Uses of Interface
edu.cmu.tetrad.graph.Graph
Packages that use Graph
Package
Description
Contains classes for searching for (mostly structural) causal models given data.
Contains classes for various various sorts of scores for running score-based algorithms.
Contains classes for running conditional independence tests for various sorts of data.
Contains some utility classes for search algorithms.
Contains some classes that aren't ready for prime time.
-
Uses of Graph in edu.cmu.tetrad.algcomparison
Methods in edu.cmu.tetrad.algcomparison with parameters of type GraphModifier and TypeMethodDescriptionstatic @NotNull String
CompareTwoGraphs.getEdgewiseComparisonString
(Graph trueGraph, Graph targetGraph) Returns an edgewise comparison of two graphs.static @NotNull String
CompareTwoGraphs.getMisclassificationTable
(Graph trueGraph, Graph targetGraph) Returns a misclassification comparison of two graphs.static String
CompareTwoGraphs.getStatsListTable
(Graph trueGraph, Graph targetGraph) Returns a string representing a table of statistics that can be printed.static String
CompareTwoGraphs.getStatsListTable
(Graph trueGraph, Graph targetGraph, DataModel dataModel) Returns a string representing a table of statistics that can be printed. -
Uses of Graph in edu.cmu.tetrad.algcomparison.algorithm
Methods in edu.cmu.tetrad.algcomparison.algorithm that return GraphModifier and TypeMethodDescriptionAlgorithm.getComparisonGraph
(Graph graph) Returns that graph that the result should be compared to.FirstInflection.getComparisonGraph
(Graph graph) StabilitySelection.getComparisonGraph
(Graph graph) StARS.getComparisonGraph
(Graph graph) Algorithm.search
(DataModel dataSet, Parameters parameters) Runs the search.FirstInflection.search
(DataModel dataSet, Parameters parameters) MultiDataSetAlgorithm.search
(List<DataModel> dataSets, Parameters parameters) Runs the search.StabilitySelection.search
(DataModel dataSet, Parameters parameters) StARS.search
(DataModel dataSet, Parameters parameters) Methods in edu.cmu.tetrad.algcomparison.algorithm that return types with arguments of type GraphMethods in edu.cmu.tetrad.algcomparison.algorithm with parameters of type GraphModifier and TypeMethodDescriptionstatic Algorithm
AlgorithmFactory.create
(Class<? extends Algorithm> algoClass, IndependenceWrapper test, ScoreWrapper score, Graph externalGraph) Creates an algorithm.static Algorithm
AlgorithmFactory.create
(Class<? extends Algorithm> algoClass, Class<? extends IndependenceWrapper> indTestClass, Class<? extends ScoreWrapper> scoreClass, Graph externalGraph) Creates an algorithm.Algorithm.getComparisonGraph
(Graph graph) Returns that graph that the result should be compared to.FirstInflection.getComparisonGraph
(Graph graph) StabilitySelection.getComparisonGraph
(Graph graph) StARS.getComparisonGraph
(Graph graph) -
Uses of Graph in edu.cmu.tetrad.algcomparison.algorithm.cluster
Methods in edu.cmu.tetrad.algcomparison.algorithm.cluster that return GraphModifier and TypeMethodDescriptionBpc.getComparisonGraph
(Graph graph) Fofc.getComparisonGraph
(Graph graph) Ftfc.getComparisonGraph
(Graph graph) Bpc.search
(DataModel dataSet, Parameters parameters) Fofc.search
(DataModel dataSet, Parameters parameters) Ftfc.search
(DataModel dataSet, Parameters parameters) Methods in edu.cmu.tetrad.algcomparison.algorithm.cluster with parameters of type GraphModifier and TypeMethodDescriptionBpc.getComparisonGraph
(Graph graph) Fofc.getComparisonGraph
(Graph graph) Ftfc.getComparisonGraph
(Graph graph) -
Uses of Graph in edu.cmu.tetrad.algcomparison.algorithm.continuous.dag
Methods in edu.cmu.tetrad.algcomparison.algorithm.continuous.dag that return GraphModifier and TypeMethodDescriptionDagma.getComparisonGraph
(Graph graph) DirectLingam.getComparisonGraph
(Graph graph) IcaLingam.getComparisonGraph
(Graph graph) IcaLingD.getComparisonGraph
(Graph graph) Dagma.search
(DataModel dataSet, Parameters parameters) DirectLingam.search
(DataModel dataSet, Parameters parameters) IcaLingam.search
(DataModel dataSet, Parameters parameters) IcaLingD.search
(DataModel dataSet, Parameters parameters) Methods in edu.cmu.tetrad.algcomparison.algorithm.continuous.dag that return types with arguments of type GraphModifier and TypeMethodDescriptionDagma.getBootstrapGraphs()
DirectLingam.getBootstrapGraphs()
IcaLingam.getBootstrapGraphs()
IcaLingD.getBootstrapGraphs()
Methods in edu.cmu.tetrad.algcomparison.algorithm.continuous.dag with parameters of type GraphModifier and TypeMethodDescriptionDagma.getComparisonGraph
(Graph graph) DirectLingam.getComparisonGraph
(Graph graph) IcaLingam.getComparisonGraph
(Graph graph) IcaLingD.getComparisonGraph
(Graph graph) -
Uses of Graph in edu.cmu.tetrad.algcomparison.algorithm.external
Methods in edu.cmu.tetrad.algcomparison.algorithm.external that return GraphModifier and TypeMethodDescriptionExternalAlgorithmBnlearnMmhc.getComparisonGraph
(Graph graph) Returns the CPDAG of the supplied DAG.ExternalAlgorithmBNTPc.getComparisonGraph
(Graph graph) Returns the CPDAG of the supplied DAG.ExternalAlgorithmIntersection.getComparisonGraph
(Graph graph) Returns the CPDAG of the supplied DAG.ExternalAlgorithmPcalgGes.getComparisonGraph
(Graph graph) Returns the CPDAG of the supplied DAG.ExternalAlgorithmPcalgPc.getComparisonGraph
(Graph graph) Returns the CPDAG of the supplied DAG.ExternalAlgorithmTetrad.getComparisonGraph
(Graph graph) Returns the CPDAG of the supplied DAG.static Graph
ExternalAlgorithmPcalgPc.loadGraphPcAlgMatrix
(DataSet dataSet) ExternalAlgorithmBnlearnMmhc.search
(DataModel dataSet, Parameters parameters) Reads in the relevant graph from the file (see above) and returns it.ExternalAlgorithmBNTPc.search
(DataModel dataSet, Parameters parameters) Reads in the relevant graph from the file (see above) and returns it.ExternalAlgorithmIntersection.search
(DataModel dataSet, Parameters parameters) Reads in the relevant graph from the file (see above) and returns it.ExternalAlgorithmPcalgGes.search
(DataModel dataSet, Parameters parameters) Reads in the relevant graph from the file (see above) and returns it.ExternalAlgorithmPcalgPc.search
(DataModel dataSet, Parameters parameters) Reads in the relevant graph from the file (see above) and returns it.ExternalAlgorithmTetrad.search
(DataModel dataSet, Parameters parameters) Reads in the relevant graph from the file and returns it.Methods in edu.cmu.tetrad.algcomparison.algorithm.external with parameters of type GraphModifier and TypeMethodDescriptionExternalAlgorithmBnlearnMmhc.getComparisonGraph
(Graph graph) Returns the CPDAG of the supplied DAG.ExternalAlgorithmBNTPc.getComparisonGraph
(Graph graph) Returns the CPDAG of the supplied DAG.ExternalAlgorithmIntersection.getComparisonGraph
(Graph graph) Returns the CPDAG of the supplied DAG.ExternalAlgorithmPcalgGes.getComparisonGraph
(Graph graph) Returns the CPDAG of the supplied DAG.ExternalAlgorithmPcalgPc.getComparisonGraph
(Graph graph) Returns the CPDAG of the supplied DAG.ExternalAlgorithmTetrad.getComparisonGraph
(Graph graph) Returns the CPDAG of the supplied DAG. -
Uses of Graph in edu.cmu.tetrad.algcomparison.algorithm.mixed
Methods in edu.cmu.tetrad.algcomparison.algorithm.mixed that return GraphModifier and TypeMethodDescriptionMgm.getComparisonGraph
(Graph graph) Mgm.search
(DataModel ds, Parameters parameters) Methods in edu.cmu.tetrad.algcomparison.algorithm.mixed with parameters of type Graph -
Uses of Graph in edu.cmu.tetrad.algcomparison.algorithm.multi
Methods in edu.cmu.tetrad.algcomparison.algorithm.multi that return GraphModifier and TypeMethodDescriptionFask.getComparisonGraph
(Graph graph) FaskConcatenated.getComparisonGraph
(Graph graph) FaskLofsConcatenated.getComparisonGraph
(Graph graph) FaskVote.getComparisonGraph
(Graph graph) FasLofs.getComparisonGraph
(Graph graph) FciIod.getComparisonGraph
(Graph graph) FgesConcatenated.getComparisonGraph
(Graph graph) Images.getComparisonGraph
(Graph graph) Fask.search
(DataModel dataSet, Parameters parameters) FaskConcatenated.search
(DataModel dataSet, Parameters parameters) FaskConcatenated.search
(List<DataModel> dataSets, Parameters parameters) FaskLofsConcatenated.search
(DataModel dataSet, Parameters parameters) FaskLofsConcatenated.search
(List<DataModel> dataModels, Parameters parameters) FaskVote.search
(DataModel dataSet, Parameters parameters) FaskVote.search
(List<DataModel> dataSets, Parameters parameters) FasLofs.search
(DataModel dataSet, Parameters parameters) FciIod.search
(DataModel dataSet, Parameters parameters) FciIod.search
(List<DataModel> dataSets, Parameters parameters) FgesConcatenated.search
(DataModel dataSet, Parameters parameters) FgesConcatenated.search
