pitt.dbmi.algo.resampling.GeneralResamplingSearch
- setSamplePrior(double) - Method in class edu.cmu.tetrad.search.score.BdeScore
-
BDe does not use a sample prior.
- setSamplePrior(double) - Method in class edu.cmu.tetrad.search.score.BdeuScore
-
Set the sample prior
- setSamplePrior(double) - Method in class edu.cmu.tetrad.search.score.DiscreteBicScore
-
This method is not used for this score.
- setSamplePrior(double) - Method in interface edu.cmu.tetrad.search.score.DiscreteScore
-
Sets the sample prior.
- setSamplePrior(double) - Method in class edu.cmu.tetrad.search.SvarFges
-
Deprecated.Use the setters on the individual scores instead.
- setSamplePrior(double) - Method in class edu.cmu.tetrad.search.utils.FgesOrienter
-
For BDeu score for discrete search; see Chickering (2002).
- setSamplePrior(double) - Method in class edu.cmu.tetrad.study.performance.ComparisonParameters
- setSampleSampleVariability(double) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.simulation.MeasurementSimulator
-
Sets the sample to sample variability.
- setSampleSampleVariability(double) - Method in class edu.cmu.tetrad.study.gene.tetradapp.model.MeasurementSimulatorParams
- setSampleSize(int) - Method in class edu.cmu.tetrad.data.CorrelationMatrixOnTheFly
- setSampleSize(int) - Method in class edu.cmu.tetrad.data.CovarianceMatrix
- setSampleSize(int) - Method in class edu.cmu.tetrad.data.CovarianceMatrixOnTheFly
- setSampleSize(int) - Method in interface edu.cmu.tetrad.data.ICovarianceMatrix
- setSampleSize(int) - Method in class edu.cmu.tetrad.study.performance.ComparisonParameters
- setSampleStyle(Cstar.SampleStyle) - Method in class edu.cmu.tetrad.search.Cstar
-
Sets the sample style.
- setSaveCPDAGs(boolean) - Method in class edu.cmu.tetrad.algcomparison.Comparison
- setSaveCPDAGs(boolean) - Method in class edu.cmu.tetrad.algcomparison.TimeoutComparison
- setSaveData(boolean) - Method in class edu.cmu.tetrad.algcomparison.Comparison
- setSaveGraphs(boolean) - Method in class edu.cmu.tetrad.algcomparison.Comparison
- setSaveGraphs(boolean) - Method in class edu.cmu.tetrad.algcomparison.TimeoutComparison
- setSavePags(boolean) - Method in class edu.cmu.tetrad.algcomparison.Comparison
- setSavePags(boolean) - Method in class edu.cmu.tetrad.algcomparison.TimeoutComparison
- setScore(Lofs.Score) - Method in class edu.cmu.tetrad.search.Lofs
-
Sets the (LoFS) score to use.
- setScore(ScoreType) - Method in class edu.cmu.tetrad.study.performance.ComparisonParameters
- setScoreType(ScoreType) - Method in class edu.cmu.tetrad.sem.SemEstimator
- setScoreType(ScoreType) - Method in class edu.cmu.tetrad.sem.SemIm
- setScoreWrapper(ScoreWrapper) - Method in class edu.cmu.tetrad.algcomparison.algorithm.continuous.dag.DirectLingam
- setScoreWrapper(ScoreWrapper) - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.Fask
- setScoreWrapper(ScoreWrapper) - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FaskConcatenated
- setScoreWrapper(ScoreWrapper) - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FaskLofsConcatenated
- setScoreWrapper(ScoreWrapper) - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FaskVote
- setScoreWrapper(ScoreWrapper) - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FciIod
- setScoreWrapper(ScoreWrapper) - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.FgesConcatenated
- setScoreWrapper(ScoreWrapper) - Method in class edu.cmu.tetrad.algcomparison.algorithm.multi.Images
- setScoreWrapper(ScoreWrapper) - Method in interface edu.cmu.tetrad.algcomparison.algorithm.MultiDataSetAlgorithm
-
Sets a score wrapper if not null.
- setScoreWrapper(ScoreWrapper) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Boss
- setScoreWrapper(ScoreWrapper) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Fges
- setScoreWrapper(ScoreWrapper) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.FgesMb
- setScoreWrapper(ScoreWrapper) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Grasp
- setScoreWrapper(ScoreWrapper) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.PcLingam
- setScoreWrapper(ScoreWrapper) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.RestrictedBoss
- setScoreWrapper(ScoreWrapper) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Sp
- setScoreWrapper(ScoreWrapper) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Bfci
- setScoreWrapper(ScoreWrapper) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Gfci
- setScoreWrapper(ScoreWrapper) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.GraspFci
- setScoreWrapper(ScoreWrapper) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.SpFci
- setScoreWrapper(ScoreWrapper) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.SvarGfci
- setScoreWrapper(ScoreWrapper) - Method in class edu.cmu.tetrad.algcomparison.algorithm.oracle.pattern.Cstar
- setScoreWrapper(ScoreWrapper) - Method in interface edu.cmu.tetrad.algcomparison.utils.UsesScoreWrapper
- setScoreWrapper(ScoreWrapper) - Method in class edu.pitt.dbmi.algo.resampling.GeneralResamplingSearch
- setScoreWrapper(ScoreWrapper) - Method in class edu.pitt.dbmi.algo.resampling.GeneralResamplingTest
- setScoreWrapper(ScoreWrapper) - Method in class edu.pitt.dbmi.algo.resampling.task.GeneralResamplingSearchRunnable
- setSd(double) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.AbstractNbComponent
-
Sets the standard deviation.
- setSeed(long) - Method in class edu.cmu.tetrad.util.RandomUtil
-
Sets the seed to the given value.
- setSelected(Node, boolean) - Method in class edu.cmu.tetrad.data.BoxDataSet
-
Marks the given column as selected if 'selected' is true or deselected if 'selected' is false.
- setSelected(Node, boolean) - Method in interface edu.cmu.tetrad.data.DataSet
-
Marks the given column as selected if 'selected' is true or deselected if 'selected' is false.
- setSelected(Node, boolean) - Method in class edu.cmu.tetrad.data.NumberObjectDataSet
-
Marks the given column as selected if 'selected' is true or deselected if 'selected' is false.
- setSelectedModel(DataModel) - Method in class edu.cmu.tetrad.data.DataModelList
- setSelectionAlpha(double) - Method in class edu.cmu.tetrad.search.Cstar
-
Sets the selection alpha.
- setSelfLoopCoef(double) - Method in class edu.cmu.tetrad.sem.LargeScaleSimulation
- setSelfLoopStrength(double) - Method in class edu.cmu.tetrad.search.Lofs
-
Sets the self-loop strength, if applicable.
- setSemIm(SemIm) - Method in class edu.cmu.tetrad.search.work_in_progress.SampleVcpc
- setSemIm(SemIm) - Method in class edu.cmu.tetrad.search.work_in_progress.SampleVcpcFast
- setSemOptimizer(SemOptimizer) - Method in class edu.cmu.tetrad.sem.SemEstimator
- setSemPm(SemPm) - Method in class edu.cmu.tetrad.search.work_in_progress.SampleVcpc
- setSemPm(SemPm) - Method in class edu.cmu.tetrad.search.work_in_progress.SampleVcpcFast
- setSessionChanged(boolean) - Method in class edu.cmu.tetrad.session.Session
- setSetType(MarkovCheck.ConditioningSetType) - Method in class edu.cmu.tetrad.search.MarkovCheck
-
Sets the type of conditioning sets to use in the Markov check.
- setShortDescription(String) - Method in class edu.cmu.tetrad.util.ParamDescription
- setShowAlgorithmIndices(boolean) - Method in class edu.cmu.tetrad.algcomparison.Comparison
- setShowAlgorithmIndices(boolean) - Method in class edu.cmu.tetrad.algcomparison.TimeoutComparison
- setShowErrorTerms(boolean) - Method in class edu.cmu.tetrad.graph.SemGraph
- setShowSimulationIndices(boolean) - Method in class edu.cmu.tetrad.algcomparison.Comparison
- setShowSimulationIndices(boolean) - Method in class edu.cmu.tetrad.algcomparison.TimeoutComparison
- setShowUtilities(boolean) - Method in class edu.cmu.tetrad.algcomparison.Comparison
- setShowUtilities(boolean) - Method in class edu.cmu.tetrad.algcomparison.TimeoutComparison
- setSignificance(double) - Method in interface edu.cmu.tetrad.search.utils.TetradTest
- setSignificance(double) - Method in class edu.cmu.tetrad.search.utils.TetradTestContinuous
- setSignificance(double) - Method in class edu.cmu.tetrad.search.utils.TetradTestDiscrete
- setSignificance(double) - Method in class edu.cmu.tetrad.search.utils.TetradTestPopulation
- setSignificanceChecked(boolean) - Method in class edu.cmu.tetrad.search.Fofc
-
Sets whether the significance of the cluster should be checked for each cluster.
- setSimIndex(int) - Method in class edu.cmu.tetrad.algcomparison.algorithm.ExternalAlgorithm
- setSimulation(Simulation) - Method in class edu.cmu.tetrad.algcomparison.algorithm.ExternalAlgorithm
- setSimulator(MeasurementSimulatorParams) - Method in class edu.cmu.tetrad.study.gene.tetradapp.model.BooleanGlassGeneIm
- setSingularDepth(int) - Method in class edu.cmu.tetrad.search.GraspFci
- setSkewEdgeThreshold(double) - Method in class edu.cmu.tetrad.search.Fask
-
Sets the skew-edge threshold.
- setSortByUtility(boolean) - Method in class edu.cmu.tetrad.algcomparison.Comparison
- setSortByUtility(boolean) - Method in class edu.cmu.tetrad.algcomparison.TimeoutComparison
- setSpineThreshold(double) - Method in class edu.cmu.tetrad.search.IcaLingD
-
Sets the threshold used to prune the matrix for the purpose of searching for alternative strong diagonals.
- setSpringConstant(double) - Method in class edu.cmu.tetrad.graph.LayoutUtil.KamadaKawaiLayout
- setStable(boolean) - Method in class edu.cmu.tetrad.search.Cpc
-
Sets whether the stable adjacency search should be used.
- setStable(boolean) - Method in class edu.cmu.tetrad.search.Fas
-
Sets whether the stable adjacency search should be used.
- setStable(boolean) - Method in class edu.cmu.tetrad.search.Fci
-
Sets whether the stable options should be used in the initial adjacency search.
- setStable(boolean) - Method in class edu.cmu.tetrad.search.FciMax
-
Sets whether the stable option will be used for search.
- setStable(boolean) - Method in class edu.cmu.tetrad.search.Pc
-
Sets whether the stable adjacency search should be used.
- setStable(boolean) - Method in class edu.cmu.tetrad.search.work_in_progress.Fas2
- setStable(boolean) - Method in class edu.cmu.tetrad.search.work_in_progress.Fas3
-
Sets whether the stable adjacency search should be used.
- setStartIm(SemIm) - Method in class edu.cmu.tetrad.sem.SemEstimatorGibbsParams
- setStartingValue(double) - Method in class edu.cmu.tetrad.sem.Parameter
-
Sets the starting value in case this is a fixed parameter.
- setStartsWith(String, String, GeneralizedSemPm) - Static method in class edu.pitt.csb.mgm.MixedUtils
-
Set all existing parameters that begins with sta to template and also set template for any new parameters
- setStartsWithParametersEstimationInitializaationTemplate(String, String) - Method in class edu.cmu.tetrad.sem.GeneralizedSemPm
- setStartsWithParametersTemplate(String, String) - Method in class edu.cmu.tetrad.sem.GeneralizedSemPm
- setStdout(PrintStream) - Method in class edu.cmu.tetrad.data.simulation.LoadDataAndGraphs
- setStepsGenerated(int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.simulation.MeasurementSimulator
-
Sets the number of time steps to generate.
- setStepsGenerated(int) - Method in class edu.cmu.tetrad.study.gene.tetradapp.model.MeasurementSimulatorParams
- setStopEnergy(double) - Method in class edu.cmu.tetrad.graph.LayoutUtil.KamadaKawaiLayout
- setStretch(double) - Method in class edu.cmu.tetrad.sem.SemEstimatorGibbsParams
- setStructurePrior(double) - Method in class edu.cmu.tetrad.search.score.BdeScore
-
BDe does not use a structure prior.
- setStructurePrior(double) - Method in class edu.cmu.tetrad.search.score.BdeuScore
-
Sets the structure prior
- setStructurePrior(double) - Method in class edu.cmu.tetrad.search.score.ConditionalGaussianScore
- setStructurePrior(double) - Method in class edu.cmu.tetrad.search.score.DiscreteBicScore
-
Sets the structure prior.
- setStructurePrior(double) - Method in interface edu.cmu.tetrad.search.score.DiscreteScore
-
Sets the structure prior.
- setStructurePrior(double) - Method in class edu.cmu.tetrad.search.score.SemBicScore
- setStructurePrior(double) - Method in class edu.cmu.tetrad.search.SvarFges
-
Deprecated.Use the setters on the individual scores instead.
- setStructurePrior(double) - Method in class edu.cmu.tetrad.search.utils.FgesOrienter
-
For BDeu score for discrete search; see Chickering (2002).
- setStructurePrior(double) - Method in class edu.cmu.tetrad.study.performance.ComparisonParameters
- setSubstitutions(Map<String, Double>) - Method in class edu.cmu.tetrad.sem.GeneralizedSemIm
- setSymmetricFirstStep(boolean) - Method in class edu.cmu.tetrad.search.Fges
-
Sets whether the first step of the procedure will score both X->Y and Y->X and prefer the higher score (for adding X--Y to the graph).
- setSymmetricFirstStep(boolean) - Method in class edu.cmu.tetrad.search.FgesMb
-
Sets whether the first step of the procedure will score both X->Y and Y->X and prefer the higher score (for adding X--Y to the graph).
- setTabDelimitedTables(boolean) - Method in class edu.cmu.tetrad.algcomparison.Comparison
- setTabDelimitedTables(boolean) - Method in class edu.cmu.tetrad.algcomparison.TimeoutComparison
- setTarget(String) - Method in class edu.cmu.tetrad.classify.ClassifierBayesUpdaterDiscrete
-
Sets the target variable.
- setTestType(BpcTestType) - Method in class edu.cmu.tetrad.search.utils.TetradTestContinuous
- setTetradLoggerConfig(TetradLoggerConfig) - Method in class edu.cmu.tetrad.util.TetradLogger
-
Sets what configuration should be used to determine which events to log.
- setTheta(DoubleMatrix2D) - Method in class edu.pitt.csb.mgm.Mgm.MGMParams
- setThr(double) - Method in class edu.cmu.tetrad.search.work_in_progress.Glasso
- setThreshold(boolean) - Method in class edu.cmu.tetrad.search.test.IndTestProbabilistic
- setThreshold(boolean) - Method in class edu.pitt.dbmi.algo.bayesian.constraint.search.PagSamplingRfci
- setThreshold(double) - Method in class edu.cmu.tetrad.search.FactorAnalysis
-
Sets the threshold.
- setThreshold(double) - Method in class edu.cmu.tetrad.search.test.Kci
-
Sets the threshold.
- setThresholdNoRandomConstrainSearch(boolean) - Method in class edu.pitt.dbmi.algo.bayesian.constraint.search.RfciBsc
- setThresholdNoRandomDataSearch(boolean) - Method in class edu.pitt.dbmi.algo.bayesian.constraint.search.RfciBsc
- setTier(int, List<String>) - Method in class edu.cmu.tetrad.data.Knowledge
-
Sets the variable in a given tier to the specified list.
- setTierForbiddenWithin(int, boolean) - Method in class edu.cmu.tetrad.data.Knowledge
-
Forbids any variable from being parent of any other variable within the given tier, or cancels this forbidding.
- setToken(int, int, String) - Method in class edu.cmu.tetrad.util.TextTable
-
Sets the token at the given row and column, each of which must be >= 0 and less than the number of rows or columns, respectively.
- setTolerance(double) - Method in class edu.cmu.tetrad.search.FastIca
-
Sets a positive scalar giving the tolerance at which the un-mixing matrix is considered to have converged.
- setToleranceDepth(int) - Method in class edu.cmu.tetrad.search.work_in_progress.GraspTol
- setToTautology() - Method in class edu.cmu.tetrad.bayes.Proposition
-
Specifies that all variables in the proposition are either completely allowed (true) or completely disallowed (false) for all of their categories.
- setTrial(int) - Method in class edu.cmu.tetrad.study.performance.ComparisonParameters
- setTrimmingStyle(int) - Method in class edu.cmu.tetrad.search.FgesMb
- setTrueDag(Graph) - Method in class edu.cmu.tetrad.study.performance.ComparisonResult
- setTrueGraph(Graph) - Method in class edu.cmu.tetrad.search.SvarFges
-
If the true graph is set, asterisks will be printed in log output for the true edges.
- setTrueGraph(Graph) - Method in class edu.cmu.tetrad.search.utils.FgesOrienter
-
If the true graph is set, askterisks will be printed in log output for the true edges.
- setTrueGraph(Graph) - Method in interface edu.cmu.tetrad.search.utils.IPurify
- setTrueGraph(Graph) - Method in class edu.cmu.tetrad.search.utils.PurifyScoreBased
- setTrueGraph(Graph) - Method in class edu.cmu.tetrad.search.utils.PurifyTetradBased
- setTrueInputs(int[]) - Method in class edu.cmu.tetrad.search.work_in_progress.DMSearch
- setTruePag(Graph) - Method in class edu.cmu.tetrad.search.utils.FciOrient
-
Sets the true PAG for comparison.
- setTruePag(Graph) - Method in class edu.cmu.tetrad.search.utils.SvarFciOrient
- setTruePag(Graph) - Method in class edu.cmu.tetrad.search.utils.TsDagToPag
- setTwoCycleScreeningCutoff(double) - Method in class edu.cmu.tetrad.search.Fask
-
Sets the cutoff for two-cycle screening.
- setType(ParamConstraintType) - Method in class edu.cmu.tetrad.sem.ParamConstraint
- setUncoveredDepth(int) - Method in class edu.cmu.tetrad.search.Grasp
-
Sets the maximum depth at which uncovered tucks can be performed within the depth-first search of GRaSP.
- setUncoveredDepth(int) - Method in class edu.cmu.tetrad.search.work_in_progress.GraspTol
- setUnderLineTriples(Set<Triple>) - Method in class edu.cmu.tetrad.graph.Dag
- setUnderLineTriples(Set<Triple>) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
- setUnderLineTriples(Set<Triple>) - Method in interface edu.cmu.tetrad.graph.Graph
- setUnderLineTriples(Set<Triple>) - Method in class edu.cmu.tetrad.graph.LagGraph
- setUnderLineTriples(Set<Triple>) - Method in class edu.cmu.tetrad.graph.SemGraph
- setUnderLineTriples(Set<Triple>) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- setUnderLineTriples(Set<Triple>) - Method in class edu.cmu.tetrad.graph.Underlines
- setUp() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.TestSimpleRandomizer
-
Sets up a graph to randomize with 100 variables in it.
- setUp() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.simulation.TestMeasurementSimulator
-
Sets up a GeneHistory object in the format for Richard's diagnostic.
