Uses of Interface
edu.cmu.tetrad.graph.Graph

Packages that use Graph

Package	Description
edu.cmu.tetrad.algcomparison
edu.cmu.tetrad.algcomparison.algorithm
edu.cmu.tetrad.algcomparison.algorithm.cluster
edu.cmu.tetrad.algcomparison.algorithm.continuous.dag
edu.cmu.tetrad.algcomparison.algorithm.external
edu.cmu.tetrad.algcomparison.algorithm.mixed
edu.cmu.tetrad.algcomparison.algorithm.multi
edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag
edu.cmu.tetrad.algcomparison.algorithm.oracle.pag
edu.cmu.tetrad.algcomparison.algorithm.oracle.pattern
edu.cmu.tetrad.algcomparison.algorithm.other
edu.cmu.tetrad.algcomparison.algorithm.pairwise
edu.cmu.tetrad.algcomparison.comparegraphs
edu.cmu.tetrad.algcomparison.graph
edu.cmu.tetrad.algcomparison.independence
edu.cmu.tetrad.algcomparison.score
edu.cmu.tetrad.algcomparison.simulation
edu.cmu.tetrad.algcomparison.statistic
edu.cmu.tetrad.algcomparison.statistic.utils
edu.cmu.tetrad.bayes
edu.cmu.tetrad.calibration
edu.cmu.tetrad.data
edu.cmu.tetrad.data.simulation
edu.cmu.tetrad.graph
edu.cmu.tetrad.regression
edu.cmu.tetrad.search	Contains classes for searching for (mostly structural) causal models given data.
edu.cmu.tetrad.search.score	Contains classes for various sorts of scores for running score-based algorithms.
edu.cmu.tetrad.search.test	Contains classes for running conditional independence tests for various sorts of data.
edu.cmu.tetrad.search.utils	Contains some utility classes for search algorithms.
edu.cmu.tetrad.search.work_in_progress	Contains some classes that aren't ready for prime time.
edu.cmu.tetrad.sem
edu.cmu.tetrad.simulation
edu.cmu.tetrad.study.performance
edu.cmu.tetrad.util
edu.pitt.csb.mgm
edu.pitt.csb.stability
edu.pitt.dbmi.algo.bayesian.constraint.search
edu.pitt.dbmi.algo.resampling
edu.pitt.dbmi.algo.resampling.task

Uses of Graph in edu.cmu.tetrad.algcomparison

Methods in edu.cmu.tetrad.algcomparison with parameters of type Graph

Modifier and Type	Method	Description
static @NotNull String	CompareTwoGraphs.getEdgewiseComparisonString(Graph trueGraph, Graph targetGraph)	Returns an edgewise comparison of two graphs.
static @NotNull String	CompareTwoGraphs.getMisclassificationTable(Graph trueGraph, Graph targetGraph)	Returns a misclassification comparison of two graphs.
static String	CompareTwoGraphs.getStatsListTable(Graph trueGraph, Graph targetGraph)	Returns a string representing a table of statistics that can be printed.
static String	CompareTwoGraphs.getStatsListTable(Graph trueGraph, Graph targetGraph, DataModel dataModel)	Returns a string representing a table of statistics that can be printed.

Uses of Graph in edu.cmu.tetrad.algcomparison.algorithm

Methods in edu.cmu.tetrad.algcomparison.algorithm that return Graph

Modifier and Type	Method	Description
Graph	Algorithm.getComparisonGraph(Graph graph)	Returns that graph that the result should be compared to.
Graph	FirstInflection.getComparisonGraph(Graph graph)
Graph	StabilitySelection.getComparisonGraph(Graph graph)
Graph	StARS.getComparisonGraph(Graph graph)
Graph	Algorithm.search(DataModel dataSet, Parameters parameters)	Runs the search.
Graph	FirstInflection.search(DataModel dataSet, Parameters parameters)
Graph	MultiDataSetAlgorithm.search(List<DataModel> dataSets, Parameters parameters)	Runs the search.
Graph	StabilitySelection.search(DataModel dataSet, Parameters parameters)
Graph	StARS.search(DataModel dataSet, Parameters parameters)

Methods in edu.cmu.tetrad.algcomparison.algorithm that return types with arguments of type Graph

Modifier and Type	Method	Description
List<Graph>	ReturnsBootstrapGraphs.getBootstrapGraphs()	Returns the bootstrap graphs.