(List<DataModel> dataModels, Parameters parameters) Images.search
(DataModel dataSet, Parameters parameters) Images.search
(List<DataModel> dataSets, Parameters parameters) Methods in edu.cmu.tetrad.algcomparison.algorithm.multi with parameters of type GraphModifier and TypeMethodDescriptionFask.getComparisonGraph
(Graph graph) FaskConcatenated.getComparisonGraph
(Graph graph) FaskLofsConcatenated.getComparisonGraph
(Graph graph) FaskVote.getComparisonGraph
(Graph graph) FasLofs.getComparisonGraph
(Graph graph) FciIod.getComparisonGraph
(Graph graph) FgesConcatenated.getComparisonGraph
(Graph graph) Images.getComparisonGraph
(Graph graph) -
Uses of Graph in edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag
Methods in edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag that return GraphModifier and TypeMethodDescriptionBoss.getComparisonGraph
(Graph graph) Cpc.getComparisonGraph
(Graph graph) Fas.getComparisonGraph
(Graph graph) Fges.getComparisonGraph
(Graph graph) FgesMb.getComparisonGraph
(Graph graph) FgesMeasurement.getComparisonGraph
(Graph graph) GesMe.getComparisonGraph
(Graph graph) Grasp.getComparisonGraph
(Graph graph) Pc.getComparisonGraph
(Graph graph) Pcd.getComparisonGraph
(Graph graph) PcLingam.getComparisonGraph
(Graph graph) PcMb.getComparisonGraph
(Graph graph) RestrictedBoss.getComparisonGraph
(Graph graph) SingleGraphAlg.getComparisonGraph
(Graph graph) Sp.getComparisonGraph
(Graph graph) Boss.search
(DataModel dataModel, Parameters parameters) Cpc.search
(DataModel dataModel, Parameters parameters) Fas.search
(DataModel dataSet, Parameters parameters) Fges.search
(DataModel dataModel, Parameters parameters) FgesMb.search
(DataModel dataSet, Parameters parameters) FgesMeasurement.search
(DataModel dataModel, Parameters parameters) GesMe.search
(DataModel dataSet, Parameters parameters) Grasp.search
(DataModel dataModel, Parameters parameters) Pc.search
(DataModel dataModel, Parameters parameters) Pcd.search
(DataModel dataSet, Parameters parameters) PcLingam.search
(DataModel dataModel, Parameters parameters) PcMb.search
(DataModel dataSet, Parameters parameters) RestrictedBoss.search
(DataModel dataModel, Parameters parameters) SingleGraphAlg.search
(DataModel dataSet, Parameters parameters) Sp.search
(DataModel dataModel, Parameters parameters) Methods in edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag that return types with arguments of type GraphModifier and TypeMethodDescriptionBoss.getBootstrapGraphs()
Cpc.getBootstrapGraphs()
Fas.getBootstrapGraphs()
Fges.getBootstrapGraphs()
FgesMb.getBootstrapGraphs()
FgesMeasurement.getBootstrapGraphs()
GesMe.getBootstrapGraphs()
Grasp.getBootstrapGraphs()
Pc.getBootstrapGraphs()
Pcd.getBootstrapGraphs()
PcLingam.getBootstrapGraphs()
PcMb.getBootstrapGraphs()
RestrictedBoss.getBootstrapGraphs()
Sp.getBootstrapGraphs()
Methods in edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag with parameters of type GraphModifier and TypeMethodDescriptionBoss.getComparisonGraph
(Graph graph) Cpc.getComparisonGraph
(Graph graph) Fas.getComparisonGraph
(Graph graph) Fges.getComparisonGraph
(Graph graph) FgesMb.getComparisonGraph
(Graph graph) FgesMeasurement.getComparisonGraph
(Graph graph) GesMe.getComparisonGraph
(Graph graph) Grasp.getComparisonGraph
(Graph graph) Pc.getComparisonGraph
(Graph graph) Pcd.getComparisonGraph
(Graph graph) PcLingam.getComparisonGraph
(Graph graph) PcMb.getComparisonGraph
(Graph graph) RestrictedBoss.getComparisonGraph
(Graph graph) SingleGraphAlg.getComparisonGraph
(Graph graph) Sp.getComparisonGraph
(Graph graph) Constructors in edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag with parameters of type Graph -
Uses of Graph in edu.cmu.tetrad.algcomparison.algorithm.oracle.pag
Methods in edu.cmu.tetrad.algcomparison.algorithm.oracle.pag that return GraphModifier and TypeMethodDescriptionBfci.getComparisonGraph
(Graph graph) Ccd.getComparisonGraph
(Graph graph) Cfci.getComparisonGraph
(Graph graph) Fci.getComparisonGraph
(Graph graph) FciMax.getComparisonGraph
(Graph graph) Gfci.getComparisonGraph
(Graph graph) GraspFci.getComparisonGraph
(Graph graph) PagSampleRfci.getComparisonGraph
(Graph graph) Rfci.getComparisonGraph
(Graph graph) RfciBsc.getComparisonGraph
(Graph graph) SpFci.getComparisonGraph
(Graph graph) SvarFci.getComparisonGraph
(Graph graph) SvarGfci.getComparisonGraph
(Graph graph) Bfci.search
(DataModel dataModel, Parameters parameters) Ccd.search
(DataModel dataSet, Parameters parameters) Cfci.search
(DataModel dataModel, Parameters parameters) Fci.search
(DataModel dataModel, Parameters parameters) FciMax.search
(DataModel dataModel, Parameters parameters) Gfci.search
(DataModel dataModel, Parameters parameters) GraspFci.search
(DataModel dataModel, Parameters parameters) PagSampleRfci.search
(DataModel dataSet, Parameters parameters) Rfci.search
(DataModel dataModel, Parameters parameters) RfciBsc.search
(DataModel dataSet, Parameters parameters) SpFci.search
(DataModel dataModel, Parameters parameters) SvarFci.search
(DataModel dataModel, Parameters parameters) SvarGfci.search
(DataModel dataModel, Parameters parameters) Methods in edu.cmu.tetrad.algcomparison.algorithm.oracle.pag that return types with arguments of type GraphModifier and TypeMethodDescriptionBfci.getBootstrapGraphs()
Ccd.getBootstrapGraphs()
Cfci.getBootstrapGraphs()
Fci.getBootstrapGraphs()
FciMax.getBootstrapGraphs()
Gfci.getBootstrapGraphs()
GraspFci.getBootstrapGraphs()
Rfci.getBootstrapGraphs()
SpFci.getBootstrapGraphs()
SvarFci.getBootstrapGraphs()
SvarGfci.getBootstrapGraphs()
Methods in edu.cmu.tetrad.algcomparison.algorithm.oracle.pag with parameters of type GraphModifier and TypeMethodDescriptionBfci.getComparisonGraph
(Graph graph) Ccd.getComparisonGraph
(Graph graph) Cfci.getComparisonGraph
(Graph graph) Fci.getComparisonGraph
(Graph graph) FciMax.getComparisonGraph
(Graph graph) Gfci.getComparisonGraph
(Graph graph) GraspFci.getComparisonGraph
(Graph graph) PagSampleRfci.getComparisonGraph
(Graph graph) Rfci.getComparisonGraph
(Graph graph) RfciBsc.getComparisonGraph
(Graph graph) SpFci.getComparisonGraph
(Graph graph) SvarFci.getComparisonGraph
(Graph graph) SvarGfci.getComparisonGraph
(Graph graph) -
Uses of Graph in edu.cmu.tetrad.algcomparison.algorithm.oracle.pattern
Methods in edu.cmu.tetrad.algcomparison.algorithm.oracle.pattern that return GraphModifier and TypeMethodDescriptionCstar.getComparisonGraph
(Graph graph) Cstar.search
(DataModel dataSet, Parameters parameters) Methods in edu.cmu.tetrad.algcomparison.algorithm.oracle.pattern with parameters of type Graph -
Uses of Graph in edu.cmu.tetrad.algcomparison.algorithm.other
Methods in edu.cmu.tetrad.algcomparison.algorithm.other that return GraphModifier and TypeMethodDescriptionFactorAnalysis.getComparisonGraph
(Graph graph) Glasso.getComparisonGraph
(Graph graph) FactorAnalysis.search
(DataModel ds, Parameters parameters) Glasso.search
(DataModel ds, Parameters parameters) Methods in edu.cmu.tetrad.algcomparison.algorithm.other with parameters of type GraphModifier and TypeMethodDescriptionFactorAnalysis.getComparisonGraph
(Graph graph) Glasso.getComparisonGraph
(Graph graph) -
Uses of Graph in edu.cmu.tetrad.algcomparison.algorithm.pairwise
Methods in edu.cmu.tetrad.algcomparison.algorithm.pairwise that return GraphModifier and TypeMethodDescriptionEb.getComparisonGraph
(Graph graph) FaskPw.getComparisonGraph
(Graph graph) R1.getComparisonGraph
(Graph graph) R2.getComparisonGraph
(Graph graph) R3.getComparisonGraph
(Graph graph) Rskew.getComparisonGraph
(Graph graph) RskewE.getComparisonGraph
(Graph graph) Skew.getComparisonGraph
(Graph graph) SkewE.getComparisonGraph
(Graph graph) Tanh.getComparisonGraph
(Graph graph) Eb.search
(DataModel dataSet, Parameters parameters) FaskPw.search
(DataModel dataModel, Parameters parameters) R1.search
(DataModel dataSet, Parameters parameters) R2.search
(DataModel dataSet, Parameters parameters) R3.search
(DataModel dataSet, Parameters parameters) Rskew.search
(DataModel dataSet, Parameters parameters) RskewE.search
(DataModel dataSet, Parameters parameters) Skew.search
(DataModel dataSet, Parameters parameters) SkewE.search
(DataModel dataSet, Parameters parameters) Tanh.search
(DataModel dataSet, Parameters parameters) Methods in edu.cmu.tetrad.algcomparison.algorithm.pairwise with parameters of type GraphModifier and TypeMethodDescriptionEb.getComparisonGraph
(Graph graph) FaskPw.getComparisonGraph
(Graph graph) R1.getComparisonGraph
(Graph graph) R2.getComparisonGraph
(Graph graph) R3.getComparisonGraph
(Graph graph) Rskew.getComparisonGraph
(Graph graph) RskewE.getComparisonGraph
