Serialized Form
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Package edu.cmu.tetrad.algcomparison
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Class edu.cmu.tetrad.algcomparison.Comparison
class Comparison extends Object implements Serializable- serialVersionUID:
- 23L
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Serialized Fields
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comparisonGraph
Comparison.ComparisonGraph comparisonGraph
The comparison graph type. -
dataPath
String dataPath
The data path. -
graphTypeUsed
boolean[] graphTypeUsed
The graph type used. -
knowledge
Knowledge knowledge
Represents a variable for storing knowledge. -
parallelism
int parallelism
The number of threads to use. -
resultsPath
String resultsPath
The result path. -
saveCPDAGs
boolean saveCPDAGs
Whether to save the CPDAGs. -
saveData
boolean saveData
Whether to save the data. -
saveGraphs
boolean saveGraphs
Whether to save the graphs. -
savePags
boolean savePags
Whether to save the PAGs. -
setAlgorithmKnowledge
boolean setAlgorithmKnowledge
True if knowledge should be set on the algorithms (if supplied). -
showUtilities
boolean showUtilities
Whether to show the utility calculations. -
sortByUtility
boolean sortByUtility
Whether to sort by utility. -
tabDelimitedTables
boolean tabDelimitedTables
Indicates whether the tables are tab-delimited.
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Package edu.cmu.tetrad.algcomparison.algorithm
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Class edu.cmu.tetrad.algcomparison.algorithm.AbstractBootstrapAlgorithm
class AbstractBootstrapAlgorithm extends Object implements Serializable -
Class edu.cmu.tetrad.algcomparison.algorithm.Algorithms
class Algorithms extends Object implements Serializable- serialVersionUID:
- 23L
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Serialization Methods
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readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
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writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
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Serialized Fields
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Class edu.cmu.tetrad.algcomparison.algorithm.ExternalAlgorithm
class ExternalAlgorithm extends Object implements Serializable-
Serialized Fields
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path
String path
The path to the external graph. -
simIndex
int simIndex
The index of the simulation. -
simulation
Simulation simulation
The simulation. -
usedParameters
List<String> usedParameters
The parameters used in the search.
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Class edu.cmu.tetrad.algcomparison.algorithm.FirstInflection
class FirstInflection extends Object implements Serializable- serialVersionUID:
- 23L
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Serialized Fields
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Class edu.cmu.tetrad.algcomparison.algorithm.StabilitySelection
class StabilitySelection extends Object implements Serializable- serialVersionUID:
- 23L
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Serialized Fields
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algorithm
Algorithm algorithm
The algorithm to use for the initial graph.
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Class edu.cmu.tetrad.algcomparison.algorithm.StARS
class StARS extends Object implements Serializable- serialVersionUID:
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Package edu.cmu.tetrad.algcomparison.algorithm.cluster
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Class edu.cmu.tetrad.algcomparison.algorithm.cluster.Bpc
class Bpc extends Object implements Serializable- serialVersionUID:
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Class edu.cmu.tetrad.algcomparison.algorithm.cluster.Fofc
class Fofc extends AbstractBootstrapAlgorithm implements Serializable- serialVersionUID:
- 23L
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Serialized Fields
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knowledge
Knowledge knowledge
The knowledge.
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Class edu.cmu.tetrad.algcomparison.algorithm.cluster.Ftfc
class Ftfc extends AbstractBootstrapAlgorithm implements Serializable- serialVersionUID:
- 23L
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Serialized Fields
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knowledge
Knowledge knowledge
The knowledge.
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-
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Package edu.cmu.tetrad.algcomparison.algorithm.continuous.dag
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Class edu.cmu.tetrad.algcomparison.algorithm.continuous.dag.Dagma
class Dagma extends AbstractBootstrapAlgorithm implements Serializable- serialVersionUID:
- 23L
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Class edu.cmu.tetrad.algcomparison.algorithm.continuous.dag.DirectLingam
class DirectLingam extends AbstractBootstrapAlgorithm implements Serializable- serialVersionUID:
- 23L
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Serialized Fields
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score
ScoreWrapper score
The score.
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Class edu.cmu.tetrad.algcomparison.algorithm.continuous.dag.Fask
class Fask extends AbstractBootstrapAlgorithm implements Serializable- serialVersionUID:
- 23L
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Serialized Fields
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algorithm
Algorithm algorithm
The algorithm. -
knowledge
Knowledge knowledge
The knowledge. -
score
ScoreWrapper score
The score to use.
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Class edu.cmu.tetrad.algcomparison.algorithm.continuous.dag.FaskOrig
class FaskOrig extends AbstractBootstrapAlgorithm implements Serializable- serialVersionUID:
- 23L
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Serialized Fields
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algorithm
Algorithm algorithm
The algorithm. -
externalGraph
Graph externalGraph
The external graph. -
knowledge
Knowledge knowledge
The knowledge. -
score
ScoreWrapper score
The score to use. -
test
IndependenceWrapper test
The independence test to use.
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Class edu.cmu.tetrad.algcomparison.algorithm.continuous.dag.IcaLingam
class IcaLingam extends AbstractBootstrapAlgorithm implements Serializable- serialVersionUID:
- 23L
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Serialized Fields
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bHat
Matrix bHat
The bHat variable represents the estimated B matrix generated by the algorithm. The B matrix is a matrix that encodes the causal relationships between the variables in the data set. The bHat variable is implemented as an instance of the Matrix class from the Tetrad library. The Matrix class provides methods for creating and manipulating matrices.The bHat variable is a private member of the IcaLingam class and is accessible only within the class itself. It is initialized as an empty matrix during the construction of an instance of the IcaLingam algorithm.
To retrieve the estimated B matrix generated by the algorithm, use the getBHat() method. This method returns a reference to the bHat variable, allowing access to the estimated B matrix.
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Class edu.cmu.tetrad.algcomparison.algorithm.continuous.dag.IcaLingD
class IcaLingD extends AbstractBootstrapAlgorithm implements Serializable- serialVersionUID:
- 23L
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Serialized Fields
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stableBHats
List<Matrix> stableBHats
A list of stable B matrices generated by the algorithm.- See Also:
-
stableGraphs
List<Graph> stableGraphs
The stableGraphs variable represents a list of stable graphs generated by the algorithm. A stable graph is a directed graph that satisfies certain criteria and is considered to be a valid result of the algorithm. The list is implemented using the ArrayList class from the Java Collections Framework. The elements in the list are of type Graph, which represents a directed graph.The stableGraphs variable is a private member of the IcaLingD class and is accessible only within the class itself. It is initialized as an empty list during the construction of an instance of the IcaLingD algorithm.
To retrieve the list of stable graphs generated by the algorithm, use the getStableGraphs() method. This method returns a reference to the stableGraphs variable, allowing access to the list of stable graphs.
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unstableBHats
List<Matrix> unstableBHats
Represents a list of unstable B matrices generated by the algorithm. -
unstableGraphs
List<Graph> unstableGraphs
Private variable to store a list of unstable graphs.This variable is used in the IcaLingD class to store a list of unstable graphs generated by the algorithm.
- See Also:
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Package edu.cmu.tetrad.algcomparison.algorithm.mixed
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Class edu.cmu.tetrad.algcomparison.algorithm.mixed.Mgm
class Mgm extends AbstractBootstrapAlgorithm implements Serializable- serialVersionUID:
- 23L
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Package edu.cmu.tetrad.algcomparison.algorithm.multi
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Class edu.cmu.tetrad.algcomparison.algorithm.multi.FaskConcatenated
class FaskConcatenated extends Object implements Serializable- serialVersionUID:
- 23L
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Serialized Fields
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knowledge
Knowledge knowledge
The knowledge. -
score
ScoreWrapper score
The score to use. -
test
IndependenceWrapper test
The independence test to use.
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Class edu.cmu.tetrad.algcomparison.algorithm.multi.FaskLofsConcatenated
class FaskLofsConcatenated extends Object implements Serializable- serialVersionUID:
- 23L
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Class edu.cmu.tetrad.algcomparison.algorithm.multi.FaskVote
class FaskVote extends Object implements Serializable- serialVersionUID:
- 23L
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Serialized Fields
-
knowledge
Knowledge knowledge
The knowledge. -
score
ScoreWrapper score
The score to use. -
test
IndependenceWrapper test
The independence test to use.
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Class edu.cmu.tetrad.algcomparison.algorithm.multi.FasLofs
class FasLofs extends Object implements Serializable- serialVersionUID:
- 23L
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Class edu.cmu.tetrad.algcomparison.algorithm.multi.FciIod
class FciIod extends Object implements Serializable- serialVersionUID:
- 23L
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Serialized Fields
-
knowledge
Knowledge knowledge
The knowledge. -
test
IndependenceWrapper test
The independence test to use.
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Class edu.cmu.tetrad.algcomparison.algorithm.multi.FgesConcatenated
class FgesConcatenated extends Object implements Serializable- serialVersionUID:
- 23L
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Serialized Fields
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compareToTrue
boolean compareToTrue
True if the result should be compared to the true graph, false if to the CPDAG of the true graph. -
externalGraph
Algorithm externalGraph
The external graph. -
knowledge
Knowledge knowledge
The knowledge. -
score
ScoreWrapper score
The score to use.
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Class edu.cmu.tetrad.algcomparison.algorithm.multi.Images
class Images extends Object implements Serializable- serialVersionUID:
- 23L
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Serialized Fields
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knowledge
Knowledge knowledge
The knowledge. -
score
ScoreWrapper score
The score to use.
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Class edu.cmu.tetrad.algcomparison.algorithm.multi.ImagesBoss
class ImagesBoss extends Object implements Serializable- serialVersionUID:
- 23L
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Serialized Fields
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knowledge
Knowledge knowledge
The knowledge. -
score
ScoreWrapper score
The score to use.
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-
-
Package edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag
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Class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Boss
class Boss extends AbstractBootstrapAlgorithm implements Serializable- serialVersionUID:
- 23L
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Serialized Fields
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knowledge
Knowledge knowledge
The knowledge. -
score
ScoreWrapper score
The score to use.
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Class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.BossLingam
class BossLingam extends AbstractBootstrapAlgorithm implements Serializable- serialVersionUID:
- 23L
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Serialized Fields
-
knowledge
Knowledge knowledge
The knowledge. -
score
ScoreWrapper score
The score to use.
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-
Class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Cpc
class Cpc extends AbstractBootstrapAlgorithm implements Serializable- serialVersionUID:
- 23L
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Serialized Fields
-
knowledge
Knowledge knowledge
The knowledge. -
test
IndependenceWrapper test
The independence test.
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Class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Cstar
class Cstar extends Object implements Serializable- serialVersionUID:
- 23L
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Serialized Fields
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records
LinkedList<Cstar.Record> records
The records. -
score
ScoreWrapper score
The score to use. -
test
IndependenceWrapper test
The independence test to use.
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Class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Fas
class Fas extends AbstractBootstrapAlgorithm implements Serializable- serialVersionUID:
- 23L
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Serialized Fields
-
knowledge
Knowledge knowledge
The knowledge. -
test
IndependenceWrapper test
The independence test to use.
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-
Class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Fges
class Fges extends AbstractBootstrapAlgorithm implements Serializable- serialVersionUID:
- 23L
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Serialized Fields
-
knowledge
Knowledge knowledge
The knowledge. -
score
ScoreWrapper score
The score to use.
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Class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.FgesMb
class FgesMb extends AbstractBootstrapAlgorithm implements Serializable- serialVersionUID:
- 23L
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Serialized Fields
-
knowledge
Knowledge knowledge
The knowledge. -
score
ScoreWrapper score
The score to use. -
targets
List<Node> targets
The targets.
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Class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.FgesMeasurement
class FgesMeasurement extends AbstractBootstrapAlgorithm implements Serializable- serialVersionUID:
- 23L
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Serialized Fields
-
knowledge
Knowledge knowledge
The knowledge. -
score
ScoreWrapper score
The score to use.
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Class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Grasp
class Grasp extends AbstractBootstrapAlgorithm implements Serializable- serialVersionUID:
- 23L
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Serialized Fields
-
knowledge
Knowledge knowledge
The knowledge. -
score
ScoreWrapper score
The score to use. -
test
IndependenceWrapper test
The independence test to use.
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Class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Pc
class Pc extends AbstractBootstrapAlgorithm implements Serializable- serialVersionUID:
- 23L
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Serialized Fields
-
knowledge
Knowledge knowledge
The knowledge. -
test
IndependenceWrapper test
The independence test to use.
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-
Class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Pcd
class Pcd extends AbstractBootstrapAlgorithm implements Serializable- serialVersionUID:
- 23L
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Serialized Fields
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knowledge
Knowledge knowledge
The knowledge.
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Class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.PcMb
class PcMb extends AbstractBootstrapAlgorithm implements Serializable- serialVersionUID:
- 23L
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Serialized Fields
-
knowledge
Knowledge knowledge
The knowledge. -
targets
List<Node> targets
The targets. -
test
IndependenceWrapper test
The independence test to use.
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Class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.RestrictedBoss
class RestrictedBoss extends AbstractBootstrapAlgorithm implements Serializable- serialVersionUID:
- 23L
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Serialized Fields
-
score
ScoreWrapper score
The score to use.
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-
Class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.SingleGraphAlg
class SingleGraphAlg extends Object implements Serializable- serialVersionUID:
- 23L
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Serialized Fields
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graph
Graph graph
The graph.
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Class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Sp
class Sp extends AbstractBootstrapAlgorithm implements Serializable- serialVersionUID:
- 23L
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Serialized Fields
-
knowledge
Knowledge knowledge
The knowledge. -
score
ScoreWrapper score
The score to use.
-
-
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Package edu.cmu.tetrad.algcomparison.algorithm.oracle.pag
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Class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Bfci
class Bfci extends AbstractBootstrapAlgorithm implements Serializable- serialVersionUID:
- 23L
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Serialized Fields
-
knowledge
Knowledge knowledge
The knowledge. -
score
ScoreWrapper score
The score to use. -
test
IndependenceWrapper test
The independence test to use.
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-
Class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.BossDumb
class BossDumb extends AbstractBootstrapAlgorithm implements Serializable- serialVersionUID:
- 23L
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Serialized Fields
-
knowledge
Knowledge knowledge
The knowledge. -
score
ScoreWrapper score
The score to use.
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-
Class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.BossPag
class BossPag extends AbstractBootstrapAlgorithm implements Serializable- serialVersionUID:
- 23L
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Serialized Fields
-
knowledge
Knowledge knowledge
The knowledge. -
score
ScoreWrapper score
The score to use.