- setUpperBound(double) - Method in class edu.pitt.dbmi.algo.bayesian.constraint.search.RfciBsc
- setUpperBoundDouble(double) - Method in class edu.cmu.tetrad.util.ParamDescription
- setUpperBoundInt(int) - Method in class edu.cmu.tetrad.util.ParamDescription
- setUpperBoundLong(long) - Method in class edu.cmu.tetrad.util.ParamDescription
- setUseBes(boolean) - Method in class edu.cmu.tetrad.search.Boss
-
Sets up BOSS to use the BES algorithm to render BOSS correct under the faithfulness assumption.
- setUseDataOrder(boolean) - Method in class edu.cmu.tetrad.search.Boss
-
True if the order of the variables in the data should be used for an initial best-order search, false if a random permutation should be used.
- setUseDataOrder(boolean) - Method in class edu.cmu.tetrad.search.Grasp
-
True if the order of the variables in the data should be used for an initial best-order search, false if a random permutation should be used.
- setUseDataOrder(boolean) - Method in class edu.cmu.tetrad.search.GraspFci
- setUseDataOrder(boolean) - Method in class edu.cmu.tetrad.search.work_in_progress.GraspTol
- setUseDataOrder(boolean) - Method in class edu.cmu.tetrad.search.work_in_progress.OtherPermAlgs
- setUseDisplayNames(boolean) - Method in class edu.cmu.tetrad.search.utils.BayesImParser
-
Sets whether to use display names.
- setUseFgES(boolean) - Method in class edu.cmu.tetrad.search.work_in_progress.DMSearch
- setUseHeuristic(boolean) - Method in class edu.cmu.tetrad.search.utils.MaxP
-
Sets whether the max P heuristic should be used.
- setUseMaxPHeuristic(boolean) - Method in class edu.cmu.tetrad.search.Pc
-
Sets whether the max-p heuristic should be used for collider discovery.
- setUsePearl(boolean) - Method in class edu.cmu.tetrad.search.work_in_progress.OtherPermAlgs
- setUseRaskuttiUhler(boolean) - Method in class edu.cmu.tetrad.search.Grasp
-
True if the Raskutti-Uhler method should be used, false if the Verma-Pearl method should be used.
- setUseRaskuttiUhler(boolean) - Method in class edu.cmu.tetrad.search.GraspFci
- setUseRaskuttiUhler(boolean) - Method in class edu.cmu.tetrad.search.utils.TeyssierScorer
- setUseRaskuttiUhler(boolean) - Method in class edu.cmu.tetrad.search.work_in_progress.GraspTol
- setUseScore(boolean) - Method in class edu.cmu.tetrad.search.Grasp
-
True if the score should be used (if both a score and a test are provided), false if not.
- setUseScore(boolean) - Method in class edu.cmu.tetrad.search.GraspFci
- setUseScore(boolean) - Method in class edu.cmu.tetrad.search.utils.TeyssierScorer
- setUseScore(boolean) - Method in class edu.cmu.tetrad.search.work_in_progress.GraspTol
- setUseScore(boolean) - Method in class edu.cmu.tetrad.search.work_in_progress.OtherPermAlgs
- setValue(double) - Method in class edu.cmu.tetrad.sem.Mapping
-
Sets the value of the array element at the stored coordinates (i, j).
- setValue(double) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.AbstractNbComponent
- setValue(double) - Method in interface edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.NbComponent
-
Sets the parents of this component.
- setValue(int[], int) - Method in class edu.cmu.tetrad.util.MultiDimIntTable
-
Sets the value at the given coordinates to the given value, returning the new value.
- setValue(int, boolean) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.BooleanFunction
-
Sets the boolean value in a given row of the table.
- setValue(int, double) - Method in class edu.cmu.tetrad.sem.SemProposition
- setValue(int, int, double) - Method in class edu.cmu.tetrad.data.CorrelationMatrixOnTheFly
- setValue(int, int, double) - Method in class edu.cmu.tetrad.data.CovarianceMatrix
- setValue(int, int, double) - Method in class edu.cmu.tetrad.data.CovarianceMatrixOnTheFly
- setValue(int, int, double) - Method in interface edu.cmu.tetrad.data.ICovarianceMatrix
- setValue(int, int, double) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.LTMatrixF
-
Assigns double x to matrix element (r, c).
- setValue(int, int, double) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.MatrixF
-
Assigns double x to matrix element at (r, c).
- setValue(int, int, double) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.SymMatrixF
-
Sets the value of element (
row,col) tox - setValue(int, int, float) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.LTMatrixF
-
Assigns float x to matrix element (r, c)
- setValue(int, int, float) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.MatrixF
-
Assigns float x to matrix element at (r, c)
- setValue(int, int, float) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.SymMatrixF
-
Sets the value of element (
row,col) tox - setValue(int, int, int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.LTMatrix
-
Assigns integer x to matrix element (r, c).
- setValue(int, int, int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.Matrix
-
Assigns integer x to matrix element at (r, c).
- setValue(int, int, int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.SymMatrix
-
Sets the value of element (
row,col) tox - setValue(int, int, short) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.LTMatrix
-
Assigns short x to matrix element (r, c)
- setValue(int, int, short) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.Matrix
-
Assigns short x to matrix element at (r, c)
- setValue(int, int, short) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.SymMatrix
-
Sets the value of element (
row,col) tox - setValue(Node, double) - Method in class edu.cmu.tetrad.sem.SemProposition
- setVarHigh(double) - Method in class edu.cmu.tetrad.algcomparison.simulation.ConditionalGaussianSimulation
- setVarHigh(double) - Method in class edu.cmu.tetrad.algcomparison.simulation.LinearSineSimulation
- setVariable(int, boolean) - Method in class edu.cmu.tetrad.bayes.Proposition
-
Specifies that all categories for the given variable are either all allowed (true) or all disallowed (false).
- setVariables(List<Node>) - Method in class edu.cmu.tetrad.data.CorrelationMatrixOnTheFly
- setVariables(List<Node>) - Method in class edu.cmu.tetrad.data.CovarianceMatrix
- setVariables(List<Node>) - Method in class edu.cmu.tetrad.data.CovarianceMatrixOnTheFly
- setVariables(List<Node>) - Method in interface edu.cmu.tetrad.data.ICovarianceMatrix
- setVariables(List<Node>) - Method in class edu.cmu.tetrad.search.PcMb
- setVariables(List<Node>) - Method in class edu.cmu.tetrad.search.score.DiscreteBicScore
-
Sets the variables to a new list of the same size.
- setVariables(List<Node>) - Method in class edu.cmu.tetrad.search.score.GicScores
- setVariables(List<Node>) - Method in class edu.cmu.tetrad.search.score.SemBicScore
- setVariables(List<Node>) - Method in class edu.cmu.tetrad.search.test.IndTestFisherZ
-
Sets the variables to a new list of the same size.
- setVariables(List<Node>) - Method in class edu.cmu.tetrad.search.test.IndTestTrekSep
-
Sets the varialbe to this list (of the same length).
- setVariables(List<Node>) - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestFisherZRecursive
- setVariables(List<Node>) - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestPositiveCorr
- setVariables(List<Node>) - Method in class edu.cmu.tetrad.search.work_in_progress.SemBicScoreDeterministic
- setVariablesCopied(boolean) - Method in class edu.cmu.tetrad.data.Discretizer
- setVariablesTemplate(String) - Method in class edu.cmu.tetrad.sem.GeneralizedSemPm
- setVarLow(double) - Method in class edu.cmu.tetrad.algcomparison.simulation.ConditionalGaussianSimulation
- setVarLow(double) - Method in class edu.cmu.tetrad.algcomparison.simulation.LinearSineSimulation
- setVarRange(double, double) - Method in class edu.cmu.tetrad.sem.LargeScaleSimulation
- setVarsPerInd(int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.LagGraphParams
- setVarsPerInd(int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ManualLagGraphParams
-
Sets the number of variables per individual.
- setVerbose(boolean) - Method in interface edu.cmu.tetrad.cluster.ClusteringAlgorithm
-
True iff verbose output should be printed.
- setVerbose(boolean) - Method in class edu.cmu.tetrad.cluster.KMeans
- setVerbose(boolean) - Method in class edu.cmu.tetrad.data.CorrelationMatrixOnTheFly
- setVerbose(boolean) - Method in class edu.cmu.tetrad.data.CovarianceMatrixOnTheFly
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.BFci
-
Sets whether verbose output should be printed.
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.Boss
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.Cfci
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.Cpc
-
Sets whether verbose output should be printed.
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.Cstar
-
Sets whether verbose output will be printed.
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.Fas
-
Sets whether verbose output should be printed.
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.Fasd
-
Sets whether verbose output will be printed.
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.FastIca
-
Sets whether verbose output should be printed.
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.Fci
-
Sets whether verbose output should be printed.
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.FciMax
-
Sets whether verbose output should be printed.
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.Fges
-
Sets whether verbose output should be produced.
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.FgesMb
-
Sets whether verbose output should be produced.
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.Fofc
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.Ftfc
-
Sets whether verbose output should be printed.
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.GFci
-
Sets whether verbose output should be printed.
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.Grasp
-
Sets whether verbose output is printed.
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.GraspFci
-
Sets whether verbose output should be printed.
- setVerbose(boolean) - Method in interface edu.cmu.tetrad.search.IFas
-
Sets whether verbose output should be printed.
- setVerbose(boolean) - Method in interface edu.cmu.tetrad.search.IndependenceTest
-
Sets whether this test will print verbose output.
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.IndTestIod
-
Sets the test to verbose or not.
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.Pc
-
Sets whether verbose output should be given.
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.Pcd
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.Rfci
-
Sets whether verbose output is printed.
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.score.GicScores
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.score.IndTestScore
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.score.PoissonPriorScore
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.score.SemBicScore
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.SpFci
-
Sets whether verbose output is printed.
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.SvarFas
-
Sets whether verbose output should be printed.
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.SvarFci
-
Sets whether verbose output is to be printed.
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.SvarFges
-
Sets whether verbose output should be produced.
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.SvarGfci
-
Sets whether verbose output is printed.
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.test.IndTestChiSquare
-
Sets whether verbose output should be printed.
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.test.IndTestConditionalCorrelation
-
Sets whether verbose output should be printed.
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.test.IndTestConditionalGaussianLrt
-
Sets whether verbose output should be printed.
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.test.IndTestDegenerateGaussianLrt
-
Sets whether verbose output should be printed.
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.test.IndTestFisherZ
-
Sets whether verbose output should be printed.
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.test.IndTestFisherZConcatenateResiduals
-
Sets whether verbose output is printed.
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.test.IndTestFisherZFisherPValue
-
Sets whether verbose output is printed.
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.test.IndTestGSquare
-
Sets whether verbose output is printed.
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.test.IndTestHsic
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.test.IndTestIndependenceFacts
-
Sets whether verbose output is to be printed.
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.test.IndTestMulti
-
Sets whether this test will print verbose output.
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.test.IndTestMvpLrt
-
Returns whether verbose output should be printed.
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.test.IndTestProbabilistic
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.test.IndTestRegression
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.test.IndTestTrekSep
-
Sets whether verbose output should be printed.
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.test.Kci
-
Sets whether verbose output is printed.
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.test.MsepTest
-
Sets whether verbose output should be printed.
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.test.ScoreIndTest
-
Sets whether verbose output should be printed.
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.utils.Bes
-
Sets whether verbose output should be printed.
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.utils.BesPermutation
-
Sets whether verbose output should be printed.
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.utils.DagSepsets
-
Thsi method is not used.
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.utils.DagToPag
-
Setws whether verbose output should be printed.
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.utils.FciOrient
-
Sets whether verbose output is printed.
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.utils.FgesOrienter
-
Sets whether verbose output should be produced.
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.utils.MeekRules
-
Sets whether verbose output should be printed.
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.utils.PcCommon
-
Sets whether verbose output should be printed.
- setVerbose(boolean) - Method in interface edu.cmu.tetrad.search.utils.SepsetProducer
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.utils.SepsetsConservative
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.utils.SepsetsGreedy
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.utils.SepsetsPossibleMsep
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.utils.SepsetsSet
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.utils.SvarFciOrient
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.utils.TsDagToPag
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.work_in_progress.Fas2
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.work_in_progress.Fas3
-
Sets whether verbose output should be printed.
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.work_in_progress.FasFdr
-
Sets whether verbose output will be printed.
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.work_in_progress.GraspTol
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestCramerT
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestFisherZGeneralizedInverse
-
Sets whether verbose output should be printed.
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestFisherZPercentIndependent
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestFisherZRecursive
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestMixedMultipleTTest
-
Sets whether verbose output should be printed.
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestMnlrLr
-
Sets whether this test will print verbose output.
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestMultinomialLogisticRegression
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestPositiveCorr
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestSepsetDci
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestUniformScatter
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.work_in_progress.Kpc
-
Sets whether verbose output should be printed.
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.work_in_progress.OtherPermAlgs
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.work_in_progress.ProbabilisticMapIndependence
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.work_in_progress.SampleVcpc
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.work_in_progress.SampleVcpcFast
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.work_in_progress.SemBicScoreDeterministic
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.work_in_progress.VcFas
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.work_in_progress.VcPc
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.work_in_progress.VcPcAlt
- setVerbose(boolean) - Method in class edu.cmu.tetrad.search.work_in_progress.VcPcFast
- setVerbose(boolean) - Method in class edu.cmu.tetrad.sem.LargeScaleSimulation
- setVerbose(boolean) - Method in class edu.cmu.tetrad.simulation.GdistanceRandom
- setVerbose(boolean) - Method in class edu.cmu.tetrad.simulation.HsimAutoC
- setVerbose(boolean) - Method in class edu.cmu.tetrad.simulation.HsimAutoRun
- setVerbose(boolean) - Method in class edu.cmu.tetrad.simulation.HsimRepeatAC
- setVerbose(boolean) - Method in class edu.cmu.tetrad.simulation.HsimRepeatAutoRun
- setVerbose(boolean) - Method in class edu.pitt.csb.mgm.IndTestMultinomialLogisticRegressionWald
- setVerbose(boolean) - Method in class edu.pitt.dbmi.algo.bayesian.constraint.search.PagSamplingRfci
- setVerbose(boolean) - Method in class edu.pitt.dbmi.algo.bayesian.constraint.search.RfciBsc
-
Sets whether verbose output should be produced.
- setVerbose(boolean) - Method in class edu.pitt.dbmi.algo.resampling.GeneralResamplingSearch
- setVerbose(boolean) - Method in class edu.pitt.dbmi.algo.resampling.GeneralResamplingTest
-
Sets whether verbose output should be produced.
- setWeight(String, double) - Method in class edu.cmu.tetrad.algcomparison.statistic.Statistics
-
Sets the utility weight of the statistic by the given name.
- setWidth(double) - Method in class edu.cmu.tetrad.search.test.ConditionalCorrelationIndependence
-
Sets the kernel width.
- setWidthMultiplier(double) - Method in class edu.cmu.tetrad.search.test.Kci
-
Sets the width multiplier.
- setWInit(Matrix) - Method in class edu.cmu.tetrad.search.FastIca
-
Sets the initial un-mixing matrix of dimension (n.comp,n.comp).
- setWithoutReplacements(boolean) - Method in class edu.cmu.tetrad.data.BootstrapSampler
- setWrite(boolean) - Method in class edu.cmu.tetrad.simulation.HsimAutoC
- setWrite(boolean) - Method in class edu.cmu.tetrad.simulation.HsimAutoRun
- setWrite(boolean) - Method in class edu.cmu.tetrad.simulation.HsimRepeatAC
- setWrite(boolean) - Method in class edu.cmu.tetrad.simulation.HsimRepeatAutoRun
- setWThreshold(double) - Method in class edu.cmu.tetrad.search.Dagma
- severe(String) - Method in class edu.cmu.tetrad.util.LogUtils
- Sextad - Class in edu.cmu.tetrad.search.utils
-
Represents an ordered sextad of nodes.
- Sextad - Class in edu.cmu.tetrad.search.work_in_progress
-
Represents an ordered sextad of variables.
- Sextad(int, int, int, int, int, int) - Constructor for class edu.cmu.tetrad.search.utils.Sextad
-
Constructor.
- Sextad(Node[]) - Constructor for class edu.cmu.tetrad.search.work_in_progress.Sextad
- Sextad(Node, Node, Node, Node, Node, Node) - Constructor for class edu.cmu.tetrad.search.work_in_progress.Sextad
- SHD - Enum constant in enum class edu.cmu.tetrad.study.performance.Comparison.TableColumn
- SHD - Enum constant in enum class edu.cmu.tetrad.study.performance.Comparison2.TableColumn
- ShiftSearch - Class in edu.cmu.tetrad.search.utils
-
Tries to find a good shifting of variables to minimize average BIC for time-series data.
- ShiftSearch(List<DataModel>) - Constructor for class edu.cmu.tetrad.search.utils.ShiftSearch
- ShortDataBox - Class in edu.cmu.tetrad.data
-
Stores a 2D array of short data.
- ShortDataBox(int, int) - Constructor for class edu.cmu.tetrad.data.ShortDataBox
-
Constructs an 2D short array consisting entirely of missing values (-99).
- ShortDataBox(short[][]) - Constructor for class edu.cmu.tetrad.data.ShortDataBox
-
Constructs a new data box using the given 2D short data array as data.
- shuffle(List<?>) - Static method in class edu.cmu.tetrad.util.RandomUtil
-
This is just the RandomUtil.shuffle method (thanks!) but using the Tetrad RandomUtil to get random numbers.
- shuffleColumns(DataSet) - Static method in class edu.cmu.tetrad.data.DataTransforms
- shuffleColumns2(List<DataSet>) - Static method in class edu.cmu.tetrad.data.DataTransforms
- Significance - Enum constant in enum class edu.cmu.tetrad.search.utils.ClusterSignificance.CheckType
- SIGNIFICANCE_CHECKED - Static variable in class edu.cmu.tetrad.util.Params
- significant(List<Integer>, double) - Method in class edu.cmu.tetrad.search.utils.ClusterSignificance
- simIndex - Variable in class edu.cmu.tetrad.algcomparison.algorithm.ExternalAlgorithm
- SimpleDataLoader - Class in edu.cmu.tetrad.data
- SimpleDataLoader() - Constructor for class edu.cmu.tetrad.data.SimpleDataLoader
- SimpleRandomizer - Class in edu.cmu.tetrad.study.gene.tetrad.gene.history
-
Randomizes a graph using existing factors by first removing all edges and then adding for each factor (a) an edge from the same factor at time lag 1 and (b) a given number of factors chosen uniformly from all lagged factors with lag > 0.
- SimpleRandomizer(int, int, int, double) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.history.SimpleRandomizer
- SIMPLIFIED_BPC - Enum constant in enum class edu.cmu.tetrad.search.utils.BpcAlgorithmType
- SIMPLIFIED_BPC_DEPTH_0 - Enum constant in enum class edu.cmu.tetrad.search.utils.BpcAlgorithmType
- SIMPLIFIED_BPC_DEPTH_1 - Enum constant in enum class edu.cmu.tetrad.search.utils.BpcAlgorithmType
- simulate(GeneHistory) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.simulation.MeasurementSimulator
-
Simulates (optionally) neither, either, or both of two three-dimensionaly data sets, rawData and measuredData.