(Graph graph) Skew.getComparisonGraph
(Graph graph) SkewE.getComparisonGraph
(Graph graph) Tanh.getComparisonGraph
(Graph graph) -
Uses of Graph in edu.cmu.tetrad.algcomparison.comparegraphs
Constructors in edu.cmu.tetrad.algcomparison.comparegraphs with parameters of type Graph -
Uses of Graph in edu.cmu.tetrad.algcomparison.graph
Methods in edu.cmu.tetrad.algcomparison.graph that return GraphModifier and TypeMethodDescriptionCyclic.createGraph
(Parameters parameters) ErdosRenyi.createGraph
(Parameters parameters) RandomForward.createGraph
(Parameters parameters) RandomGraph.createGraph
(Parameters parameters) RandomSingleFactorMim.createGraph
(Parameters parameters) RandomTwoFactorMim.createGraph
(Parameters parameters) ScaleFree.createGraph
(Parameters parameters) SingleGraph.createGraph
(Parameters parameters) Constructors in edu.cmu.tetrad.algcomparison.graph with parameters of type Graph -
Uses of Graph in edu.cmu.tetrad.algcomparison.independence
Methods in edu.cmu.tetrad.algcomparison.independence with parameters of type GraphModifier and TypeMethodDescriptionvoid
void
Constructors in edu.cmu.tetrad.algcomparison.independence with parameters of type Graph -
Uses of Graph in edu.cmu.tetrad.algcomparison.score
Methods in edu.cmu.tetrad.algcomparison.score with parameters of type GraphConstructors in edu.cmu.tetrad.algcomparison.score with parameters of type Graph -
Uses of Graph in edu.cmu.tetrad.algcomparison.simulation
Methods in edu.cmu.tetrad.algcomparison.simulation that return GraphModifier and TypeMethodDescriptionBayesNetSimulation.getTrueGraph
(int index) Returns the true graph.BooleanGlassSimulation.getTrueGraph
(int index) ConditionalGaussianSimulation.getTrueGraph
(int index) GeneralSemSimulation.getTrueGraph
(int index) GeneralSemSimulationSpecial1.getTrueGraph
(int index) LeeHastieSimulation.getTrueGraph
(int index) LinearFisherModel.getTrueGraph
(int index) LinearSineSimulation.getTrueGraph
(int index) NLSemSimulation.getTrueGraph
(int index) SemSimulation.getTrueGraph
(int index) SemThenDiscretize.getTrueGraph
(int index) Simulation.getTrueGraph
(int index) Returns the true graph at the given index.StandardizedSemSimulation.getTrueGraph
(int index) TimeSeriesSemSimulation.getTrueGraph
(int index) -
Uses of Graph in edu.cmu.tetrad.algcomparison.statistic
Methods in edu.cmu.tetrad.algcomparison.statistic with parameters of type GraphModifier and TypeMethodDescriptionstatic boolean
CommonAncestorTruePositiveBidirected.existsCommonAncestor
(Graph trueGraph, Edge edge) static boolean
NumCommonMeasuredAncestorBidirected.existsCommonAncestor
(Graph trueGraph, Edge edge) boolean
NumDirectedEdgeNoMeasureAncestors.existsDirectedPathFromTo
(Graph graph, Node node1, Node node2) static boolean
LatentCommonAncestorTruePositiveBidirected.existsLatentCommonAncestor
(Graph trueGraph, Edge edge) double
Returns the value of the statistic, given the true graph and the estimated graph.double
double
Returns the value of the statistic, given the true graph and the estimated graph.double
double
double
Returns the value of the statistic, given the true graph and the estimated graph.double
Returns the value of the statistic, given the true graph and the estimated graph.double
Returns the value of the statistic, given the true graph and the estimated graph.double
Calculates the F1 statistic for adjacencies.double
Calculates the statistic.double
Calculates the statistic.double
Calculates the statistic.double
Calculates the statistic.double
double
double
double
double
double
double
double
double
double
double
double
double
double
double
double
double
double
double
double
double
double
double
CommonAncestorFalseNegativeBidirected.getValue
(Graph trueGraph, Graph estGraph, DataModel dataModel) double
CommonAncestorFalsePositiveBidirected.getValue
(Graph trueGraph, Graph estGraph, DataModel dataModel) double
double
CommonMeasuredAncestorRecallBidirected.getValue
(Graph trueGraph, Graph estGraph, DataModel dataModel) double
double
double
double
double
double
double
double
double
double
double
double
double
double
double
LatentCommonAncestorFalseNegativeBidirected.getValue
(Graph trueGraph, Graph estGraph, DataModel dataModel) double
LatentCommonAncestorFalsePositiveBidirected.getValue
(Graph trueGraph, Graph estGraph, DataModel dataModel) double
double
LatentCommonAncestorTruePositiveBidirected.getValue
(Graph trueGraph, Graph estGraph, DataModel dataModel) double
double
double
double
double
double
double
double
double
double
double
double
double
double
double
double
double
double
double
double
double
double
double
double
double
double
double
double
NumCompatibleDefiniteDirectedEdgeAncestors.getValue
(Graph trueGraph, Graph estGraph, DataModel dataModel) double
double
NumCompatibleDirectedEdgeNonAncestors.getValue
(Graph trueGraph, Graph estGraph, DataModel dataModel) double
double
NumCompatiblePossiblyDirectedEdgeAncestors.getValue
(Graph trueGraph, Graph estGraph, DataModel dataModel) double
NumCompatiblePossiblyDirectedEdgeNonAncestors.getValue
(Graph trueGraph, Graph estGraph, DataModel dataModel) double
double
double
double
double
double
double
double
double
NumDirectedEdgeBnaMeasuredCounfounded.getValue
(Graph trueGraph, Graph estGraph, DataModel dataModel) double
double
double
double
double
double
double
double
double
double
double
double
double
double
double
double
double
double
double
double
double
double
double
double
double
ProportionSemidirectedPathsNotReversedEst.getValue
(Graph trueGraph, Graph estGraph, DataModel dataModel) double
ProportionSemidirectedPathsNotReversedTrue.getValue
(Graph trueGraph, Graph estGraph, DataModel dataModel) double
double
double
double
double
double
Returns the value of this statistic, given the true graph and the estimated graph.double
double
double
double
double
double
double
double
double
double
double
double
double
TrueDagTruePositiveDirectedPathNonancestor.getValue
(Graph trueGraph, Graph estGraph, DataModel dataModel) double
double
double
double
double
double
-
Uses of Graph in edu.cmu.tetrad.algcomparison.statistic.utils
Constructors in edu.cmu.tetrad.algcomparison.statistic.utils with parameters of type GraphModifierConstructorDescriptionAdjacencyConfusion
(Graph truth, Graph est) Constructs a new AdjacencyConfusion object from the given graphs.ArrowConfusion
(Graph truth, Graph est) Constructs a new ArrowConfusion object.ArrowConfusion
(Graph truth, Graph est, boolean truthAdj) Constructs a new ArrowConfusion object.BidirectedConfusion
(Graph truth, Graph est) OrientationConfusion
(Graph truth, Graph est) TailConfusion
(Graph truth, Graph est) -
Uses of Graph in edu.cmu.tetrad.bayes
Methods in edu.cmu.tetrad.bayes that return GraphModifier and TypeMethodDescriptionBayesIm.getDag()
$DescriptionBayesPm.getDag()
Returns the DAG.DirichletBayesIm.getDag()
MlBayesIm.getDag()
MlBayesImObs.getDag()
UpdatedBayesIm.getDag()
ApproximateUpdater.getManipulatedGraph()
CptInvariantUpdater.getManipulatedGraph()
Identifiability.getManipulatedGraph()
JunctionTreeUpdater.getManipulatedGraph()
ManipulatingBayesUpdater.getManipulatedGraph()
Returns the manipulated graph.RowSummingExactUpdater.getManipulatedGraph()
static Graph
Create a moral graph.Methods in edu.cmu.tetrad.bayes that return types with arguments of type GraphModifier and TypeMethodDescriptionThis 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.Methods in edu.cmu.tetrad.bayes with parameters of type GraphModifier and TypeMethodDescriptionstatic void
Apply Tarjan and Yannakakis (1984) fill in algorithm for graph triangulation.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.GraphTools.getCliques
(Node[] ordering, Graph graph) Get cliques in a decomposable graph.BayesProperties.getLikelihoodRatioP
(Graph graph) Calculates the p-value of the graph with respect to the given data.static Node[]
GraphTools.getMaximumCardinalityOrdering
(Graph graph) Perform Tarjan and Yannakakis (1984) maximum cardinality search (MCS) to get the maximum cardinality ordering.static Graph
Create a moral graph.void
Constructors in edu.cmu.tetrad.bayes with parameters of type GraphModifierConstructorDescriptionConstruct 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.Constructs a new BayesPm from the given DAG, assigning each variable a random number of values betweenlowerBound
andupperBound
.Constructs a new BayesPm using a given DAG, using as much information from the old BayesPm as possible.Constructs a new BayesPm from the given DAG, using as much information from the old BayesPm as possible.EmBayesProperties
(DataSet dataSet, Graph graph) JunctionTreeAlgorithm
(Graph graph, DataModel dataModel) -
Uses of Graph in edu.cmu.tetrad.calibration