-
-
Class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Ccd
class Ccd extends AbstractBootstrapAlgorithm implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
test
IndependenceWrapper test
The independence test to use.
-
-
Class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Cfci
class Cfci extends AbstractBootstrapAlgorithm implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
knowledge
Knowledge knowledge
The knowledge. -
test
IndependenceWrapper test
The independence test to use.
-
-
Class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Fci
class Fci extends AbstractBootstrapAlgorithm implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
knowledge
Knowledge knowledge
The knowledge. -
test
IndependenceWrapper test
The independence test to use.
-
-
Class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.FciMax
class FciMax extends AbstractBootstrapAlgorithm implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
knowledge
Knowledge knowledge
The knowledge. -
test
IndependenceWrapper test
The independence test to use.
-
-
Class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Gfci
class Gfci extends AbstractBootstrapAlgorithm implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
knowledge
Knowledge knowledge
The knowledge. -
score
ScoreWrapper score
The score to use. -
test
IndependenceWrapper test
The independence test to use.
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-
Class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.GraspFci
class GraspFci extends AbstractBootstrapAlgorithm implements Serializable- serialVersionUID:
- 23L
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Serialized Fields
-
knowledge
Knowledge knowledge
The knowledge. -
score
ScoreWrapper score
The score to use. -
test
IndependenceWrapper test
The independence test to use.
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-
Class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.LvLite
class LvLite extends AbstractBootstrapAlgorithm implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
knowledge
Knowledge knowledge
The knowledge. -
score
ScoreWrapper score
The score to use. -
test
IndependenceWrapper test
The independence test to use.
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-
Class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.PagSampleRfci
class PagSampleRfci extends AbstractBootstrapAlgorithm implements Serializable- serialVersionUID:
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Serialized Fields
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knowledge
Knowledge knowledge
The knowledge -
test
IndependenceWrapper test
The probabilistic test
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-
Class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Rfci
class Rfci extends AbstractBootstrapAlgorithm implements Serializable- serialVersionUID:
- 23L
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Serialized Fields
-
knowledge
Knowledge knowledge
Represents the knowledge variable. This variable stores the knowledge associated with the given algorithm. The type of the variable is Knowledge.- See Also:
-
test
IndependenceWrapper test
The independence test to use.
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Class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.RfciBsc
class RfciBsc extends AbstractBootstrapAlgorithm implements Serializable- serialVersionUID:
- 23L
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Serialized Fields
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knowledge
Knowledge knowledge
Knowledge -
test
IndependenceWrapper test
Independence test; must the ProbabilisticTest.
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Class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.SpFci
class SpFci extends AbstractBootstrapAlgorithm implements Serializable- serialVersionUID:
- 23L
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Serialized Fields
-
knowledge
Knowledge knowledge
The knowledge. -
score
ScoreWrapper score
The score to use. -
test
IndependenceWrapper test
The independence wrapper used for testing the independence between variables in a dataset.
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Class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.SvarFci
class SvarFci extends AbstractBootstrapAlgorithm implements Serializable- serialVersionUID:
- 23L
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Serialized Fields
-
knowledge
Knowledge knowledge
Represents the private variable `knowledge` in the class `SvarFci`.This variable stores the knowledge used by the `SvarFci` algorithm. The type of `knowledge` is `Knowledge`.
- See Also:
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test
IndependenceWrapper test
The independence test to use.
-
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Class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.SvarGfci
class SvarGfci extends AbstractBootstrapAlgorithm implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
knowledge
Knowledge knowledge
The knowledge. -
score
ScoreWrapper score
The score to use. -
test
IndependenceWrapper test
The independence test to use.
-
-
-
Package edu.cmu.tetrad.algcomparison.algorithm.other
-
Class edu.cmu.tetrad.algcomparison.algorithm.other.FactorAnalysis
class FactorAnalysis extends AbstractBootstrapAlgorithm implements Serializable- serialVersionUID:
- 23L
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Class edu.cmu.tetrad.algcomparison.algorithm.other.Glasso
class Glasso extends AbstractBootstrapAlgorithm implements Serializable- serialVersionUID:
- 23L
-
-
Package edu.cmu.tetrad.algcomparison.algorithm.pairwise
-
Class edu.cmu.tetrad.algcomparison.algorithm.pairwise.Eb
class Eb extends AbstractBootstrapAlgorithm implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.algorithm.pairwise.FaskPw
class FaskPw extends AbstractBootstrapAlgorithm implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.algorithm.pairwise.R1
class R1 extends AbstractBootstrapAlgorithm implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.algorithm.pairwise.R2
class R2 extends AbstractBootstrapAlgorithm implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.algorithm.pairwise.R3
class R3 extends AbstractBootstrapAlgorithm implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.algorithm.pairwise.Rskew
class Rskew extends AbstractBootstrapAlgorithm implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.algorithm.pairwise.RskewE
class RskewE extends AbstractBootstrapAlgorithm implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.algorithm.pairwise.Skew
class Skew extends AbstractBootstrapAlgorithm implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.algorithm.pairwise.SkewE
class SkewE extends AbstractBootstrapAlgorithm implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.algorithm.pairwise.Tanh
class Tanh extends AbstractBootstrapAlgorithm implements Serializable- serialVersionUID:
- 23L
-
-
Package edu.cmu.tetrad.algcomparison.graph
-
Class edu.cmu.tetrad.algcomparison.graph.Cyclic
class Cyclic extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.graph.ErdosRenyi
class ErdosRenyi extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.graph.RandomForward
class RandomForward extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.graph.RandomSingleFactorMim
class RandomSingleFactorMim extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.graph.RandomTwoFactorMim
class RandomTwoFactorMim extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.graph.ScaleFree
class ScaleFree extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.graph.SingleGraph
class SingleGraph extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
graph
Graph graph
The graph to be used.
-
-
-
Package edu.cmu.tetrad.algcomparison.independence
-
Class edu.cmu.tetrad.algcomparison.independence.BasisFunctionBicTest
class BasisFunctionBicTest extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.independence.BdeuTest
class BdeuTest extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.independence.CciTest
class CciTest extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.independence.ChiSquare
class ChiSquare extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.independence.ConditionalGaussianLRT
class ConditionalGaussianLRT extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.independence.DegenerateGaussianLRT
class DegenerateGaussianLRT extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.independence.DiscreteBicTest
class DiscreteBicTest extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.independence.FisherZ
class FisherZ extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.independence.GICScoreTests
class GICScoreTests extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.independence.GSquare
class GSquare extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.independence.Kci
class Kci extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
verbose
boolean verbose
-
-
Class edu.cmu.tetrad.algcomparison.independence.MagSemBicTest
class MagSemBicTest extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.independence.Mnlrlrt
class Mnlrlrt extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.independence.MSeparationTest
class MSeparationTest extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
graph
Graph graph
The true graph.
-
-
Class edu.cmu.tetrad.algcomparison.independence.MultinomialLogisticRegressionWald
class MultinomialLogisticRegressionWald extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.independence.Mvplrt
class Mvplrt extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.independence.PoissonPriorTest
class PoissonPriorTest extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.independence.PositiveCorr
class PositiveCorr extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
alpha
double alpha
The alpha level for the test.
-
-
Class edu.cmu.tetrad.algcomparison.independence.ProbabilisticTest
class ProbabilisticTest extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.independence.SemBicDTest
class SemBicDTest extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.independence.SemBicTest
class SemBicTest extends Object implements Serializable- serialVersionUID:
- 23L
-
-
Package edu.cmu.tetrad.algcomparison.score
-
Class edu.cmu.tetrad.algcomparison.score.BasisFunctionBicScore
class BasisFunctionBicScore extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
dataSet
DataModel dataSet
The data set.
-
-
Class edu.cmu.tetrad.algcomparison.score.BdeuScore
class BdeuScore extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
dataSet
DataModel dataSet
The data set.
-
-
Class edu.cmu.tetrad.algcomparison.score.ConditionalGaussianBicScore
class ConditionalGaussianBicScore extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
dataSet
DataModel dataSet
The data set.
-
-
Class edu.cmu.tetrad.algcomparison.score.DegenerateGaussianBicScore
class DegenerateGaussianBicScore extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
dataSet
DataModel dataSet
The data set.
-
-
Class edu.cmu.tetrad.algcomparison.score.DiscreteBicScore
class DiscreteBicScore extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
dataSet
DataModel dataSet
The data set.
-
-
Class edu.cmu.tetrad.algcomparison.score.EbicScore
class EbicScore extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
dataSet
DataModel dataSet
The data set.
-
-
Class edu.cmu.tetrad.algcomparison.score.FisherZScore
class FisherZScore extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
alpha
double alpha
The data set. -
dataSet
DataModel dataSet
The data set.
-
-
Class edu.cmu.tetrad.algcomparison.score.GicScores
class GicScores extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
dataSet
DataModel dataSet
The data set.
-
-
Class edu.cmu.tetrad.algcomparison.score.MagDgBicScore
class MagDgBicScore extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
dataSet
DataModel dataSet
The data set.
-
-
Class edu.cmu.tetrad.algcomparison.score.MSeparationScore
class MSeparationScore extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.score.MVPBicScore
class MVPBicScore extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.score.PoissonPriorScore
class PoissonPriorScore extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
dataSet
DataModel dataSet
The data set.
-
-
Class edu.cmu.tetrad.algcomparison.score.PositiveCorrScore
class PositiveCorrScore extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
alpha
double alpha
The alpha level. -
dataSet
DataModel dataSet
The data set.
-
-
Class edu.cmu.tetrad.algcomparison.score.SemBicScore
class SemBicScore extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
dataSet
DataModel dataSet
The data set.
-
-
Class edu.cmu.tetrad.algcomparison.score.SemBicScoreDeterministic
class SemBicScoreDeterministic extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
dataSet
DataModel dataSet
The data set.
-
-
Class edu.cmu.tetrad.algcomparison.score.ZhangShenBoundScore
class ZhangShenBoundScore extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
dataSet
DataModel dataSet
The data set.
-
-
-
Package edu.cmu.tetrad.algcomparison.simulation
-
Class edu.cmu.tetrad.algcomparison.simulation.BayesNetSimulation
class BayesNetSimulation extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.simulation.ConditionalGaussianSimulation
class ConditionalGaussianSimulation extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
coefHigh
double coefHigh
The high coefficient. -
coefLow
double coefLow
The low coefficient. -
coefSymmetric
boolean coefSymmetric
Whether coefficients should be drawn equally from positive or negative values. -
dataSets
List<DataSet> dataSets
The data sets. -
dataType
DataType dataType
The data type. -
graphs
List<Graph> graphs
The graphs. -
meanHigh
double meanHigh
The high mean for variables. -
meanLow
double meanLow
The low mean for variables. -
randomGraph
RandomGraph randomGraph
The random graph. -
shuffledOrder
List<Node> shuffledOrder
The shuffled order. -
varHigh
double varHigh
The high variance. -
varLow
double varLow
The low variance.
-
-
Class edu.cmu.tetrad.algcomparison.simulation.GeneralSemSimulation
class GeneralSemSimulation extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
dataSets
List<DataSet> dataSets
The data sets. -
graphs
List<Graph> graphs
The graphs. -
im
GeneralizedSemIm im
Represents the GeneralizedSemIm object used for simulation. -
ims
List<GeneralizedSemIm> ims
The SEM IMs. -
pm
GeneralizedSemPm pm
The SEM PM. -
randomGraph
RandomGraph randomGraph
The random graph.
-
-
Class edu.cmu.tetrad.algcomparison.simulation.GeneralSemSimulationSpecial1
class GeneralSemSimulationSpecial1 extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
dataSets
List<DataSet> dataSets
The graphs. -
graphs
List<Graph> graphs
The data sets. -
randomGraph
RandomGraph randomGraph
The random graph.
-
-
Class edu.cmu.tetrad.algcomparison.simulation.LeeHastieSimulation
class LeeHastieSimulation extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.simulation.LinearFisherModel
class LinearFisherModel extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.simulation.LinearSineSimulation
class LinearSineSimulation extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
betaHigh
double betaHigh
The beta high. -
betaLow
double betaLow
The beta low. -
dataSets
List<DataSet> dataSets
The data sets. -
dataType
DataType dataType
The data type. -
gammaHigh
double gammaHigh
The gamma high. -
gammaLow
double gammaLow
The gamma low. -
graphs
List<Graph> graphs
The graphs. -
interceptHigh
double interceptHigh
The intercept high. -
interceptLow
double interceptLow
The intercept low. -
linearHigh
double linearHigh
The linear high. -
linearLow
double linearLow
The linear low. -
randomGraph
RandomGraph randomGraph
The random graph. -
shuffledOrder
List<Node> shuffledOrder
The shuffled order. -
varHigh
double varHigh
The var high. -
varLow
double varLow
The var low.
-
-
Class edu.cmu.tetrad.algcomparison.simulation.NLSemSimulation
class NLSemSimulation extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
dataSets
List<DataSet> dataSets
The data sets. -
graphs
List<Graph> graphs
The graphs. -
randomGraph
RandomGraph randomGraph
The random graph.
-
-
Class edu.cmu.tetrad.algcomparison.simulation.SemSimulation
class SemSimulation extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.simulation.SemThenDiscretize
class SemThenDiscretize extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.simulation.Simulations
class Simulations extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
simulations
List<Simulation> simulations
The simulations.
-
-
Class edu.cmu.tetrad.algcomparison.simulation.SingleDatasetSimulation
class SingleDatasetSimulation extends Object implements Serializable-
Serialized Fields
-
dataSet
DataSet dataSet
ThedataSetvariable represents a single supplied data set.
-
-
-
Class edu.cmu.tetrad.algcomparison.simulation.StandardizedSemSimulation
class StandardizedSemSimulation extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
dataSets
List<DataSet> dataSets
The data sets. -
graphs
List<Graph> graphs
The graphs. -
pm
SemPm pm
The SEM PM. -
randomGraph
RandomGraph randomGraph
The random graph. -
standardizedIm
StandardizedSemIm standardizedIm
The SEM IM.