Methods in edu.cmu.tetrad.algcomparison.algorithm with parameters of type Graph

Modifier and Type	Method	Description
static Algorithm	AlgorithmFactory.create(Class<? extends Algorithm> algoClass, IndependenceWrapper test, ScoreWrapper score, Graph externalGraph)	Creates an algorithm.
static Algorithm	AlgorithmFactory.create(Class<? extends Algorithm> algoClass, Class<? extends IndependenceWrapper> indTestClass, Class<? extends ScoreWrapper> scoreClass, Graph externalGraph)	Creates an algorithm.
Graph	Algorithm.getComparisonGraph(Graph graph)	Returns that graph that the result should be compared to.
Graph	FirstInflection.getComparisonGraph(Graph graph)
Graph	StabilitySelection.getComparisonGraph(Graph graph)
Graph	StARS.getComparisonGraph(Graph graph)

Uses of Graph in edu.cmu.tetrad.algcomparison.algorithm.cluster

Methods in edu.cmu.tetrad.algcomparison.algorithm.cluster that return Graph

Modifier and Type	Method	Description
Graph	Bpc.getComparisonGraph(Graph graph)
Graph	Fofc.getComparisonGraph(Graph graph)
Graph	Ftfc.getComparisonGraph(Graph graph)
Graph	Bpc.search(DataModel dataSet, Parameters parameters)
Graph	Fofc.search(DataModel dataSet, Parameters parameters)
Graph	Ftfc.search(DataModel dataSet, Parameters parameters)

Methods in edu.cmu.tetrad.algcomparison.algorithm.cluster with parameters of type Graph

Modifier and Type	Method	Description
Graph	Bpc.getComparisonGraph(Graph graph)
Graph	Fofc.getComparisonGraph(Graph graph)
Graph	Ftfc.getComparisonGraph(Graph graph)

Uses of Graph in edu.cmu.tetrad.algcomparison.algorithm.continuous.dag

Methods in edu.cmu.tetrad.algcomparison.algorithm.continuous.dag that return Graph

Modifier and Type	Method	Description
Graph	Dagma.getComparisonGraph(Graph graph)
Graph	DirectLingam.getComparisonGraph(Graph graph)
Graph	IcaLingam.getComparisonGraph(Graph graph)
Graph	IcaLingD.getComparisonGraph(Graph graph)
Graph	Dagma.search(DataModel dataSet, Parameters parameters)
Graph	DirectLingam.search(DataModel dataSet, Parameters parameters)
Graph	IcaLingam.search(DataModel dataSet, Parameters parameters)
Graph	IcaLingD.search(DataModel dataSet, Parameters parameters)

Methods in edu.cmu.tetrad.algcomparison.algorithm.continuous.dag that return types with arguments of type Graph

Modifier and Type	Method	Description
List<Graph>	Dagma.getBootstrapGraphs()
List<Graph>	DirectLingam.getBootstrapGraphs()
List<Graph>	IcaLingam.getBootstrapGraphs()
List<Graph>	IcaLingD.getBootstrapGraphs()

Methods in edu.cmu.tetrad.algcomparison.algorithm.continuous.dag with parameters of type Graph

Modifier and Type	Method	Description
Graph	Dagma.getComparisonGraph(Graph graph)
Graph	DirectLingam.getComparisonGraph(Graph graph)
Graph	IcaLingam.getComparisonGraph(Graph graph)
Graph	IcaLingD.getComparisonGraph(Graph graph)