Methods in edu.cmu.tetrad.calibration that return GraphModifier and TypeMethodDescriptionDataForCalibrationRfci.learnBNRFCI
(DataSet bootstrapSample, int depth, Graph truePag) DataForCalibrationRfci.makeDAG
(int numVars, double edgesPerNode, int numLatentConfounders) Methods in edu.cmu.tetrad.calibration with parameters of type GraphModifier and TypeMethodDescriptionDataForCalibrationRfci.learnBNRFCI
(DataSet bootstrapSample, int depth, Graph truePag) -
Uses of Graph in edu.cmu.tetrad.data
Methods in edu.cmu.tetrad.data that return GraphModifier and TypeMethodDescriptionKnowledgeBoxInput.getResultGraph()
KnowledgeBoxInput.getSourceGraph()
static Graph
DataGraphUtils.randomBifactorModel
(int numStructuralNodes, int numStructuralEdges, int numMeasurementsPerLatent, int numLatentMeasuredImpureParents, int numMeasuredMeasuredImpureParents, int numMeasuredMeasuredImpureAssociations) First a random single factor model is created with the specified number of latent nodes and latent edges, and impurity structure.static Graph
DataGraphUtils.randomMim
(Graph graph, int numMeasurementsPerLatent, int numLatentMeasuredImpureParents, int numMeasuredMeasuredImpureParents, int numMeasuredMeasuredImpureAssociations, boolean arrangeGraph) static Graph
DataGraphUtils.randomSingleFactorModel
(int numStructuralNodes, int numStructuralEdges, int numMeasurementsPerLatent, int numLatentMeasuredImpureParents, int numMeasuredMeasuredImpureParents, int numMeasuredMeasuredImpureAssociations) Methods in edu.cmu.tetrad.data with parameters of type GraphModifier and TypeMethodDescriptionboolean
Knowledge.isViolatedBy
(Graph graph) static Graph
DataGraphUtils.randomMim
(Graph graph, int numMeasurementsPerLatent, int numLatentMeasuredImpureParents, int numMeasuredMeasuredImpureParents, int numMeasuredMeasuredImpureAssociations, boolean arrangeGraph) Constructors in edu.cmu.tetrad.data with parameters of type Graph -
Uses of Graph in edu.cmu.tetrad.data.simulation
Methods in edu.cmu.tetrad.data.simulation that return GraphModifier and TypeMethodDescriptionLoadContinuousDataAndGraphs.getTrueGraph
(int index) LoadContinuousDataAndSingleGraph.getTrueGraph
(int index) LoadContinuousDataSmithSim.getTrueGraph
(int index) LoadDataAndGraphs.getTrueGraph
(int index) LoadDataFromFileWithoutGraph.getTrueGraph
(int index) -
Uses of Graph in edu.cmu.tetrad.graph
Classes in edu.cmu.tetrad.graph that implement GraphModifier and TypeClassDescriptionfinal class
Represents a directed acyclic graph--that is, a graph containing only directed edges, with no cycles.class
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.class
Implements a graph allowing nodes in the getModel time lag to have parents taken from previous time lags.final class
Represents the graphical structure of a structural equation model.class
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.Methods in edu.cmu.tetrad.graph that return GraphModifier and TypeMethodDescriptionstatic Graph
GraphUtils.bidirectedToUndirected
(Graph graph) static Graph
GraphUtils.completeGraph
(Graph graph) static Graph
Converts a string spec of a graph--for example, "X1-->X2, X1---X3, X2o->X4, X3<->X4" to a Graph.static Graph
GraphTransforms.cpdagForDag
(Graph dag) static Graph
GraphTransforms.dagFromCPDAG
(Graph graph) static Graph
GraphTransforms.dagFromCPDAG
(Graph graph, Knowledge knowledge) static @NotNull Graph
static Graph
GraphUtils.emptyGraph
(int numNodes) static Graph
GraphUtils.getComparisonGraph
(Graph graph, Parameters params) RandomGraph.UniformGraphGenerator.getDag()
static Graph
static Graph
GraphSaveLoadUtils.loadGraphBNTPcMatrix
(List<Node> vars, DataSet dataSet) static Graph
GraphSaveLoadUtils.loadGraphJson
(File file) static Graph
GraphSaveLoadUtils.loadGraphPcalg
(File file) static Graph
GraphSaveLoadUtils.loadGraphRuben
(File file) static Graph
GraphSaveLoadUtils.loadGraphTxt
(File file) static Graph
GraphSaveLoadUtils.loadRSpecial
(File file) static Graph
GraphUtils.markovBlanketSubgraph
(Node target, Graph graph) Calculates the subgraph over the Markov blanket of a target node in a given DAG, CPDAG, MAG, or PAG.static Graph
static Graph
GraphSaveLoadUtils.parseGraphXml
(nu.xom.Element graphElement, Map<String, Node> nodes) static Graph
RandomGraph.randomCyclicGraph2
(int numNodes, int numEdges, int maxDegree) Makes a cyclic graph by repeatedly adding cycles of length of 3, 4, or 5 to the graph, then finally adding two cycles.static Graph
RandomGraph.randomCyclicGraph3
(int numNodes, int numEdges, int maxDegree, double probCycle, double probTwoCycle) Makes a cyclic graph by repeatedly adding cycles of length of 3, 4, or 5 to the graph, then finally adding two cycles.static Graph
RandomGraph.randomDag
(int numNodes, int numLatentConfounders, int maxNumEdges, int maxDegree, int maxIndegree, int maxOutdegree, boolean connected) static Graph
RandomGraph.randomGraph
(int numNodes, int numLatentConfounders, int numEdges, int maxDegree, int maxIndegree, int maxOutdegree, boolean connected) static Graph
RandomGraph.randomGraph
(List<Node> nodes, int numLatentConfounders, int maxNumEdges, int maxDegree, int maxIndegree, int maxOutdegree, boolean connected) Defaults to random forward graphs.static Graph
RandomGraph.randomGraphRandomForwardEdges
(int numNodes, int numLatentConfounders, int numEdges, int maxDegree, int maxIndegree, int maxOutdegree, boolean connected) static Graph
RandomGraph.randomGraphRandomForwardEdges
(List<Node> nodes, int numLatentConfounders, int numEdges, int maxDegree, int maxIndegree, int maxOutdegree, boolean connected) static Graph
RandomGraph.randomGraphRandomForwardEdges
(List<Node> nodes, int numLatentConfounders, int numEdges, int maxDegree, int maxIndegree, int maxOutdegree, boolean connected, boolean layoutAsCircle) static Graph
RandomGraph.randomGraphUniform
(List<Node> nodes, int numLatentConfounders, int maxNumEdges, int maxDegree, int maxIndegree, int maxOutdegree, boolean connected, int numIterations) static Graph
RandomGraph.randomScaleFreeGraph
(int numNodes, int numLatentConfounders, double alpha, double beta, double delta_in, double delta_out) static Graph
GraphSaveLoadUtils.readerToGraphJson
(Reader reader) static Graph
GraphSaveLoadUtils.readerToGraphRuben
(Reader reader) static Graph
GraphSaveLoadUtils.readerToGraphTxt
(Reader reader) static Graph
GraphSaveLoadUtils.readerToGraphTxt
(String graphString) static Graph
GraphUtils.removeBidirectedOrientations
(Graph estCpdag) static Graph
GraphUtils.replaceNodes
(Graph originalGraph, List<Node> newVariables) Converts the given graph,originalGraph
, to use the new variables (with the same names as the old).static Graph
GraphUtils.restrictToMeasured
(Graph graph) Constructs and returns a subgraph consisting of a given subset of the nodes of this graph together with the edges between them.static Graph
static Graph
GraphUtils.undirectedGraph
(Graph graph) static Graph
GraphUtils.undirectedToBidirected
(Graph graph) Methods in edu.cmu.tetrad.graph that return types with arguments of type GraphModifier and TypeMethodDescriptionGraphTransforms.generateCpdagDags
(Graph cpdag, boolean orientBidirectedEdges) Generates the list of DAGs in the given cpdag.GraphTransforms.getAllGraphsByDirectingUndirectedEdges
(Graph skeleton) GraphTransforms.getDagsInCpdagMeek
(Graph cpdag, Knowledge knowledge) Methods in edu.cmu.tetrad.graph with parameters of type GraphModifier and TypeMethodDescriptionstatic void
GraphUtils.addForbiddenReverseEdgesForDirectedEdges
(Graph graph, Knowledge knowledge) static void
GraphUtils.addPagColoring
(Graph graph) static void
RandomGraph.addTwoCycles
(Graph graph, int numTwoCycles) boolean
Triple.alongPathIn
(Graph graph) static void
LayoutUtil.arrangeByLayout
(Graph graph, HashMap<String, PointXy> layout) static boolean
LayoutUtil.arrangeBySourceGraph
(Graph resultGraph, Graph sourceGraph) Arranges the nodes in the result graph according to their positions in the source graph.static Graph
GraphUtils.bidirectedToUndirected
(Graph graph) static Graph
GraphUtils.completeGraph
(Graph graph) static boolean
GraphUtils.containsBidirectedEdge
(Graph graph) static nu.xom.Element
GraphSaveLoadUtils.convertToXml
(Graph graph) static int
GraphUtils.countAdjErrors
(Graph graph1, Graph graph2) Counts the adjacencies that are in graph1 but not in graph2.static int
GraphUtils.countArrowptErrors
(Graph graph1, Graph graph2) Counts the arrowheads that are in graph1 but not in graph2.static Graph
GraphTransforms.cpdagForDag
(Graph dag) static Graph
GraphTransforms.dagFromCPDAG
(Graph graph) static Graph
GraphTransforms.dagFromCPDAG
(Graph graph, Knowledge knowledge) static @NotNull Graph
static void
LayoutUtil.defaultLayout