-
-
Class edu.cmu.tetrad.algcomparison.simulation.TimeSeriesSemSimulation
class TimeSeriesSemSimulation extends Object implements Serializable- serialVersionUID:
- 23L
-
-
Package edu.cmu.tetrad.algcomparison.statistic
-
Class edu.cmu.tetrad.algcomparison.statistic.AdjacencyFn
class AdjacencyFn extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.AdjacencyFp
class AdjacencyFp extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.AdjacencyFpr
class AdjacencyFpr extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.AdjacencyPrecision
class AdjacencyPrecision extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.AdjacencyRecall
class AdjacencyRecall extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.AdjacencyTn
class AdjacencyTn extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.AdjacencyTp
class AdjacencyTp extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.AdjacencyTpr
class AdjacencyTpr extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.AncestorF1
class AncestorF1 extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.AncestorPrecision
class AncestorPrecision extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.AncestorRecall
class AncestorRecall extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.AncestralPrecision
class AncestralPrecision extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.AncestralRecall
class AncestralRecall extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.ArrowheadFn
class ArrowheadFn extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.ArrowheadFp
class ArrowheadFp extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.ArrowheadFpr
class ArrowheadFpr extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.ArrowheadPrecision
class ArrowheadPrecision extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.ArrowheadPrecisionCommonEdges
class ArrowheadPrecisionCommonEdges extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.ArrowheadRecall
class ArrowheadRecall extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.ArrowheadRecallCommonEdges
class ArrowheadRecallCommonEdges extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.ArrowheadTn
class ArrowheadTn extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.ArrowheadTp
class ArrowheadTp extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.AverageDegreeEst
class AverageDegreeEst extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.AverageDegreeTrue
class AverageDegreeTrue extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.BicDiff
class BicDiff extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
precomputeCovariances
boolean precomputeCovariances
Whether to precompute covariances.
-
-
Class edu.cmu.tetrad.algcomparison.statistic.BicDiffPerRecord
class BicDiffPerRecord extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
precomputeCovariances
boolean precomputeCovariances
Whether to precompute covariances.
-
-
Class edu.cmu.tetrad.algcomparison.statistic.BicEst
class BicEst extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
precomputeCovariances
boolean precomputeCovariances
Whether to precompute covariances.
-
-
Class edu.cmu.tetrad.algcomparison.statistic.BicTrue
class BicTrue extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
precomputeCovariances
boolean precomputeCovariances
Whether to precompute covariances.
-
-
Class edu.cmu.tetrad.algcomparison.statistic.BidirectedEst
class BidirectedEst extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.BidirectedFP
class BidirectedFP extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.BidirectedLatentPrecision
class BidirectedLatentPrecision extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.BidirectedPrecision
class BidirectedPrecision extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.BidirectedRecall
class BidirectedRecall extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.BidirectedTP
class BidirectedTP extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.BidirectedTrue
class BidirectedTrue extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.CommonAncestorFalseNegativeBidirected
class CommonAncestorFalseNegativeBidirected extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.CommonAncestorFalsePositiveBidirected
class CommonAncestorFalsePositiveBidirected extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.CommonAncestorTruePositiveBidirected
class CommonAncestorTruePositiveBidirected extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.CommonMeasuredAncestorRecallBidirected
class CommonMeasuredAncestorRecallBidirected extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.CorrectSkeleton
class CorrectSkeleton extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.DefiniteDirectedPathPrecision
class DefiniteDirectedPathPrecision extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.DefiniteDirectedPathRecall
class DefiniteDirectedPathRecall extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.DensityEst
class DensityEst extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.DensityTrue
class DensityTrue extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.ElapsedCpuTime
class ElapsedCpuTime extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.F1Adj
class F1Adj extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.F1All
class F1All extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.F1Arrow
class F1Arrow extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.FalseNegativesAdjacencies
class FalseNegativesAdjacencies extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.FalsePositiveAdjacencies
class FalsePositiveAdjacencies extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.FBetaAdj
class FBetaAdj extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
beta
double beta
The beta parameter.
-
-
Class edu.cmu.tetrad.algcomparison.statistic.FractionDependentUnderAlternative
class FractionDependentUnderAlternative extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
alpha
double alpha
The significance level for the independence tests.
-
-
Class edu.cmu.tetrad.algcomparison.statistic.FractionDependentUnderNull
class FractionDependentUnderNull extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
alpha
double alpha
The significance level.
-
-
Class edu.cmu.tetrad.algcomparison.statistic.GraphExactlyRight
class GraphExactlyRight extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.IdaAverageSquaredDistance
class IdaAverageSquaredDistance extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
semIm
SemIm semIm
The true SEM IM. This stat can only be used if the true SEM IM is known.
-
-
Class edu.cmu.tetrad.algcomparison.statistic.IdaCheckAvgMaxSquaredDiffEstTrue
class IdaCheckAvgMaxSquaredDiffEstTrue extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.IdaCheckAvgMinSquaredDiffEstTrue
class IdaCheckAvgMinSquaredDiffEstTrue extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.IdaCheckAvgSquaredDifference
class IdaCheckAvgSquaredDifference extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.IdaMaximumSquaredDifference
class IdaMaximumSquaredDifference extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
semIm
SemIm semIm
The true SEM IM. This stat can only be used if the true SEM IM is known.
-
-
Class edu.cmu.tetrad.algcomparison.statistic.IdaMinimumSquaredDifference
class IdaMinimumSquaredDifference extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
semIm
SemIm semIm
The true SEM IM. This stat can only be used if the true SEM IM is known.
-
-
Class edu.cmu.tetrad.algcomparison.statistic.ImpliedArrowOrientationRatioEst
class ImpliedArrowOrientationRatioEst extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.ImpliedArrowOrientationRatioEst2
class ImpliedArrowOrientationRatioEst2 extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.ImpliedOrientationRatioEst
class ImpliedOrientationRatioEst extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.ImpliesLegalMag
class ImpliesLegalMag extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.KnowledgeSatisfied
class KnowledgeSatisfied extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
knowledge
Knowledge knowledge
The `knowledge` variable represents a knowledge object. This variable is a private member of the `KnowledgeSatisfied` class, which implements the `Statistic` and `HasKnowledge` interfaces. It is used to measure whether the provided knowledge is satisfied for the estimated graph. It is initially set to `null`.- See Also:
-
-
Class edu.cmu.tetrad.algcomparison.statistic.LatentCommonAncestorFalseNegativeBidirected
class LatentCommonAncestorFalseNegativeBidirected extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.LatentCommonAncestorFalsePositiveBidirected
class LatentCommonAncestorFalsePositiveBidirected extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.LatentCommonAncestorRecallBidirected
class LatentCommonAncestorRecallBidirected extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.LatentCommonAncestorTruePositiveBidirected
class LatentCommonAncestorTruePositiveBidirected extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.LegalPag
class LegalPag extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.LocalGraphPrecision
class LocalGraphPrecision extends Object implements Serializable -
Class edu.cmu.tetrad.algcomparison.statistic.LocalGraphRecall
class LocalGraphRecall extends Object implements Serializable -
Class edu.cmu.tetrad.algcomparison.statistic.MagCgScore
class MagCgScore extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.MagDgScore
class MagDgScore extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.MagSemScore
class MagSemScore extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.MarkovCheckAdPasses
class MarkovCheckAdPasses extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.MarkovCheckAdPassesBestOf10
class MarkovCheckAdPassesBestOf10 extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.MarkovCheckAndersonDarlingP
class MarkovCheckAndersonDarlingP extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.MarkovCheckAndersonDarlingPBestOf10
class MarkovCheckAndersonDarlingPBestOf10 extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.MarkovCheckBinomialP
class MarkovCheckBinomialP extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.MarkovCheckBinomialPBestOf10
class MarkovCheckBinomialPBestOf10 extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.MarkovCheckKolmogorovSmirnoffP
class MarkovCheckKolmogorovSmirnoffP extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.MarkovCheckKolmogorovSmirnoffPBestOf10
class MarkovCheckKolmogorovSmirnoffPBestOf10 extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.MarkovCheckKsPasses
class MarkovCheckKsPasses extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.MarkovCheckKsPassesBestOf10
class MarkovCheckKsPassesBestOf10 extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.MathewsCorrAdj
class MathewsCorrAdj extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.MathewsCorrArrow
class MathewsCorrArrow extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.Maximal
class Maximal extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.MaximalityCondition
class MaximalityCondition extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NoAlmostCyclicPathsCondition
class NoAlmostCyclicPathsCondition extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NoCyclicPathsCondition
class NoCyclicPathsCondition extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NodesInCyclesPrecision
class NodesInCyclesPrecision extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NodesInCyclesRecall
class NodesInCyclesRecall extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NonancestorPrecision
class NonancestorPrecision extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NonancestorRecall
class NonancestorRecall extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NoSemidirectedF1
class NoSemidirectedF1 extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NoSemidirectedPrecision
class NoSemidirectedPrecision extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NoSemidirectedRecall
class NoSemidirectedRecall extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NumAmbiguousTriples
class NumAmbiguousTriples extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NumberArrowsEst
class NumberArrowsEst extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NumberArrowsNotInUnshieldedCollidersEst
class NumberArrowsNotInUnshieldedCollidersEst extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NumberCollidersEst
class NumberCollidersEst extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NumberEdgesEst
class NumberEdgesEst extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NumberEdgesInCollidersEst
class NumberEdgesInCollidersEst extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NumberEdgesInUnshieldedCollidersEst
class NumberEdgesInUnshieldedCollidersEst extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NumberEdgesTrue
class NumberEdgesTrue extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NumberOfEdgesEst
class NumberOfEdgesEst extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NumberOfEdgesTrue
class NumberOfEdgesTrue extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NumberTailsEst
class NumberTailsEst extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NumberUnshieldedCollidersEst
class NumberUnshieldedCollidersEst extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NumBidirectedBothNonancestorAncestor
class NumBidirectedBothNonancestorAncestor extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NumBidirectedEdgesEst
class NumBidirectedEdgesEst extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NumBidirectedEdgesTrue
class NumBidirectedEdgesTrue extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NumColoredDD
class NumColoredDD extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NumColoredNL
class NumColoredNL extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NumColoredPD
class NumColoredPD extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NumColoredPL
class NumColoredPL extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NumCommonMeasuredAncestorBidirected
class NumCommonMeasuredAncestorBidirected extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NumCompatibleDefiniteDirectedEdgeAncestors
class NumCompatibleDefiniteDirectedEdgeAncestors extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NumCompatibleDirectedEdgeConfounded
class NumCompatibleDirectedEdgeConfounded extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NumCompatibleDirectedEdgeNonAncestors
class NumCompatibleDirectedEdgeNonAncestors extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NumCompatibleEdges
class NumCompatibleEdges extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NumCompatiblePossiblyDirectedEdgeAncestors
class NumCompatiblePossiblyDirectedEdgeAncestors extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NumCompatiblePossiblyDirectedEdgeNonAncestors
class NumCompatiblePossiblyDirectedEdgeNonAncestors extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NumCompatibleVisibleNonancestors
class NumCompatibleVisibleNonancestors extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NumCorrectBidirected
class NumCorrectBidirected extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NumCorrectDDAncestors
class NumCorrectDDAncestors extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NumCorrectPDAncestors
class NumCorrectPDAncestors extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NumCorrectVisibleEdges
class NumCorrectVisibleEdges extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NumCoveringAdjacenciesInPag
class NumCoveringAdjacenciesInPag extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NumDefinitelyDirected
class NumDefinitelyDirected extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NumDefinitelyNotDirectedPaths
class NumDefinitelyNotDirectedPaths extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NumDirectedEdgeAncestors
class NumDirectedEdgeAncestors extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NumDirectedEdgeBnaMeasuredCounfounded
class NumDirectedEdgeBnaMeasuredCounfounded extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NumDirectedEdgeNoMeasureAncestors
class NumDirectedEdgeNoMeasureAncestors extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NumDirectedEdgeNotAncNotRev
class NumDirectedEdgeNotAncNotRev extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NumDirectedEdgeReversed
class NumDirectedEdgeReversed extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NumDirectedEdges
class NumDirectedEdges extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NumDirectedPathsEst
class NumDirectedPathsEst extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NumDirectedPathsTrue
class NumDirectedPathsTrue extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NumDirectedShouldBePartiallyDirected
class NumDirectedShouldBePartiallyDirected extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NumEdgeInEstInTrue
class NumEdgeInEstInTrue extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NumGenuineAdjacenciesInPag
class NumGenuineAdjacenciesInPag extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NumIncorrectDDAncestors
class NumIncorrectDDAncestors extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NumIncorrectPDAncestors
class NumIncorrectPDAncestors extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NumIncorrectVisibleAncestors
class NumIncorrectVisibleAncestors extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NumLatentCommonAncestorBidirected
class NumLatentCommonAncestorBidirected extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NumNondirectedEdges
class NumNondirectedEdges extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NumParametersEst
class NumParametersEst extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NumPartiallyOrientedEdges
class NumPartiallyOrientedEdges extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NumPossiblyDirected
class NumPossiblyDirected extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NumUndirectedEdges
class NumUndirectedEdges extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NumVisibleEdgeEst
class NumVisibleEdgeEst extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NumVisibleEdges
class NumVisibleEdges extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.NumVisibleEdgeTrue
class NumVisibleEdgeTrue extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.OrientationPrecision
class OrientationPrecision extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.OrientationRecall
class OrientationRecall extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.PagAdjacencyPrecision
class PagAdjacencyPrecision extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.PagAdjacencyRecall
class PagAdjacencyRecall extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.ParameterColumn
class ParameterColumn extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
parameter
String parameter
The name of the parameter to list. If this parameter does not exist, '*' is output.
-
-
Class edu.cmu.tetrad.algcomparison.statistic.PercentAmbiguous
class PercentAmbiguous extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.PercentBidirectedEdges
class PercentBidirectedEdges extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.ProportionSemidirectedPathsNotReversedEst
class ProportionSemidirectedPathsNotReversedEst extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.ProportionSemidirectedPathsNotReversedTrue
class ProportionSemidirectedPathsNotReversedTrue extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.PvalueDistanceToAlpha
class PvalueDistanceToAlpha extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
alpha
double alpha
The significance level for the independence tests.
-
-
Class edu.cmu.tetrad.algcomparison.statistic.PvalueUniformityUnderNull
class PvalueUniformityUnderNull extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
alpha
double alpha
The significance level for the independence tests.