- simulate(GeneHistory) - Method in class edu.cmu.tetrad.study.gene.tetradapp.model.MeasurementSimulatorParams
- simulateData() - Method in class edu.cmu.tetrad.study.gene.tetradapp.model.BooleanGlassGeneIm
-
Uses the MeasurementSimulator class to simulate a set of measurement data and optionally a set of raw cell expression data.
- simulateData(int, boolean) - Method in interface edu.cmu.tetrad.bayes.BayesIm
-
Simulates a sample with the given sample size.
- simulateData(int, boolean) - Method in class edu.cmu.tetrad.bayes.DirichletBayesIm
-
Simulates and returns a dataset with number of cases equal to
sampleSize. - simulateData(int, boolean) - Method in class edu.cmu.tetrad.bayes.MlBayesIm
- simulateData(int, boolean) - Method in class edu.cmu.tetrad.bayes.MlBayesImObs
-
Simulates a sample with the given sample size.
- simulateData(int, boolean) - Method in class edu.cmu.tetrad.bayes.UpdatedBayesIm
- simulateData(int, boolean) - Method in interface edu.cmu.tetrad.data.Simulator
-
Simulates data from the model associated with this object.
- simulateData(int, boolean) - Method in class edu.cmu.tetrad.sem.GeneralizedSemIm
- simulateData(int, boolean) - Method in class edu.cmu.tetrad.sem.SemIm
-
This simulate method uses the implied covariance metrix directly to simulate data, instead of going tier by tier.
- simulateData(int, boolean) - Method in class edu.cmu.tetrad.sem.StandardizedSemIm
-
A convenience method, in case we want to change out mind about how to simulate.
- simulateData(int, boolean, int[]) - Method in class edu.cmu.tetrad.bayes.MlBayesIm
-
Simulates a sample with the given sample size.
- simulateData(DataSet, boolean) - Method in interface edu.cmu.tetrad.bayes.BayesIm
-
Overwrites the given dataSet with a new simulated dataSet, to avoid allocating memory.
- simulateData(DataSet, boolean) - Method in class edu.cmu.tetrad.bayes.DirichletBayesIm
-
Would be nice to have this method supported, but no one's using it, so it's not.
- simulateData(DataSet, boolean) - Method in class edu.cmu.tetrad.bayes.MlBayesIm
- simulateData(DataSet, boolean) - Method in class edu.cmu.tetrad.bayes.MlBayesImObs
- simulateData(DataSet, boolean) - Method in class edu.cmu.tetrad.bayes.UpdatedBayesIm
- simulateData(DataSet, boolean, int[]) - Method in class edu.cmu.tetrad.bayes.MlBayesIm
- simulateDataAvoidInfinity(int, boolean) - Method in class edu.cmu.tetrad.sem.GeneralizedSemIm
- simulateDataCholesky(int, boolean) - Method in class edu.cmu.tetrad.sem.SemIm
-
Simulates data from this Sem using a Cholesky decomposition of the implied covariance matrix.
- simulateDataFisher(double[][], int, double) - Method in class edu.cmu.tetrad.sem.LargeScaleSimulation
-
Simulates data using the model of R.
- simulateDataFisher(int) - Method in class edu.cmu.tetrad.sem.GeneralizedSemIm
-
Simulates data using the model of R.
- simulateDataFisher(int) - Method in class edu.cmu.tetrad.sem.LargeScaleSimulation
-
Simulates data using the model of R.
- simulateDataFisher(int, int, double) - Method in class edu.cmu.tetrad.sem.GeneralizedSemIm
-
Simulates data using the model of R.
- simulateDataFisher(int, int, int, double, boolean) - Method in class edu.cmu.tetrad.sem.LargeScaleSimulation
- simulateDataMinimizeSurface(int, boolean) - Method in class edu.cmu.tetrad.sem.GeneralizedSemIm
- simulateDataNSteps(int, boolean) - Method in class edu.cmu.tetrad.sem.GeneralizedSemIm
- simulateDataRecursive(int) - Method in class edu.cmu.tetrad.sem.LargeScaleSimulation
-
This simulates data by picking random values for the exogenous terms and percolating this information down through the SEM, assuming it is acyclic.
- simulateDataRecursive(int, boolean) - Method in class edu.cmu.tetrad.sem.GeneralizedSemIm
-
This simulates data by picking random values for the exogenous terms and percolating this information down through the SEM, assuming it is acyclic.
- simulateDataRecursive(int, boolean) - Method in class edu.cmu.tetrad.sem.SemIm
- simulateDataReducedForm(int) - Method in class edu.cmu.tetrad.sem.LargeScaleSimulation
-
Simulates data using the model X = (I - B)Y^-1 * e.
- simulateDataReducedForm(int, boolean) - Method in class edu.cmu.tetrad.sem.SemIm
- simulateDataReducedForm(int, boolean) - Method in class edu.cmu.tetrad.sem.StandardizedSemIm
- SimulateNetwork - Class in edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin
- SimulateNetwork() - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.SimulateNetwork
- SimulateNetworkMain - Class in edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin
- SimulateNetworkMain() - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.SimulateNetworkMain
- simulateOneRecord(Vector) - Method in class edu.cmu.tetrad.sem.GeneralizedSemIm
- simulateOneRecord(Vector) - Method in class edu.cmu.tetrad.sem.SemIm
- simulation - Variable in class edu.cmu.tetrad.algcomparison.algorithm.ExternalAlgorithm
- Simulation - Interface in edu.cmu.tetrad.algcomparison.simulation
-
The interface that simulations must implement.
- SIMULATION_ERROR_TYPE - Static variable in class edu.cmu.tetrad.util.Params
- SIMULATION_PARAM1 - Static variable in class edu.cmu.tetrad.util.Params
- SIMULATION_PARAM2 - Static variable in class edu.cmu.tetrad.util.Params
- SimulationParamsSource - Interface in edu.cmu.tetrad.session
-
Created by jdramsey on 3/14/16.
- SimulationPath - Interface in edu.cmu.tetrad.algcomparison.statistic.utils
-
Some simulations may wish to implement this interface to specify a simulation path, which will be printed in the output.
- Simulations - Class in edu.cmu.tetrad.algcomparison.simulation
-
A list of simulations to be compared.
- Simulations() - Constructor for class edu.cmu.tetrad.algcomparison.simulation.Simulations
- SimulationStudy - Class in edu.cmu.tetrad.session
-
Runs a simulation edu.cmu.tetrad.study for a session which traverses a subtree of the session graph in depth-first order and executes each node encountered a specified number of times.
- SimulationStudy(Session) - Constructor for class edu.cmu.tetrad.session.SimulationStudy
-
Constructs a new simulation edu.cmu.tetrad.study for the given session.
- SimulationTypes - Class in edu.cmu.tetrad.algcomparison.simulation
-
Jun 4, 2019 3:10:49 PM
- SimulationUtils - Class in edu.cmu.tetrad.algcomparison.simulation
-
Jun 4, 2019 5:21:45 PM
- Simulator - Interface in edu.cmu.tetrad.data
-
Created by jdramsey on 12/22/15.
- SingleGraph - Class in edu.cmu.tetrad.algcomparison.graph
-
Stores a single graph for use in simulations, etc.
- SingleGraph(Graph) - Constructor for class edu.cmu.tetrad.algcomparison.graph.SingleGraph
- SingleGraphAlg - Class in edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag
-
PC.
- SingleGraphAlg(Graph) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.SingleGraphAlg
- SingleValue - Class in edu.cmu.tetrad.util.dist
-
A pretend distribution that always returns the given value when nextRandom() is called.
- SingleValue(double) - Constructor for class edu.cmu.tetrad.util.dist.SingleValue
-
Constructs single value "distribution" using the given value.
- size() - Method in class edu.cmu.tetrad.algcomparison.statistic.Statistics
-
The number of statistics.
- size() - Method in interface edu.cmu.tetrad.data.Covariances
-
Returns the dimensiom of the matrix.
- size() - Method in class edu.cmu.tetrad.data.CovariancesDoubleForkJoin
- size() - Method in class edu.cmu.tetrad.data.DataModelList
- size() - Method in class edu.cmu.tetrad.data.IndependenceFacts
- size() - Method in class edu.cmu.tetrad.search.utils.SepsetMap
-
Returns the number of {x, y} in the key set of the map.
- size() - Method in class edu.cmu.tetrad.search.utils.TeyssierScorer
- size() - Method in class edu.cmu.tetrad.search.work_in_progress.SepsetMapDci
- size() - Method in class edu.cmu.tetrad.util.Vector
- skeletonToMatrix(Graph) - Static method in class edu.pitt.csb.mgm.MixedUtils
- skew - Enum constant in enum class edu.cmu.tetrad.search.Lofs.Score
- skew(double[], double[], boolean) - Static method in class edu.cmu.tetrad.search.Fask
- Skew - Class in edu.cmu.tetrad.algcomparison.algorithm.pairwise
-
Skew.
- Skew - Enum constant in enum class edu.cmu.tetrad.search.Lofs.Rule
- Skew() - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.pairwise.Skew
- Skew(Algorithm) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.pairwise.Skew
- SKEW - Enum constant in enum class edu.cmu.tetrad.search.Fask.LeftRight
- SKEW_EDGE_THRESHOLD - Static variable in class edu.cmu.tetrad.util.Params
- SkewE - Class in edu.cmu.tetrad.algcomparison.algorithm.pairwise
-
SkewE.
- SkewE - Enum constant in enum class edu.cmu.tetrad.search.Lofs.Rule
- SkewE() - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.pairwise.SkewE
- SkewE(Algorithm) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.pairwise.SkewE
- skewness(double[]) - Static method in class edu.cmu.tetrad.util.StatUtils
- skewness(double[], int) - Static method in class edu.cmu.tetrad.util.StatUtils
- skewness(long[]) - Static method in class edu.cmu.tetrad.util.StatUtils
- skewness(long[], int) - Static method in class edu.cmu.tetrad.util.StatUtils
- SKIP_NUM_RECORDS - Static variable in class edu.cmu.tetrad.util.Params
- smooth(DoubleMatrix1D, DoubleMatrix1D) - Method in class edu.pitt.csb.mgm.ConvexProximal
-
Calculate value of g(X) and gradient of g(X) at the same time for efficiency reasons.
- smooth(DoubleMatrix1D, DoubleMatrix1D) - Method in class edu.pitt.csb.mgm.Mgm
-
non-penalized -log(pseudolikelihood) this is the smooth function g(x) in prox gradient this overloaded version calculates both nll and the smooth gradient at the same time any value in gradOut will be replaced by the new calculations
- smoothGradient(DoubleMatrix1D) - Method in class edu.pitt.csb.mgm.Mgm
-
Gradient of the pseudolikelihood
- smoothValue(DoubleMatrix1D) - Method in class edu.pitt.csb.mgm.Mgm
-
non-penalized -log(pseudolikelihood) this is the smooth function g(x) in prox gradient
- solve(Matrix, Matrix) - Static method in class edu.cmu.tetrad.util.TetradAlgebra
- sortEdges(List<Edge>) - Static method in class edu.cmu.tetrad.graph.Edges
- sp(TeyssierScorer) - Method in class edu.cmu.tetrad.search.work_in_progress.OtherPermAlgs
- Sp - Class in edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag
-
SP (Sparsest Permutation)
- Sp - Class in edu.cmu.tetrad.search
-
Implements the SP (Sparsest Permutation) algorithm.
- Sp() - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Sp
- Sp(ScoreWrapper) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Sp
- Sp(Score) - Constructor for class edu.cmu.tetrad.search.Sp
-
This algorithm will work with an arbitrary score.
- SP - Enum constant in enum class edu.cmu.tetrad.search.work_in_progress.OtherPermAlgs.Method
- SPACE - Enum constant in enum class edu.cmu.tetrad.util.TextTable.Delimiter
- sparseMatrix(int, int) - Static method in class edu.cmu.tetrad.util.Matrix
- sparseMatrix(int, int) - Static method in class edu.cmu.tetrad.util.Matrix2
- SpFci - Class in edu.cmu.tetrad.algcomparison.algorithm.oracle.pag
-
Adjusts GFCI to use a permutation algorithm (in this case SP) to do the initial steps of finding adjacencies and unshielded colliders.
- SpFci - Class in edu.cmu.tetrad.search
-
Uses SP in place of FGES for the initial step in the GFCI algorithm.
- SpFci() - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.SpFci
- SpFci(IndependenceWrapper, ScoreWrapper) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.SpFci
- SpFci(IndependenceTest, Score) - Constructor for class edu.cmu.tetrad.search.SpFci
-
Constructor; requires by ta test and a score, over the same variables.
- spirtesFinalOrientation(Graph) - Method in class edu.cmu.tetrad.search.utils.FciOrient
- split(DataSet, double) - Static method in class edu.cmu.tetrad.data.DataTransforms
- Split - Class in edu.cmu.tetrad.util.dist
-
Wraps a chi square distribution for purposes of drawing random samples.
- Split(double, double) - Constructor for class edu.cmu.tetrad.util.dist.Split
-
Creates a new split distribution, drawing uniformly from [-b, -a] U [a, b], where a and b are positive real numbers.
- SplitCasesSpec - Class in edu.cmu.tetrad.data
-
Specifies how a column (continuous or discrete) should be discretized.
- SplitCasesSpec(int, int[], List<String>) - Constructor for class edu.cmu.tetrad.data.SplitCasesSpec
- sqrt() - Method in class edu.cmu.tetrad.util.Matrix
- sqrt() - Method in class edu.cmu.tetrad.util.Matrix2
- sqrt(Matrix) - Static method in class jgpml.covariancefunctions.MatrixOperations
-
Computes the square root of the input
Matrix(element by element) - SquaredErrorLoss - Class in edu.cmu.tetrad.cluster.metrics
-
Euclidean dissimilarity metric--i.e., the sum of the differences in corresponding variable values.
- SquaredErrorLoss() - Constructor for class edu.cmu.tetrad.cluster.metrics.SquaredErrorLoss
- squareLayout(Graph) - Static method in class edu.cmu.tetrad.graph.LayoutUtil
- sSquare(double[]) - Static method in class edu.cmu.tetrad.util.StatUtils
- sSquare(double[], int) - Static method in class edu.cmu.tetrad.util.StatUtils
- sSquare(long[]) - Static method in class edu.cmu.tetrad.util.StatUtils
- sSquare(long[], int) - Static method in class edu.cmu.tetrad.util.StatUtils
- ssx(double[]) - Static method in class edu.cmu.tetrad.util.StatUtils
- ssx(double[], int) - Static method in class edu.cmu.tetrad.util.StatUtils
- ssx(long[]) - Static method in class edu.cmu.tetrad.util.StatUtils
- ssx(long[], int) - Static method in class edu.cmu.tetrad.util.StatUtils
- StabilitySearch(DataSet, DataGraphSearch, int, int) - Static method in class edu.pitt.csb.stability.StabilityUtils
- StabilitySearchPar(DataSet, DataGraphSearch, int, int) - Static method in class edu.pitt.csb.stability.StabilityUtils
- StabilitySelection - Class in edu.cmu.tetrad.algcomparison.algorithm
-
Stability selection.
- StabilitySelection(Algorithm) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.StabilitySelection
- StabilityUtils - Class in edu.pitt.csb.stability
-
Runs a search algorithm over a N subsamples of size b to asses stability as in "Stability Selection" and "Stability Approach to Regularization Selection"
- StabilityUtils() - Constructor for class edu.pitt.csb.stability.StabilityUtils
- STABLE - Enum constant in enum class edu.cmu.tetrad.search.utils.PcCommon.FasType
- STABLE_FAS - Static variable in class edu.cmu.tetrad.util.Params
- STANDARDIZE - Static variable in class edu.cmu.tetrad.util.Params
- STANDARDIZED_STRUCTURAL_EQUATION_MODEL - Static variable in class edu.cmu.tetrad.algcomparison.simulation.SimulationTypes
- standardizeData(double[]) - Static method in class edu.cmu.tetrad.data.DataTransforms
- standardizeData(double[]) - Static method in class edu.cmu.tetrad.util.StatUtils
- standardizeData(DoubleArrayList) - Static method in class edu.cmu.tetrad.data.DataTransforms
- standardizeData(DataSet) - Static method in class edu.cmu.tetrad.data.DataTransforms
- standardizeData(Matrix) - Static method in class edu.cmu.tetrad.data.DataTransforms
- standardizeData(List<DataSet>) - Static method in class edu.cmu.tetrad.data.DataTransforms
- standardizedFifthMoment(double[]) - Static method in class edu.cmu.tetrad.util.StatUtils
- standardizedFifthMoment(double[], int) - Static method in class edu.cmu.tetrad.util.StatUtils
- StandardizedSemIm - Class in edu.cmu.tetrad.sem
-
A special SEM model in which variances of variables are always 1 and means of variables are always 0.
- StandardizedSemIm(SemIm, StandardizedSemIm.Initialization, Parameters) - Constructor for class edu.cmu.tetrad.sem.StandardizedSemIm
-
Constructs a new standardized SEM IM from the freeParameters in the given SEM IM.
- StandardizedSemIm(SemIm, Parameters) - Constructor for class edu.cmu.tetrad.sem.StandardizedSemIm
-
Constructs a new standardized SEM IM, initializing from the freeParameters in the given SEM IM.
- StandardizedSemIm.Initialization - Enum Class in edu.cmu.tetrad.sem
- StandardizedSemIm.ParameterRange - Class in edu.cmu.tetrad.sem
-
Stores a coefficient range--i.e.
- StandardizedSemSimulation - Class in edu.cmu.tetrad.algcomparison.simulation
-
Standardized SEM simulation.
- StandardizedSemSimulation(RandomGraph) - Constructor for class edu.cmu.tetrad.algcomparison.simulation.StandardizedSemSimulation
- StandardizedSemSimulation(SemPm) - Constructor for class edu.cmu.tetrad.algcomparison.simulation.StandardizedSemSimulation
- StandardizedSemSimulation(StandardizedSemIm) - Constructor for class edu.cmu.tetrad.algcomparison.simulation.StandardizedSemSimulation
- standardizedSixthMoment(double[]) - Static method in class edu.cmu.tetrad.util.StatUtils
- standardizedSixthMoment(double[], int) - Static method in class edu.cmu.tetrad.util.StatUtils
- STAR - Enum constant in enum class edu.cmu.tetrad.graph.Endpoint
- StARS - Class in edu.cmu.tetrad.algcomparison.algorithm
-
StARS
- StARS(Algorithm, String, double, double) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.StARS
- startsWithPrefixes() - Method in class edu.cmu.tetrad.sem.GeneralizedSemPm
- Statistic - Interface in edu.cmu.tetrad.algcomparison.statistic
-
The interface that each statistic needs to implement.
- Statistics - Class in edu.cmu.tetrad.algcomparison.statistic
-
A list of statistics and their utility weights.
- Statistics() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.Statistics
- STATS_LIST - Enum constant in enum class edu.cmu.tetrad.algcomparison.comparegraphs.CompareTwoGraphs.ComparisonType
- StatUtils - Class in edu.cmu.tetrad.util
-
Contains a number of basic statistical functions.
- StatUtils() - Constructor for class edu.cmu.tetrad.util.StatUtils
- std(Matrix) - Static method in class jgpml.covariancefunctions.MatrixOperations
- stop() - Method in class edu.cmu.tetrad.search.utils.ShiftSearch
- StoredCellProbs - Class in edu.cmu.tetrad.bayes
-
Creates a table of stored cell probabilities for the given list of variables.