(Graph graph) Arranges the nodes in the graph in a circle if there are 20 or fewer nodes, otherwise arranges them in a square.static int
static int[][]
GraphUtils.edgeMisclassificationCounts
(Graph leftGraph, Graph topGraph, boolean print) static String
MisclassificationUtils.edgeMisclassifications
(Graph estGraph, Graph refGraph) static String
MisclassificationUtils.endpointMisclassification
(Graph estGraph, Graph refGraph) static void
GraphUtils.fciOrientbk
(Knowledge knowledge, Graph graph, List<Node> variables) Orients according to background knowledgestatic void
RandomGraph.fixLatents1
(int numLatentConfounders, Graph graph) static void
RandomGraph.fixLatents4
(int numLatentConfounders, Graph graph) static void
LayoutUtil.fruchtermanReingoldLayout
(Graph graph) GraphTransforms.generateCpdagDags
(Graph cpdag, boolean orientBidirectedEdges) Generates the list of DAGs in the given cpdag.GraphTransforms.getAllGraphsByDirectingUndirectedEdges
(Graph skeleton) GraphUtils.getAmbiguousTriplesFromGraph
(Node node, Graph graph) static Node
GraphUtils.getAssociatedNode
(Node errorNode, Graph graph) GraphSaveLoadUtils.getCollidersFromGraph
(Node node, Graph graph) static Graph
GraphUtils.getComparisonGraph
(Graph graph, Parameters params) GraphTransforms.getDagsInCpdagMeek
(Graph cpdag, Knowledge knowledge) static int
GraphUtils.getDottedUnderlinedTriplesFromGraph
(Node node, Graph graph) static int
GraphUtils.getIndegree
(Graph graph) static int
GraphUtils.getNumCorrectArrowpts
(Graph correct, Graph estimated) static GraphUtils.TwoCycleErrors
GraphUtils.getTwoCycleErrors
(Graph trueGraph, Graph estGraph) GraphUtils.getUnderlinedTriplesFromGraph
(Node node, Graph graph) static void
GraphUtils.gfciExtraEdgeRemovalStep
(Graph graph, Graph referenceCpdag, List<Node> nodes, SepsetProducer sepsets) The extra edge removal step for GFCI.static void
GraphUtils.gfciR0
(Graph graph, Graph referenceCpdag, SepsetProducer sepsets, Knowledge knowledge) static String
GraphUtils.graphAttributesToText
(Graph graph, String title) static String
GraphUtils.graphEdgesToText
(Graph graph, String title) static String
GraphUtils.graphNodeAttributesToText
(Graph graph, String title, char delimiter) static String
GraphUtils.graphNodesToText
(Graph graph, String title, char delimiter) static String
GraphSaveLoadUtils.graphRMatrixTxt
(Graph graph) static String
GraphSaveLoadUtils.graphToDot
(Graph graph) Converts a graph to a Graphviz .dot filestatic void
GraphSaveLoadUtils.graphToDot
(Graph graph, File file) static String
GraphSaveLoadUtils.graphToLavaan
(Graph g) static String
GraphSaveLoadUtils.graphToPcalg
(Graph g) static String
GraphUtils.graphToText
(Graph graph, boolean doPagColoring) static String
GraphSaveLoadUtils.graphToXml
(Graph graph) static boolean
GraphUtils.isClique
(Collection<Node> set, Graph graph) static boolean
boolean
Check to see if a set of variables Z satisfies the back-door criterion relative to node x and node y.static void
LayoutUtil.kamadaKawaiLayout
(Graph graph, boolean randomlyInitialized, double naturalEdgeLength, double springConstant, double stopEnergy) static void
LayoutUtil.layoutByCausalOrder
(Graph graph) static LinkedList<Triple>
GraphUtils.listColliderTriples
(Graph graph) static String
GraphSaveLoadUtils.loadGraphRMatrix
(Graph graph) GraphUtils.markovBlanket
(Node x, Graph G) Returns a Markov blanket of a node for a DAG, CPDAG, MAG, or PAG.static Graph
GraphUtils.markovBlanketSubgraph
(Node target, Graph graph) Calculates the subgraph over the Markov blanket of a target node in a given DAG, CPDAG, MAG, or PAG.GraphUtils.maximalCliques
(Graph graph, List<Node> nodes) static Graph
static String
GraphUtils.pathString
(Graph graph, Node... x) static String
GraphUtils.pathString
(Graph graph, List<Node> path) static String
Triple.pathString
(Graph graph, Node x, Node y, Node z) static Graph
GraphUtils.removeBidirectedOrientations
(Graph estCpdag) static void
GraphUtils.removeNonSkeletonEdges
(Graph graph, Knowledge knowledge) static Graph
GraphUtils.replaceNodes
(Graph originalGraph, List<Node> newVariables) Converts the given graph,originalGraph
, to use the new variables (with the same names as the old).GraphUtils.replaceNodes
(List<Node> originalNodes, Graph graph) Converts the given list of nodes,originalNodes
, to use the replacement nodes for them by the same name in the givengraph
.static Graph
GraphUtils.restrictToMeasured
(Graph graph) static PrintWriter
static void
LayoutUtil.squareLayout
(Graph graph) void
Dag.transferAttributes
(Graph graph) void
EdgeListGraph.transferAttributes
(Graph graph) void
Graph.transferAttributes
(Graph graph) void
LagGraph.transferAttributes
(Graph graph) void
SemGraph.transferAttributes
(Graph graph) void
TimeLagGraph.transferAttributes
(Graph graph) void
Dag.transferNodesAndEdges
(Graph graph) void
EdgeListGraph.transferNodesAndEdges
(Graph graph) Transfers nodes and edges from one graph to another.void
Graph.transferNodesAndEdges
(Graph graph) Transfers nodes and edges from one graph to another.void
LagGraph.transferNodesAndEdges
(Graph graph) void
SemGraph.transferNodesAndEdges
(Graph graph) void
TimeLagGraph.transferNodesAndEdges
(Graph graph) static Graph
static Graph
GraphUtils.undirectedGraph
(Graph graph) static Graph
GraphUtils.undirectedToBidirected
(Graph graph) Method parameters in edu.cmu.tetrad.graph with type arguments of type GraphModifier and TypeMethodDescriptionstatic String
GraphUtils.getIntersectionComparisonString
(List<Graph> graphs) Constructors in edu.cmu.tetrad.graph with parameters of type GraphModifierConstructorDescriptionConstructs a new directed acyclic graph from the given graph object.EdgeListGraph
(Graph graph) Constructs a EdgeListGraph using the nodes and edges of the given graph.FruchtermanReingoldLayout
(Graph graph) KamadaKawaiLayout
(Graph graph) Constructs a new SemGraph from the nodes and edges of the given graph.Underlines
(Graph graph) -
Uses of Graph in edu.cmu.tetrad.regression
Methods in edu.cmu.tetrad.regression that return GraphModifier and TypeMethodDescriptionRegression.getGraph()
RegressionCovariance.getGraph()
RegressionDataset.getGraph()
Methods in edu.cmu.tetrad.regression with parameters of type Graph -
Uses of Graph in edu.cmu.tetrad.search
Methods in edu.cmu.tetrad.search that return GraphModifier and TypeMethodDescriptionSvarFges.getAdjacencies()
SvarFges.getExternalGraph()
Mimbuild.getFullGraph()
The full graph inferred, including the edges from latents to measures.MimbuildTrek.getFullGraph()
The full graph discovered.Cpc.getGraph()
The graph that's constructed during the search.@NotNull Graph
Grasp.getGraph
(boolean cpDag) Returns the graph implied by the discovered permutation.static Graph
Construct a graph given a specification of the parents for each node.static Graph
PermutationSearch.getGraph
(List<Node> nodes, Map<Node, Set<Node>> parents, Knowledge knowledge, boolean cpDag) Construct a graph given a specification of the parents for each node.Cstar.makeGraph
(List<Cstar.Record> records) Makes a graph of the estimated predictors to the effect.static @NotNull Graph
Returns a graph given a coefficient matrix and a list of variables.Lofs.orient()
Orients the graph and returns the oriented graph.PcMb.resultGraph()
Returns the result graph.BFci.search()
Does the search and returns a PAG.Bpc.search()
Runs the search and returns the graph, or null if there is no model.Ccd.search()
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.Cfci.search()
Performs the search and returns the PAG.Cpc.search()
Runs CPC starting with a fully connected graph over all the variables in the domain of the independence test.Dagma.search()
NEEDS DOCUMENTATIONDirectLingam.search()
NEEDS DOCUMENTATIONFas.search()
Runs the search and returns the resulting (undirected) graph.Discovers all adjacencies in data.Fasd.search()
Discovers all adjacencies in data.Fask.search()
Runs the search on the concatenated data, returning a graph, possibly cyclic, possibly with two-cycles.Fci.search()
FciMax.search()
Performs the search and returns the PAG.Fges.search()
Greedy equivalence search: Start from the empty graph, add edges till the model is significant.Greedy equivalence search: Start from the empty graph, add edges till the model is significant.Fofc.search()
Runs the search and returns a graph of clusters with the ir respective latent parents.Ftfc.search()
Runs the search and returns a graph of clusters, each of which has two common latent parents.GFci.search()
Runs the graph and returns the search PAG.GraspFci.search()
Run the search and return s a PAG.IGraphSearch.search()
Runs the search and returns a graph.Mimbuild.search