Uses of Graph in edu.cmu.tetrad.algcomparison.algorithm.external

Methods in edu.cmu.tetrad.algcomparison.algorithm.external that return Graph

Modifier and Type	Method	Description
Graph	ExternalAlgorithmBnlearnMmhc.getComparisonGraph(Graph graph)	Returns the CPDAG of the supplied DAG.
Graph	ExternalAlgorithmBNTPc.getComparisonGraph(Graph graph)	Returns the CPDAG of the supplied DAG.
Graph	ExternalAlgorithmIntersection.getComparisonGraph(Graph graph)	Returns the CPDAG of the supplied DAG.
Graph	ExternalAlgorithmPcalgGes.getComparisonGraph(Graph graph)	Returns the CPDAG of the supplied DAG.
Graph	ExternalAlgorithmPcalgPc.getComparisonGraph(Graph graph)	Returns the CPDAG of the supplied DAG.
Graph	ExternalAlgorithmTetrad.getComparisonGraph(Graph graph)	Returns the CPDAG of the supplied DAG.
static Graph	ExternalAlgorithmPcalgPc.loadGraphPcAlgMatrix(DataSet dataSet)
Graph	ExternalAlgorithmBnlearnMmhc.search(DataModel dataSet, Parameters parameters)	Reads in the relevant graph from the file (see above) and returns it.
Graph	ExternalAlgorithmBNTPc.search(DataModel dataSet, Parameters parameters)	Reads in the relevant graph from the file (see above) and returns it.
Graph	ExternalAlgorithmIntersection.search(DataModel dataSet, Parameters parameters)	Reads in the relevant graph from the file (see above) and returns it.
Graph	ExternalAlgorithmPcalgGes.search(DataModel dataSet, Parameters parameters)	Reads in the relevant graph from the file (see above) and returns it.
Graph	ExternalAlgorithmPcalgPc.search(DataModel dataSet, Parameters parameters)	Reads in the relevant graph from the file (see above) and returns it.
Graph	ExternalAlgorithmTetrad.search(DataModel dataSet, Parameters parameters)	Reads in the relevant graph from the file and returns it.

Methods in edu.cmu.tetrad.algcomparison.algorithm.external with parameters of type Graph

Modifier and Type	Method	Description
Graph	ExternalAlgorithmBnlearnMmhc.getComparisonGraph(Graph graph)	Returns the CPDAG of the supplied DAG.
Graph	ExternalAlgorithmBNTPc.getComparisonGraph(Graph graph)	Returns the CPDAG of the supplied DAG.
Graph	ExternalAlgorithmIntersection.getComparisonGraph(Graph graph)	Returns the CPDAG of the supplied DAG.
Graph	ExternalAlgorithmPcalgGes.getComparisonGraph(Graph graph)	Returns the CPDAG of the supplied DAG.
Graph	ExternalAlgorithmPcalgPc.getComparisonGraph(Graph graph)	Returns the CPDAG of the supplied DAG.
Graph	ExternalAlgorithmTetrad.getComparisonGraph(Graph graph)	Returns the CPDAG of the supplied DAG.

Uses of Graph in edu.cmu.tetrad.algcomparison.algorithm.mixed

Methods in edu.cmu.tetrad.algcomparison.algorithm.mixed that return Graph

Modifier and Type	Method	Description
Graph	Mgm.getComparisonGraph(Graph graph)
Graph	Mgm.search(DataModel ds, Parameters parameters)

Methods in edu.cmu.tetrad.algcomparison.algorithm.mixed with parameters of type Graph

Modifier and Type	Method	Description
Graph	Mgm.getComparisonGraph(Graph graph)

Uses of Graph in edu.cmu.tetrad.algcomparison.algorithm.multi

Methods in edu.cmu.tetrad.algcomparison.algorithm.multi that return Graph

Modifier and Type	Method	Description
Graph	Fask.getComparisonGraph(Graph graph)
Graph	FaskConcatenated.getComparisonGraph(Graph graph)
Graph	FaskLofsConcatenated.getComparisonGraph(Graph graph)
Graph	FaskVote.getComparisonGraph(Graph graph)
Graph	FasLofs.getComparisonGraph(Graph graph)
Graph	FciIod.getComparisonGraph(Graph graph)
Graph	FgesConcatenated.getComparisonGraph(Graph graph)
Graph	Images.getComparisonGraph(Graph graph)
Graph	ImagesBoss.getComparisonGraph(Graph graph)
Graph	Fask.search(DataModel dataSet, Parameters parameters)
Graph	FaskConcatenated.search(DataModel dataSet, Parameters parameters)
Graph	FaskConcatenated.search(List<DataModel> dataSets, Parameters parameters)
Graph	FaskLofsConcatenated.search(DataModel dataSet, Parameters parameters)
Graph	FaskLofsConcatenated.search(List<DataModel> dataModels, Parameters parameters)
Graph	FaskVote.search(DataModel dataSet, Parameters parameters)
Graph	FaskVote.search(List<DataModel> dataSets, Parameters parameters)
Graph	FasLofs.search(DataModel dataSet, Parameters parameters)
Graph	FciIod.search(DataModel dataSet, Parameters parameters)
Graph	FciIod.search(List<DataModel> dataSets, Parameters parameters)
Graph	FgesConcatenated.search(DataModel dataSet, Parameters parameters)
Graph	FgesConcatenated.search(List<DataModel> dataModels, Parameters parameters)
Graph	Images.search(DataModel dataSet, Parameters parameters)
Graph	Images.search(List<DataModel> dataSets, Parameters parameters)
Graph	ImagesBoss.search(DataModel dataSet, Parameters parameters)
Graph	ImagesBoss.search(List<DataModel> dataSets, Parameters parameters)