- StoredCellProbsObs - Class in edu.cmu.tetrad.bayes
-
Creates a table of stored cell probabilities for the given list of variables.
- StoredCellProbsObs(List<Node>) - Constructor for class edu.cmu.tetrad.bayes.StoredCellProbsObs
- StoredLagGraphParams - Class in edu.cmu.tetrad.study.gene.tetrad.gene.graph
-
Stores a file for reading in a lag graph from a file.
- StoredLagGraphParams() - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.graph.StoredLagGraphParams
-
Constructs a new parameters object.
- stouffer - Enum constant in enum class edu.cmu.tetrad.search.utils.ResolveSepsets.Method
- stouffer - Enum constant in enum class edu.cmu.tetrad.search.work_in_progress.ResolveSepsetsDci.Method
- STRING - Enum constant in enum class edu.cmu.tetrad.calculator.parser.Token
- stringFrom2dArray(int[][]) - Static method in class edu.pitt.csb.mgm.MixedUtils
- strOfParents(int) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.biolingua.BiolinguaDigraph
-
Returns a string with the indexes of all parents of node i separated by spaces (useful for printouts)
- STRUCTURAL_EQUATION_MODEL - Static variable in class edu.cmu.tetrad.algcomparison.simulation.SimulationTypes
- structuralHammingDistance(Graph, Graph) - Static method in class edu.cmu.tetrad.search.utils.GraphSearchUtils
-
Tsamardinos, I., Brown, L.
- StructuralHammingDistance - Class in edu.cmu.tetrad.algcomparison.statistic
-
Calculates the structural Hamming distance (SHD) between the estimated graph and the true graph.
- StructuralHammingDistance() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.StructuralHammingDistance
- structuralVar(DataSet, int) - Static method in class edu.cmu.tetrad.search.utils.TsUtils
- STRUCTURE_PRIOR - Static variable in class edu.cmu.tetrad.util.Params
- subgraph(List<Node>) - Method in class edu.cmu.tetrad.graph.Dag
- subgraph(List<Node>) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
- subgraph(List<Node>) - Method in interface edu.cmu.tetrad.graph.Graph
-
Constructs and returns a subgraph consisting of a given subset of the nodes of this graph together with the edges between them.
- subgraph(List<Node>) - Method in class edu.cmu.tetrad.graph.LagGraph
- subgraph(List<Node>) - Method in class edu.cmu.tetrad.graph.SemGraph
- subgraph(List<Node>) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- SublistGenerator - Class in edu.cmu.tetrad.util
-
Generates (nonrecursively) all of the sublists of size b from a list of size a, where a, b are nonnegative integers and a >= b.
- SublistGenerator(int, int) - Constructor for class edu.cmu.tetrad.util.SublistGenerator
-
Constructs a new generator for sublists for a list of size b taken a at a time.
- submatrix(double[][], int) - Static method in class edu.cmu.tetrad.util.MatrixUtils
-
A copy of the original (square) matrix with the stated index row/column removed
- subMatrix(ICovarianceMatrix, Node, Node, List<Node>) - Static method in class edu.cmu.tetrad.data.DataUtils
- subMatrix(ICovarianceMatrix, Map<Node, Integer>, Node, Node, List<Node>) - Static method in class edu.cmu.tetrad.data.DataUtils
- subMatrix(Matrix, List<Node>, Node, Node, List<Node>) - Static method in class edu.cmu.tetrad.data.DataUtils
- subMatrix(Matrix, Map<Node, Integer>, Node, Node, List<Node>) - Static method in class edu.cmu.tetrad.data.DataUtils
- SuborderSearch - Interface in edu.cmu.tetrad.search
-
An interface for suborder searches for various types of permutation algorithms.
- SUBSAMPLE - Enum constant in enum class edu.cmu.tetrad.search.Cstar.SampleStyle
- subSampleNoReplacement(int, int, int) - Static method in class edu.pitt.csb.stability.StabilityUtils
- subset(List<Node>) - Method in class edu.cmu.tetrad.search.score.SemBicScore
- subsetColumns(int[]) - Method in class edu.cmu.tetrad.data.BoxDataSet
- subsetColumns(int[]) - Method in interface edu.cmu.tetrad.data.DataSet
- subsetColumns(int[]) - Method in class edu.cmu.tetrad.data.NumberObjectDataSet
- subsetColumns(List<Node>) - Method in class edu.cmu.tetrad.data.BoxDataSet
-
Creates and returns a dataset consisting of those variables in the list vars.
- subsetColumns(List<Node>) - Method in interface edu.cmu.tetrad.data.DataSet
-
Creates and returns a dataset consisting of those variables in the list vars.
- subsetColumns(List<Node>) - Method in class edu.cmu.tetrad.data.NumberObjectDataSet
-
Creates and returns a dataset consisting of those variables in the list vars.
- subsetRows(int[]) - Method in class edu.cmu.tetrad.data.BoxDataSet
- subsetRows(int[]) - Method in interface edu.cmu.tetrad.data.DataSet
- subsetRows(int[]) - Method in class edu.cmu.tetrad.data.NumberObjectDataSet
- subsetRowsColumns(int[], int[]) - Method in class edu.cmu.tetrad.data.BoxDataSet
- subsetRowsColumns(int[], int[]) - Method in interface edu.cmu.tetrad.data.DataSet
- subsetRowsColumns(int[], int[]) - Method in class edu.cmu.tetrad.data.NumberObjectDataSet
- subtract(double[][], double[][]) - Static method in class edu.cmu.tetrad.util.MatrixUtils
- subtract(double[], double[]) - Static method in class edu.cmu.tetrad.util.MatrixUtils
- successiveFactorVarimax(Matrix) - Method in class edu.cmu.tetrad.search.FactorAnalysis
-
Returns the matrix result for the varimax algorithm.
- successiveResidual() - Method in class edu.cmu.tetrad.search.FactorAnalysis
-
Successive method with residual matrix.
- suite() - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.reveal.TestRevealEvaluator
-
This method uses reflection to collect up all of the test methods from this class and return them to the test runner.
- suite() - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.TestBooleanFunction
-
This method uses reflection to collect up all of the test methods from this class and return them to the test runner.
- suite() - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.TestIndexedConnectivity
-
This method uses reflection to collect up all of the test methods from this class and return them to the test runner.
- suite() - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.TestIndexedLagGraph
-
This method uses reflection to collect up all of the test methods from this class and return them to the test runner.
- suite() - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.TestPolynomial
-
This method uses reflection to collect up all of the test methods from this class and return them to the test runner.
- suite() - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.TestPolynomialTerm
-
This method uses reflection to collect up all of the test methods from this class and return them to the test runner.
- suite() - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.TestSimpleRandomizer
-
This method uses reflection to collect up all of the test methods from this class and return them to the test runner.
- suite() - Static method in class edu.cmu.tetrad.study.gene.tetrad.gene.simulation.TestMeasurementSimulator
-
This method uses reflection to collect up all of the test methods from this class and return them to the test runner.
- sum(double[]) - Static method in class edu.cmu.tetrad.util.StatUtils
- sum(double[][], double[][]) - Static method in class edu.cmu.tetrad.util.MatrixUtils
- sum(double[], double[]) - Static method in class edu.cmu.tetrad.util.MatrixUtils
- sum(int) - Method in class edu.cmu.tetrad.util.Matrix
- sum(int) - Method in class edu.cmu.tetrad.util.Matrix2
- sum0ToN(int) - Static method in class edu.cmu.tetrad.util.MatrixUtils
- sumBits(byte[]) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.akutsu.BoolSearch
- sumBits(byte[]) - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.BoolSearch
- summarize(List<ComparisonResult>, List<Comparison.TableColumn>) - Static method in class edu.cmu.tetrad.study.performance.Comparison
- summarize(List<ComparisonResult>, List<Comparison2.TableColumn>) - Static method in class edu.cmu.tetrad.study.performance.Comparison2
- sumOfArCoefficients(DataSet, int) - Static method in class edu.cmu.tetrad.search.utils.TsUtils
- sumRows(Matrix) - Static method in class jgpml.covariancefunctions.MatrixOperations
-
Sums across the rows of the
Matrixand return the result as a single columnMAtrix - SvarFas - Class in edu.cmu.tetrad.search
-
Adapts FAS for the time series setting, assuming the data is generated by a SVAR (structural vector autoregression).
- SvarFas(IndependenceTest) - Constructor for class edu.cmu.tetrad.search.SvarFas
-
Constructs a new FastAdjacencySearch.
- SvarFci - Class in edu.cmu.tetrad.algcomparison.algorithm.oracle.pag
-
SvarFCI.
- SvarFci - Class in edu.cmu.tetrad.search
-
Adapts FCI for the time series setting, assuming the data is generated by a SVAR (structural vector autoregression).
- SvarFci() - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.SvarFci
- SvarFci(IndependenceWrapper) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.SvarFci
- SvarFci(IndependenceTest) - Constructor for class edu.cmu.tetrad.search.SvarFci
-
Constructs a new FCI search for the given independence test and background knowledge.
- SVARFCI - Enum constant in enum class edu.cmu.tetrad.study.performance.ComparisonParameters.Algorithm
- SvarFciOrient - Class in edu.cmu.tetrad.search.utils
-
Adapts FciOrient for the SvarFCI algorithm.
- SvarFciOrient(SepsetProducer, IndependenceTest) - Constructor for class edu.cmu.tetrad.search.utils.SvarFciOrient
-
Constructs a new FCI search for the given independence test and background knowledge.
- SvarFges - Class in edu.cmu.tetrad.search
-
Adapts FGES for the time series setting, assuming the data is generated by a SVAR (structural vector autoregression).
- SvarFges(Score) - Constructor for class edu.cmu.tetrad.search.SvarFges
-
Construct a Score and pass it in here.
- SvarGfci - Class in edu.cmu.tetrad.algcomparison.algorithm.oracle.pag
-
SvarFCI.
- SvarGfci - Class in edu.cmu.tetrad.search
-
Adapts GFCI for the time series setting, assuming the data is generated by a SVAR (structural vector autoregression).
- SvarGfci() - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.SvarGfci
- SvarGfci(IndependenceWrapper, ScoreWrapper) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.SvarGfci
- SvarGfci(IndependenceTest, Score) - Constructor for class edu.cmu.tetrad.search.SvarGfci
-
Constructs a new GFCI search for the given independence test and background knowledge.
- swap(Node, Node) - Method in class edu.cmu.tetrad.search.utils.TeyssierScorer
-
Swaps m and n in the permutation.
- SWAP - Enum constant in enum class edu.cmu.tetrad.search.work_in_progress.HbsmsBeam.Move.Type
- swaptuck(Node, Node) - Method in class edu.cmu.tetrad.search.utils.TeyssierScorer
-
Performs a tuck operation.
- sxy(double[], double[]) - Static method in class edu.cmu.tetrad.util.StatUtils
- sxy(double[], double[], int) - Static method in class edu.cmu.tetrad.util.StatUtils
- sxy(long[], long[]) - Static method in class edu.cmu.tetrad.util.StatUtils
- sxy(long[], long[], int) - Static method in class edu.cmu.tetrad.util.StatUtils
- sxy(Vector, Vector, int) - Static method in class edu.cmu.tetrad.util.StatUtils
- SymMatrix - Class in edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util
-
Implements a space-efficient symmetric matrix (of elements of type
short), storing only the lower triangular portion of it - SymMatrix(String) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.SymMatrix
-
Creates a symmetric matrix reading it from file
fname. - SymMatrix(String, int) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.SymMatrix
-
Creates a symmetric matrix with
nrowsrows. - SymMatrixF - Class in edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util
-
Implements a space-efficient symmetric matrix (of elements of type
short), storing only the lower triangular portion of it - SymMatrixF(String) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.SymMatrixF
-
Creates a symmetric matrix reading it from file
fname. - SymMatrixF(String, int) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.SymMatrixF
-
Creates a symmetric matrix with
nrowsrows. - SYMMETRIC_FIRST_STEP - Static variable in class edu.cmu.tetrad.util.Params
- symmetricDirichletIm(BayesPm, double) - Static method in class edu.cmu.tetrad.bayes.DirichletBayesIm
- symmetricInverse() - Method in class edu.cmu.tetrad.util.Matrix
- symmetricInverse() - Method in class edu.cmu.tetrad.util.Matrix2
- symmetry() - Method in class edu.cmu.tetrad.search.utils.GraphoidAxioms
-
Checks is symmetry holds--i.e., X ⊥⊥ Y | Z ==> Y ⊥⊥ X | Z
T
- ta - Enum constant in enum class edu.cmu.tetrad.graph.EdgeTypeProbability.EdgeType
- TAB - Enum constant in enum class edu.cmu.tetrad.util.TextTable.Delimiter
- TAB - Static variable in class edu.cmu.tetrad.data.DelimiterType
- TAIL - Enum constant in enum class edu.cmu.tetrad.graph.Endpoint
- TailConfusion - Class in edu.cmu.tetrad.algcomparison.statistic.utils
-
A confusion matrix for tails--i.e.
- TailConfusion(Graph, Graph) - Constructor for class edu.cmu.tetrad.algcomparison.statistic.utils.TailConfusion
- TailPrecision - Class in edu.cmu.tetrad.algcomparison.statistic
-
The arrow precision.
- TailPrecision() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.TailPrecision
- TailRecall - Class in edu.cmu.tetrad.algcomparison.statistic
-
The arrow recall.
- TailRecall() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.TailRecall
- TakesData - Interface in edu.cmu.tetrad.algcomparison.utils
-
Tags a gadget that takes a data model list as argument to its constructor.
- takesExternalGraph(Class) - Method in class edu.cmu.tetrad.annotation.AlgorithmAnnotations
-
Checks if the algorithm takes an external graph.
- TakesExternalGraph - Interface in edu.cmu.tetrad.algcomparison.utils
-
Tags an algorithm that can take an external graph as input.
- TakesGraph - Interface in edu.cmu.tetrad.algcomparison.independence
- TakesIndependenceWrapper - Interface in edu.cmu.tetrad.algcomparison.utils
-
Author : Jeremy Espino MD Created 7/13/17 2:25 PM
- takesKnowledge(Class) - Method in class edu.cmu.tetrad.annotation.AlgorithmAnnotations
-
Checks if the algorithm takes knowledge.
- takesMultipleDataset(Class) - Method in class edu.cmu.tetrad.annotation.AlgorithmAnnotations
-
Checks if the algorithm takes multiple data sets.
- Tanh - Class in edu.cmu.tetrad.algcomparison.algorithm.pairwise
-
Tanh.
- Tanh - Enum constant in enum class edu.cmu.tetrad.search.Lofs.Rule
- Tanh(Algorithm) - Constructor for class edu.cmu.tetrad.algcomparison.algorithm.pairwise.Tanh
- TANH - Enum constant in enum class edu.cmu.tetrad.search.Fask.LeftRight
- TARGET_NAME - Static variable in class edu.cmu.tetrad.util.Params
- TARGETS - Static variable in class edu.cmu.tetrad.util.Params
- TaskManager - Class in edu.cmu.tetrad.util
-
This cancels all processes that check the TaskManager.getInstance().isCanceled() method.
- TaskManager() - Constructor for class edu.cmu.tetrad.util.TaskManager
- tautology(VariableSource) - Static method in class edu.cmu.tetrad.bayes.Evidence
- tautology(VariableSource) - Static method in class edu.cmu.tetrad.bayes.Proposition
- tautology(SemIm) - Static method in class edu.cmu.tetrad.sem.SemProposition
- tCdf(double, double) - Static method in class edu.cmu.tetrad.util.ProbUtils
-
CACM Algorithm 395, by G.
- tearDown() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.TestSimpleRandomizer
- TemplateExpander - Class in edu.cmu.tetrad.sem
-
Expands templates for the generalized SEM PM.
- TestBooleanFunction - Class in edu.cmu.tetrad.study.gene.tetrad.gene.history
-
Tests the BooleanFunction class.
- TestBooleanFunction(String) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.history.TestBooleanFunction
-
Standard constructor for JUnit test cases.
- TestBoss - Class in edu.cmu.tetrad.algcomparison.examples
-
Test the degenerate Gaussian score.
- TestBoss() - Constructor for class edu.cmu.tetrad.algcomparison.examples.TestBoss
- testChipToChipError() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.simulation.TestMeasurementSimulator
-
Turn on chip to chip error, turn off all other sources of error, simulate 1 dish of data with 1000 samples per dish and look to see whether in the aggregated data the standard deviations for Gene2:t1, Gene3:t1, and Gene1:t2 are 0.3.
- testCompareDagToCPDAG(int) - Method in class edu.cmu.tetrad.study.performance.PerformanceTests
- testComparePcVersions(int, double, int) - Method in class edu.cmu.tetrad.study.performance.PerformanceTests
- testConstantIndegree() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.TestSimpleRandomizer
-
Tests whether the randomizer can randomly make a graph where all of the factors have the same indegree.
- testConstruction() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.TestIndexedConnectivity
- testConstruction() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.TestIndexedLagGraph
- testConstruction() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.TestPolynomial
-
Tests to make sure that null parent throw an exception.
- testConstruction() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.TestPolynomialTerm
-
Tests to make sure that null parent throw an exception.
- testCpc(int, double, int) - Method in class edu.cmu.tetrad.study.performance.PerformanceTests
- testCpcStable(int, double, int, double) - Method in class edu.cmu.tetrad.study.performance.PerformanceTests
- testDefaultParameterSettings() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.simulation.TestMeasurementSimulator
-
Test to make sure the accessor methods are working correctly.
- TestDegenerateGaussian - Class in edu.cmu.tetrad.algcomparison.examples
-
Test the degenerate Gaussian score.
- TestDegenerateGaussian() - Constructor for class edu.cmu.tetrad.algcomparison.examples.TestDegenerateGaussian
- testDishToDishVariability() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.simulation.TestMeasurementSimulator
-
Turn on dish-to-dish variability error, turn off all other sources of error, simulate 100 dishes of data with 1 sample per dish, and look to see whether in the aggregated data Gene2:t1 and Gene3:t1 have standard deviations that are 10% of their respective means.
- testEvaluation() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.TestPolynomial
-
Test the evaluation of terms.
- testEvaluation() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.TestPolynomialTerm
-
Test the evaluation of terms.
- testFci(int, double, int) - Method in class edu.cmu.tetrad.study.performance.PerformanceTests
- testFges(int, double, int, double) - Method in class edu.cmu.tetrad.study.performance.PerformanceTests
- testFgesComparisonContinuous(int, double, int, int) - Method in class edu.cmu.tetrad.study.performance.PerformanceTests
- testFgesComparisonDiscrete(int, double, int, int) - Method in class edu.cmu.tetrad.study.performance.PerformanceTests
- testFgesMbComparisonContinuous(int, double, int, int) - Method in class edu.cmu.tetrad.study.performance.PerformanceTests
- testFgesMbComparisonDiscrete(int, double, int, int) - Method in class edu.cmu.tetrad.study.performance.PerformanceTests
- testGfci(int, double) - Method in class edu.cmu.tetrad.study.performance.PerformanceTests
- testGFciComparison() - Method in class edu.cmu.tetrad.study.performance.PerformanceTests
- TestIndexedConnectivity - Class in edu.cmu.tetrad.study.gene.tetrad.gene.history
-
Tests the IndexedConnectivity class by constructing graphs with randomly chosen parameters and seeing if they have the required properties.