-
-
Class edu.cmu.tetrad.algcomparison.statistic.SemidirectedPathF1
class SemidirectedPathF1 extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.SemidirectedPrecision
class SemidirectedPrecision extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.SemidirectedRecall
class SemidirectedRecall extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.Statistics
class Statistics extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
Class edu.cmu.tetrad.algcomparison.statistic.StructuralHammingDistance
class StructuralHammingDistance extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.TailPrecision
class TailPrecision extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.TailRecall
class TailRecall extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.TrueDagFalseNegativesArrows
class TrueDagFalseNegativesArrows extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.TrueDagFalseNegativesTails
class TrueDagFalseNegativesTails extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.TrueDagFalsePositiveArrow
class TrueDagFalsePositiveArrow extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.TrueDagFalsePositiveTails
class TrueDagFalsePositiveTails extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.TrueDagPrecisionArrow
class TrueDagPrecisionArrow extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.TrueDagPrecisionTails
class TrueDagPrecisionTails extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.TrueDagRecallArrows
class TrueDagRecallArrows extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.TrueDagRecallTails
class TrueDagRecallTails extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.TrueDagTruePositiveArrow
class TrueDagTruePositiveArrow extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.TrueDagTruePositiveDirectedPathNonancestor
class TrueDagTruePositiveDirectedPathNonancestor extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.TrueDagTruePositiveTails
class TrueDagTruePositiveTails extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.TwoCycleFalseNegative
class TwoCycleFalseNegative extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.TwoCycleFalsePositive
class TwoCycleFalsePositive extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.TwoCyclePrecision
class TwoCyclePrecision extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.TwoCycleRecall
class TwoCycleRecall extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.algcomparison.statistic.TwoCycleTruePositive
class TwoCycleTruePositive extends Object implements Serializable- serialVersionUID:
- 23L
-
-
Package edu.cmu.tetrad.annotation
-
Class edu.cmu.tetrad.annotation.AnnotatedClass
class AnnotatedClass extends Object implements Serializable- serialVersionUID:
- 5060798016477163171L
-
Serialized Fields
-
annotation
T extends Annotation annotation
AnnotatedClass represents a class along with its associated annotation. -
clazz
Class<?> clazz
Represents a Class used as a parameter to an AnnotatedClass object. It is stored as a private final member in the AnnotatedClass class.Example usage:
AnnotatedClass<MyAnnotation> annotatedClass = new AnnotatedClass<>(MyClass.class, myAnnotation); Class<?> clazz = annotatedClass.clazz();
- See Also:
-
-
-
Package edu.cmu.tetrad.bayes
-
Class edu.cmu.tetrad.bayes.ApproximateUpdater
class ApproximateUpdater extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
bayesIm
BayesIm bayesIm
The IM which this updater modifies.Cannot be null. -
counts
int[][] counts
Counts of data points for each variable value. -
evidence
Evidence evidence
Stores evidence for all variables.Cannot be null. -
manipulatedBayesIm
BayesIm manipulatedBayesIm
This is the source BayesIm after manipulation; all data simulations should be taken from this.
-
-
Class edu.cmu.tetrad.bayes.BayesImProbs
class BayesImProbs extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
Class edu.cmu.tetrad.bayes.BayesPm
class BayesPm extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
dag
Graph dag
The underlying graph that's being parameterized.Cannot be null. -
nodesToVariables
Map<Node,
DiscreteVariable> nodesToVariables The map from nodes to variables.Cannot be null.
-
-
Class edu.cmu.tetrad.bayes.CptInvariantMarginalCalculator
class CptInvariantMarginalCalculator extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
bayesIm
BayesIm bayesIm
The Bayes net. -
evidence
Evidence evidence
The evidence. -
storedMarginals
double[][] storedMarginals
The stored marginals. -
updatedBayesIm
UpdatedBayesIm updatedBayesIm
The updated Bayes net.
-
-
Class edu.cmu.tetrad.bayes.CptInvariantUpdater
class CptInvariantUpdater extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
bayesIm
BayesIm bayesIm
The IM which this updater modifies.Cannot be null. -
cptInvariantMarginalCalculator
CptInvariantMarginalCalculator cptInvariantMarginalCalculator
The gadget that calculates marginals. -
evidence
Evidence evidence
Stores evidence for all variables.Cannot be null -
manipulatedBayesIm
BayesIm manipulatedBayesIm
The manipulated Bayes IM--that is, bayesIm after the manipulations in evidence have been applied to it. -
updatedBayesIm
UpdatedBayesIm updatedBayesIm
The IM after update.
-
-
Class edu.cmu.tetrad.bayes.CptMapCounts
class CptMapCounts extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
cellCounts
Map<Integer,
Integer> cellCounts Constructs a new count map, a map from a unique integer index for a particular node to the count for that value, where 0's are not stored. -
numColumns
int numColumns
The number of columns in the table. -
numRows
int numRows
The number of rows in the table. -
priorCount
double priorCount
The prior count for all cells. '0' is maximimum likelihood estimate. -
rowCounts
Map<Integer,
Integer> rowCounts Constructs a new row count map, a map from a unique integer index for a particular node to the count for that row, where 0's are not stored.
-
-
Class edu.cmu.tetrad.bayes.CptMapProbs
class CptMapProbs extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
map
Map<Integer,
Double> map Constructs a new probability map, a map from a unique integer index for a particular node to the probability of that node taking on that value, where NaN's are not stored. -
numColumns
int numColumns
The number of columns in the table. -
numRows
int numRows
The number of rows in the table.
-
-
Class edu.cmu.tetrad.bayes.DirichletBayesIm
class DirichletBayesIm extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
bayesPm
BayesPm bayesPm
The associated Bayes PM model. -
nextRowTotal
double nextRowTotal
1.0000 The default row size for randomly creating new rows. -
nodes
Node[] nodes
The array of nodes from the graph. Order is important. -
parentDims
int[][] parentDims
The array of dimensionality (number of values for each node) for each of the subarrays of 'parents'. -
parents
int[][] parents
The list of parents for each node from the graph. Order or nodes corresponds to the order of nodes in 'nodes', and order in subarrays is important. -
pseudocounts
double[][][] pseudocounts
The main data structure; stores the values of all of the pseudocounts for the Dirichlet Bayes net of the form row by row, for each node. The first dimension is the node N, in the order of 'nodes'. The second dimension is the row index for the table of parameters associated with node N; the third dimension is the column index. The row index is calculated by the function getRowIndex(int[] values) where 'values' is an array of numerical indices for each of the parent values; the order of the values in this array is the same as the order of node in 'parents'; the value indices are obtained from the Bayes PM for each node. The column is the index of the value of N, where this index is obtained from the Bayes PM. If a pseudocount is -1, that means its value should be filled in manually.
-
-
Class edu.cmu.tetrad.bayes.Evidence
class Evidence extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
manipulation
Manipulation manipulation
A manipulation indicating how the bayes Im should be manipulated before updating. -
proposition
Proposition proposition
A proposition stating what we know for each variable.
-
-
Class edu.cmu.tetrad.bayes.Identifiability
class Identifiability extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
Class edu.cmu.tetrad.bayes.JunctionTreeAlgorithm
class JunctionTreeAlgorithm extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
bayesIm
BayesIm bayesIm
The BayesIm. -
bayesPm
BayesPm bayesPm
The BayesPm. -
graphNodes
Node[] graphNodes
The nodes in the graph. -
margins
double[][] margins
The marginal probabilities of the nodes. -
maxCardOrdering
Node[] maxCardOrdering
The maximum cardinality ordering of the nodes. -
root
edu.cmu.tetrad.bayes.JunctionTreeAlgorithm.TreeNode root
The root of the junction tree. -
treeNodes
Map<Node,
edu.cmu.tetrad.bayes.JunctionTreeAlgorithm.TreeNode> treeNodes The tree nodes.
-
-
Class edu.cmu.tetrad.bayes.JunctionTreeUpdater
class JunctionTreeUpdater extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
bayesIm
BayesIm bayesIm
The BayesIm which this updater modifies. -
evidence
Evidence evidence
Stores evidence for all variables. -
jta
JunctionTreeAlgorithm jta
Calculates probabilities from the manipulated Bayes IM. -
manipulatedBayesIm
BayesIm manipulatedBayesIm
The last manipulated BayesIm. -
updatedBayesIm
BayesIm updatedBayesIm
The BayesIm after update, if this was calculated.
-
-
Class edu.cmu.tetrad.bayes.Manipulation
class Manipulation extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
manipulated
boolean[] manipulated
An array indicating whether each variable in turn is manipulated. -
variableSource
VariableSource variableSource
The variable source for which this manipulation is defined.
-
-
Class edu.cmu.tetrad.bayes.MlBayesIm
class MlBayesIm extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
bayesPm
BayesPm bayesPm
The associated Bayes PM model. -
cptMapType
MlBayesIm.CptMapType cptMapType
The type of CPT map used to store the probabilities. -
nodes
Node[] nodes
The array of nodes from the graph. Order is important. -
parentDims
int[][] parentDims
The array of dimensionality (number of categories for each node) for each of the subarrays of 'parents'. -
parents
int[][] parents
The list of parents for each node from the graph. Order or nodes corresponds to the order of nodes in 'nodes', and order in subarrays is important. -
probMatrices
CptMap[] probMatrices
The array of CPT maps for each node. The index of the node corresponds to the index of the probability map in this array. Replaces the probs array. -
probs
double[][][] probs
The main data structure; stores the values of all of the conditional probabilities for the Bayes net of the form P(N=v0 | P1=v1, P2=v2,...). The first dimension is the node N, in the order of 'nodes'. The second dimension is the row index for the table of parameters associated with node N; the third dimension is the column index. The row index is calculated by the function getRowIndex(int[] values) where 'values' is an array of numerical indices for each of the parent values; the order of the values in this array is the same as the order of node in 'parents'; the value indices are obtained from the Bayes PM for each node. The column is the index of the value of N, where this index is obtained from the Bayes PM.This is kept here for backward compatibility. The new way of storing the probabilities is in the probMatrices array.
-
-
Class edu.cmu.tetrad.bayes.MlBayesImObs
class MlBayesImObs extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
bayesImObs
BayesIm bayesImObs
BayesIm containing only the observed variables. Only used to 1) construct propositions (mapped from the original allowUnfaithfulness bayesIm) in Identifiability 2) to avoid summing over rows in jpd when only the latent variables have changed values (only sum when all the latent variables have value 0) This is a MlBayesIm instead of a MlBayesImObs because otherwise there will be an infinite loop attempting to creating the MlBayesImObs -
bayesImRandomize
BayesIm bayesImRandomize
a regular MlBayesIm used to create randomized CPDs so that the values can be marginalized to a consistent observed jpd -
bayesPm
BayesPm bayesPm
The associated Bayes PM model. -
jpd
StoredCellProbsObs jpd
joint probability table -
nodes
Node[] nodes
The array of nodes from the graph. Order is important. -
parentDims
int[][] parentDims
The array of dimensionality (number of categories for each node) for each of the subarrays of 'parents'. -
parents
int[][] parents
The list of parents for each node from the graph. Order or nodes corresponds to the order of nodes in 'nodes', and order in subarrays is important. -
probs
double[][][] probs
The main data structure; stores the values of all of the conditional probabilities for the Bayes net of the form P(N=v0 | P1=v1, P2=v2,...). The first dimension is the node N, in the order of 'nodes'. The second dimension is the row index for the table of parameters associated with node N; the third dimension is the column index. The row index is calculated by the function getRowIndex(int[] values) where 'values' is an array of numerical indices for each of the parent values; the order of the values in this array is the same as the order of node in 'parents'; the value indices are obtained from the Bayes PM for each node. The column is the index of the value of N, where this index is obtained from the Bayes PM.
-
-
Class edu.cmu.tetrad.bayes.Proposition
class Proposition extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
allowedCategories
boolean[][] allowedCategories
An array indicating whether each category for each variable is allowed. -
variableSource
VariableSource variableSource
The Bayes IM that this is a proposition for.
-
-
Class edu.cmu.tetrad.bayes.RowSummingExactUpdater
class RowSummingExactUpdater extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.- Parameters:
s- anObjectInputStreamobject- Throws:
IOException- If any.ClassNotFoundException- If any.
-
-
Serialized Fields
-
bayesIm
BayesIm bayesIm
The BayesIm which this updater modifies. -
bayesImProbs
BayesImProbs bayesImProbs
Calculates probabilities from the manipulated Bayes IM. -
evidence
Evidence evidence
Stores evidence for all variables. -
manipulatedBayesIm
BayesIm manipulatedBayesIm
The last manipulated BayesIm. -
updatedBayesIm
BayesIm updatedBayesIm
The BayesIm after update, if this was calculated.
-
-
Class edu.cmu.tetrad.bayes.StoredCellProbs
class StoredCellProbs extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
Class edu.cmu.tetrad.bayes.StoredCellProbsObs
class StoredCellProbsObs extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.bayes.UpdatedBayesIm
class UpdatedBayesIm extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.- Parameters:
s- aObjectInputStreamobject- Throws:
IOException- If any.ClassNotFoundException- If any.
-
-
Serialized Fields
-
affectedVars
boolean[] affectedVars
A boolean array that is true at a position if the node at that index is an ancestor or a child of one of the evidence variables. -
bayesIm
BayesIm bayesIm
The wrapped BayesIm. Unmodified conditional probability values will be retrieved from here. -
changedProbs
double[][][] changedProbs
Stores probs that change with respect to the underlying bayesIm, calculated on the fly. -
evidence
Evidence evidence
The evidence updated on.
-
-
-
Package edu.cmu.tetrad.calculator.expression
-
Class edu.cmu.tetrad.calculator.expression.AbstractExpressionDescriptor.Signature
class Signature extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.calculator.expression.ConstantExpression
class ConstantExpression extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
name
String name
The name of the constant or null if there isn't one. Constants with names are things like PI or E. -
value
double value
THe value of the expression.
-
-
Class edu.cmu.tetrad.calculator.expression.EvaluationExpression
class EvaluationExpression extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
string
String string
The string you are testing the variable against. -
variable
VariableExpression variable
The variable part of the expression.
-
-
Exception Class edu.cmu.tetrad.calculator.expression.ExpressionInitializationException
class ExpressionInitializationException extends Exception implements Serializable -
Class edu.cmu.tetrad.calculator.expression.VariableExpression
class VariableExpression extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
variable
String variable
The variable that is being evaluated.
-
-
-
Package edu.cmu.tetrad.classify
-
Class edu.cmu.tetrad.classify.ClassifierBayesUpdaterDiscrete
class ClassifierBayesUpdaterDiscrete extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.)- Parameters:
s- The input stream.- Throws:
IOException- If an IO error occurs.ClassNotFoundException- If a class is not found.