(List<List<Node>> clustering, List<String> latentNames, ICovarianceMatrix measuresCov) Does a Mimbuild search.MimbuildTrek.search
(List<List<Node>> clustering, List<String> latentNames, ICovarianceMatrix measuresCov) Does the search and returns the graph.Pc.search()
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.Runs the search using a particular implementation of the fast adjacency search (FAS), over the given sublist of nodes.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.Pcd.search()
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.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.PcLingam.search()
Runs the search and returns the result graph.PcMb.search()
Does the search.Searches for the MB CPDAG for the given targets.PermutationSearch.search()
Performe the search and return a CPDAG.Rfci.search()
Runs the search and returns the RFCI PAG.Runs the search and returns the RFCI PAG.Searches of a specific sublist of nodes.SpFci.search()
Runs the search and returns the discovered PAG.SvarFas.search()
Discovers all adjacencies in data.SvarFci.search()
Runs the search and returns the PAG.Runs the search using a particular implementation of FAS.SvarFges.search()
Greedy equivalence search: Start from the empty graph, add edges till the model is significant.SvarGfci.search()
Runs the search and returns a PAG.Methods in edu.cmu.tetrad.search with parameters of type GraphModifier and TypeMethodDescriptionstatic @NotNull MarkovCheck.AllSubsetsIndependenceFacts
MarkovCheck.getAllSubsetsIndependenceFacts
(Graph graph) double
double
double
double
Scores the given DAG, up to a constant.void
SvarFges.setAdjacencies
(Graph adjacencies) Sets the set of preset adjacencies for the algorithm; edges not in this adjacencies graph will not be added.void
Fges.setBoundGraph
(Graph boundGraph) If non-null, edges not adjacent in this graph will not be added.void
FgesMb.setBoundGraph
(Graph boundGraph) If non-null, edges not adjacent in this graph will not be added.void
Fasd.setExternalGraph
(Graph externalGraph) Sets the external graph.void
Fask.setExternalGraph
(Graph externalGraph) Sets the external graph to use.void
SvarFas.setExternalGraph
(Graph externalGraph) Sets an external graph.void
SvarFges.setExternalGraph
(Graph externalGraph) Sets the initial graph.void
Fges.setInitialGraph
(Graph initialGraph) void
FgesMb.setInitialGraph
(Graph initialGraph) void
SvarFges.setTrueGraph
(Graph trueGraph) If the true graph is set, asterisks will be printed in log output for the true edges.double
Ida.trueEffect
(Node x, Node y, Graph trueDag) Calculates the true effect of (x, y) given the true DAG (which must be provided).Constructors in edu.cmu.tetrad.search with parameters of type GraphModifierConstructorDescriptionConstructor.Constructor.MarkovCheck
(Graph graph, IndependenceTest independenceTest, MarkovCheck.ConditioningSetType setType) Constructor.Constructor. -
Uses of Graph in edu.cmu.tetrad.search.score
Methods in edu.cmu.tetrad.search.score that return GraphModifier and TypeMethodDescriptionGraphScore.getDag()
Returns a copy of the DAG being searched over.ScoredGraph.getGraph()
Methods in edu.cmu.tetrad.search.score with parameters of type GraphModifier and TypeMethodDescriptionstatic double
Scores the given DAG using the given data model, usimg a BIC score.static double
SemBicScorer.scoreDag
(Graph dag, DataModel data, double penaltyDiscount, boolean precomputeCovariances) Scores the given DAG using the given data model, usimg a BIC score.Constructors in edu.cmu.tetrad.search.score with parameters of type GraphModifierConstructorDescriptionGraphScore
(Graph dag) ConstructorScoredGraph
(Graph graph, Double score) -
Uses of Graph in edu.cmu.tetrad.search.test
Methods in edu.cmu.tetrad.search.test that return GraphModifier and TypeMethodDescriptionMsepTest.getGraph()
Returns the underlying graph that is being used to calculate d-separation relationships.Constructors in edu.cmu.tetrad.search.test with parameters of type Graph -
Uses of Graph in edu.cmu.tetrad.search.utils
Methods in edu.cmu.tetrad.search.utils that return GraphModifier and TypeMethodDescriptionDagToPag.convert()
This method does the convertion of DAG to PAG.TsDagToPag.convert()
static Graph
ClusterUtils.convertSearchGraph
(List<int[]> clusters, String[] varNames) static Graph
Purify.convertSearchGraph
(SemGraph input) FgesOrienter.getAdjacencies()
TsUtils.VarResult.getCollapsedVarGraph()
DagSepsets.getDag()
Returns the DAG being analyzed.SepsetsGreedy.getDag()
FgesOrienter.getExternalGraph()
TeyssierScorer.getGraph
(boolean cpDag) Returns the DAG build for the current permutation, or its CPDAG.static Graph
MbUtils.getOneMbDag
(Graph mbCpdag) Returns an example DAG from the given MB CPDAG.PossibleMConnectingPath.getPag()
FciOrient.getTruePag()
The true PAG if available.SvarFciOrient.getTruePag()
The true PAG if available.TsDagToPag.getTruePag()
DagInCpcagIterator.next()
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.DagIterator.next()
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.Performs final FCI orientation on the given graph.FgesOrienter.search()
Greedy equivalence search: Start from the empty graph, add edges till model is significant.PcCommon.search()
Runs the search and returns the search graph.Runs the search over the given list of nodes only, returning the serach graph.Purify.search()
****************************************************** SEARCH INTERFACE *******************************************************Methods in edu.cmu.tetrad.search.utils that return types with arguments of type GraphModifier and TypeMethodDescriptionMbUtils.generateMbDags
(Graph mbCPDAG, boolean orientBidirectedEdges, IndependenceTest test, int depth, Node target) Generates the list of MB DAGs consistent with the MB CPDAG returned by the previous search.Methods in edu.cmu.tetrad.search.utils with parameters of type GraphModifier and TypeMethodDescriptionstatic void
GraphSearchUtils.arrangeByKnowledgeTiers
(Graph graph) static void
GraphSearchUtils.arrangeByKnowledgeTiers
(Graph graph, Knowledge knowledge) static void
GraphSearchUtils.basicCpdag
(Graph graph) Get a graph and direct only the unshielded colliders.static void
GraphSearchUtils.basicCpdagRestricted2
(Graph graph, Node node) void
Runs BES for a graph over the given list of variablesvoid
Runs BES.static Clusters
MimUtils.convertToClusters
(Graph clusterGraph) static Clusters
MimUtils.convertToClusters
(Graph clusterGraph, List<Node> measuredVariables) Converts a disconnected multiple indicator model into a set of clusters.MimUtils.convertToClusters2
(Graph clusterGraph) void
a method to search "back from a" to find a DDP.void
a method to search "back from a" to find a DDP.boolean
Orients the edges inside the definte discriminating path triangle.void
FciOrient.doFinalOrientation
(Graph graph) Orients the graph according to rules in the graph (FCI step D).void
SvarFciOrient.doFinalOrientation
(Graph graph) Orients the graph according to rules in the graph (FCI step D).static boolean
DagToPag.existsInducingPathInto
(Node x, Node y, Graph graph) static boolean
TsDagToPag.existsInducingPathInto
(Node x, Node y, Graph graph, Knowledge knowledge) static boolean
TsDagToPag.existsInducingPathVisitts
(Graph graph, Node a, Node b, Node x, Node y, LinkedList<Node> path, Knowledge knowledge) void
FciOrient.fciOrientbk
(Knowledge bk, Graph graph, List<Node> variables) Orients according to background knowledgestatic List<PossibleMConnectingPath>
PossibleMConnectingPath.findMConnectingPaths
(Graph pag, Node x, Node y, Collection<Node> z) Finds all possible D-connection undirectedPaths as sub-graphs of the pag given at construction time from x to y given z.static List<PossibleMConnectingPath>
PossibleMConnectingPath.findMConnectingPathsOfLength
(Graph pag, Node x, Node y, Collection<Node> z, Integer length) 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.MbUtils.generateMbDags
(Graph mbCPDAG, boolean orientBidirectedEdges, IndependenceTest test, int depth, Node target) Generates the list of MB DAGs consistent with the MB CPDAG returned by the previous search.GraphSearchUtils.getCpcTripleType
(Node x, Node y, Node z, IndependenceTest test, int depth, Graph graph) static String
GraphSearchUtils.getEdgewiseComparisonString
(String trueGraphName, Graph trueGraph, String targetGraphName, Graph targetGraph) static GraphUtils.GraphComparison
GraphSearchUtils.getGraphComparison
(Graph trueGraph, Graph targetGraph) Just counts arrowhead errors--for cyclic edges counts an arrowhead at each node.static Knowledge
TsUtils.getKnowledge
(Graph graph) static Graph
MbUtils.getOneMbDag
(Graph mbCpdag) Returns an example DAG from the given MB CPDAG.GraphSearchUtils.getReachableNodes