- TestIndexedConnectivity(String) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.history.TestIndexedConnectivity
-
Change the name of this constructor to match the name of the test class.
- TestIndexedLagGraph - Class in edu.cmu.tetrad.study.gene.tetrad.gene.history
-
Tests the IndexedLagGraph class by constructing graphs with randomly chosen parameters and seeing if they have the required properties.
- TestIndexedLagGraph(String) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.history.TestIndexedLagGraph
-
Change the name of this constructor to match the name of the test class.
- testIsCanalyzing() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.TestBooleanFunction
-
Tests to see whether some known canalyzing functions (AND, OR, ...) pass the isCanalyzing() test.
- testIsEffective() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.TestBooleanFunction
-
Tests to see whether some known effective functions pass the isEffective() test.
- testLiangFigure6() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.reveal.TestRevealEvaluator
-
Tests whether the calculations in Liang, Figure 6 come out to the correct values.
- testMain() - Method in class edu.pitt.dbmi.algo.bayesian.constraint.inference.BayesianConstraintInferenceTest
-
Test of main method, of class BayesianConstraintInference.
- testMaxIndegree() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.TestSimpleRandomizer
-
Tests whether the randomizer can randomly make a graph where the maximum indegree across factors is the given factor.
- testMeanIndegree() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.TestSimpleRandomizer
-
Tests whether the randomizer can randomly make a graph where the mean ofindegree across factors is the given number.
- TestMeasurementSimulator - Class in edu.cmu.tetrad.study.gene.tetrad.gene.simulation
-
Tests the MeasurementSimulator class using diagnostics devised by Richard Scheines.
- TestMeasurementSimulator(String) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.simulation.TestMeasurementSimulator
-
Standard constructor for JUnit test cases.
- testNullConstruction() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.TestBooleanFunction
-
Tests to make sure that null parent throw an exception.
- TestOfIndependence - Annotation Interface in edu.cmu.tetrad.annotation
-
Aug 31, 2017 4:42:08 PM
- TestOfIndependenceAnnotations - Class in edu.cmu.tetrad.annotation
-
Sep 26, 2017 1:18:28 AM
- testPc(int, double, int, double) - Method in class edu.cmu.tetrad.study.performance.PerformanceTests
- testPcStable(int, double, int, double) - Method in class edu.cmu.tetrad.study.performance.PerformanceTests
- testPixelError() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.simulation.TestMeasurementSimulator
-
Turn on pixel digitalization error, turn off all other sources of error, simulate 1 dish of data with 1000 samples per dish and look to see whether in the aggregated data the standard deviations for Gene2:t1, Gene3:t1 and Gene1:t2 are 0.3.
- TestPolynomial - Class in edu.cmu.tetrad.study.gene.tetrad.gene.history
-
Tests the Polynomial class.
- TestPolynomial(String) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.history.TestPolynomial
-
Standard constructor for JUnit test cases.
- TestPolynomialTerm - Class in edu.cmu.tetrad.study.gene.tetrad.gene.history
-
Tests the PolynomialTerm class.
- TestPolynomialTerm(String) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.history.TestPolynomialTerm
-
Standard constructor for JUnit test cases.
- testPrint(int) - Static method in class edu.cmu.tetrad.util.PermutationGenerator
-
This static method will print the series of combinations for numObjects choose b to System.out.
- testPrint(int) - Static method in class edu.cmu.tetrad.util.SelectionGenerator
-
This static method will print the series of combinations for a choose b to System.out.
- testPrint(int[]) - Static method in class edu.cmu.tetrad.util.CombinationGenerator
-
This static method will print the series of combinations for a choose b to System.out.
- testPrint(int, int) - Static method in class edu.cmu.tetrad.util.ChoiceGenerator
-
This static method will print the series of combinations for a choose b to System.out.
- testPrint(int, int) - Static method in class edu.cmu.tetrad.util.SublistGenerator
-
This static method will print the series of combinations for a choose depth to System.out.
- TestRevealEvaluator - Class in edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.reveal
-
Test the Reveal evaluator.
- TestRevealEvaluator(String) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.reveal.TestRevealEvaluator
-
Standard constructor for JUnit test cases.
- testRowOrder() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.TestBooleanFunction
-
Tests whether rows are stored in the correct order.
- testSampleToSampleError() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.simulation.TestMeasurementSimulator
-
Turn on sample-to-sample error, turn off all other sources of error, simulate 1 dish of data with 1000 samples per dish, and look to see whether in the aggregated data the standard deviations of Gene2:t1 and Gene3:t1 are 0.2.
- TestSimpleRandomizer - Class in edu.cmu.tetrad.study.gene.tetrad.gene.history
-
Tests the SimpleRandomizer class by constructing graphs with randomly chosen parameters and seeing if they have the required properties.
- TestSimpleRandomizer(String) - Constructor for class edu.cmu.tetrad.study.gene.tetrad.gene.history.TestSimpleRandomizer
-
Change the name of this constructor to match the name of the test class.
- testTableSize() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.TestBooleanFunction
-
Tests to make sure the table is the correct size.
- testTranscriptionError() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.simulation.TestMeasurementSimulator
-
Save out the raw data using default parameters and make sure that Gene1:t2 has the specified standard deviation.
- Tetrad - Class in edu.cmu.tetrad.search.utils
-
Represents a ordered tetrad of variables, (i, j, k, l).
- Tetrad(Node, Node, Node, Node) - Constructor for class edu.cmu.tetrad.search.utils.Tetrad
- Tetrad(Node, Node, Node, Node, double) - Constructor for class edu.cmu.tetrad.search.utils.Tetrad
- TETRAD_BASED - Enum constant in enum class edu.cmu.tetrad.search.utils.BpcTestType
- TETRAD_BOLLEN - Enum constant in enum class edu.cmu.tetrad.search.utils.BpcTestType
- TETRAD_DELTA - Enum constant in enum class edu.cmu.tetrad.search.utils.BpcTestType
- TETRAD_PURIFY_WASHDOWN - Enum constant in enum class edu.cmu.tetrad.search.utils.BpcAlgorithmType
- TETRAD_WISHART - Enum constant in enum class edu.cmu.tetrad.search.utils.BpcTestType
- TetradAlgebra - Class in edu.cmu.tetrad.util
-
Some algebra methods.
- TetradAlgebra() - Constructor for class edu.cmu.tetrad.util.TetradAlgebra
- tetradHolds(int, int, int, int) - Method in interface edu.cmu.tetrad.search.utils.TetradTest
- tetradHolds(int, int, int, int) - Method in class edu.cmu.tetrad.search.utils.TetradTestContinuous
- tetradHolds(int, int, int, int) - Method in class edu.cmu.tetrad.search.utils.TetradTestDiscrete
- tetradHolds(int, int, int, int) - Method in class edu.cmu.tetrad.search.utils.TetradTestPopulation
- TetradLogger - Class in edu.cmu.tetrad.util
-
Represents a logging utility used throughout tetrad.
- TetradLogger.EmptyConfig - Class in edu.cmu.tetrad.util
-
A empty config, where no event is active.
- TetradLogger.LogDisplayOutputStream - Interface in edu.cmu.tetrad.util
-
Represents an output stream that can get its own length.
- TetradLoggerConfig - Interface in edu.cmu.tetrad.util
-
Represents the configuration for the logger.
- TetradLoggerConfig.Event - Interface in edu.cmu.tetrad.util
-
Represents an event which is just an id and a description.
- TetradLoggerEvent - Class in edu.cmu.tetrad.util
-
An event associated with the
TetradLoggerListener. - TetradLoggerEvent(Object, TetradLoggerConfig) - Constructor for class edu.cmu.tetrad.util.TetradLoggerEvent
-
Constructs the event given the source and the
TetradLoggerConfigassociated with the event if there is one - TetradLoggerListener - Interface in edu.cmu.tetrad.util
-
A listener for tetrad's logger.
- TetradProperties - Class in edu.cmu.tetrad.util
-
Nov 10, 2017 4:14:31 PM
- tetradPValue(int, int, int, int) - Method in interface edu.cmu.tetrad.search.utils.TetradTest
- tetradPValue(int, int, int, int) - Method in class edu.cmu.tetrad.search.utils.TetradTestContinuous
- tetradPValue(int, int, int, int) - Method in class edu.cmu.tetrad.search.utils.TetradTestDiscrete
- tetradPValue(int, int, int, int) - Method in class edu.cmu.tetrad.search.utils.TetradTestPopulation
- tetradScore(int, int, int, int) - Method in interface edu.cmu.tetrad.search.utils.TetradTest
- tetradScore(int, int, int, int) - Method in class edu.cmu.tetrad.search.utils.TetradTestContinuous
- tetradScore(int, int, int, int) - Method in class edu.cmu.tetrad.search.utils.TetradTestDiscrete
- tetradScore(int, int, int, int) - Method in class edu.cmu.tetrad.search.utils.TetradTestPopulation
-
Population scores: assumes CorrelationMatrix is the population covariance CorrelationMatrix.
- tetradScore1(int, int, int, int) - Method in interface edu.cmu.tetrad.search.utils.TetradTest
- tetradScore1(int, int, int, int) - Method in class edu.cmu.tetrad.search.utils.TetradTestContinuous
-
Tests the tetrad (v1, v3) x (v2, v4) = (v1, v4) x (v2, v3)
- tetradScore1(int, int, int, int) - Method in class edu.cmu.tetrad.search.utils.TetradTestDiscrete
-
Tests the tetrad (v1, v3) x (v2, v4) = (v1, v4) x (v2, v3), and only that.
- tetradScore1(int, int, int, int) - Method in class edu.cmu.tetrad.search.utils.TetradTestPopulation
- tetradScore3(int, int, int, int) - Method in interface edu.cmu.tetrad.search.utils.TetradTest
- tetradScore3(int, int, int, int) - Method in class edu.cmu.tetrad.search.utils.TetradTestContinuous
-
Tests if all tetrad constraints hold
- tetradScore3(int, int, int, int) - Method in class edu.cmu.tetrad.search.utils.TetradTestDiscrete
-
Tests if all tetrad constraints hold
- tetradScore3(int, int, int, int) - Method in class edu.cmu.tetrad.search.utils.TetradTestPopulation
- TetradSerializable - Interface in edu.cmu.tetrad.util
-
Interface to tag a class that is part of the set of serializable classes in the Tetrad API.
- TetradSerializableExcluded - Interface in edu.cmu.tetrad.util
-
Interface to tag a class that should be exluded from the set of TetradSerializable classes, even if it implements the TetradSerializable interface.
- TetradSerializableUtils - Class in edu.cmu.tetrad.util
-
Contains methods used by TestSerialization to ensure that previous "stable" versions of Tetrad will by loadable by later "stable" versions of Tetrad.
- TetradSerializableUtils(String, String, String) - Constructor for class edu.cmu.tetrad.util.TetradSerializableUtils
-
Blank constructor.
- TetradTest - Interface in edu.cmu.tetrad.search.utils
-
Provides an interface for classes that test tetrad constraints.
- TetradTestContinuous - Class in edu.cmu.tetrad.search.utils
-
Implements different tests of tetrad constraints: using Wishart's test (CPS, Wishart 1928); Bollen's test (Bollen, 1990) or a more computationally intensive test that fits one/two factor Gaussian models.
- TetradTestContinuous(CorrelationMatrix, BpcTestType, double) - Constructor for class edu.cmu.tetrad.search.utils.TetradTestContinuous
- TetradTestContinuous(DataSet, BpcTestType, double) - Constructor for class edu.cmu.tetrad.search.utils.TetradTestContinuous
- TetradTestContinuous(ICovarianceMatrix, BpcTestType, double) - Constructor for class edu.cmu.tetrad.search.utils.TetradTestContinuous
- TetradTestDiscrete - Class in edu.cmu.tetrad.search.utils
-
Implements a test of tetrad constraints with discrete variables.
- TetradTestDiscrete(DataSet, double) - Constructor for class edu.cmu.tetrad.search.utils.TetradTestDiscrete
- TetradTestPopulation - Class in edu.cmu.tetrad.search.utils
-
Implements a test of tetrad constraints in a known correlation matrix.
- TetradTestPopulation(CorrelationMatrix) - Constructor for class edu.cmu.tetrad.search.utils.TetradTestPopulation
- TextTable - Class in edu.cmu.tetrad.util
-
Stores a 2D array of Strings for printing out tables.
- TextTable(int, int) - Constructor for class edu.cmu.tetrad.util.TextTable
-
Construct the text table; the table has a fixed number of rows and columns, each greater than zero.
- TextTable.Delimiter - Enum Class in edu.cmu.tetrad.util
- TeyssierScorer - Class in edu.cmu.tetrad.search.utils
-
Implements and extends a scorer extending Teyssier, M., and Koller, D.
- TeyssierScorer(IndependenceTest, Score) - Constructor for class edu.cmu.tetrad.search.utils.TeyssierScorer
-
Constructor that takes both a test or a score.
- THR - Static variable in class edu.cmu.tetrad.util.Params
- threshold(Matrix, double) - Static method in class edu.cmu.tetrad.search.IcaLingD
-
Thresholds the given matrix, sending any small entries in absolute value to zero.
- Threshold - Enum constant in enum class edu.pitt.dbmi.algo.resampling.ResamplingEdgeEnsemble
- THRESHOLD_B - Static variable in class edu.cmu.tetrad.util.Params
- THRESHOLD_FOR_NUM_EIGENVALUES - Static variable in class edu.cmu.tetrad.util.Params
- THRESHOLD_NO_RANDOM_CONSTRAIN_SEARCH - Static variable in class edu.cmu.tetrad.util.Params
- THRESHOLD_NO_RANDOM_DATA_SEARCH - Static variable in class edu.cmu.tetrad.util.Params
- THRESHOLD_SPINE - Static variable in class edu.cmu.tetrad.util.Params
- TIME_LAG - Static variable in class edu.cmu.tetrad.util.Params
- TIME_SERIES - Static variable in class edu.cmu.tetrad.algcomparison.simulation.SimulationTypes
- TimeLagGraph - Class in edu.cmu.tetrad.graph
-
Represents a time series graph--that is, a graph with a fixed number S of lags, with edges into initial lags only--that is, into nodes in the first R lags, for some R.
- TimeLagGraph() - Constructor for class edu.cmu.tetrad.graph.TimeLagGraph
- TimeLagGraph(TimeLagGraph) - Constructor for class edu.cmu.tetrad.graph.TimeLagGraph
- TimeLagGraph.NodeId - Class in edu.cmu.tetrad.graph
- timeMillis() - Static method in class edu.cmu.tetrad.util.MillisecondTimes
- TIMEOUT - Static variable in class edu.cmu.tetrad.util.Params
- TimeoutComparison - Class in edu.cmu.tetrad.algcomparison
-
Nov 14, 2017 12:00:31 PM
- TimeoutComparison() - Constructor for class edu.cmu.tetrad.algcomparison.TimeoutComparison
- TimeoutComparison.ComparisonGraph - Enum Class in edu.cmu.tetrad.algcomparison
- times(Matrix) - Method in class edu.cmu.tetrad.util.Matrix
- times(Matrix2) - Method in class edu.cmu.tetrad.util.Matrix2
- times(Vector) - Method in class edu.cmu.tetrad.util.Matrix
- times(Vector) - Method in class edu.cmu.tetrad.util.Matrix2
- TimeSeries - Annotation Interface in edu.cmu.tetrad.annotation
-
Aug 7, 2019 6:17:29 PM
- TimeSeriesData - Class in edu.cmu.tetrad.data
-
Stores time series data as a list of continuous columns.
- TimeSeriesData(Matrix, List<String>) - Constructor for class edu.cmu.tetrad.data.TimeSeriesData
-
Constructs a new time series data contains for the given row-major data array and the given list of variables.
- TimeSeriesSemSimulation - Class in edu.cmu.tetrad.algcomparison.simulation
-
Time series SEM simulation.
- TimeSeriesSemSimulation(RandomGraph) - Constructor for class edu.cmu.tetrad.algcomparison.simulation.TimeSeriesSemSimulation
- tippett - Enum constant in enum class edu.cmu.tetrad.search.utils.ResolveSepsets.Method
- tippett - Enum constant in enum class edu.cmu.tetrad.search.work_in_progress.ResolveSepsetsDci.Method
- toArray() - Method in class edu.cmu.tetrad.simulation.PRAOerrors
- toArray() - Method in class edu.cmu.tetrad.util.Matrix
- toArray() - Method in class edu.cmu.tetrad.util.Matrix2
- toArray() - Method in class edu.cmu.tetrad.util.Vector
- toContinuousDataModel(ContinuousData) - Static method in class edu.cmu.tetrad.util.DataConvertUtils
- toCovarianceMatrix(CovarianceData) - Static method in class edu.cmu.tetrad.util.DataConvertUtils
- toDataModel(Data) - Static method in class edu.cmu.tetrad.util.DataConvertUtils
- toDataModel(Data, Metadata) - Static method in class edu.cmu.tetrad.util.DataConvertUtils
- toDelimiter(char) - Static method in class edu.cmu.tetrad.util.DelimiterUtils
-
Get the enum delimiter corresponding to char delimiter: tab, space, comma, colon, semicolon, pipe.
- Token - Enum Class in edu.cmu.tetrad.calculator.parser
-
Allowable tokens.
- toMatrix1D() - Method in class edu.pitt.csb.mgm.Mgm.MGMParams
-
Copy all params into a single vector
- toMixedDataBox(MixedTabularData) - Static method in class edu.cmu.tetrad.util.DataConvertUtils
- toMixedDataBox(MixedTabularData, Metadata) - Static method in class edu.cmu.tetrad.util.DataConvertUtils
-
Converting using metadata
- toNodes(DataColumn[]) - Static method in class edu.cmu.tetrad.util.DataConvertUtils
- toNodes(DiscreteDataColumn[]) - Static method in class edu.cmu.tetrad.util.DataConvertUtils
- toNodes(List<String>) - Static method in class edu.cmu.tetrad.util.DataConvertUtils
- TOP_BRACKET - Static variable in class edu.cmu.tetrad.util.Params
- topToBottomLayout(TimeLagGraph) - Static method in class edu.cmu.tetrad.algcomparison.simulation.BooleanGlassSimulation
- topToBottomLayout(TimeLagGraph) - Static method in class edu.cmu.tetrad.algcomparison.simulation.TimeSeriesSemSimulation
- toString() - Method in class edu.cmu.tetrad.bayes.ApproximateUpdater
-
Prints out the most recent marginal.
- toString() - Method in interface edu.cmu.tetrad.bayes.BayesIm
-
Returns a string representation for this Bayes net.
- toString() - Method in class edu.cmu.tetrad.bayes.BayesPm
-
Prints out the list of values for each node.
- toString() - Method in class edu.cmu.tetrad.bayes.CptInvariantUpdater
-
Prints out the most recent marginal.
- toString() - Method in class edu.cmu.tetrad.bayes.DirichletBayesIm
-
Prints out the probability table for each variable.
- toString() - Method in class edu.cmu.tetrad.bayes.Evidence
- toString() - Method in class edu.cmu.tetrad.bayes.Identifiability
- toString() - Method in class edu.cmu.tetrad.bayes.JunctionTreeAlgorithm
- toString() - Method in class edu.cmu.tetrad.bayes.JunctionTreeUpdater
- toString() - Method in class edu.cmu.tetrad.bayes.Manipulation
- toString() - Method in class edu.cmu.tetrad.bayes.MlBayesIm
-
Prints out the probability table for each variable.