-
-
Serialized Fields
-
bayesIm
BayesIm bayesIm
The BayesIm instance used to create an updater. Supplied as an argument to the constructor. -
bayesImVars
List<Node> bayesImVars
The variables in the dataset to be classified. These should be the same variables as in the training dataset according to the "equals" method of DiscreteVariable. -
classifications
int[] classifications
The classifications of the target variable. -
marginals
double[][] marginals
The marginals. -
numCases
int numCases
The number of cases in the dataset. -
percentCorrect
double percentCorrect
The percentage of correct estimates of the target variable. This will be set to a meaningful value upon completion of the crossTabulate method. -
targetVariable
DiscreteVariable targetVariable
The target variable (inferred from its name). -
testData
DataSet testData
The dataset to be classified. -
totalUsableCases
int totalUsableCases
The number of usable cases in the dataset.
-
-
-
Package edu.cmu.tetrad.data
-
Class edu.cmu.tetrad.data.AbstractVariable
class AbstractVariable extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
name
String name
Name of this variable. -
selectionBias
boolean selectionBias
True just in case this node is a selection bias node.
-
-
Class edu.cmu.tetrad.data.BoxDataSet
class BoxDataSet extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
caseIds
Map<Integer,
String> caseIds Case ID's. These are strings associated with some or all of the cases of the dataset. -
columnToTooltip
Map<String,
String> columnToTooltip The name of the data model. This is not used internally; it is only here in case an external class wants this dataset to have a name. -
dataBox
DataBox dataBox
The container storing the data. Rows are cases; columns are variables. The order of columns is coordinated with the order of variables in getVariables(). -
knowledge
Knowledge knowledge
The knowledge associated with this data. -
multipliers
Map<Integer,
Integer> multipliers A map from cases to case multipliers. If a case is not in the domain of this map, its case multiplier is by default 1. This is the number of repetitions of the case in the dataset. The sample size is obtained by summing over these multipliers. -
name
String name
The name of the data model. This is not used internally; it is only here in case an external class wants this dataset to have a name. -
outputDelimiter
char outputDelimiter
The character used as a delimiter when the dataset is printed. -
selection
Set<Node> selection
The set of selected variables. -
variables
List<Node> variables
The list of variables. These correspond columnwise to the columns ofdata.
-
-
Class edu.cmu.tetrad.data.ByteDataBox
class ByteDataBox extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
data
byte[][] data
The stored byte data. -
numCols
int numCols
The number of columns (tracked because it may be zero). -
numRows
int numRows
The number of rows (tracked because it may be zero).
-
-
Class edu.cmu.tetrad.data.Clusters
class Clusters extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
clusters
Map<String,
Integer> clusters This is used to store information on pure measurement models (when the graph is a measurement/structural model). The information is stored variable clusters, and is used by algorithm such as Purify and MIM Build (R. Silva, 04/2003) -
names
Map<Integer,
String> names Node names. -
numClusters
int numClusters
The number of clusters represented. If there is no fixed upper bound, set this to -1.
-
-
Class edu.cmu.tetrad.data.ContinuousDiscretizationSpec
class ContinuousDiscretizationSpec extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
Class edu.cmu.tetrad.data.ContinuousVariable
class ContinuousVariable extends AbstractVariable implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
attributes
Map<String,
Object> attributes The node type. -
centerX
int centerX
The x coordinate of the center of the node. -
centerY
int centerY
The y coordinate of the center of the node. -
nodeType
NodeType nodeType
The node type. -
nodeVariableType
NodeVariableType nodeVariableType
Node variable type (domain, interventional status, interventional value..) of this node variable
-
-
Class edu.cmu.tetrad.data.CorrelationMatrix
class CorrelationMatrix extends CovarianceMatrix implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.data.CorrelationMatrixOnTheFly
class CorrelationMatrixOnTheFly extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
cov
ICovarianceMatrix cov
The covariance matrix. Cannot be null. Must be symmetric and positive definite. -
matrixC
cern.colt.matrix.DoubleMatrix2D matrixC
The matrix data. Should be square. This may be set by derived classes, but it must always be set to a legitimate covariance matrix. -
selectedVariables
Set<Node> selectedVariables
The list of selected variables. -
variables
List<Node> variables
The variables (in order) for this covariance matrix. -
verbose
boolean verbose
Whether to print out verbose messages.
-
-
Class edu.cmu.tetrad.data.CovarianceMatrix
class CovarianceMatrix extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
_covariancesMatrix
Matrix _covariancesMatrix
The wrapped covariance matrix data. -
knowledge
Knowledge knowledge
The knowledge for this data. -
name
String name
The name of the covariance matrix. -
sampleSize
int sampleSize
The size of the sample from which this covariance matrix was calculated. -
selectedVariables
Set<Node> selectedVariables
The list of selected variables. -
variables
List<Node> variables
The variables (in order) for this covariance matrix.
-
-
Class edu.cmu.tetrad.data.CovarianceMatrixOnTheFly
class CovarianceMatrixOnTheFly extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
knowledge
Knowledge knowledge
The knowledge for this data. -
matrix
Matrix matrix
Stored matrix data. Should be square. This may be set by derived classes, but it must always be set to a legitimate covariance matrix. -
name
String name
The name of the covariance matrix. -
sampleSize
int sampleSize
The size of the sample from which this covariance matrix was calculated. -
selectedVariables
Set<Node> selectedVariables
The list of selected variables. -
variables
List<Node> variables
The variables (in order) for this covariance matrix. -
variances
double[] variances
The variances of the variables. -
vectors
double[][] vectors
The vectors for the variables. -
verbose
boolean verbose
Whether to print out verbose information.
-
-
Class edu.cmu.tetrad.data.DataModelList
- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
Class edu.cmu.tetrad.data.DelimiterType
class DelimiterType extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
readResolve
readResolve.
- Throws:
ObjectStreamException- if any.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
ordinal
int ordinal
The ordinal of this type.
-
-
Class edu.cmu.tetrad.data.DiscreteDiscretizationSpec
class DiscreteDiscretizationSpec extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
Class edu.cmu.tetrad.data.DiscreteVariable
class DiscreteVariable extends AbstractVariable implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
accommodateNewCategories
boolean accommodateNewCategories
True iff new variables should be allowed to be constructed to replace this one, accommodating new categories. -
attributes
Map<String,
Object> attributes Attributes of the node. -
categoriesCopy
List<String> categoriesCopy
A copy of the category list is stored here for when the discrete variable is deserialized. On deserialization, STORED_CATEGORY_LISTS will be constructed if it hasn't been already, and this list will be looked up on the "bulletin board" to see if a permutation of it already exists. -
categoryNamesDisplayed
boolean categoryNamesDisplayed
True iff the category categories for this variable should be displayed; false if the integer indices of categories should be displayed. -
centerX
int centerX
The x coordinate of the center of the node. -
centerY
int centerY
The y coordinate of the center of the node. -
discreteVariableType
DiscreteVariableType discreteVariableType
The discreteVariableType of discrete variable this is. -
nodeType
NodeType nodeType
The node discreteVariableType. -
nodeVariableType
NodeVariableType nodeVariableType
Node variable type (domain, interventional status, interventional value, ...) of this node variable
-
-
Class edu.cmu.tetrad.data.DiscreteVariableType
class DiscreteVariableType extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
readResolve
Returns the ordinal of this type.- Throws:
ObjectStreamException- if any.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
ordinal
int ordinal
The ordinal of this type.
-
-
Class edu.cmu.tetrad.data.DoubleDataBox
class DoubleDataBox extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
data
double[][] data
The stored double data. -
numCols
int numCols
The number of columns (tracked because it may be zero). -
numRows
int numRows
The number of rows (tracked because it may be zero).
-
-
Class edu.cmu.tetrad.data.FloatDataBox
class FloatDataBox extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
data
float[][] data
The stored float data.
-
-
Class edu.cmu.tetrad.data.IndependenceFacts
class IndependenceFacts extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.data.IntDataBox
class IntDataBox extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
data
int[][] data
The stored short data. -
numCols
int numCols
The number of columns (tracked because it may be zero). -
numRows
int numRows
The number of rows (tracked because it may be zero).
-
-
Class edu.cmu.tetrad.data.Knowledge
class Knowledge extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
defaultToKnowledgeLayout
boolean defaultToKnowledgeLayout
The default to knowledge layout. -
forbiddenRulesSpecs
List<OrderedPair<Set<String>>> forbiddenRulesSpecs
This needs to be a list for backward compatibility. Need to check when adding a new spec whether it's already in the list. -
knowledgeGroupRules
Map<KnowledgeGroup,
OrderedPair<Set<String>>> knowledgeGroupRules The knowledge group rules. -
knowledgeGroups
List<KnowledgeGroup> knowledgeGroups
The knowledge groups. -
requiredRulesSpecs
List<OrderedPair<Set<String>>> requiredRulesSpecs
This needs to be a list for backward compatibility. Need to check when adding a new spec whether it's already in the list. -
tierSpecs
List<Set<String>> tierSpecs
The tier specs. -
variables
Set<String> variables
The variable names.
-
-
Class edu.cmu.tetrad.data.KnowledgeEdge
class KnowledgeEdge extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
Class edu.cmu.tetrad.data.KnowledgeGroup
class KnowledgeGroup extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
Class edu.cmu.tetrad.data.LongDataBox
class LongDataBox extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
data
long[][] data
The stored long data. -
numCols
int numCols
The number of columns (tracked because it may be zero). -
numRows
int numRows
The number of rows (tracked because it may be zero).
-
-
Class edu.cmu.tetrad.data.MixedDataBox
class MixedDataBox extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.data.NumberObjectDataSet
class NumberObjectDataSet extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
columnToTooltip
Map<String,
String> columnToTooltip The map from column names to tooltips. -
data
Number[][] data
The container storing the data. Rows are cases; columns are variables. The order of columns is coordinated with the order of variables in getVariable(). -
knowledge
Knowledge knowledge
The knowledge associated with this data. -
name
String name
The name of the data model. This is not used internally; it is only here in case an external class wants this dataset to have a name. -
outputDelimiter
char outputDelimiter
The character used as a delimiter when the dataset is printed. -
selection
Set<Node> selection
The set of selected variables. -
variables
List<Node> variables
The list of variables. These correspond columnwise to the columns ofdata.
-
-
Class edu.cmu.tetrad.data.ShortDataBox
class ShortDataBox extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
data
short[][] data
The stored short data. -
numCols
int numCols
The number of columns (tracked because it may be zero). -
numRows
int numRows
The number of rows (tracked because it may be zero).
-
-
Class edu.cmu.tetrad.data.SplitCasesSpec
class SplitCasesSpec extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
Class edu.cmu.tetrad.data.TimeSeriesData
class TimeSeriesData extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
Class edu.cmu.tetrad.data.VerticalDoubleDataBox
class VerticalDoubleDataBox extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
data
double[][] data
The stored double data. -
numCols
int numCols
The number of columns (tracked because it may be zero). -
numRows
int numRows
The number of rows (tracked because it may be zero).
-
-
Class edu.cmu.tetrad.data.VerticalIntDataBox
class VerticalIntDataBox extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
data
int[][] data
The stored int data. -
numCols
int numCols
The number of columns (tracked because it may be zero). -
numRows
int numRows
The number of rows (tracked because it may be zero).
-
-
-
Package edu.cmu.tetrad.data.simulation
-
Class edu.cmu.tetrad.data.simulation.LoadContinuousDataAndGraphs
class LoadContinuousDataAndGraphs extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.data.simulation.LoadContinuousDataAndSingleGraph
class LoadContinuousDataAndSingleGraph extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.data.simulation.LoadContinuousDataSmithSim
class LoadContinuousDataSmithSim extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.data.simulation.LoadDataAndGraphs
class LoadDataAndGraphs extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.data.simulation.LoadDataFromFileWithoutGraph
class LoadDataFromFileWithoutGraph extends Object implements Serializable- serialVersionUID:
- 23L
-
-
Package edu.cmu.tetrad.graph
-
Class edu.cmu.tetrad.graph.Dag
class Dag extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.)- Parameters:
s- The object input stream.- Throws:
IOException- If any.ClassNotFoundException- If any.
-
-
Serialized Fields
-
Class edu.cmu.tetrad.graph.Edge
class Edge extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
bold
boolean bold
Whether the edge is bold. -
edgeTypeProbabilities
List<EdgeTypeProbability> edgeTypeProbabilities
The edge type probabilities. -
endpoint1
Endpoint endpoint1
The endpoint at the first node. -
endpoint2
Endpoint endpoint2
The endpoint at the second node. -
highlighted
boolean highlighted
Whether the edge is highlighted. -
node1
Node node1
The first node. -
node2
Node node2
The second node. -
probability
double probability
The probability. -
properties
List<Edge.Property> properties
The properties.
-
-
Class edu.cmu.tetrad.graph.EdgeListGraph
class EdgeListGraph extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.)- Parameters:
s- aObjectInputStreamobject- Throws:
IOException- if any.ClassNotFoundException- if any.
-
-
Serialized Fields
-
ambiguousTriples
Set<Triple> ambiguousTriples
The ambiguous triples. -
ancestorCache
Map<org.apache.commons.lang3.tuple.Pair<Node,
Node>, Boolean> ancestorCache The cache for the ancestor relationships -
attributes
Map<String,
Object> attributes The attributes. -
dottedUnderLineTriples
Set<Triple> dottedUnderLineTriples
The dotted underline triples. -
edgeLists
Map<Node,
Set<Edge>> edgeLists Map from each node to the List of edges connected to that node. -
edgesSet
Set<Edge> edgesSet
The edges in the graph. -
namesHash
Map<String,
Node> namesHash A hash from node names to nodes; -
nodes
List<Node> nodes
A list of the nodes in the graph, in the order in which they were added. -
parentsHash
Map<Node,
List<Node>> parentsHash The parents hash. -
semidirectedPathCache
Map<org.apache.commons.lang3.tuple.Pair<Node,
Node>, Boolean> semidirectedPathCache The cache for the semidirected path relationships -
underLineTriples
Set<Triple> underLineTriples
The underline triples.
-
-
Class edu.cmu.tetrad.graph.EdgeTypeProbability
class EdgeTypeProbability extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
edgeType
EdgeTypeProbability.EdgeType edgeType
The edge type. -
probability
double probability
The probability. -
properties
List<Edge.Property> properties
The properties.