(List<Node> initialNodes, LegalPairs legalPairs, List<Node> c, List<Node> d, Graph graph, int maxPathLength) double
FciOrient.getUcCirclePaths
(Node n1, Node n2, Graph graph) 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.FciOrient.getUcPdPaths
(Node n1, Node n2, Graph graph) Gets a list of every uncovered partially directed path between two nodes in the graph.static int[][]
GraphSearchUtils.graphComparison
(Graph trueCpdag, Graph estCpdag, PrintStream out) static boolean
GraphInPag.graphInPagStep0
(Graph pag, Graph dag) This method implements step (1) of the definition.static boolean
GraphInPag.graphInPagStep1
(Graph pag, Graph dag) static boolean
GraphInPag.graphInPagStep2
(Graph pag, Graph dag) static boolean
GraphInPag.graphInPagStep3
(Graph pag, Graph dag) static boolean
GraphInPag.graphInPagStep4
(Graph pag, Graph dag) static boolean
GraphInPag.graphInPagStep5
(Graph pag, Graph dag) static TimeLagGraph
TsUtils.graphToLagGraph
(Graph _graph, int numLags) static boolean
FciOrient.isArrowheadAllowed
(Node x, Node y, Graph graph, Knowledge knowledge) static GraphSearchUtils.LegalPagRet
GraphSearchUtils.isLegalPag
(Graph pag) static Clusters
ClusterUtils.mimClusters
(Graph mim) Performs final FCI orientation on the given graph.void
void
Adds colliders to the given graph using the max P rule.static void
PcCommon.orientCollider
(Node x, Node y, Node z, PcCommon.ConflictRule conflictRule, Graph graph) Orient a single unshielded triple, x*-*y*-*z, in a graph.static void
GraphSearchUtils.orientCollidersUsingSepsets
(SepsetMap set, Knowledge knowledge, Graph graph, boolean verbose, boolean enforceCpdag) Step C of PC; orients colliders using specified sepset.MeekRules.orientImplied
(Graph graph) Uses the Meek rules to do as many orientations in the given graph as possible.void
FciOrient.orientTailPath
(List<Node> path, Graph graph) Orients every edge on a path as undirected (i.e.static void
GraphSearchUtils.pcdOrientC
(IndependenceTest test, Knowledge knowledge, Graph graph) 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).static void
GraphSearchUtils.pcOrientbk
(Knowledge bk, Graph graph, List<Node> nodes) Orients according to background knowledge.void
Orients colliders in the graph.void
Orients colliders in the graph.void
void
Tries to apply Zhang's rule R10 to a pair of nodes A and C which are assumed to be such that Ao->C.void
void
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.void
Implements the double-triangle orientation rule, which states that if D*-oB, A*->B<-*C and A*-oDo-*C, then D*->B.void
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.void
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.void
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.void
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.void
Implements Zhang's rules R6 and R7, applies them over the graph once.void
Implements Zhang's rules R6 and R7, applies them over the graph once.boolean
Tries to apply Zhang's rule R8 to a pair of nodes A and C which are assumed to be such that Ao->C.boolean
Tries to apply Zhang's rule R9 to a pair of nodes A and C which are assumed to be such that Ao->C.void
FciOrient.rulesR1R2cycle
(Graph graph) void
SvarFciOrient.rulesR1R2cycle
(Graph graph) void
FciOrient.rulesR8R9R10
(Graph graph) Implements Zhang's rules R8, R9, R10, applies them over the graph once.void
SvarFciOrient.rulesR8R9R10
(Graph graph) Implements Zhang's rules R8, R9, R10, applies them over the graph once.double
double
Scores the given DAG, up to a constant.void
FgesOrienter.setAdjacencies
(Graph adjacencies) Sets the set of preset adjacenies for the algorithm; edges not in this adjacencies graph will not be added.void
FgesOrienter.setExternalGraph
(Graph externalGraph) Sets the initial graph.void
FgesOrienter.setTrueGraph
(Graph trueGraph) If the true graph is set, askterisks will be printed in log output for the true edges.void
IPurify.setTrueGraph
(Graph mim) void
PurifyScoreBased.setTrueGraph
(Graph mim) void
PurifyTetradBased.setTrueGraph
(Graph mim) void
FciOrient.setTruePag
(Graph truePag) Sets the true PAG for comparison.void
SvarFciOrient.setTruePag
(Graph truePag) void
TsDagToPag.setTruePag
(Graph truePag) void
FciOrient.spirtesFinalOrientation
(Graph graph) static int
GraphSearchUtils.structuralHammingDistance
(Graph trueGraph, Graph estGraph) Tsamardinos, I., Brown, L.static void
MbUtils.trimEdgesAmongParents
(Graph graph, Node target) Removes edges among the parents of the target.static void
MbUtils.trimEdgesAmongParentsOfChildren
(Graph graph, Node target) Removes edges among the parents of children of the target.static void
MbUtils.trimToAdjacents
(Graph graph, Node target) Trims the graph to just the adjacents of the target.static void
MbUtils.trimToMbNodes
(Graph graph, Node target, boolean includeBidirected) Trims the graph to the target, the parents and children of the target, and the parents of the children of the target.void
FciOrient.zhangFinalOrientation
(Graph graph) Constructors in edu.cmu.tetrad.search.utils with parameters of type GraphModifierConstructorDescriptionDagInCpcagIterator
(Graph CPDAG) The given CPDAG must be a CPDAG.DagInCpcagIterator
(Graph CPDAG, Knowledge knowledge) The given CPDAG must be a CPDAG.DagInCpcagIterator
(Graph CPDAG, Knowledge knowledge, boolean allowArbitraryOrientations, boolean allowNewColliders) The given CPDAG must be a CPDAG.DagIterator
(Graph CPDAG) The given CPDAG must be a CPDAG.DagSepsets
(Graph dag) Constructs a new DagSepsets object for the given DAG.Constructs a new FCI search for the given independence test and background knowledge.PossibleMsepFci
(Graph graph, IndependenceTest test) Creates a new SepSet and assumes that none of the variables have yet been checked.SepsetsConservative
(Graph graph, IndependenceTest independenceTest, SepsetMap extraSepsets, int depth) SepsetsGreedy
(Graph graph, IndependenceTest independenceTest, SepsetMap extraSepsets, int depth, Knowledge knowledge) SepsetsPossibleMsep
(Graph graph, IndependenceTest test, Knowledge knowledge, int depth, int maxPathLength) TsDagToPag
(Graph dag) Constructs a new FCI search for the given independence test and background knowledge. -
Uses of Graph in edu.cmu.tetrad.search.work_in_progress
Methods in edu.cmu.tetrad.search.work_in_progress that return GraphModifier and TypeMethodDescriptionOutputs a new PAG, a copy of the input excepting the applied changes of this object.@NotNull Graph
GraspTol.getGraph
(boolean cpDag) HbsmsBeam.getGraph()
HbsmsGes.getGraph()
HbsmsGes.GraphWithPValue.getGraph()
@NotNull Graph
OtherPermAlgs.getGraph
(boolean cpDag) SampleVcpc.getGraph()
The graph that's constructed during the search.SampleVcpcFast.getGraph()
The graph that's constructed during the search.VcPc.getGraph()
The graph that's constructed during the search.VcPcAlt.getGraph()
The graph that's constructed during the search.VcPcFast.getGraph()
The graph that's constructed during the search.MagSemBicScore.getMag()
Returns the wrapped MAG.DMSearch.LatentStructure.latentStructToEdgeListGraph
(DMSearch.LatentStructure structure) HbsmsBeam.removeZeroEdges
(Graph bestGraph) BpcTetradPurifyWashdown.search()
Runs the search and returns a graph.DMSearch.search()
Fas2.search()
Discovers all adjacencies in data.Fas3.search()
Runs the search and returns the resulting (undirected) graph.Discovers all adjacencies in data.FasFdr.search()
Discovers all adjacencies in data.FaskVote.search
(Parameters parameters) Does the search.FasLofs.search()
Runs the search on the concatenated data, returning a graph, possibly cyclic, possibly with two-cycles.Hbsms.search()
HbsmsBeam.search()
HbsmsGes.search()
InverseCorrelation.search()
Kpc.search()
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.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.Mmhc.search()
Runs PC starting with a fully connected graph over all of the variables in the domain of the independence test.SampleVcpc.search()
SampleVcpcFast.search()
VcFas.search()
Discovers all adjacencies in data.VcPc.search()
VcPcAlt.search()
VcPcFast.search()
Washdown.search()
Runs the Washdown algorithm and return a graph.Methods in edu.cmu.tetrad.search.work_in_progress that return types with arguments of type GraphModifier and TypeMethodDescriptionDci.search()
Begins the DCI search procedure, described at each stepIon.search()
Runs the ION search and returns a list of compatible graphs.Methods in edu.cmu.tetrad.search.work_in_progress with parameters of type GraphModifier and TypeMethodDescriptionDMSearch.applyDmSearch
(Graph pattern, Set<String> inputString, double penalty) Outputs a new PAG, a copy of the input excepting the applied changes of this object.static void