- toString() - Method in class edu.cmu.tetrad.bayes.MlBayesImObs
-
Prints out the probability table for each variable.
- toString() - Method in class edu.cmu.tetrad.bayes.Proposition
- toString() - Method in class edu.cmu.tetrad.bayes.RowSummingExactUpdater
-
Prints out the most recent marginal.
- toString() - Method in class edu.cmu.tetrad.bayes.StoredCellProbs
- toString() - Method in class edu.cmu.tetrad.bayes.StoredCellProbsObs
- toString() - Method in class edu.cmu.tetrad.bayes.UpdatedBayesIm
-
Prints out the probability table for each variable.
- toString() - Method in class edu.cmu.tetrad.calculator.expression.ConstantExpression
- toString() - Method in class edu.cmu.tetrad.calculator.expression.VariableExpression
- toString() - Method in class edu.cmu.tetrad.cluster.KMeans
- toString() - Method in class edu.cmu.tetrad.data.AbstractVariable
- toString() - Method in class edu.cmu.tetrad.data.BoxDataSet
- toString() - Method in class edu.cmu.tetrad.data.Clusters
- toString() - Method in class edu.cmu.tetrad.data.CorrelationMatrixOnTheFly
-
Prints out the matrix
- toString() - Method in class edu.cmu.tetrad.data.CovarianceMatrix
-
Prints out the matrix
- toString() - Method in class edu.cmu.tetrad.data.CovarianceMatrixOnTheFly
-
Prints out the matrix
- toString() - Method in interface edu.cmu.tetrad.data.DataModel
-
Renders the data model as as String.
- toString() - Method in class edu.cmu.tetrad.data.DataModelList
- toString() - Method in interface edu.cmu.tetrad.data.DataSet
- toString() - Method in class edu.cmu.tetrad.data.DelimiterType
-
Prints out the name of the type.
- toString() - Method in class edu.cmu.tetrad.data.DiscreteVariable
- toString() - Method in class edu.cmu.tetrad.data.DiscreteVariableType
-
Prints out the name of the type.
- toString() - Method in class edu.cmu.tetrad.data.Discretizer.Discretization
- toString() - Method in interface edu.cmu.tetrad.data.ICovarianceMatrix
- toString() - Method in class edu.cmu.tetrad.data.IndependenceFacts
- toString() - Method in class edu.cmu.tetrad.data.Knowledge
- toString() - Method in class edu.cmu.tetrad.data.KnowledgeEdge
- toString() - Method in class edu.cmu.tetrad.data.NumberObjectDataSet
- toString() - Method in class edu.cmu.tetrad.graph.Dag
- toString() - Method in class edu.cmu.tetrad.graph.Edge
-
Produces a string representation of the edge.
- toString() - Method in class edu.cmu.tetrad.graph.EdgeListGraph
- toString() - Method in interface edu.cmu.tetrad.graph.Graph
- toString() - Method in class edu.cmu.tetrad.graph.GraphNode
- toString() - Method in class edu.cmu.tetrad.graph.GraphUtils.TwoCycleErrors
- toString() - Method in class edu.cmu.tetrad.graph.IndependenceFact
- toString() - Method in interface edu.cmu.tetrad.graph.Node
-
Returns the intervention type for this node.
- toString() - Method in class edu.cmu.tetrad.graph.NodePair
- toString() - Method in class edu.cmu.tetrad.graph.NodeType
-
Prints out the name of the type.
- toString() - Method in class edu.cmu.tetrad.graph.OrderedPair
- toString() - Method in class edu.cmu.tetrad.graph.RandomGraph.UniformGraphGenerator
- toString() - Method in class edu.cmu.tetrad.graph.SemGraph
- toString() - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- toString() - Method in class edu.cmu.tetrad.graph.Triple
- toString() - Method in class edu.cmu.tetrad.regression.LogisticRegression.Result
- toString() - Method in class edu.cmu.tetrad.regression.RegressionResult
- toString() - Method in class edu.cmu.tetrad.search.FastIca.IcaResult
- toString() - Method in class edu.cmu.tetrad.search.Ida.NodeEffects
- toString() - Method in interface edu.cmu.tetrad.search.IndependenceTest
-
Returns a string representation of this test.
- toString() - Method in class edu.cmu.tetrad.search.IndTestIod
-
Returns a string representation of this test.
- toString() - Method in class edu.cmu.tetrad.search.score.BdeScore
-
Returns "BDe Score".
- toString() - Method in class edu.cmu.tetrad.search.score.BdeuScore
-
Returns a string representation of this score.
- toString() - Method in class edu.cmu.tetrad.search.score.ConditionalGaussianLikelihood.Ret
- toString() - Method in class edu.cmu.tetrad.search.score.ConditionalGaussianScore
- toString() - Method in class edu.cmu.tetrad.search.score.DegenerateGaussianScore
- toString() - Method in class edu.cmu.tetrad.search.score.DiscreteBicScore
-
Returns a string representation of this score.
- toString() - Method in class edu.cmu.tetrad.search.score.GicScores
- toString() - Method in interface edu.cmu.tetrad.search.score.Score
-
A string representation of the score.
- toString() - Method in class edu.cmu.tetrad.search.score.SemBicScore
- toString() - Method in class edu.cmu.tetrad.search.test.IndependenceResult
-
Returns a string represnetation of this independence fact.
- toString() - Method in class edu.cmu.tetrad.search.test.IndTestChiSquare
-
Returns a string representation of this test.
- toString() - Method in class edu.cmu.tetrad.search.test.IndTestConditionalCorrelation
-
Returns a string representation of this test.
- toString() - Method in class edu.cmu.tetrad.search.test.IndTestConditionalGaussianLrt
-
Returns a string representation of this test.
- toString() - Method in class edu.cmu.tetrad.search.test.IndTestDegenerateGaussianLrt.Ret
- toString() - Method in class edu.cmu.tetrad.search.test.IndTestDegenerateGaussianLrt
-
Returns a string representation of this test.
- toString() - Method in class edu.cmu.tetrad.search.test.IndTestFisherZ
- toString() - Method in class edu.cmu.tetrad.search.test.IndTestFisherZConcatenateResiduals
- toString() - Method in class edu.cmu.tetrad.search.test.IndTestFisherZFisherPValue
-
Returns a string representation of this test.
- toString() - Method in class edu.cmu.tetrad.search.test.IndTestGSquare
-
Returns a String representation of this test.
- toString() - Method in class edu.cmu.tetrad.search.test.IndTestHsic
-
Returns a string representation of this test.
- toString() - Method in class edu.cmu.tetrad.search.test.IndTestMulti
- toString() - Method in class edu.cmu.tetrad.search.test.IndTestRegression
- toString() - Method in class edu.cmu.tetrad.search.test.IndTestTrekSep
-
Returns a string representation of this test.
- toString() - Method in class edu.cmu.tetrad.search.test.Kci
-
Returns a string representation of this test.
- toString() - Method in class edu.cmu.tetrad.search.test.MsepTest
-
Returns a string representation of this test.
- toString() - Method in class edu.cmu.tetrad.search.test.ScoreIndTest
-
Returns a String representation of this test.
- toString() - Method in class edu.cmu.tetrad.search.utils.GraphoidAxioms.GraphoidIndFact
- toString() - Method in class edu.cmu.tetrad.search.utils.PermutationMatrixPair
-
Prints a string representation of this.
- toString() - Method in class edu.cmu.tetrad.search.utils.PossibleMConnectingPath
- toString() - Method in class edu.cmu.tetrad.search.utils.SepsetMap
-
Returns a string representation of this sepset map.
- toString() - Method in class edu.cmu.tetrad.search.utils.Sextad
- toString() - Method in class edu.cmu.tetrad.search.utils.Tetrad
- toString() - Method in class edu.cmu.tetrad.search.work_in_progress.DMSearch.LatentStructure
- toString() - Method in class edu.cmu.tetrad.search.work_in_progress.GraphChange
-
Anly outputs ops which have elements, not empty structures.
- toString() - Method in class edu.cmu.tetrad.search.work_in_progress.HbsmsBeam.Move
- toString() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestCramerT
- toString() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestFisherZGeneralizedInverse
- toString() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestFisherZPercentIndependent
- toString() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestFisherZRecursive
- toString() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestMixedMultipleTTest
- toString() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestMnlrLr
- toString() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestMultinomialLogisticRegression
- toString() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestPositiveCorr
- toString() - Method in class edu.cmu.tetrad.search.work_in_progress.IndTestSepsetDci
- toString() - Method in class edu.cmu.tetrad.search.work_in_progress.MagSemBicScore
- toString() - Method in class edu.cmu.tetrad.search.work_in_progress.SepsetMapDci
- toString() - Method in class edu.cmu.tetrad.search.work_in_progress.Sextad
- toString() - Method in class edu.cmu.tetrad.sem.DagScorer
- toString() - Method in class edu.cmu.tetrad.sem.GeneralizedSemIm
- toString() - Method in class edu.cmu.tetrad.sem.GeneralizedSemPm
-
Returns a relatively brief String representation of this SEM PM--the equations and distributions of the model.
- toString() - Method in class edu.cmu.tetrad.sem.Mapping
- toString() - Method in class edu.cmu.tetrad.sem.ParamComparison
-
Prints out the name of the type.
- toString() - Method in class edu.cmu.tetrad.sem.ParamConstraintType
-
Prints out the name of the type.
- toString() - Method in class edu.cmu.tetrad.sem.Parameter
- toString() - Method in class edu.cmu.tetrad.sem.ParamType
-
Prints out the name of the type.
- toString() - Method in class edu.cmu.tetrad.sem.Ricf.FitConGraphResult
- toString() - Method in class edu.cmu.tetrad.sem.Ricf.RicfResult
- toString() - Method in interface edu.cmu.tetrad.sem.Scorer
- toString() - Method in class edu.cmu.tetrad.sem.SemEstimator
- toString() - Method in class edu.cmu.tetrad.sem.SemEstimatorGibbs
- toString() - Method in class edu.cmu.tetrad.sem.SemEvidence
- toString() - Method in class edu.cmu.tetrad.sem.SemIm
- toString() - Method in class edu.cmu.tetrad.sem.SemManipulation
- toString() - Method in class edu.cmu.tetrad.sem.SemOptimizerEm
- toString() - Method in class edu.cmu.tetrad.sem.SemOptimizerPowell
- toString() - Method in class edu.cmu.tetrad.sem.SemOptimizerRegression
- toString() - Method in class edu.cmu.tetrad.sem.SemOptimizerRicf
- toString() - Method in class edu.cmu.tetrad.sem.SemOptimizerScattershot
- toString() - Method in class edu.cmu.tetrad.sem.SemPm
- toString() - Method in class edu.cmu.tetrad.sem.SemProposition
- toString() - Method in class edu.cmu.tetrad.sem.StandardizedSemIm.ParameterRange
- toString() - Method in class edu.cmu.tetrad.sem.StandardizedSemIm
- toString() - Method in class edu.cmu.tetrad.session.SessionNode
-
Prints out the name of the session node.
- toString() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.biolingua.BiolinguaDigraph
-
Returns a specially formatted string with all the contents of this Graph.
- toString() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.BasicGraph
-
Returns a specially formatted string with all the contents of this Graph.
- toString() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.BasicLTMatrix
-
Returns a specially formatted string with all the contents of this matrix
- toString() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.BasicMatrix
-
Returns a specially formatted string with all the contents of this matrix
- toString() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.LTMatrix
-
Returns a specially formatted string with all the contents of this matrix
- toString() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.Matrix
-
Returns a specially formatted string with all the contents of this matrix
- toString() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.SymMatrix
-
Returns a specially formatted string with all the contents of this matrix
- toString() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.util.SymMatrixF
-
Returns a specially formatted string with all the contents of this matrix
- toString() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ManualLagGraph
- toString() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.BasicLagGraph
-
Returns a string representation of the graph, indicating for each factor which lagged factors map into it.
- toString() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.BooleanFunction
-
Returns a string representation of the boolean function.
- toString() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.IndexedConnectivity
-
Returns a string representation of the graph, indicating for each factor which lagged factors map into it.
- toString() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.IndexedLagGraph
-
Returns a string representation of the graph, indicating for each factor which lagged factors map into it.
- toString() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.IndexedParent
-
Prints out the factor index and lag.
- toString() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.LaggedFactor
-
Returns a string representing this lagged factor.
- toString() - Method in interface edu.cmu.tetrad.study.gene.tetrad.gene.history.LagGraph
-
Returns a string representation of the graph, indicating for each factor which lagged factors map into it.
- toString() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.LinearFunction
-
Prints out the linear function of each factor of its parents.
- toString() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.Polynomial
-
Prints out a representation of the term.
- toString() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.PolynomialTerm
-
Prints out a representation of the term.
- toString() - Method in class edu.cmu.tetrad.study.performance.ComparisonParameters
- toString() - Method in class edu.cmu.tetrad.study.performance.ComparisonResult
- toString() - Method in class edu.cmu.tetrad.util.DefaultTetradLoggerConfig.DefaultEvent
- toString() - Method in class edu.cmu.tetrad.util.DefaultTetradLoggerConfig
- toString() - Method in class edu.cmu.tetrad.util.dist.Beta
-
A string representation of the distribution.
- toString() - Method in class edu.cmu.tetrad.util.dist.ChiSquare
- toString() - Method in class edu.cmu.tetrad.util.dist.Discrete
- toString() - Method in class edu.cmu.tetrad.util.dist.Exponential
- toString() - Method in class edu.cmu.tetrad.util.dist.Gamma
- toString() - Method in class edu.cmu.tetrad.util.dist.Indicator
- toString() - Method in class edu.cmu.tetrad.util.dist.LogNormal
- toString() - Method in class edu.cmu.tetrad.util.dist.MixtureOfGaussians
- toString() - Method in class edu.cmu.tetrad.util.dist.Normal
- toString() - Method in class edu.cmu.tetrad.util.dist.Poisson
- toString() - Method in class edu.cmu.tetrad.util.dist.SingleValue
- toString() - Method in class edu.cmu.tetrad.util.dist.Split
- toString() - Method in class edu.cmu.tetrad.util.dist.TruncatedNormal
- toString() - Method in class edu.cmu.tetrad.util.dist.Uniform
- toString() - Method in interface edu.cmu.tetrad.util.Function
- toString() - Method in class edu.cmu.tetrad.util.Matrix
- toString() - Method in class edu.cmu.tetrad.util.Matrix2
- toString() - Method in class edu.cmu.tetrad.util.Parameters
-
Returns a list of the parameters whose values were actually used in the course of the simulation.
- toString() - Method in class edu.cmu.tetrad.util.PartialCorrelationPdf
- toString() - Method in class edu.cmu.tetrad.util.Point
- toString() - Method in class edu.cmu.tetrad.util.PointXy
- toString() - Method in class edu.cmu.tetrad.util.SublistGenerator
- toString() - Method in interface edu.cmu.tetrad.util.TetradLoggerConfig
- toString() - Method in class edu.cmu.tetrad.util.TextTable
- toString() - Method in class edu.cmu.tetrad.util.Vector
- toString() - Method in class edu.cmu.tetrad.util.Version
- toString() - Method in class edu.pitt.csb.mgm.IndTestMultinomialLogisticRegressionWald
- toString() - Method in class edu.pitt.csb.mgm.Mgm.MGMParams
- toString(boolean[][]) - Static method in class edu.cmu.tetrad.util.MatrixUtils
-
Copies the given array, starting each line with a tab character..
- toString(double[]) - Static method in class edu.cmu.tetrad.util.MatrixUtils
- toString(double[][]) - Static method in class edu.cmu.tetrad.util.MatrixUtils
-
Copies the given array, using a standard scientific notation number formatter and beginning each line with a tab character.
- toString(double[][], List<String>) - Static method in class edu.cmu.tetrad.util.MatrixUtils
- toString(double[], NumberFormat) - Static method in class edu.cmu.tetrad.util.MatrixUtils
- toString(int[]) - Static method in class edu.cmu.tetrad.util.MatrixUtils
- toString(int[][]) - Static method in class edu.cmu.tetrad.util.MatrixUtils
- toString(int[][], List<String>) - Static method in class edu.cmu.tetrad.util.MatrixUtils
- toStringDep() - Method in class edu.cmu.tetrad.search.MarkovCheck.AllSubsetsIndependenceFacts
- toStringIndep() - Method in class edu.cmu.tetrad.search.MarkovCheck.AllSubsetsIndependenceFacts
- toStringSquare(double[][], NumberFormat, List<String>) - Static method in class edu.cmu.tetrad.util.MatrixUtils
- toStringSquare(double[][], List<String>) - Static method in class edu.cmu.tetrad.util.MatrixUtils
- toStringSquare(int[][], List<String>) - Static method in class edu.cmu.tetrad.util.MatrixUtils
- totalInstabilityDir(DoubleMatrix2D, List<Node>) - Static method in class edu.pitt.csb.stability.StabilityUtils
- totalInstabilityUndir(DoubleMatrix2D, List<Node>) - Static method in class edu.pitt.csb.stability.StabilityUtils
- toVector() - Method in class edu.pitt.csb.mgm.Mgm.MGMParams
- toVerticalDiscreteDataModel(VerticalDiscreteTabularData) - Static method in class edu.cmu.tetrad.util.DataConvertUtils
- toVerticalDiscreteDataModel(VerticalDiscreteTabularData, Metadata) - Static method in class edu.cmu.tetrad.util.DataConvertUtils
-
Converting using metadata
- toXML() - Method in class edu.pitt.isp.sverchkov.data.AdTree
-
Converts to XML.
- toXML(DocumentBuilder) - Method in class edu.pitt.isp.sverchkov.data.AdTree
-
Converts to XML.
- tPdf(double, double) - Static method in class edu.cmu.tetrad.util.ProbUtils
- tQuantile(double, double) - Static method in class edu.cmu.tetrad.util.ProbUtils
-
CACM Algorithm 396, by G.
- trace() - Method in class edu.cmu.tetrad.util.Matrix
- trace() - Method in class edu.cmu.tetrad.util.Matrix2
- trace(double[][]) - Static method in class edu.cmu.tetrad.util.MatrixUtils
- trace(Set<Node>, Set<Node>) - Method in class edu.cmu.tetrad.search.utils.GrowShrinkTree
- trace(Set<Node>, Set<Node>, Set<Node>) - Method in class edu.cmu.tetrad.search.utils.GrowShrinkTree
- train(Matrix, Matrix, Matrix) - Method in class jgpml.GaussianProcess
-
Trains the GP Hyperparameters maximizing the marginal likelihood.
- train(Matrix, Matrix, Matrix, int) - Method in class jgpml.GaussianProcess
-
Trains the GP Hyperparameters maximizing the marginal likelihood.
- tRand(double) - Static method in class edu.cmu.tetrad.util.ProbUtils
-
T distribution random generator.
- transferAttributes(Graph) - Method in class edu.cmu.tetrad.graph.Dag
- transferAttributes(Graph) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
- transferAttributes(Graph) - Method in interface edu.cmu.tetrad.graph.Graph
- transferAttributes(Graph) - Method in class edu.cmu.tetrad.graph.LagGraph
- transferAttributes(Graph) - Method in class edu.cmu.tetrad.graph.SemGraph
- transferAttributes(Graph) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- transferNodesAndEdges(Graph) - Method in class edu.cmu.tetrad.graph.Dag
- transferNodesAndEdges(Graph) - Method in class edu.cmu.tetrad.graph.EdgeListGraph
-
Transfers nodes and edges from one graph to another.