-
-
Class edu.cmu.tetrad.graph.GraphNode
class GraphNode extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.- Parameters:
s- The input stream.- Throws:
IOException- If any.ClassNotFoundException- If any.
-
-
Serialized Fields
-
attributes
Map<String,
Object> attributes The attributes of the node. -
centerX
int centerX
The x coordinate of the center of the node. -
centerY
int centerY
The y coordinate of the center of the node. -
name
String name
The name of the node. -
nodeType
NodeType nodeType
The type of the node.- See Also:
-
nodeVariableType
NodeVariableType nodeVariableType
Node variable type (domain, interventional status, interventional value..) of this node variable -
selectionBias
boolean selectionBias
Whether the node is selected as a bias node.
-
-
Class edu.cmu.tetrad.graph.IndependenceFact
class IndependenceFact extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
Class edu.cmu.tetrad.graph.LagGraph
class LagGraph extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
ambiguousTriples
Set<Triple> ambiguousTriples
The set of ambiguous triples. -
attributes
Map<String,
Object> attributes The map from variables to their attributes. -
dottedUnderLineTriples
Set<Triple> dottedUnderLineTriples
The set of dotted underline triples. -
graph
Dag graph
The graph. -
laggedVariables
Map<String,
List<Node>> laggedVariables The map from variables to their lagged variables. -
paths
Paths paths
The paths -
underLineTriples
Set<Triple> underLineTriples
The set of underline triples. -
variables
List<String> variables
The list of variables in the getModel time lag.
-
-
Class edu.cmu.tetrad.graph.OrderedPair
class OrderedPair extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
Class edu.cmu.tetrad.graph.Paths
class Paths extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
graph
Graph graph
The graph.
-
-
Class edu.cmu.tetrad.graph.SemGraph
class SemGraph extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.)- Parameters:
s- The object input stream.- Throws:
IOException- If any.ClassNotFoundException- If any.
-
-
Serialized Fields
-
ambiguousTriples
Set<Triple> ambiguousTriples
The ambiguous triples. -
attributes
Map<String,
Object> attributes The attributes of the graph. -
cpdag
boolean cpdag
True if the graph is a CPDAG. -
dottedUnderLineTriples
Set<Triple> dottedUnderLineTriples
The dotted underlines. -
errorNodes
Map<Node,
Node> errorNodes A map from nodes to their error nodes, if they exist. This includes variables nodes to their error nodes and error nodes to themselves. Added because looking them up in the graph was not scalable. -
graph
Graph graph
The underlying graph that stores all the information. This needs to be an EdgeListGraph or something at least that can allow nodes to quickly be added or removed. -
pag
boolean pag
True if the graph is a PAG. -
paths
Paths paths
The paths of the graph. -
showErrorTerms
boolean showErrorTerms
True if error terms for exogenous terms should be shown. -
underLineTriples
Set<Triple> underLineTriples
The underlines.
-
-
Class edu.cmu.tetrad.graph.TimeLagGraph
class TimeLagGraph extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
ambiguousTriples
Set<Triple> ambiguousTriples
The set of ambiguous triples. -
attributes
Map<String,
Object> attributes A node in a time lag graph. -
cpdag
boolean cpdag
Whether the graph is a CPDAG. -
dottedUnderLineTriples
Set<Triple> dottedUnderLineTriples
The set of dotted underlined triples. -
graph
EdgeListGraph graph
A node in a time lag graph. -
lag0Nodes
List<Node> lag0Nodes
The nodes in lag 0. -
maxLag
int maxLag
The maximum lag. -
numInitialLags
int numInitialLags
The number of initial lags. -
pag
boolean pag
Whether the graph is a PAG. -
paths
Paths paths
The paths in the graph. -
underLineTriples
Set<Triple> underLineTriples
The set of underlined triples.
-
-
Class edu.cmu.tetrad.graph.Triple
class Triple extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
Class edu.cmu.tetrad.graph.Underlines
class Underlines extends Object implements Serializable- serialVersionUID:
- 23L
-
-
Package edu.cmu.tetrad.regression
-
Class edu.cmu.tetrad.regression.LogisticRegression
class LogisticRegression extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.- Parameters:
s- aObjectInputStreamobject- Throws:
IOException- if an error occursClassNotFoundException- if an error occurs
-
-
Serialized Fields
-
alpha
double alpha
The default alpha level which may be specified otherwise in the GUI -
dataCols
double[][] dataCols
The data converted into column major, to avoid unnecessary copying. -
dataSet
DataSet dataSet
The data set that was supplied. -
rows
int[] rows
The rows in the data used for regression.
-
-
Class edu.cmu.tetrad.regression.LogisticRegression.Result
class Result extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
alpha
double alpha
The alpha level. -
chiSq
double chiSq
The chi square statistic. -
coefs
double[] coefs
The array of regression coefficients. -
intercept
double intercept
The intercept. -
logLikelihood
double logLikelihood
The log likelihood of the regression. -
numRegressors
int numRegressors
The number of regressors. -
ny0
int ny0
The number of cases with target = 0. -
ny1
int ny1
The number of cases with target = 1. -
probs
double[] probs
The array of coefP-values for the regression coefficients. -
regressorNames
List<String> regressorNames
The names of the regressors. -
stdErrs
double[] stdErrs
The array of standard errors for the regression coefficients. -
target
String target
The target. -
xMeans
double[] xMeans
The array of means. -
xStdDevs
double[] xStdDevs
The array of standard devs.
-
-
Class edu.cmu.tetrad.regression.RegressionResult
class RegressionResult extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
alpha
double alpha
Alpha value to determine significance.- See Also:
-
b
double[] b
The array of regression coefficients.- See Also:
-
n
int n
The number of data points.- See Also:
-
p
double[] p
The array of p-values for the regression coefficients.- See Also:
-
r2
double r2
R square value.- See Also:
-
regressorNames
String[] regressorNames
Regressor names.- See Also:
-
res
Vector res
The residuals. -
rss
double rss
Residual sums of squares.- See Also:
-
se
double[] se
Standard errors of the coefficients- See Also:
-
t
double[] t
The array of t-statistics for the regression coefficients.- See Also:
-
zeroInterceptAssumed
boolean zeroInterceptAssumed
True iff this model assumes a zero intercept.- See Also:
-
-
-
Package edu.cmu.tetrad.search
-
Class edu.cmu.tetrad.search.Cstar.Record
class Record extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
causeNode
Node causeNode
The cause node. -
effect
double effect
The minimum effect size of the predictor on the target across subsamples calculated by IDA. -
numCauses
int numCauses
The number of possible causes of the target. -
numEffects
int numEffects
The number of possible effects of the target. -
pi
double pi
The percentage of the time the predictor is a cause of the target across subsamples. -
target
Node target
The effect node.
-
-
-
Package edu.cmu.tetrad.search.score
-
Class edu.cmu.tetrad.search.score.ScoredGraph
class ScoredGraph extends Object implements Serializable- serialVersionUID:
- 23L
-
-
Package edu.cmu.tetrad.search.test
-
Class edu.cmu.tetrad.search.test.IndependenceResult
class IndependenceResult extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
fact
IndependenceFact fact
The fact itself. -
indep
boolean indep
The conditional independence result, true if the fact holds, false if not. -
isValid
boolean isValid
Whether the result is valid or not. A test is not valid if the test is not able to determine whether the fact holds or not. -
pValue
double pValue
The p-values of the independence result, under the null (independence) hypothesis. -
score
double score
The score of the test, which is alpha - p if the test returns a p-value or else a bump if the test is based on a score.
-
-
-
Package edu.cmu.tetrad.search.utils
-
Class edu.cmu.tetrad.search.utils.AlmostCycleRemover
class AlmostCycleRemover extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.search.utils.SepsetMap
class SepsetMap extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help).- Parameters:
s- aObjectInputStreamobject- Throws:
IOException- if an error occursClassNotFoundException- if an error occurs
-
-
Serialized Fields
-
Class edu.cmu.tetrad.search.utils.Sextad
class Sextad extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
i
int i
The first node. -
j
int j
The second node. -
k
int k
The third node. -
l
int l
The fourth node. -
m
int m
The fifth node. -
n
int n
The sixth node.
-
-
-
Package edu.cmu.tetrad.search.work_in_progress
-
Class edu.cmu.tetrad.search.work_in_progress.Sextad
class Sextad extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
-
Package edu.cmu.tetrad.sem
-
Class edu.cmu.tetrad.sem.DagScorer
class DagScorer extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
covMatrix
ICovarianceMatrix covMatrix
The covariance matrix. -
dag
Graph dag
The DAG. -
dataSet
DataSet dataSet
The data set. -
edgeCoef
Matrix edgeCoef
The edge coefficients. -
errorCovar
Matrix errorCovar
The error covariance. -
fml
double fml
The fml score. -
implCovarMeasC
Matrix implCovarMeasC
The implied covariance matrix for the measured variables. -
logDetSample
double logDetSample
The log determinant of the sample covariance matrix. -
sampleCovar
Matrix sampleCovar
The sample covariance. -
variables
List<Node> variables
The variables.
-
-
Class edu.cmu.tetrad.sem.GeneralizedSemIm
class GeneralizedSemIm extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
guaranteeIid
boolean guaranteeIid
Whether to guarantee that the IID is preserved when simulating data. -
parameterValues
Map<String,
Double> parameterValues A map from freeParameters names to their values--these form the context for evaluating expressions. Variables do not appear in this list. All freeParameters are double-valued. -
pm
GeneralizedSemPm pm
The wrapped PM, that holds all the expressions and structure for the model.
-
-
Class edu.cmu.tetrad.sem.GeneralizedSemPm
class GeneralizedSemPm extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
errorNodes
List<Node> errorNodes
The error nodes. -
errorsTemplate
String errorsTemplate
The stored template for error terms. -
graph
SemGraph graph
The structural model graph that this sem parametric model is based on.Cannot be null. -
measuredNodes
List<Node> measuredNodes
The measured nodes. -
namesToNodes
Map<String,
Node> namesToNodes A map from names to nodes, speedup. -
nodeExpressions
Map<Node,
Expression> nodeExpressions The map from variable nodes to equations. -
nodeExpressionStrings
Map<Node,
String> nodeExpressionStrings The String representations of equations that were set. -
nodes
List<Node> nodes
The list of all nodes (unmodifiable).Cannot be null. -
parameterEstimationInitializationExpressions
Map<String,
Expression> parameterEstimationInitializationExpressions Distributions from which initial values for freeParameters are drawn. -
parameterEstimationInitializationExpressionStrings
Map<String,
String> parameterEstimationInitializationExpressionStrings String representations of initial parameter distributions. A map from parameter names to expression strings. -
parameterExpressions
Map<String,
Expression> parameterExpressions Distributions from which initial values for freeParameters are drawn. -
parameterExpressionStrings
Map<String,
String> parameterExpressionStrings String representations of initial parameter distributions. A map from parameter names to expression strings. -
parametersEstimationInitializationTemplate
String parametersEstimationInitializationTemplate
The stored template for freeParameters. -
parametersTemplate
String parametersTemplate
The stored template for freeParameters. -
parameterSubscript
Map<String,
Integer> parameterSubscript A map from names to nodes, speedup. -
referencedNodes
Map<Node,
Set<Node>> referencedNodes The nodes of the model, variable nodes or error nodes, mapped to the other nodes that they are associated with. -
referencedParameters
Map<String,
Set<Node>> referencedParameters The freeParameters in the model, mapped to the nodes that they are associated with. Each parameter may be associated with more than one node. When freeParameters are removed from an equation or error distribution, the associated nodes should be removed from the relevant set in this map, and if the set is empty, the parameter should be removed from the map. Also, before adding a parameter to this map, it must be checked whether a parameter by the same name already exists. If one such parameter by the same name already exists, that one should be used instead of the new one. This is needed both to avoid confusion and to allow freeParameters to be reused in different parts of the interface, creating equality constraints.Cannot be null. -
startsWithParametersEstimationInitializationTemplates
Map<String,
String> startsWithParametersEstimationInitializationTemplates A map from initial name strings to parameter templates. -
startsWithParametersTemplates
Map<String,
String> startsWithParametersTemplates A map from initial name strings to parameter templates. -
variableNames
List<String> variableNames
The list of variable names. -
variableNodes
List<Node> variableNodes
The latent and measured nodes. -
variablesTemplate
String variablesTemplate
The stored template for variables.
-
-
Class edu.cmu.tetrad.sem.Mapping
class Mapping extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
a
Matrix a
The 2D double array whose element at (i, j) to be manipulated.Can't be null. -
i
int i
The left-hand coordinate of a[i][j].Any value. -
j
int j
The right-hand coordinate of a[i][j].Any value. -
parameter
Parameter parameter
The parameter this mapping maps.Can't be null. -
semIm
ISemIm semIm
The SemIm for which this is a mapping.Can't be null.
-
-
Class edu.cmu.tetrad.sem.ParamConstraint
class ParamConstraint extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
number
double number
The number of the constraint. -
param2
Parameter param2
The first parameter. -
semIm
SemIm semIm
The SEM. -
type
ParamConstraintType type
The type of the constraint.
-
-
Class edu.cmu.tetrad.sem.Parameter
class Parameter extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
distribution
Distribution distribution
If this parameter is initialized randomly, the initial value is drawn from this distribution.Cannot be null. -
fixed
boolean fixed
True iff this parameter is fixed in estimation.Any value. -
initializedRandomly
boolean initializedRandomly
True iff this parameter should be initialized randomly.Any value. -
name
String name
The name of the parameter.Cannot be null. -
nodeA
Node nodeA
One of the anchor endpoints specifying the parameter this is.Cannot be null. -
nodeB
Node nodeB
One of the anchor endpoints specifying the parameter this is.Cannot be null. -
startingValue
double startingValue
If this parameter is either fixed or not initialized randomly, returns its starting value.Any value. -
type
ParamType type
The type of parameter--coefficient, covariance, or variance.Cannot be null. Should be ParamType.VAR if nodeA != nodeB and ParamType.COVAR if nodeA == nodeB.
-
-
Class edu.cmu.tetrad.sem.ParameterPair
class ParameterPair extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
Class edu.cmu.tetrad.sem.SemEstimator
class SemEstimator extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
covMatrix
ICovarianceMatrix covMatrix
The covariance matrix used to estimate the SemIm. Note that the variables names in the covariance matrix must be in the same order as the variable names in the semPm. -
dataSet
DataSet dataSet
The data set being estimated from (needed to calculate means of variables). May be null in which case means are set to zero. -
estimatedSem
SemIm estimatedSem
The most recently estimated model, or null if no model has been estimated yet. -
numRestarts
int numRestarts
The number of restarts to use. -
scoreType
ScoreType scoreType
The score type used to optimize the SEM. -
semOptimizer
SemOptimizer semOptimizer
The algorithm that minimizes the fitting function for the SEM. -
semPm
SemPm semPm
The SemPm containing the graph and the freeParameters to be estimated.