Methods in edu.cmu.tetrad.algcomparison.algorithm.multi with parameters of type Graph

Modifier and Type	Method	Description
Graph	Fask.getComparisonGraph(Graph graph)
Graph	FaskConcatenated.getComparisonGraph(Graph graph)
Graph	FaskLofsConcatenated.getComparisonGraph(Graph graph)
Graph	FaskVote.getComparisonGraph(Graph graph)
Graph	FasLofs.getComparisonGraph(Graph graph)
Graph	FciIod.getComparisonGraph(Graph graph)
Graph	FgesConcatenated.getComparisonGraph(Graph graph)
Graph	Images.getComparisonGraph(Graph graph)
Graph	ImagesBoss.getComparisonGraph(Graph graph)

Uses of Graph in edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag

Methods in edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag that return Graph

Modifier and Type	Method	Description
Graph	Boss.getComparisonGraph(Graph graph)
Graph	BossLingam.getComparisonGraph(Graph graph)
Graph	Cpc.getComparisonGraph(Graph graph)
Graph	Fas.getComparisonGraph(Graph graph)
Graph	Fges.getComparisonGraph(Graph graph)
Graph	FgesMb.getComparisonGraph(Graph graph)
Graph	FgesMeasurement.getComparisonGraph(Graph graph)
Graph	GesMe.getComparisonGraph(Graph graph)
Graph	Grasp.getComparisonGraph(Graph graph)
Graph	Pc.getComparisonGraph(Graph graph)
Graph	Pcd.getComparisonGraph(Graph graph)
Graph	PcMb.getComparisonGraph(Graph graph)
Graph	RestrictedBoss.getComparisonGraph(Graph graph)
Graph	SingleGraphAlg.getComparisonGraph(Graph graph)
Graph	Sp.getComparisonGraph(Graph graph)
Graph	Boss.search(DataModel dataModel, Parameters parameters)
Graph	BossLingam.search(DataModel dataModel, Parameters parameters)
Graph	Cpc.search(DataModel dataModel, Parameters parameters)
Graph	Fas.search(DataModel dataSet, Parameters parameters)
Graph	Fges.search(DataModel dataModel, Parameters parameters)
Graph	FgesMb.search(DataModel dataSet, Parameters parameters)
Graph	FgesMeasurement.search(DataModel dataModel, Parameters parameters)
Graph	GesMe.search(DataModel dataSet, Parameters parameters)
Graph	Grasp.search(DataModel dataModel, Parameters parameters)
Graph	Pc.search(DataModel dataModel, Parameters parameters)
Graph	Pcd.search(DataModel dataSet, Parameters parameters)
Graph	PcMb.search(DataModel dataSet, Parameters parameters)
Graph	RestrictedBoss.search(DataModel dataModel, Parameters parameters)
Graph	SingleGraphAlg.search(DataModel dataSet, Parameters parameters)
Graph	Sp.search(DataModel dataModel, Parameters parameters)

Methods in edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag that return types with arguments of type Graph