- transferNodesAndEdges(Graph) - Method in interface edu.cmu.tetrad.graph.Graph
-
Transfers nodes and edges from one graph to another.
- transferNodesAndEdges(Graph) - Method in class edu.cmu.tetrad.graph.LagGraph
- transferNodesAndEdges(Graph) - Method in class edu.cmu.tetrad.graph.SemGraph
- transferNodesAndEdges(Graph) - Method in class edu.cmu.tetrad.graph.TimeLagGraph
- transform(DataSet, String...) - Static method in class edu.cmu.tetrad.calculator.Transformation
-
Transforms the given data using the given representations of transforming equations.
- Transformation - Class in edu.cmu.tetrad.calculator
-
Represents a transformation on some dataset.
- translate(String, List<Node>) - Static method in class edu.cmu.tetrad.search.utils.GraphSearchUtils
- transpose() - Method in class edu.cmu.tetrad.util.Matrix
- transpose() - Method in class edu.cmu.tetrad.util.Matrix2
- transpose(double[][]) - Static method in class edu.cmu.tetrad.util.MatrixUtils
- transposeWithoutCopy(RealMatrix) - Static method in class edu.cmu.tetrad.util.MatrixUtils
- traverse(Node, Edge) - Static method in class edu.cmu.tetrad.graph.Edges
- traverseDirected(Node, Edge) - Static method in class edu.cmu.tetrad.graph.Edges
-
For A -> B, given A, returns B; otherwise returns null.
- traverseReverseDirected(Node, Edge) - Static method in class edu.cmu.tetrad.graph.Edges
-
For A -> B, given B, returns A; otherwise returns null.
- traverseSemiDirected(Node, Edge) - Static method in class edu.cmu.tetrad.graph.Edges
-
For A --* B or A o-* B, given A, returns B.
- traverseSemiDirected(Node, Edge) - Static method in class edu.cmu.tetrad.graph.GraphUtils
- treks(Graph, Node, Node) - Static method in class edu.cmu.tetrad.search.work_in_progress.Ion
- treks(Node, Node, int) - Method in class edu.cmu.tetrad.graph.Paths
- treksIncludingBidirected(Node, Node) - Method in class edu.cmu.tetrad.graph.Paths
- triangle(Node, Node, Node) - Method in class edu.cmu.tetrad.search.utils.TeyssierScorer
-
Returns true iff [a, b, c] is a triangle.
- trimEdgesAmongParents(Graph, Node) - Static method in class edu.cmu.tetrad.search.utils.MbUtils
-
Removes edges among the parents of the target.
- trimEdgesAmongParentsOfChildren(Graph, Node) - Static method in class edu.cmu.tetrad.search.utils.MbUtils
-
Removes edges among the parents of children of the target.
- trimGraph(List<Node>, Graph, int) - Static method in class edu.cmu.tetrad.graph.GraphUtils
- TRIMMING_STYLE - Static variable in class edu.cmu.tetrad.util.Params
- trimToAdjacents(Graph, Node) - Static method in class edu.cmu.tetrad.search.utils.MbUtils
-
Trims the graph to just the adjacents of the target.
- trimToMbNodes(Graph, Node, boolean) - Static method in class edu.cmu.tetrad.search.utils.MbUtils
-
Trims the graph to the target, the parents and children of the target, and the parents of the children of the target.
- Triple - Class in edu.cmu.tetrad.graph
-
Stores a triple (x, y, z) of nodes.
- Triple(Node, Node, Node) - Constructor for class edu.cmu.tetrad.graph.Triple
-
Constructs a triple of nodes.
- TripleClassifier - Interface in edu.cmu.tetrad.graph
-
Marks a search algorithm as a triad classifier and returns the triad classifications if makes.
- triplesToText(Set<Triple>, String) - Static method in class edu.cmu.tetrad.graph.GraphUtils
- true_DAG - Enum constant in enum class edu.cmu.tetrad.algcomparison.Comparison.ComparisonGraph
- true_DAG - Enum constant in enum class edu.cmu.tetrad.algcomparison.TimeoutComparison.ComparisonGraph
- TrueDagFalseNegativesArrows - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- TrueDagFalseNegativesArrows() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.TrueDagFalseNegativesArrows
- TrueDagFalseNegativesTails - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- TrueDagFalseNegativesTails() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.TrueDagFalseNegativesTails
- TrueDagFalsePositiveArrow - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- TrueDagFalsePositiveArrow() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.TrueDagFalsePositiveArrow
- TrueDagFalsePositiveTails - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- TrueDagFalsePositiveTails() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.TrueDagFalsePositiveTails
- TrueDagPrecisionArrow - Class in edu.cmu.tetrad.algcomparison.statistic
-
The proportion of X*->Y in the estimated graph for which there is no path Y~~>X in the true graph.
- TrueDagPrecisionArrow() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.TrueDagPrecisionArrow
- TrueDagPrecisionTails - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- TrueDagPrecisionTails() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.TrueDagPrecisionTails
- TrueDagRecallArrows - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- TrueDagRecallArrows() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.TrueDagRecallArrows
- TrueDagRecallTails - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- TrueDagRecallTails() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.TrueDagRecallTails
- TrueDagTruePositiveArrow - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- TrueDagTruePositiveArrow() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.TrueDagTruePositiveArrow
- TrueDagTruePositiveDirectedPathNonancestor - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- TrueDagTruePositiveDirectedPathNonancestor() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.TrueDagTruePositiveDirectedPathNonancestor
- TrueDagTruePositiveTails - Class in edu.cmu.tetrad.algcomparison.statistic
-
The bidirected true positives.
- TrueDagTruePositiveTails() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.TrueDagTruePositiveTails
- trueEffect(Node, Node, Graph) - Method in class edu.cmu.tetrad.search.Ida
-
Calculates the true effect of (x, y) given the true DAG (which must be provided).
- TruncatedNormal - Class in edu.cmu.tetrad.util.dist
-
A normal distribution that allows its parameters to be set and allows random sampling.
- TsDagToPag - Class in edu.cmu.tetrad.search.utils
-
Finds the PAG to which a DAG belongs, for a time series model.
- TsDagToPag(Graph) - Constructor for class edu.cmu.tetrad.search.utils.TsDagToPag
-
Constructs a new FCI search for the given independence test and background knowledge.
- TsUtils - Class in edu.cmu.tetrad.search.utils
-
Contains some utilities for doing autoregression.
- TsUtils() - Constructor for class edu.cmu.tetrad.search.utils.TsUtils
- TsUtils.VarResult - Class in edu.cmu.tetrad.search.utils
-
Gives a result consisting of the residuals and collapsed var graphs.
- tt - Enum constant in enum class edu.cmu.tetrad.graph.EdgeTypeProbability.EdgeType
- tuck(Node, int) - Method in class edu.cmu.tetrad.search.utils.TeyssierScorer
- TWO_CYCLE_ALPHA - Static variable in class edu.cmu.tetrad.util.Params
- TWO_CYCLE_SCREENING_THRESHOLD - Static variable in class edu.cmu.tetrad.util.Params
- twoCycCor - Variable in class edu.cmu.tetrad.graph.GraphUtils.TwoCycleErrors
- twoCycFn - Variable in class edu.cmu.tetrad.graph.GraphUtils.TwoCycleErrors
- twoCycFp - Variable in class edu.cmu.tetrad.graph.GraphUtils.TwoCycleErrors
- TwoCycleErrors(int, int, int) - Constructor for class edu.cmu.tetrad.graph.GraphUtils.TwoCycleErrors
- TwoCycleFalseNegative - Class in edu.cmu.tetrad.algcomparison.statistic
-
The 2-cycle precision.
- TwoCycleFalseNegative() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.TwoCycleFalseNegative
- TwoCycleFalsePositive - Class in edu.cmu.tetrad.algcomparison.statistic
-
The 2-cycle precision.
- TwoCycleFalsePositive() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.TwoCycleFalsePositive
- TwoCyclePrecision - Class in edu.cmu.tetrad.algcomparison.statistic
-
The 2-cycle precision.
- TwoCyclePrecision() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.TwoCyclePrecision
- TwoCycleRecall - Class in edu.cmu.tetrad.algcomparison.statistic
-
The 2-cycle recall.
- TwoCycleRecall() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.TwoCycleRecall
- TwoCycleTruePositive - Class in edu.cmu.tetrad.algcomparison.statistic
-
The 2-cycle precision.
- TwoCycleTruePositive() - Constructor for class edu.cmu.tetrad.algcomparison.statistic.TwoCycleTruePositive
- twoFactorTest(int, int, int, int) - Method in interface edu.cmu.tetrad.search.utils.TetradTest
- twoFactorTest(int, int, int, int) - Method in class edu.cmu.tetrad.search.utils.TetradTestContinuous
- twoFactorTest(int, int, int, int) - Method in class edu.cmu.tetrad.search.utils.TetradTestDiscrete
- twoFactorTest(int, int, int, int) - Method in class edu.cmu.tetrad.search.utils.TetradTestPopulation
- twoFactorTest(int, int, int, int, int) - Method in interface edu.cmu.tetrad.search.utils.TetradTest
- twoFactorTest(int, int, int, int, int) - Method in class edu.cmu.tetrad.search.utils.TetradTestContinuous
- twoFactorTest(int, int, int, int, int) - Method in class edu.cmu.tetrad.search.utils.TetradTestDiscrete
- twoFactorTest(int, int, int, int, int) - Method in class edu.cmu.tetrad.search.utils.TetradTestPopulation
- twoFactorTest(int, int, int, int, int, int) - Method in interface edu.cmu.tetrad.search.utils.TetradTest
- twoFactorTest(int, int, int, int, int, int) - Method in class edu.cmu.tetrad.search.utils.TetradTestContinuous
- twoFactorTest(int, int, int, int, int, int) - Method in class edu.cmu.tetrad.search.utils.TetradTestDiscrete
- twoFactorTest(int, int, int, int, int, int) - Method in class edu.cmu.tetrad.search.utils.TetradTestPopulation
- type - Static variable in class edu.cmu.tetrad.util.MillisecondTimes
- Type1 - Class in edu.cmu.tetrad.session
-
A sample class to be wrapped in a SessionNode as a model.
- Type1(Type2, Type3, Parameters) - Constructor for class edu.cmu.tetrad.session.Type1
-
A sample constructor that takes Model 2 and Type3 as parent.
- Type10 - Class in edu.cmu.tetrad.session
-
A sample class to be wrapped in a SessionNode as a model.
- Type10(Type6, Type6, Parameters) - Constructor for class edu.cmu.tetrad.session.Type10
- Type11 - Class in edu.cmu.tetrad.session
-
A sample class to be wrapped in a SessionNode as a model.
- Type11(Parameters) - Constructor for class edu.cmu.tetrad.session.Type11
- Type12 - Class in edu.cmu.tetrad.session
-
A sample class to be wrapped in a SessionNode as a model.
- Type12(Type11, Parameters) - Constructor for class edu.cmu.tetrad.session.Type12
- Type12(Type12, Parameters) - Constructor for class edu.cmu.tetrad.session.Type12
- Type2 - Class in edu.cmu.tetrad.session
-
A sample class to be wrapped in a SessionNode as a model.
- Type2(Parameters) - Constructor for class edu.cmu.tetrad.session.Type2
-
A sample constructor that takes Model 2 and Type3 as parent.
- Type3 - Class in edu.cmu.tetrad.session
-
A sample class to be wrapped in a SessionNode as a model.
- Type3(Type2, Type4) - Constructor for class edu.cmu.tetrad.session.Type3
-
It should also be possible to construct a Type3-model with two parents: a Type1-node and a Type2-node.
- Type3(Type2, Parameters) - Constructor for class edu.cmu.tetrad.session.Type3
-
It should be possible to construct a Type3-model with a Type1-node as parent.
- Type4 - Class in edu.cmu.tetrad.session
-
A sample class to be wrapped in a SessionNode as a model.
- Type4(Type1, Parameters) - Constructor for class edu.cmu.tetrad.session.Type4
-
It should be possible to construct a Type4-model with a Type1-node as parent.
- Type4(Type2, Type3) - Constructor for class edu.cmu.tetrad.session.Type4
-
It should be possible to construct a Type4-model with both Type2 and Type2-nodes as parents.
- Type5 - Class in edu.cmu.tetrad.session
-
A sample class to be wrapped in a SessionNode as a model.
- Type5(Type1, Type1, Parameters) - Constructor for class edu.cmu.tetrad.session.Type5
-
It should not be possible to constuct Type5, because it contains two arguments of the same type.
- Type6 - Class in edu.cmu.tetrad.session
-
A sample class to be wrapped in a SessionNode as a model.
- Type6(Type7, Type8, Parameters) - Constructor for class edu.cmu.tetrad.session.Type6
- Type7 - Class in edu.cmu.tetrad.session
-
A sample class to be wrapped in a SessionNode as a model.
- Type7(Parameters) - Constructor for class edu.cmu.tetrad.session.Type7
- Type8 - Class in edu.cmu.tetrad.session
-
A sample class to be wrapped in a SessionNode as a model.
- Type8(Type7, Type9, Parameters) - Constructor for class edu.cmu.tetrad.session.Type8
- Type8(Type7, Parameters) - Constructor for class edu.cmu.tetrad.session.Type8
- Type9 - Class in edu.cmu.tetrad.session
-
A sample class to be wrapped in a SessionNode as a model.
- Type9(Type6, Parameters) - Constructor for class edu.cmu.tetrad.session.Type9
- Type9(Type7, Type8, Parameters) - Constructor for class edu.cmu.tetrad.session.Type9
- TYPES - Static variable in class edu.cmu.tetrad.graph.NodeType
U
- Underlines - Class in edu.cmu.tetrad.graph
- Underlines(Graph) - Constructor for class edu.cmu.tetrad.graph.Underlines
- Underlines(Underlines) - Constructor for class edu.cmu.tetrad.graph.Underlines
- undirectedEdge(Node, Node) - Static method in class edu.cmu.tetrad.graph.Edges
-
Constructs a new undirected edge from nodeA to nodeB (--).
- undirectedGraph(Graph) - Static method in class edu.cmu.tetrad.graph.GraphUtils
- undirectedToBidirected(Graph) - Static method in class edu.cmu.tetrad.graph.GraphUtils
- Uniform - Class in edu.cmu.tetrad.util.dist
-
For given a, b (a < b), returns a point chosen uniformly from [a, b].
- Uniform(double, double) - Constructor for class edu.cmu.tetrad.util.dist.Uniform
- UniformGraphGenerator(int) - Constructor for class edu.cmu.tetrad.graph.RandomGraph.UniformGraphGenerator
-
Constructs a random graph generator for the given structure.
- UniformityTest - Class in edu.cmu.tetrad.util
- UniformityTest() - Constructor for class edu.cmu.tetrad.util.UniformityTest
- uniformRand() - Static method in class edu.cmu.tetrad.util.ProbUtils
- UniformScatterTest - Class in edu.cmu.tetrad.algcomparison.independence
-
Wrapper for Fisher Z test.
- UniformScatterTest() - Constructor for class edu.cmu.tetrad.algcomparison.independence.UniformScatterTest
- uniformSeeds(long, long) - Static method in class edu.cmu.tetrad.util.ProbUtils
- union(GraphChange) - Method in class edu.cmu.tetrad.search.work_in_progress.GraphChange
-
Absorbs all changes from the GraphChange other into the calling GraphChange.
- UNKNOWN - Enum constant in enum class edu.cmu.tetrad.calculator.parser.Token
- Unmarshallable - Interface in edu.cmu.tetrad.util
-
Interface to tag classes that should not be cloned by marshalling.> 0
- UnmeasuredConfounder - Annotation Interface in edu.cmu.tetrad.annotation
-
Sep 19, 2017 1:56:20 PM
- unregisterEditor(JComponent) - Static method in class edu.cmu.tetrad.session.ModificationRegistery
- unregisterSessionNode(SessionNode) - Static method in class edu.cmu.tetrad.session.ModificationRegistery
-
Removes the given session node from the list of sessions nodes for which changes have been made.
- update() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.AbstractNbComponent
-
Updates.
- update() - Method in interface edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.NbComponent
-
Updates.
- update() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.NbFunction
- update() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.NbFunctionAnd
- update() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.NbFunctionOr
- update() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.NbFunctionSum
- update() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.NbFunctionSV
- update() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.NbGene
- update() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.NbGeneAnd
- update() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.urchin.NbGeneOr
- update() - Method in class edu.cmu.tetrad.study.gene.tetrad.gene.history.GeneHistory
-
Updates the history to the next time slice using some formula.
- UpdatedBayesIm - Class in edu.cmu.tetrad.bayes
-
Represents a Bayes IM in which all of the conditional probability tables have been updated to take into account evidence.
- UpdatedBayesIm(BayesIm) - Constructor for class edu.cmu.tetrad.bayes.UpdatedBayesIm
-
Constructs Bayes net in which CPT's updated for the given evidence are calculated on the fly.
- UpdatedBayesIm(BayesIm, Evidence) - Constructor for class edu.cmu.tetrad.bayes.UpdatedBayesIm
-
Constructs Bayes net in which CPT's updated for the given evidence are calculated on the fly.
- updatedIm(Matrix, Vector) - Method in class edu.cmu.tetrad.sem.SemIm
- UpdateFunction - Interface in edu.cmu.tetrad.study.gene.tetrad.gene.history
-
Implements a function from the previous time steps of a history array to the getModel time step.
- UPPER_BOUND - Static variable in class edu.cmu.tetrad.util.Params
- upperTri(DoubleMatrix2D, int) - Static method in class edu.pitt.csb.mgm.Mgm
- USE_BES - Static variable in class edu.cmu.tetrad.util.Params
- USE_CORR_DIFF_ADJACENCIES - Static variable in class edu.cmu.tetrad.util.Params
- USE_DATA_ORDER - Static variable in class edu.cmu.tetrad.util.Params
- USE_FAS_ADJACENCIES - Static variable in class edu.cmu.tetrad.util.Params
- USE_GAP - Static variable in class edu.cmu.tetrad.util.Params
- USE_MAX_P_HEURISTIC - Static variable in class edu.cmu.tetrad.util.Params
- USE_MAX_P_ORIENTATION_HEURISTIC - Static variable in class edu.cmu.tetrad.util.Params
- USE_SKEW_ADJACENCIES - Static variable in class edu.cmu.tetrad.util.Params
- USE_WISHART - Static variable in class edu.cmu.tetrad.util.Params
- useClonedModel() - Method in class edu.cmu.tetrad.session.SessionNode
- usedParameters - Variable in class edu.cmu.tetrad.algcomparison.algorithm.ExternalAlgorithm
- User - Enum constant in enum class edu.cmu.tetrad.util.MillisecondTimes.Type
- userTimeMillis() - Static method in class edu.cmu.tetrad.util.MillisecondTimes
- UsesScoreWrapper - Interface in edu.cmu.tetrad.algcomparison.utils
-
Author : Jeremy Espino MD Created 7/6/17 2:19 PM
V
- valSet(DoubleMatrix1D) - Static method in class edu.pitt.csb.mgm.MixedUtils
- valueAt(double) - Method in interface edu.cmu.tetrad.util.Function
- valueAt(double) - Method in class edu.cmu.tetrad.util.PartialCorrelationPdf
-
Calculates the value of the function at the given domain point.