-
-
Class edu.cmu.tetrad.sem.SemEstimatorGibbsParams
class SemEstimatorGibbsParams extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
flatPrior
boolean flatPrior
Whether to use a flat prior. -
numIterations
int numIterations
The number of iterations to run. -
startIm
SemIm startIm
The initial SEM. -
stretch
double stretch
The stretch factor. -
tolerance
double tolerance
The tolerance for convergence.
-
-
Class edu.cmu.tetrad.sem.SemEvidence
class SemEvidence extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
manipulation
SemManipulation manipulation
A manipulation indicating how the bayes Im should be manipulated before updating. -
proposition
SemProposition proposition
A proposition stating what we know for each variable.Cannot be null. -
semIm
SemIm semIm
Bayes IM that this is evidence for.
-
-
Class edu.cmu.tetrad.sem.SemIm
class SemIm extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
cyclic
boolean cyclic
True just in case the graph for the SEM is cyclic. -
cyclicChecked
boolean cyclicChecked
True just in case cyclicity has already been checked. -
distributions
Map<Node,
Distribution> distributions Stores a distribution for each variable. Initialized to N(0, 1) for each. -
edgeCoef
Matrix edgeCoef
Matrix of edge coefficients. edgeCoefC[i][j] is the coefficient of the edge from getVariableNodes().get(i) to getVariableNodes().get(j), or 0.0 if this edge is not in the graph. The values of these may be changed, but the array itself may not. -
errCovar
Matrix errCovar
Matrix of error covariances. errCovar[i][j] is the covariance of the error term of getExoNodes().get(i) and getExoNodes().get(j), with the special case (duh!) that errCovar[i][i] is the variance of getExoNodes.get(i). The values of these may be changed, but the array itself may not. -
errorParam1
double errorParam1
Error distribution parameters. -
errorParam2
double errorParam2
Error distribution parameters. -
estimated
boolean estimated
True iff this SemIm is estimated. -
fixedMappings
List<Mapping> fixedMappings
The list of fixed freeParameters (Unmodifiable). This must be in the same order as this.fixedParameters. -
fixedParameters
List<Parameter> fixedParameters
The list of fixed freeParameters (Unmodifiable). This must be in the same order as this.fixedMappings. -
freeMappings
List<Mapping> freeMappings
The list of freeMappings. This is an unmodifiable list. It is fixed (up to order) by the SemPm. This must be in the same order as this.freeParameters. -
freeParameters
List<Parameter> freeParameters
The list of free freeParameters (Unmodifiable). This must be in the same order as this.freeMappings. -
functions
Map<Node,
ConnectionFunction> functions Stores the connection functions of specified nodes. -
implCovar
Matrix implCovar
Replaced by implCovarC. Please do not delete. Required for serialization backward compatibility. -
meanParameters
List<Parameter> meanParameters
The list of mean freeParameters (Unmodifiable). This must be in the same order as variableMeans. -
measuredNodes
List<Node> measuredNodes
The list of measured variableNodes from the semPm. (Unmodifiable.) -
numRandomCalls
int numRandomCalls
Number of random calls. -
parameterBoundsEnforced
boolean parameterBoundsEnforced
True iff setting freeParameters to out-of-bound values throws exceptions. -
params
Parameters params
Parameters to help guide how values are chosen for freeParameters. -
sampleCovarC
Matrix sampleCovarC
Replaced by sampleCovar. Please do not delete. Required for serialization backward compatibility. -
sampleCovInv
Matrix sampleCovInv
The type of score to use for estimation. -
sampleSize
int sampleSize
The sample size. -
scoreType
ScoreType scoreType
Types of scores that yield a chi square value when minimized. -
semPm
SemPm semPm
The Sem PM containing the graph and the freeParameters to be estimated. For now a defensive copy of this is not being constructed, since it is not used anywhere in the code except in the the constructor and in its accessor method. If somebody changes it, it's their own fault, but it won't affect this class. -
standardErrors
double[] standardErrors
Stores the standard errors for the freeParameters. May be null. -
variableMeans
double[] variableMeans
Means of variables. These will not be counted for purposes of calculating degrees of freedom, since the increase in dof is exactly balanced by a decrease in dof. -
variableMeansStdDev
double[] variableMeansStdDev
Standard Deviations of means. Needed to calculate standard errors. -
variableNodes
List<Node> variableNodes
The list of measured and latent variableNodes for the semPm. (Unmodifiable.) -
variablesHash
Map<Node,
Integer> variablesHash The type of score to use for estimation.
-
-
Class edu.cmu.tetrad.sem.SemManipulation
class SemManipulation extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
manipulated
boolean[] manipulated
An array indicating whether each variable in turn is manipulated.Cannot be null. -
semIm
SemIm semIm
Bayes IM that this is evidence for.Cannot be null.
-
-
Class edu.cmu.tetrad.sem.SemOptimizerEm
class SemOptimizerEm extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
errorParent
Node[] errorParent
Error parent of each node. -
expectedCov
Matrix expectedCov
Expected covariance matrix. -
graph
SemGraph graph
The SEM graph. -
idxLatent
int[] idxLatent
Indices of the latent variables. -
idxObserved
int[] idxObserved
Indices of the latent variables. -
nodeParentsCov
double[][] nodeParentsCov
Covariance of each node with its parents. -
numLatent
int numLatent
Number of observed and latent variables. -
numObserved
int numObserved
Number of observed and latent variables. -
numRestarts
int numRestarts
Number of restarts. -
parents
int[][] parents
Indices of the parents of each node. -
parentsCov
double[][][] parentsCov
Parents covariance matrix. -
semIm
SemIm semIm
The SEM to optimize. -
yCov
Matrix yCov
The sample covariance matrix. -
yCovModel
Matrix yCovModel
Partitions of the modeled cov. -
yzCovModel
Matrix yzCovModel
Partitions of the modeled cov. -
zCovModel
Matrix zCovModel
Partitions of the modeled cov.
-
-
Class edu.cmu.tetrad.sem.SemOptimizerPowell
class SemOptimizerPowell extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
numRestarts
int numRestarts
The number of restarts.
-
-
Class edu.cmu.tetrad.sem.SemOptimizerRegression
class SemOptimizerRegression extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
numRestarts
int numRestarts
The number of restarts.
-
-
Class edu.cmu.tetrad.sem.SemOptimizerRicf
class SemOptimizerRicf extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
numRestarts
int numRestarts
The number of restarts to use.
-
-
Class edu.cmu.tetrad.sem.SemOptimizerScattershot
class SemOptimizerScattershot extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
numRestarts
int numRestarts
The number of restarts to use.
-
-
Class edu.cmu.tetrad.sem.SemPm
class SemPm extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
bIndex
int bIndex
The index of the most recent "B" parameter. (These are edge coefficients.)Range >= 0. -
graph
SemGraph graph
The structural model graph that this sem parametric model is based on.Cannot be null. -
mIndex
int mIndex
The index of the most recent "M" parameter. (These are means.)Range >= 0. -
nodes
List<Node> nodes
The list of all nodes (unmodifiable).Cannot be null. -
paramComparisons
Map<ParameterPair,
ParamComparison> paramComparisons The set of parameter comparisons.Cannot be null. -
parameters
List<Parameter> parameters
The list of Parameters (unmodifiable).Cannot be null. -
tIndex
int tIndex
The index of the most recent "T" parameter. (These are variance and covariance terms.)Range >= 0. -
variableNodes
List<Node> variableNodes
The list of variable nodes (unmodifiable).Cannot be null.
-
-
Class edu.cmu.tetrad.sem.SemProposition
class SemProposition extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
semIm
SemIm semIm
Represents a final variable semIm. -
values
double[] values
Represents a private final array of double values.This variable is part of the SemProposition class in the Tetrad API. SemProposition is a class that represents a Proposition for a Bayes IM (Bayesian Inference Model). It allows for semantic checks when deserializing.
The values array contains the double values associated with the Proposition.
-
-
Class edu.cmu.tetrad.sem.SemUpdater
class SemUpdater extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
evidence
SemEvidence evidence
The evidence to be used in the update. -
semIm
SemIm semIm
The SEM to be updated.
-
-
Class edu.cmu.tetrad.sem.StandardizedSemIm
class StandardizedSemIm extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
edgeCoef
Matrix edgeCoef
The edge coefficient matrix of the model, a la SemIm. Note that this will normally need to be transposed, since [a][b] is the edge coefficient for a-->b, not b-->a. Sorry. History. THESE ARE PARAMETERS OF THE MODEL--THE ONLY PARAMETERS. -
edgeParameters
Map<Edge,
Double> edgeParameters A map from edges in the graph to their coefficients. These are the only freeParameters in the model. This includes coefficients for directed as well as bidirected edges. -
editingEdge
Edge editingEdge
The edge being edited. -
errorCovar
Matrix errorCovar
The error covariance matrix of the model. i.e. [a][b] is the covariance of E_a and E_b, with [a][a] of course being the variance of E_a. THESE ARE NOT PARAMETERS OF THE MODEL; THEY ARE CALCULATED. Note that elements of this matrix may be Double.NaN; this indicates that these elements cannot be calculated. -
errorVariances
Map<Node,
Double> errorVariances A map from error nodes in the graph to their error variances. These are not freeParameters in the model; their values are always calculated as residual variances, under the constraint that the variances of each variable must be 1. -
implCovar
Matrix implCovar
The implied covariance matrix over all the variables. -
implCovarMeas
Matrix implCovarMeas
The implied covariance matrix over the measured variables only. -
range
StandardizedSemIm.ParameterRange range
The range of the parameter being edited. -
sampleSize
int sampleSize
The sample size for the model. -
semGraph
SemGraph semGraph
The graph of the model. Stored internally because it must be ensured that the error terms are showing. -
semPm
SemPm semPm
The SEM model.
-
-
Class edu.cmu.tetrad.sem.StandardizedSemIm.ParameterRange
class ParameterRange extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
coef
double coef
The coefficient value for which the range is needed. -
edge
Edge edge
The edge for which the range is needed. -
high
double high
The high end of the range to which the coefficient value may be adjusted. -
low
double low
The low end of the range to which the coefficient value may be adjusted.
-
-
-
Package edu.cmu.tetrad.study.gene.tetrad.gene.graph
-
Class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ActiveLagGraph
class ActiveLagGraph extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.- Parameters:
s- anObjectInputStreamobject- Throws:
IOException- If any.ClassNotFoundException- If any.
-
-
Serialized Fields
-
lagGraph
LagGraph lagGraph
Underlying graph representing the update graph.
-
-
Class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ManualLagGraph
class ManualLagGraph extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.- Parameters:
s- anObjectInputStreamobject- Throws:
IOException- If any.ClassNotFoundException- If any.
-
-
Serialized Fields
-
lagGraph
BasicLagGraph lagGraph
The lag graph.
-
-
Class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ManualLagGraphParams
class ManualLagGraphParams extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.- Parameters:
s- anObjectInputStreamobject- Throws:
IOException- if any.ClassNotFoundException- if any.
-
-
Serialized Fields
-
mlag
int mlag
The maximum lag of the lag graph. -
varsPerInd
int varsPerInd
The number of variables per individual.
-
-
Class edu.cmu.tetrad.study.gene.tetrad.gene.graph.StoredLagGraphParams
class StoredLagGraphParams extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
filename
String filename
The filename of the stored lag graph.
-
-
-
Package edu.cmu.tetrad.study.gene.tetrad.gene.history
-
Class edu.cmu.tetrad.study.gene.tetrad.gene.history.BasalInitializer
class BasalInitializer extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.- Parameters:
s- anObjectInputStreamobject- Throws:
IOException- If any.ClassNotFoundException- If any.
-
-
Serialized Fields
-
basalExpression
double basalExpression
The average expression level that all unregulated genes are initialized to. -
initStDev
double initStDev
The standard deviation of a normal distribution N(basalExpression, sem.D.) that random initial values for unregulated genes are set to. -
updateFunction
UpdateFunction updateFunction
The update function this is initializing for.
-
-
Class edu.cmu.tetrad.study.gene.tetrad.gene.history.BasicLagGraph
class BasicLagGraph extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.- Parameters:
s- anObjectInputStreamobject- Throws:
IOException- If any.ClassNotFoundException- If any.
-
-
Serialized Fields
-
connectivity
SortedMap<String,
SortedSet<LaggedFactor>> connectivity For each factor, stores the set of lagged factors which map into it. (Maps Strings to SortedSets of Strings.) This is the main data structure for the graph. -
locations
Map<String,
PointXy> locations Stores the locations of the points for a directed graph. -
maxLagAllowable
int maxLagAllowable
The maximum allowable lag. edges may not be added with lags greater than this. The value must be >= 1.
-
-
Class edu.cmu.tetrad.study.gene.tetrad.gene.history.BooleanFunction
class BooleanFunction extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
lookupTable
boolean[] lookupTable
The stored boolean function. The order of the rows (for the given parents array, for two parents) is 00, 01, 10, 11, and so on for higher numbers of parents. -
parents
IndexedParent[] parents
The array of parents for the stored boolean function.
-
-
Class edu.cmu.tetrad.study.gene.tetrad.gene.history.BooleanGlassFunction
class BooleanGlassFunction extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.- Parameters:
s- anObjectInputStreamobject- Throws:
IOException- If any.ClassNotFoundException- If any.
-
-
Serialized Fields
-
basalExpression
double basalExpression
The basalExpression for determining whether history expression levels should be mapped to "true" or "false" for purposes of looking up output values in the Boolean function table. -
booleanFunctions
BooleanFunction[] booleanFunctions
Stores a boolean function for each factor from a preselected set of lagged factors to the given factor. -
booleanInfluenceRate
double booleanInfluenceRate
The rate at which the F function (with outputs -1 and +1) affects the update for a gene. -
connectivity
IndexedLagGraph connectivity
The indexed connectivity "snapshot" of the lag graph. -
decayRate
double decayRate
The rate at which expression levels for a gene tend to return to basal level. -
errorDistributions
Distribution[] errorDistributions
Error distributions from which errors are drawn for each of the factors. -
lowerBound
double lowerBound
The lower bound for expression levels. Expression levels that wander below this bound will be set to this bound.