Modifier and Type	Method	Description
List<Graph>	Boss.getBootstrapGraphs()
List<Graph>	BossLingam.getBootstrapGraphs()
List<Graph>	Cpc.getBootstrapGraphs()
List<Graph>	Fas.getBootstrapGraphs()
List<Graph>	Fges.getBootstrapGraphs()
List<Graph>	FgesMb.getBootstrapGraphs()
List<Graph>	FgesMeasurement.getBootstrapGraphs()
List<Graph>	GesMe.getBootstrapGraphs()
List<Graph>	Grasp.getBootstrapGraphs()
List<Graph>	Pc.getBootstrapGraphs()
List<Graph>	Pcd.getBootstrapGraphs()
List<Graph>	PcMb.getBootstrapGraphs()
List<Graph>	RestrictedBoss.getBootstrapGraphs()
List<Graph>	Sp.getBootstrapGraphs()

Methods in edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag with parameters of type Graph

Modifier and Type	Method	Description
Graph	Boss.getComparisonGraph(Graph graph)
Graph	BossLingam.getComparisonGraph(Graph graph)
Graph	Cpc.getComparisonGraph(Graph graph)
Graph	Fas.getComparisonGraph(Graph graph)
Graph	Fges.getComparisonGraph(Graph graph)
Graph	FgesMb.getComparisonGraph(Graph graph)
Graph	FgesMeasurement.getComparisonGraph(Graph graph)
Graph	GesMe.getComparisonGraph(Graph graph)
Graph	Grasp.getComparisonGraph(Graph graph)
Graph	Pc.getComparisonGraph(Graph graph)
Graph	Pcd.getComparisonGraph(Graph graph)
Graph	PcMb.getComparisonGraph(Graph graph)
Graph	RestrictedBoss.getComparisonGraph(Graph graph)
Graph	SingleGraphAlg.getComparisonGraph(Graph graph)
Graph	Sp.getComparisonGraph(Graph graph)

Constructors in edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag with parameters of type Graph

Modifier	Constructor	Description
	SingleGraphAlg(Graph graph)

Uses of Graph in edu.cmu.tetrad.algcomparison.algorithm.oracle.pag

Methods in edu.cmu.tetrad.algcomparison.algorithm.oracle.pag that return Graph

Modifier and Type	Method	Description
Graph	Bfci.getComparisonGraph(Graph graph)
Graph	Ccd.getComparisonGraph(Graph graph)
Graph	Cfci.getComparisonGraph(Graph graph)
Graph	Fci.getComparisonGraph(Graph graph)
Graph	FciMax.getComparisonGraph(Graph graph)
Graph	Gfci.getComparisonGraph(Graph graph)
Graph	GraspFci.getComparisonGraph(Graph graph)
Graph	PagSampleRfci.getComparisonGraph(Graph graph)
Graph	Rfci.getComparisonGraph(Graph graph)
Graph	RfciBsc.getComparisonGraph(Graph graph)
Graph	SpFci.getComparisonGraph(Graph graph)
Graph	SvarFci.getComparisonGraph(Graph graph)
Graph	SvarGfci.getComparisonGraph(Graph graph)
Graph	Bfci.search(DataModel dataModel, Parameters parameters)
Graph	Ccd.search(DataModel dataSet, Parameters parameters)
Graph	Cfci.search(DataModel dataModel, Parameters parameters)
Graph	Fci.search(DataModel dataModel, Parameters parameters)
Graph	FciMax.search(DataModel dataModel, Parameters parameters)
Graph	Gfci.search(DataModel dataModel, Parameters parameters)
Graph	GraspFci.search(DataModel dataModel, Parameters parameters)
Graph	PagSampleRfci.search(DataModel dataSet, Parameters parameters)
Graph	Rfci.search(DataModel dataModel, Parameters parameters)
Graph	RfciBsc.search(DataModel dataSet, Parameters parameters)
Graph	SpFci.search(DataModel dataModel, Parameters parameters)
Graph	SvarFci.search(DataModel dataModel, Parameters parameters)
Graph	SvarGfci.search(DataModel dataModel, Parameters parameters)

Methods in edu.cmu.tetrad.algcomparison.algorithm.oracle.pag that return types with arguments of type Graph

Modifier and Type	Method	Description
List<Graph>	Bfci.getBootstrapGraphs()
List<Graph>	Ccd.getBootstrapGraphs()
List<Graph>	Cfci.getBootstrapGraphs()
List<Graph>	Fci.getBootstrapGraphs()
List<Graph>	FciMax.getBootstrapGraphs()
List<Graph>	Gfci.getBootstrapGraphs()
List<Graph>	GraspFci.getBootstrapGraphs()
List<Graph>	Rfci.getBootstrapGraphs()
List<Graph>	SpFci.getBootstrapGraphs()
List<Graph>	SvarFci.getBootstrapGraphs()
List<Graph>	SvarGfci.getBootstrapGraphs()