SampleVcpc.futureNodeVisit
(Graph graph, Node b, LinkedList<Node> path, Set<Node> futureNodes) static void
SampleVcpcFast.futureNodeVisit
(Graph graph, Node b, LinkedList<Node> path, Set<Node> futureNodes) static void
VcPc.futureNodeVisit
(Graph graph, Node b, LinkedList<Node> path, Set<Node> futureNodes) static void
VcPcAlt.futureNodeVisit
(Graph graph, Node b, LinkedList<Node> path, Set<Node> futureNodes) static void
VcPcFast.futureNodeVisit
(Graph graph, Node b, LinkedList<Node> path, Set<Node> futureNodes) VcPc.getPopulationTripleType
(Node x, Node y, Node z, IndependenceTest test, int depth, Graph graph, boolean verbose) VcPcFast.getPopulationTripleType
(Node x, Node y, Node z, IndependenceTest test, int depth, Graph graph, boolean verbose) HbsmsBeam.removeZeroEdges
(Graph bestGraph) HbsmsBeam.scoreGraph
(Graph graph) HbsmsGes.scoreGraph
(Graph graph) void
VcFas.setExternalGraph
(Graph externalGraph) void
void
void
void
void
void
Sets the MAG to wrap.Constructors in edu.cmu.tetrad.search.work_in_progress with parameters of type GraphModifierConstructorDescriptionFas2
(Graph initialGraph, IndependenceTest test) Constructs a new FastAdjacencySearch.FasDci
(Graph graph, IndependenceTest independenceTest) Constructs a new FastAdjacencySearch for DCI.FasDci
(Graph graph, IndependenceTest independenceTest, ResolveSepsets.Method method, List<Set<Node>> marginalVars, List<IndependenceTest> independenceTests, SepsetMapDci knownIndependencies, SepsetMapDci knownAssociations) Constructs a new FastAdjacencySearch for DCI with independence test pooling to resolve inconsistencies.GraphWithPValue
(Graph graph, double pValue) HbsmsBeam
(Graph graph, CovarianceMatrix cov, Knowledge knowledge) Constructor parameters in edu.cmu.tetrad.search.work_in_progress with type arguments of type Graph -
Uses of Graph in edu.cmu.tetrad.sem
Methods in edu.cmu.tetrad.sem that return GraphModifier and TypeMethodDescriptionLargeScaleSimulation.getGraph()
SemUpdater.getManipulatedGraph()
Methods in edu.cmu.tetrad.sem with parameters of type GraphModifier and TypeMethodDescriptionLargeScaleSimulation.getKnowledge
(Graph graph) ReidentifyVariables.getLatents
(Graph graph) ReidentifyVariables.reidentifyVariables1
(List<List<Node>> partition, Graph trueGraph) Ricf.ricf2
(Graph mag, ICovarianceMatrix covMatrix, double tolerance) same as above but takes a Graph instead of a SemGraphdouble
Runs the estimator on the data and SemPm passed in through the constructor.double
Constructors in edu.cmu.tetrad.sem with parameters of type GraphModifierConstructorDescriptionGeneralizedSemPm
(Graph graph) Constructs a BayesPm from the given Graph, which must be convertible first into a ProtoSemGraph and then into a SemGraph.LargeScaleSimulation
(Graph graph) LargeScaleSimulation
(Graph graph, List<Node> nodes, int[] tierIndices) Constructs a BayesPm from the given Graph, which must be convertible first into a ProtoSemGraph and then into a SemGraph. -
Uses of Graph in edu.cmu.tetrad.simulation
Methods in edu.cmu.tetrad.simulation that return GraphModifier and TypeMethodDescriptionstatic Graph
static Graph
HsimUtils.mkRandSEMDAG
(int numVars, int numEdges) Methods in edu.cmu.tetrad.simulation with parameters of type GraphModifier and TypeMethodDescriptionstatic double[]
static Graph
HsimUtils.getAllParents
(Graph inputgraph, Set<Node> inputnodes) -
Uses of Graph in edu.cmu.tetrad.study.performance
Methods in edu.cmu.tetrad.study.performance that return GraphModifier and TypeMethodDescriptionComparisonResult.getCorrectResult()
ComparisonResult.getResultGraph()
ComparisonResult.getTrueDag()
Methods in edu.cmu.tetrad.study.performance with parameters of type GraphModifier and TypeMethodDescriptionstatic String
PerformanceTests.endpointMisclassification
(List<Node> _nodes, Graph estGraph, Graph refGraph) static Knowledge
Comparison2.getKnowledge
(Graph graph) void
ComparisonResult.setCorrectResult
(Graph correctResult) void
ComparisonResult.setResultGraph
(Graph graph) void
ComparisonResult.setTrueDag
(Graph trueDag) -
Uses of Graph in edu.cmu.tetrad.util
Methods in edu.cmu.tetrad.util that return GraphModifier and TypeMethodDescriptionstatic Graph
GraphSampling.createDisplayGraph
(Graph graph, ResamplingEdgeEnsemble ensemble) Create a graph for displaying and print out.static Graph
GraphSampling.createGraphWithHighProbabilityEdges
(List<Graph> graphs) Combine all the edges from the list of graphs onto one graph with the edge type that has the highest frequency probability.static Graph
GraphSampling.createGraphWithHighProbabilityEdges
(List<Graph> graphs, ResamplingEdgeEnsemble ensemble) static Graph
GraphSampling.createGraphWithoutNullEdges
(Graph graph) Create a graph from the given graph that contains no null edges.static Graph
JsonUtils.parseJSONObjectToTetradGraph
(String jsonResponse) static Graph
JsonUtils.parseJSONObjectToTetradGraph
(org.json.JSONObject jObj) Methods in edu.cmu.tetrad.util with parameters of type GraphModifier and TypeMethodDescriptionstatic Graph
GraphSampling.createDisplayGraph
(Graph graph, ResamplingEdgeEnsemble ensemble) Create a graph for displaying and print out.static Graph
GraphSampling.createGraphWithoutNullEdges
(Graph graph) Create a graph from the given graph that contains no null edges.JsonUtils.parseJSONArrayToTetradEdges
(Graph graph, org.json.JSONArray jArray) static Edge
JsonUtils.parseJSONObjectToTetradEdge
(Graph graph, org.json.JSONObject jObj) Method parameters in edu.cmu.tetrad.util with type arguments of type GraphModifier and TypeMethodDescriptionstatic Graph
GraphSampling.createGraphWithHighProbabilityEdges
(List<Graph> graphs) Combine all the edges from the list of graphs onto one graph with the edge type that has the highest frequency probability.static Graph
GraphSampling.createGraphWithHighProbabilityEdges
(List<Graph> graphs, ResamplingEdgeEnsemble ensemble) static Set<edu.cmu.tetrad.util.GraphSampling.NodePair>
GraphSampling.getEdgeNodePairs
(List<Graph> graphs) -
Uses of Graph in edu.pitt.csb.mgm
Methods in edu.pitt.csb.mgm that return GraphModifier and TypeMethodDescriptionMgm.graphFromMGM()
Converts MGM object to Graph object with edges if edge parameters are non-zero.static Graph
MixedUtils.makeMixedGraph
(Graph g, Map<String, Integer> m) Mgm.search()
Simple search command for GraphSearch implementation.Methods in edu.pitt.csb.mgm with parameters of type GraphModifier and TypeMethodDescriptionstatic int[][]
MixedUtils.allEdgeStats
(Graph pT, Graph pE) static int[][]
static GeneralizedSemPm
MixedUtils.GaussianCategoricalPm
(Graph trueGraph, String paramTemplate) static GeneralizedSemPm
MixedUtils.GaussianTrinaryPm
(Graph trueGraph, HashMap<String, String> nodeDists, int maxSample, String paramTemplate) MixedUtils.getNodeDists
(Graph g) static cern.colt.matrix.DoubleMatrix2D
MixedUtils.graphToMatrix
(Graph graph) static cern.colt.matrix.DoubleMatrix2D
MixedUtils.graphToMatrix
(Graph graph, double undirectedWeight, double directedWeight) static Graph
MixedUtils.makeMixedGraph
(Graph g, Map<String, Integer> m) static cern.colt.matrix.DoubleMatrix2D
MixedUtils.skeletonToMatrix
(Graph graph) -
Uses of Graph in edu.pitt.csb.stability
Methods in edu.pitt.csb.stability that return Graph -
Uses of Graph in edu.pitt.dbmi.algo.bayesian.constraint.search
Methods in edu.pitt.dbmi.algo.bayesian.constraint.search that return GraphModifier and TypeMethodDescriptionRfciBsc.getGraphRBD()
RfciBsc.getGraphRBI()
PagSamplingRfci.search()
RfciBsc.search()
-
Uses of Graph in edu.pitt.dbmi.algo.resampling
Methods in edu.pitt.dbmi.algo.resampling that return GraphMethods in edu.pitt.dbmi.algo.resampling that return types with arguments of type GraphModifier and TypeMethodDescriptionGeneralResamplingTest.getGraphs()
Returns the individual bootstrap result graphs.GeneralResamplingSearch.search()
Methods in edu.pitt.dbmi.algo.resampling with parameters of type GraphModifier and TypeMethodDescriptionstatic int[][]
GeneralResamplingTest.getAdjConfusionMatrix
(Graph truth, Graph estimate) static int[][]
GeneralResamplingTest.getEdgeTypeConfusionMatrix
(Graph truth, Graph estimate) void
GeneralResamplingSearch.setExternalGraph
(Graph externalGraph) void
GeneralResamplingTest.setExternalGraph
(Graph externalGraph) Sets the initial graph. -
Uses of Graph in edu.pitt.dbmi.algo.resampling.task
Methods in edu.pitt.dbmi.algo.resampling.task that return GraphModifier and TypeMethodDescriptionGeneralResamplingSearchRunnable.call()
GeneralResamplingSearchRunnable.getExternalGraph()
Methods in edu.pitt.dbmi.algo.resampling.task with parameters of type GraphModifier and TypeMethodDescriptionvoid
GeneralResamplingSearchRunnable.setExternalGraph
(Graph externalGraph)