-
-
Class edu.cmu.tetrad.study.gene.tetrad.gene.history.DishModel
class DishModel extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
dishBumps
double[] dishBumps
An array of dish bumps for each dish. -
dishBumpStDev
double dishBumpStDev
The standard deviation of the normal distribution from which dish bump values are drawn, in percent. The distribution has a mean of 100%. -
dishNumber
int dishNumber
The number of the getModel dish.
-
-
Class edu.cmu.tetrad.study.gene.tetrad.gene.history.GeneHistory
class GeneHistory extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
dishModel
DishModel dishModel
A model of the differences in expression levels due to the particular dish a sample is taken from. -
historyArray
double[][] historyArray
A history of time slices of values for each factor, extending back as far as is necessary for the update function to be applied properly (that is, from maxlag up to 0, the getModel time step). Note that the firs subscript is the time slice, whereas the second subscript is the expression level for each gene. -
initializer
Initializer initializer
The initializer for the history. -
initSync
boolean initSync
Indicates whether initialization should be synchronized or not. If it's synchronized, then the same (or almost the same) set of initial random values are used each time the initialize() method is called. Otherwise, a new set of random values is chosen each time. Note that this is a "first pass" attempt at "shocking" the simulated cells. -
step
int step
The getModel time step, which is the number of steps after the initialization period. In other words, time step 0 is the first update step after the initialization, or the first step at which the Glass updating function has been applied. (Markov process.) -
syncInitialization
double[][] syncInitialization
A stored copy of the initial values for the history array, to be used if synchronized initialization is desired. If synchonized initialization is selected, then on the first pass through the initialization method, this array is calculated, and for each individual simulated, the history array for that individual is initialized using values from this array. -
updateFunction
UpdateFunction updateFunction
The update function for the history. -
updatePeriods
int[] updatePeriods
To simulate asynchronous updating, update periods for each factor are allowed to be different. (Note: this was a brilliant idea somebody had a long time ago that has never yet been used. jdramsey 2/22/02)
-
-
Class edu.cmu.tetrad.study.gene.tetrad.gene.history.IndexedConnectivity
class IndexedConnectivity extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
factors
List<String> factors
The factors in the graph, in the order that they are used. -
parents
IndexedParent[][] parents
The graph that this "snapshot" of indexedConnectivity was taken from.
-
-
Class edu.cmu.tetrad.study.gene.tetrad.gene.history.IndexedLagGraph
class IndexedLagGraph extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
factors
List<String> factors
The factors in the graph, in the order that they are used. -
parents
IndexedParent[][] parents
The graph that this "snapshot" of indexedLagGraph was taken from.
-
-
Class edu.cmu.tetrad.study.gene.tetrad.gene.history.IndexedParent
class IndexedParent extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
index
int index
The index of the parent. -
lag
int lag
The lag of the parent.
-
-
Class edu.cmu.tetrad.study.gene.tetrad.gene.history.LaggedEdge
class LaggedEdge extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
factor
String factor
The name of the factor. -
laggedFactor
LaggedFactor laggedFactor
The lagged factor.
-
-
Class edu.cmu.tetrad.study.gene.tetrad.gene.history.LaggedFactor
class LaggedFactor extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.- Parameters:
s- anObjectInputStreamobject- Throws:
IOException- if any.ClassNotFoundException- if any.
-
-
Serialized Fields
-
factor
String factor
The name of the factor. -
lag
int lag
The number of time steps back for the lagged factor.
-
-
Class edu.cmu.tetrad.study.gene.tetrad.gene.history.LinearFunction
class LinearFunction extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.- Parameters:
s- anObjectInputStreamobject- Throws:
IOException- if any.ClassNotFoundException- if any.
-
-
Serialized Fields
-
polynomialFunction
PolynomialFunction polynomialFunction
The wrapped polynomial function that's doing all the work.
-
-
Class edu.cmu.tetrad.study.gene.tetrad.gene.history.Polynomial
class Polynomial extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
terms
List<PolynomialTerm> terms
The terms of the polynomial.
-
-
Class edu.cmu.tetrad.study.gene.tetrad.gene.history.PolynomialFunction
class PolynomialFunction extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.- Parameters:
s- The input stream from which this object is being deserialized.- Throws:
IOException- If any.ClassNotFoundException- If any.
-
-
Serialized Fields
-
connectivity
IndexedLagGraph connectivity
The "snapshot" indexed connectivity of the initial lag graph. -
errorDistributions
Distribution[] errorDistributions
Error distributions from which errors are drawn for each of the factors. -
polynomials
Polynomial[] polynomials
The polynomials of each factor given its parents.
-
-
Class edu.cmu.tetrad.study.gene.tetrad.gene.history.PolynomialTerm
class PolynomialTerm extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
coefficient
double coefficient
The coefficient of the term. -
variables
int[] variables
The variables of the term.
-
-
-
Package edu.cmu.tetrad.study.gene.tetrad.gene.simulation
-
Class edu.cmu.tetrad.study.gene.tetrad.gene.simulation.MeasurementSimulator
class MeasurementSimulator extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
cellNumber
int cellNumber
The cellNumber variable represents the number of a cell. It is a private integer variable with an initial value of -1. -
dishNumber
int dishNumber
The dishNumber variable stores the number of a dish. It is an integer value and is initially set to -1. -
history
GeneHistory history
The history that will be used to simulate the data. -
measuredData
double[][][] measuredData
Array variable to store measured data.This variable is a 3-dimensional array of type double to store measured data. It is used to store data collected from various measures or experiments. The first dimension represents the measure index, the second dimension represents the sample index within the measure, and the third dimension represents the data value.
The structure of the array is as follows:
- The first dimension represents the measure index, ranging from 0 to n-1.
- The second dimension represents the sample index within the measure, ranging from 0 to m-1.
- The third dimension represents the data value, ranging from 0 to k-1.
The data values in the array are of type double, allowing for the storage of decimal values. The array dimensions and size may vary based on the specific application and requirements.
Access to this variable is restricted to the private scope to ensure encapsulation and proper data management.
Usage example: measuredData[1][2][3]
-
parameters
Parameters parameters
The parameters for this simulation. -
rawData
double[][][] rawData
This variable stores raw data in a three-dimensional array.The first dimension represents the rows in the data.
The second dimension represents the columns in the data.
The third dimension represents additional dimensions for the data, which can be used for organizing multidimensional data.
The values stored in this array are of type double.
Access to this variable is private, meaning it can only be accessed from within the class it is declared in.
Modifying this variable should be done with caution, as it contains sensitive raw data.
-
timeSteps
int[] timeSteps
Represents an array of time steps.This variable is used to store an array of integers representing different time steps.
-
-
-
Package edu.cmu.tetrad.study.gene.tetradapp.model
-
Class edu.cmu.tetrad.study.gene.tetradapp.model.GenePm
class GenePm extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
lagGraph
LagGraph lagGraph
The wrapped lag workbench.
-
-
Class edu.cmu.tetrad.study.gene.tetradapp.model.MeasurementSimulatorParams
class MeasurementSimulatorParams extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
includeDishAndChipVariables
boolean includeDishAndChipVariables
Whether to include dish and chip variables in the simulation. -
simulator
MeasurementSimulator simulator
The wrapped measurement simulator.
-
-
-
Package edu.cmu.tetrad.util
-
Class edu.cmu.tetrad.util.DefaultTetradLoggerConfig
class DefaultTetradLoggerConfig extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
active
Set<String> active
The event ids that are currently active. -
events
List<TetradLoggerConfig.Event> events
The events that are supported.
-
-
Class edu.cmu.tetrad.util.DefaultTetradLoggerConfig.DefaultEvent
class DefaultEvent extends Object implements Serializable- serialVersionUID:
- 23L
-
Class edu.cmu.tetrad.util.Matrix
class Matrix extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
apacheData
org.apache.commons.math3.linear.RealMatrix apacheData
The Apache math3 matrix. -
m
int m
The number of rows. -
n
int n
The number of columns.
-
-
Class edu.cmu.tetrad.util.Parameters
class Parameters extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
Class edu.cmu.tetrad.util.PartialCorrelationPdf
class PartialCorrelationPdf extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
constant
double constant
The aggregate value of the constant expression in the distribution function for zero partial correlation. -
k
int k
Number of compared variables--that is, 2 + (#conditioning variables). -
n
int n
Number of data points in the sample. -
outsideExp
double outsideExp
The power to which the variable expression is raised in the distribution function for zero partial correlation.
-
-
Class edu.cmu.tetrad.util.PointXy
class PointXy extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
x
int x
The x coordinate. -
y
int y
The y coordinate.
-
-
Class edu.cmu.tetrad.util.TetradLogger.EmptyConfig
class EmptyConfig extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
active
boolean active
Represents the activation status of an event in the logger configuration.
-
-
Class edu.cmu.tetrad.util.TetradLoggerEvent
class TetradLoggerEvent extends EventObject implements Serializable-
Serialized Fields
-
config
TetradLoggerConfig config
The config associated with the event, may be null.
-
-
-
Class edu.cmu.tetrad.util.Vector
class Vector extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
data
org.apache.commons.math3.linear.RealVector data
The data.
-
-
Class edu.cmu.tetrad.util.Version
class Version extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
incrementalRelease
int incrementalRelease
The incremental release number. In release a.b.c-d, d. This number increases without bound until the next major version, minor version, or minor subversion release, at which point is goes back to zero. If it is zero, release a.b.c.dx may be referred to as a.b.c.With maven snapshots the incremental release number refers to the snapshot build date. If this field is SNAPSHOT it is set to max int
Range greater than or equal to 0. -
majorVersion
int majorVersion
The major version number. In release a.b.c-d, a. At time of creating this class, it's 4, and the minor version is 3. This should increase only for truly substantial and essentially complete new releases of Tetrad.Range greater than or equal to 0. -
minorSubversion
int minorSubversion
The minor release number. In release a.b.c-d, c. This number increases without bound until the next major or minor release, at which point it goes back to zero.Range greater than or equal to 0. -
minorVersion
int minorVersion
The minor version number. In release a.b.c-d, b. This number increases without bound until the next major release, at which point it goes back to zero.Range greater than or equal to 0.
-
-
-
Package edu.cmu.tetrad.util.dist
-
Class edu.cmu.tetrad.util.dist.Beta
class Beta extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
alpha
double alpha
Ibid. -
beta
double beta
Ibid.
-
-
Class edu.cmu.tetrad.util.dist.ChiSquare
class ChiSquare extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
df
double df
The stored degrees of freedom. Needed because the wrapped distribution does not provide getters for its parameters.
-
-
Class edu.cmu.tetrad.util.dist.Discrete
class Discrete extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
p
double[] p
The probabilities of the different values.
-
-
Class edu.cmu.tetrad.util.dist.Exponential
class Exponential extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
lambda
double lambda
The rate parameter.
-
-
Class edu.cmu.tetrad.util.dist.Gamma
class Gamma extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
alpha
double alpha
The shape parameter. -
lambda
double lambda
The rate parameter.
-
-
Class edu.cmu.tetrad.util.dist.GaussianPower
class GaussianPower extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
name
String name
The name. -
power
double power
The power. -
sd
double sd
The standard deviation of the Gaussian distribution.
-
-
Class edu.cmu.tetrad.util.dist.Indicator
class Indicator extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
p
double p
The probability of returning 1.
-
-
Class edu.cmu.tetrad.util.dist.LogNormal
class LogNormal extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
sd
double sd
The standard deviation.
-
-
Class edu.cmu.tetrad.util.dist.MixtureOfGaussians
class MixtureOfGaussians extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
a
double a
The mixing parameter. -
mean1
double mean1
The mean of the first Gaussian. -
mean2
double mean2
The mean of the second Gaussian. -
sd1
double sd1
The standard deviation of the first Gaussian. -
sd2
double sd2
The standard deviation of the second Gaussian.
-
-
Class edu.cmu.tetrad.util.dist.Normal
class Normal extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
mean
double mean
The mean of the distribution. -
sd
double sd
The standard deviation of the distribution.
-
-
Class edu.cmu.tetrad.util.dist.Poisson
class Poisson extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
mean
double mean
The mean of the Poisson distribution.
-
-
Class edu.cmu.tetrad.util.dist.SingleValue
class SingleValue extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialized Fields
-
value
double value
Represents a single value in a statistical distribution.
-
-
Class edu.cmu.tetrad.util.dist.Split
class Split extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
a
double a
Represents the variable 'a' in the Split distribution. -
b
double b
A private variable representing the value of `b`.
-
-
Class edu.cmu.tetrad.util.dist.TruncatedNormal
class TruncatedNormal extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
high
double high
The standard devision of the distribution. -
low
double low
The standard devision of the distribution. -
mean
double mean
The mean of the distribution. -
sd
double sd
The standard devision of the distribution.
-
-
Class edu.cmu.tetrad.util.dist.Uniform
class Uniform extends Object implements Serializable- serialVersionUID:
- 23L
-
Serialization Methods
-
readObject
Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.- Parameters:
in- The ObjectInputStream to read the object from.- Throws:
IOException- If an I/O error occurs.ClassNotFoundException- If the class of the serialized object cannot be found.
-
writeObject
Writes the object to the specified ObjectOutputStream.- Parameters:
out- The ObjectOutputStream to write the object to.- Throws:
IOException- If an I/O error occurs.
-
-
Serialized Fields
-
a
double a
The lower bound of the range from which numbers are drawn uniformly. -
b
double b
The upper bound of the range from which numbers are drawn uniformly.
-
-
-
Package edu.pitt.isp.sverchkov.data
-
Class edu.pitt.isp.sverchkov.data.AdTree
class AdTree extends edu.pitt.isp.sverchkov.data.AdTreeHelper implements Serializable-
Serialized Fields
-
-
Class edu.pitt.isp.sverchkov.data.AdTreeHelper.CountNode
class CountNode extends Object implements Serializable-
Serialized Fields
-
attr
int attr
The attribute of this node. -
count
int count
The number of instances in the data set. -
vary
edu.pitt.isp.sverchkov.data.AdTreeHelper.VaryNode[] vary
The children of this node.
-
-
-
Class edu.pitt.isp.sverchkov.data.AdTreeHelper.VaryNode
class VaryNode extends Object implements Serializable-
Serialized Fields
-
mcv
int mcv
The most common value of the attribute. -
values
edu.pitt.isp.sverchkov.data.AdTreeHelper.CountNode[] values
The values of the attribute.
-
-
-