Methods in edu.cmu.tetrad.algcomparison.algorithm.oracle.pag with parameters of type Graph

Modifier and Type	Method	Description
Graph	Bfci.getComparisonGraph(Graph graph)
Graph	Ccd.getComparisonGraph(Graph graph)
Graph	Cfci.getComparisonGraph(Graph graph)
Graph	Fci.getComparisonGraph(Graph graph)
Graph	FciMax.getComparisonGraph(Graph graph)
Graph	Gfci.getComparisonGraph(Graph graph)
Graph	GraspFci.getComparisonGraph(Graph graph)
Graph	PagSampleRfci.getComparisonGraph(Graph graph)
Graph	Rfci.getComparisonGraph(Graph graph)
Graph	RfciBsc.getComparisonGraph(Graph graph)
Graph	SpFci.getComparisonGraph(Graph graph)
Graph	SvarFci.getComparisonGraph(Graph graph)
Graph	SvarGfci.getComparisonGraph(Graph graph)

Uses of Graph in edu.cmu.tetrad.algcomparison.algorithm.oracle.pattern

Methods in edu.cmu.tetrad.algcomparison.algorithm.oracle.pattern that return Graph

Modifier and Type	Method	Description
Graph	Cstar.getComparisonGraph(Graph graph)
Graph	Cstar.search(DataModel dataSet, Parameters parameters)

Methods in edu.cmu.tetrad.algcomparison.algorithm.oracle.pattern with parameters of type Graph

Modifier and Type	Method	Description
Graph	Cstar.getComparisonGraph(Graph graph)

Uses of Graph in edu.cmu.tetrad.algcomparison.algorithm.other

Methods in edu.cmu.tetrad.algcomparison.algorithm.other that return Graph

Modifier and Type	Method	Description
Graph	FactorAnalysis.getComparisonGraph(Graph graph)
Graph	Glasso.getComparisonGraph(Graph graph)
Graph	FactorAnalysis.search(DataModel ds, Parameters parameters)
Graph	Glasso.search(DataModel ds, Parameters parameters)

Methods in edu.cmu.tetrad.algcomparison.algorithm.other with parameters of type Graph

Modifier and Type	Method	Description
Graph	FactorAnalysis.getComparisonGraph(Graph graph)
Graph	Glasso.getComparisonGraph(Graph graph)

Uses of Graph in edu.cmu.tetrad.algcomparison.algorithm.pairwise

Methods in edu.cmu.tetrad.algcomparison.algorithm.pairwise that return Graph

Modifier and Type	Method	Description
Graph	Eb.getComparisonGraph(Graph graph)
Graph	FaskPw.getComparisonGraph(Graph graph)
Graph	R1.getComparisonGraph(Graph graph)
Graph	R2.getComparisonGraph(Graph graph)
Graph	R3.getComparisonGraph(Graph graph)
Graph	Rskew.getComparisonGraph(Graph graph)
Graph	RskewE.getComparisonGraph(Graph graph)
Graph	Skew.getComparisonGraph(Graph graph)
Graph	SkewE.getComparisonGraph(Graph graph)
Graph	Tanh.getComparisonGraph(Graph graph)
Graph	Eb.search(DataModel dataSet, Parameters parameters)
Graph	FaskPw.search(DataModel dataModel, Parameters parameters)
Graph	R1.search(DataModel dataSet, Parameters parameters)
Graph	R2.search(DataModel dataSet, Parameters parameters)
Graph	R3.search(DataModel dataSet, Parameters parameters)
Graph	Rskew.search(DataModel dataSet, Parameters parameters)
Graph	RskewE.search(DataModel dataSet, Parameters parameters)
Graph	Skew.search(DataModel dataSet, Parameters parameters)
Graph	SkewE.search(DataModel dataSet, Parameters parameters)
Graph	Tanh.search(DataModel dataSet, Parameters parameters)