- valueAt(double...) - Method in interface edu.cmu.tetrad.sem.ConnectionFunction
- valueOf(String) - Static method in enum class edu.cmu.tetrad.algcomparison.comparegraphs.CompareTwoGraphs.CompareToType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.cmu.tetrad.algcomparison.comparegraphs.CompareTwoGraphs.ComparisonType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.cmu.tetrad.algcomparison.Comparison.ComparisonGraph
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.cmu.tetrad.algcomparison.TimeoutComparison.ComparisonGraph
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.cmu.tetrad.annotation.AlgType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.cmu.tetrad.calculator.expression.ExpressionDescriptor.Position
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.cmu.tetrad.calculator.parser.ExpressionParser.RestrictionType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.cmu.tetrad.calculator.parser.Token
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.cmu.tetrad.data.DataType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.cmu.tetrad.graph.Edge.Property
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.cmu.tetrad.graph.EdgeTypeProbability.EdgeType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.cmu.tetrad.graph.Endpoint
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.cmu.tetrad.graph.NodeVariableType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.cmu.tetrad.search.Cstar.CpdagAlgorithm
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.cmu.tetrad.search.Cstar.SampleStyle
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.cmu.tetrad.search.Fask.AdjacencyMethod
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.cmu.tetrad.search.Fask.LeftRight
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.cmu.tetrad.search.FgesMb.TrimmingStyle
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.cmu.tetrad.search.Fofc.Algorithm
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.cmu.tetrad.search.Ftfc.Algorithm
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.cmu.tetrad.search.Lofs.Rule
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.cmu.tetrad.search.Lofs.Score
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.cmu.tetrad.search.MarkovCheck.ConditioningSetType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.cmu.tetrad.search.score.GicScores.RuleType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.cmu.tetrad.search.score.SemBicScore.RuleType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.cmu.tetrad.search.test.ConditionalCorrelationIndependence.Basis
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.cmu.tetrad.search.test.ConditionalCorrelationIndependence.Kernel
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.cmu.tetrad.search.utils.BpcAlgorithmType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.cmu.tetrad.search.utils.BpcTestType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.cmu.tetrad.search.utils.ClusterSignificance.CheckType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.cmu.tetrad.search.utils.GraphSearchUtils.CpcTripleType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.cmu.tetrad.search.utils.PcCommon.ColliderDiscovery
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.cmu.tetrad.search.utils.PcCommon.ConflictRule
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.cmu.tetrad.search.utils.PcCommon.FasType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.cmu.tetrad.search.utils.PcCommon.PcHeuristicType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.cmu.tetrad.search.utils.ResolveSepsets.Method
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.cmu.tetrad.search.work_in_progress.HbsmsBeam.Move.Type
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.cmu.tetrad.search.work_in_progress.OtherPermAlgs.Method
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.cmu.tetrad.search.work_in_progress.ResolveSepsetsDci.Method
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.cmu.tetrad.search.work_in_progress.VcPc.CpcTripleType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.cmu.tetrad.search.work_in_progress.VcPcFast.CpcTripleType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.cmu.tetrad.sem.ScoreType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.cmu.tetrad.sem.StandardizedSemIm.Initialization
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.cmu.tetrad.study.performance.Comparison.TableColumn
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.cmu.tetrad.study.performance.Comparison2.TableColumn
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.cmu.tetrad.study.performance.ComparisonParameters.Algorithm
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.cmu.tetrad.study.performance.ComparisonParameters.DataType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.cmu.tetrad.study.performance.ComparisonParameters.IndependenceTestType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.cmu.tetrad.study.performance.ComparisonParameters.ResultType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.cmu.tetrad.util.MillisecondTimes.Type
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.cmu.tetrad.util.TextTable.Delimiter
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.pitt.dbmi.algo.bayesian.constraint.inference.BCCausalInference.OP
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.pitt.dbmi.algo.bayesian.constraint.inference.BCInference.OP
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.pitt.dbmi.algo.resampling.ResamplingEdgeEnsemble
-
Returns the enum constant of this class with the specified name.
- values() - Static method in enum class edu.cmu.tetrad.algcomparison.comparegraphs.CompareTwoGraphs.CompareToType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.cmu.tetrad.algcomparison.comparegraphs.CompareTwoGraphs.ComparisonType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.cmu.tetrad.algcomparison.Comparison.ComparisonGraph
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.cmu.tetrad.algcomparison.TimeoutComparison.ComparisonGraph
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.cmu.tetrad.annotation.AlgType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.cmu.tetrad.calculator.expression.ExpressionDescriptor.Position
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.cmu.tetrad.calculator.parser.ExpressionParser.RestrictionType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.cmu.tetrad.calculator.parser.Token
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.cmu.tetrad.data.DataType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.cmu.tetrad.graph.Edge.Property
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.cmu.tetrad.graph.EdgeTypeProbability.EdgeType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.cmu.tetrad.graph.Endpoint
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.cmu.tetrad.graph.NodeVariableType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.cmu.tetrad.search.Cstar.CpdagAlgorithm
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.cmu.tetrad.search.Cstar.SampleStyle
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.cmu.tetrad.search.Fask.AdjacencyMethod
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.cmu.tetrad.search.Fask.LeftRight
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.cmu.tetrad.search.FgesMb.TrimmingStyle
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.cmu.tetrad.search.Fofc.Algorithm
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.cmu.tetrad.search.Ftfc.Algorithm
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.cmu.tetrad.search.Lofs.Rule
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.cmu.tetrad.search.Lofs.Score
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.cmu.tetrad.search.MarkovCheck.ConditioningSetType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.cmu.tetrad.search.score.GicScores.RuleType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.cmu.tetrad.search.score.SemBicScore.RuleType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.cmu.tetrad.search.test.ConditionalCorrelationIndependence.Basis
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.cmu.tetrad.search.test.ConditionalCorrelationIndependence.Kernel
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.cmu.tetrad.search.utils.BpcAlgorithmType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.cmu.tetrad.search.utils.BpcTestType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.cmu.tetrad.search.utils.ClusterSignificance.CheckType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.cmu.tetrad.search.utils.GraphSearchUtils.CpcTripleType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.cmu.tetrad.search.utils.PcCommon.ColliderDiscovery
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.cmu.tetrad.search.utils.PcCommon.ConflictRule
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.cmu.tetrad.search.utils.PcCommon.FasType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.cmu.tetrad.search.utils.PcCommon.PcHeuristicType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.cmu.tetrad.search.utils.ResolveSepsets.Method
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.cmu.tetrad.search.work_in_progress.HbsmsBeam.Move.Type
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.cmu.tetrad.search.work_in_progress.OtherPermAlgs.Method
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.cmu.tetrad.search.work_in_progress.ResolveSepsetsDci.Method
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.cmu.tetrad.search.work_in_progress.VcPc.CpcTripleType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.cmu.tetrad.search.work_in_progress.VcPcFast.CpcTripleType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.cmu.tetrad.sem.ScoreType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.cmu.tetrad.sem.StandardizedSemIm.Initialization
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.cmu.tetrad.study.performance.Comparison.TableColumn
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.cmu.tetrad.study.performance.Comparison2.TableColumn
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.cmu.tetrad.study.performance.ComparisonParameters.Algorithm
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.cmu.tetrad.study.performance.ComparisonParameters.DataType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.cmu.tetrad.study.performance.ComparisonParameters.IndependenceTestType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.cmu.tetrad.study.performance.ComparisonParameters.ResultType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.cmu.tetrad.util.MillisecondTimes.Type
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.cmu.tetrad.util.TextTable.Delimiter
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.pitt.dbmi.algo.bayesian.constraint.inference.BCCausalInference.OP
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.pitt.dbmi.algo.bayesian.constraint.inference.BCInference.OP
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.pitt.dbmi.algo.resampling.ResamplingEdgeEnsemble
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values(A) - Method in class edu.pitt.isp.sverchkov.data.AdTree
-
Returns the number of rows in the data set.
- valuesToString() - Method in class edu.cmu.tetrad.simulation.PRAOerrors
- VAR - Static variable in class edu.cmu.tetrad.sem.ParamType
-
A variance parameter.
- VAR_HIGH - Static variable in class edu.cmu.tetrad.util.Params
- VAR_LOW - Static variable in class edu.cmu.tetrad.util.Params
- varHat(double[]) - Static method in class edu.cmu.tetrad.util.StatUtils
- varHat(double[], int) - Static method in class edu.cmu.tetrad.util.StatUtils
- varHat(long[]) - Static method in class edu.cmu.tetrad.util.StatUtils
- varHat(long[], int) - Static method in class edu.cmu.tetrad.util.StatUtils
- Variable - Interface in edu.cmu.tetrad.data
-
Interface implemented by classes, instantiations of which are capable of serving as variables for columns in a DataSet.
- VariableExpression - Class in edu.cmu.tetrad.calculator.expression
-
An Expression for a variable.
- VariableExpression(String) - Constructor for class edu.cmu.tetrad.calculator.expression.VariableExpression
- variables() - Method in interface edu.pitt.isp.sverchkov.data.DataTable
- variables() - Method in class edu.pitt.isp.sverchkov.data.DataTableImpl
- variablesForIndices(List<Integer>, List<Node>) - Static method in class edu.cmu.tetrad.search.utils.ClusterSignificance
- variablesForIndices2(Set<List<Integer>>, List<Node>) - Static method in class edu.cmu.tetrad.search.utils.ClusterSignificance
- VariableSource - Interface in edu.cmu.tetrad.data
-
Inteface implemented by classes, instantiations of which are associated with lists of variables.
- variance(double[]) - Static method in class edu.cmu.tetrad.util.StatUtils
- variance(double[], int) - Static method in class edu.cmu.tetrad.util.StatUtils
- variance(long[]) - Static method in class edu.cmu.tetrad.util.StatUtils
- variance(long[], int) - Static method in class edu.cmu.tetrad.util.StatUtils
- Variance - Interface in edu.cmu.tetrad.stat
-
Feb 9, 2016 3:18:03 PM
- VarianceVector - Class in edu.cmu.tetrad.stat
-
Feb 9, 2016 3:18:44 PM
- VarianceVector(float[][]) - Constructor for class edu.cmu.tetrad.stat.VarianceVector
- VarianceVectorForkJoin - Class in edu.cmu.tetrad.stat
-
Feb 9, 2016 3:19:52 PM
- VarianceVectorForkJoin(float[][], int) - Constructor for class edu.cmu.tetrad.stat.VarianceVectorForkJoin
- VarResult(DataSet, Graph) - Constructor for class edu.cmu.tetrad.search.utils.TsUtils.VarResult
- VcFas - Class in edu.cmu.tetrad.search.work_in_progress
-
Implements the "fast adjacency search" used in several causal algorithm in this package.
- VcFas(IndependenceTest) - Constructor for class edu.cmu.tetrad.search.work_in_progress.VcFas
- VcPc - Class in edu.cmu.tetrad.search.work_in_progress
-
Implements a convervative version of PC, in which the Markov condition is assumed but faithfulness is tested locally.
- VcPc(IndependenceTest) - Constructor for class edu.cmu.tetrad.search.work_in_progress.VcPc
-
Constructs a CPC algorithm that uses the given independence test as oracle.
- VcPc.CpcTripleType - Enum Class in edu.cmu.tetrad.search.work_in_progress
- VcPcAlt - Class in edu.cmu.tetrad.search.work_in_progress
-
Implements a convervative version of PC, in which the Markov condition is assumed but faithfulness is tested locally.
- VcPcAlt(IndependenceTest) - Constructor for class edu.cmu.tetrad.search.work_in_progress.VcPcAlt
-
Constructs a CPC algorithm that uses the given independence test as oracle.
- VcPcFast - Class in edu.cmu.tetrad.search.work_in_progress
-
Implements a convervative version of PC, in which the Markov condition is assumed but faithfulness is tested locally.
- VcPcFast(IndependenceTest) - Constructor for class edu.cmu.tetrad.search.work_in_progress.VcPcFast
-
Constructs a CPC algorithm that uses the given independence test as oracle.
- VcPcFast.CpcTripleType - Enum Class in edu.cmu.tetrad.search.work_in_progress
- vec(double[][]) - Static method in class edu.cmu.tetrad.util.MatrixUtils
- vech(double[][]) - Static method in class edu.cmu.tetrad.util.MatrixUtils
- vechToVecLeft(int) - Static method in class edu.cmu.tetrad.util.MatrixUtils
-
The matrix which, when postmultiplied by vech, return vec.
- vecMax(DoubleMatrix1D) - Static method in class edu.pitt.csb.mgm.MixedUtils
- Vector - Class in edu.cmu.tetrad.util
-
Vector wrapping matrix library.
- Vector(double[]) - Constructor for class edu.cmu.tetrad.util.Vector
- Vector(int) - Constructor for class edu.cmu.tetrad.util.Vector
- verbose - Variable in class edu.cmu.tetrad.search.utils.TetradTestDiscrete
- VERBOSE - Static variable in class edu.cmu.tetrad.util.Params
- Version - Class in edu.cmu.tetrad.util
-
Represents the getModel Tetrad version.
- Version(String) - Constructor for class edu.cmu.tetrad.util.Version
-
Parses string version specs into Versions.
- VerticalDoubleDataBox - Class in edu.cmu.tetrad.data
-
Stores a 2D array of double data.
- VerticalDoubleDataBox(double[][]) - Constructor for class edu.cmu.tetrad.data.VerticalDoubleDataBox
-
Constructs a new data box using the given 2D double data array as data.
- VerticalDoubleDataBox(int, int) - Constructor for class edu.cmu.tetrad.data.VerticalDoubleDataBox
-
Constructs an 2D double array consisting entirely of missing values (Double.NaN).
- VerticalDoubleDataBox(DataBox) - Constructor for class edu.cmu.tetrad.data.VerticalDoubleDataBox
-
Copies the data from the given data box into this one.
- VerticalIntDataBox - Class in edu.cmu.tetrad.data
-
Stores a 2D array of int data.
- VerticalIntDataBox(int[][]) - Constructor for class edu.cmu.tetrad.data.VerticalIntDataBox
-
Constructs a new data box using the given 2D int data array as data.
- VerticalIntDataBox(int, int) - Constructor for class edu.cmu.tetrad.data.VerticalIntDataBox
-
Constructs an 2D int array consisting entirely of missing values (int.NaN).
- VerticalIntDataBox(DataBox) - Constructor for class edu.cmu.tetrad.data.VerticalIntDataBox
- Vicinity - Class in edu.cmu.tetrad.simulation
-
This version of Vicinity finds nearby nodes by searching with an expanding cube Prior to Vicinity4, versions of Vicinity looked at the 3 axis independently instead of collectively.
- Vicinity(List<Edge>, DataSet, int, int, int, int, int, int, double, double, double) - Constructor for class edu.cmu.tetrad.simulation.Vicinity
- viewSelection(int[]) - Method in class edu.cmu.tetrad.util.Vector
- viewSelection(int[], int[]) - Method in class edu.cmu.tetrad.data.ByteDataBox
- viewSelection(int[], int[]) - Method in interface edu.cmu.tetrad.data.DataBox
- viewSelection(int[], int[]) - Method in class edu.cmu.tetrad.data.DoubleDataBox
- viewSelection(int[], int[]) - Method in class edu.cmu.tetrad.data.FloatDataBox
- viewSelection(int[], int[]) - Method in class edu.cmu.tetrad.data.IntDataBox
- viewSelection(int[], int[]) - Method in class edu.cmu.tetrad.data.LongDataBox
- viewSelection(int[], int[]) - Method in class edu.cmu.tetrad.data.MixedDataBox
- viewSelection(int[], int[]) - Method in class edu.cmu.tetrad.data.ShortDataBox
- viewSelection(int[], int[]) - Method in class edu.cmu.tetrad.data.VerticalDoubleDataBox
- viewSelection(int[], int[]) - Method in class edu.cmu.tetrad.data.VerticalIntDataBox
W
- W_THRESHOLD - Static variable in class edu.cmu.tetrad.util.Params
- Wall - Enum constant in enum class edu.cmu.tetrad.util.MillisecondTimes.Type
- wallTimeMillis() - Static method in class edu.cmu.tetrad.util.MillisecondTimes
- warning(String) - Method in class edu.cmu.tetrad.util.LogUtils
- Washdown - Class in edu.cmu.tetrad.search.work_in_progress
-
Implements the Washdown algorithm,
- Washdown(DataSet, double) - Constructor for class edu.cmu.tetrad.search.work_in_progress.Washdown
-
Constructor.
- Washdown(ICovarianceMatrix, double) - Constructor for class edu.cmu.tetrad.search.work_in_progress.Washdown
-
Constructor.
- weakUnion() - Method in class edu.cmu.tetrad.search.utils.GraphoidAxioms
-
Checks is weak union holds, e.g., X _||_ Y U W | Z ==> X _||_ Y | Z U W
- WHITESPACE - Enum constant in enum class edu.cmu.tetrad.calculator.parser.Token
- WHITESPACE - Static variable in class edu.cmu.tetrad.data.DelimiterType
- worsleyfriston - Enum constant in enum class edu.cmu.tetrad.search.utils.ResolveSepsets.Method
- worsleyfriston - Enum constant in enum class edu.cmu.tetrad.search.work_in_progress.ResolveSepsetsDci.Method
- wouldBeSatisfied(double) - Method in class edu.cmu.tetrad.sem.ParamConstraint
-
This method is for testing whether a value that might be assigned to a parameter would satisfy it.
- writeCovMatrix(ICovarianceMatrix, PrintWriter, NumberFormat) - Static method in class edu.cmu.tetrad.data.DataWriter
-
Writes the lower triangle of a covariance matrix to file.
- writeRectangularData(DataSet, Writer, char) - Static method in class edu.cmu.tetrad.data.DataWriter
-
Writes a dataset to file.
X
- X - Variable in class jgpml.GaussianProcess
-
input data points
Z
- zeros(int, int) - Static method in class edu.cmu.tetrad.util.MatrixUtils
- zhangFinalOrientation(Graph) - Method in class edu.cmu.tetrad.search.utils.FciOrient
- ZhangShenBoundScore - Class in edu.cmu.tetrad.algcomparison.score
-
Wrapper for linear, Gaussian Extended BIC score (Chen and Chen).
- ZhangShenBoundScore() - Constructor for class edu.cmu.tetrad.algcomparison.score.ZhangShenBoundScore
- ZS_RISK_BOUND - Static variable in class edu.cmu.tetrad.util.Params
- ZsbScore - Class in edu.cmu.tetrad.search.score
-
Implements an unpublished score based on a risk bound due to Zhang and Shen.
- ZsbScore(DataSet, boolean) - Constructor for class edu.cmu.tetrad.search.score.ZsbScore
-
Constructs the score using a covariance matrix.
- ZsbScore(ICovarianceMatrix) - Constructor for class edu.cmu.tetrad.search.score.ZsbScore
-
Constructs the score using a covariance matrix.
- zSum() - Method in class edu.cmu.tetrad.util.Matrix
- zSum() - Method in class edu.cmu.tetrad.util.Matrix2
- zSum(double[][]) - Static method in class edu.cmu.tetrad.util.MatrixUtils
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