Methods in edu.cmu.tetrad.algcomparison.algorithm.pairwise with parameters of type Graph

Modifier and Type	Method	Description
Graph	Eb.getComparisonGraph(Graph graph)
Graph	FaskPw.getComparisonGraph(Graph graph)
Graph	R1.getComparisonGraph(Graph graph)
Graph	R2.getComparisonGraph(Graph graph)
Graph	R3.getComparisonGraph(Graph graph)
Graph	Rskew.getComparisonGraph(Graph graph)
Graph	RskewE.getComparisonGraph(Graph graph)
Graph	Skew.getComparisonGraph(Graph graph)
Graph	SkewE.getComparisonGraph(Graph graph)
Graph	Tanh.getComparisonGraph(Graph graph)

Uses of Graph in edu.cmu.tetrad.algcomparison.comparegraphs

Constructors in edu.cmu.tetrad.algcomparison.comparegraphs with parameters of type Graph

Modifier	Constructor	Description
	CompareTwoGraphs(Graph target, Graph reference)

Uses of Graph in edu.cmu.tetrad.algcomparison.graph

Methods in edu.cmu.tetrad.algcomparison.graph that return Graph

Modifier and Type	Method	Description
Graph	Cyclic.createGraph(Parameters parameters)
Graph	ErdosRenyi.createGraph(Parameters parameters)
Graph	RandomForward.createGraph(Parameters parameters)
Graph	RandomGraph.createGraph(Parameters parameters)
Graph	RandomSingleFactorMim.createGraph(Parameters parameters)
Graph	RandomTwoFactorMim.createGraph(Parameters parameters)
Graph	ScaleFree.createGraph(Parameters parameters)
Graph	SingleGraph.createGraph(Parameters parameters)

Constructors in edu.cmu.tetrad.algcomparison.graph with parameters of type Graph

Modifier	Constructor	Description
	SingleGraph(Graph graph)

Uses of Graph in edu.cmu.tetrad.algcomparison.independence

Methods in edu.cmu.tetrad.algcomparison.independence with parameters of type Graph

Modifier and Type	Method	Description
void	MSeparationTest.setGraph(Graph graph)
void	TakesGraph.setGraph(Graph graph)

Constructors in edu.cmu.tetrad.algcomparison.independence with parameters of type Graph

Modifier	Constructor	Description
	MSeparationTest(Graph graph)

Uses of Graph in edu.cmu.tetrad.algcomparison.score

Methods in edu.cmu.tetrad.algcomparison.score with parameters of type Graph

Modifier and Type	Method	Description
void	MSeparationScore.setGraph(Graph graph)

Constructors in edu.cmu.tetrad.algcomparison.score with parameters of type Graph

Modifier	Constructor	Description
	MSeparationScore(Graph graph)

Uses of Graph in edu.cmu.tetrad.algcomparison.simulation

Methods in edu.cmu.tetrad.algcomparison.simulation that return Graph

Modifier and Type	Method	Description
Graph	BayesNetSimulation.getTrueGraph(int index)	Returns the true graph.
Graph	BooleanGlassSimulation.getTrueGraph(int index)
Graph	ConditionalGaussianSimulation.getTrueGraph(int index)
Graph	GeneralSemSimulation.getTrueGraph(int index)
Graph	GeneralSemSimulationSpecial1.getTrueGraph(int index)
Graph	LeeHastieSimulation.getTrueGraph(int index)
Graph	LinearFisherModel.getTrueGraph(int index)
Graph	LinearSineSimulation.getTrueGraph(int index)
Graph	NLSemSimulation.getTrueGraph(int index)
Graph	SemSimulation.getTrueGraph(int index)
Graph	SemThenDiscretize.getTrueGraph(int index)
Graph	Simulation.getTrueGraph(int index)	Returns the true graph at the given index.
Graph	StandardizedSemSimulation.getTrueGraph(int index)
Graph	TimeSeriesSemSimulation.getTrueGraph(int index)

Uses of Graph in edu.cmu.tetrad.algcomparison.statistic

Methods in edu.cmu.tetrad.algcomparison.statistic with parameters of type Graph

Modifier and Type	Method	Description
static boolean	CommonAncestorTruePositiveBidirected.existsCommonAncestor(Graph trueGraph, Edge edge)
static boolean	NumCommonMeasuredAncestorBidirected.existsCommonAncestor(Graph trueGraph, Edge edge)
boolean	NumDirectedEdgeNoMeasureAncestors.existsDirectedPathFromTo(Graph graph, Node node1, Node node2)
static boolean	LatentCommonAncestorTruePositiveBidirected.existsLatentCommonAncestor(Graph trueGraph, Edge edge)
double	AdjacencyFn.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)	Returns the value of the statistic, given the true graph and the estimated graph.
double	AdjacencyFp.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	AdjacencyFpr.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)	Returns the value of the statistic, given the true graph and the estimated graph.
double	AdjacencyPrecision.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	AdjacencyRecall.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	AdjacencyTn.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)	Returns the value of the statistic, given the true graph and the estimated graph.
double	AdjacencyTp.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)	Returns the value of the statistic, given the true graph and the estimated graph.
double	AdjacencyTpr.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)	Returns the value of the statistic, given the true graph and the estimated graph.
double	AncestorF1.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)	Calculates the F1 statistic for adjacencies.
double	AncestorPrecision.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)	Calculates the statistic.
double	AncestorRecall.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)	Calculates the statistic.
double	AncestralPrecision.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)	Calculates the statistic.
double	AncestralRecall.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)	Calculates the statistic.
double	ArrowheadFn.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	ArrowheadFp.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	ArrowheadFpr.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	ArrowheadPrecision.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	ArrowheadPrecisionCommonEdges.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	ArrowheadRecall.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	ArrowheadRecallCommonEdges.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	ArrowheadTn.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	ArrowheadTp.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	AverageDegreeEst.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	AverageDegreeTrue.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	BicDiff.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)	Returns the value of the statistic.
double	BicDiffPerRecord.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)	Returns the difference between the true and estimated BIC scores, divided by the sample size.
double	BicEst.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)	Returns the value of the statistic.
double	BicTrue.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)	Returns the value of the statistic.
double	BidirectedEst.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	BidirectedFP.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	BidirectedLatentPrecision.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	BidirectedPrecision.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	BidirectedRecall.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	BidirectedTP.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	BidirectedTrue.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	CommonAncestorFalseNegativeBidirected.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	CommonAncestorFalsePositiveBidirected.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	CommonAncestorTruePositiveBidirected.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	CommonMeasuredAncestorRecallBidirected.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	CorrectSkeleton.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	DefiniteDirectedPathPrecision.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	DefiniteDirectedPathRecall.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	DensityEst.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	DensityTrue.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	ElapsedCpuTime.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	F1Adj.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	F1All.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	F1Arrow.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	FalseNegativesAdjacencies.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	FalsePositiveAdjacencies.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	FBetaAdj.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	FractionDependentUnderAlternative.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	FractionDependentUnderNull.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	GraphExactlyRight.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	LatentCommonAncestorFalseNegativeBidirected.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	LatentCommonAncestorFalsePositiveBidirected.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	LatentCommonAncestorRecallBidirected.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	LatentCommonAncestorTruePositiveBidirected.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	LegalPag.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	MathewsCorrAdj.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	MathewsCorrArrow.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	MaximalityCondition.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	NoAlmostCyclicPathsCondition.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	NoAlmostCyclicPathsInMagCondition.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	NoCyclicPathsCondition.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	NoCyclicPathsInMagCondition.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	NodesInCyclesPrecision.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	NodesInCyclesRecall.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	NonancestorPrecision.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	NonancestorRecall.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	NoSemidirectedF1.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	NoSemidirectedPrecision.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	NoSemidirectedRecall.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	NumAmbiguousTriples.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	NumberOfEdgesEst.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	NumberOfEdgesTrue.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	NumBidirectedBothNonancestorAncestor.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	NumBidirectedEdgesEst.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	NumBidirectedEdgesTrue.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	NumColoredDD.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	NumColoredNL.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	NumColoredPD.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	NumColoredPL.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	NumCommonMeasuredAncestorBidirected.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	NumCompatibleDefiniteDirectedEdgeAncestors.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	NumCompatibleDirectedEdgeConfounded.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	NumCompatibleDirectedEdgeNonAncestors.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	NumCompatibleEdges.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	NumCompatiblePossiblyDirectedEdgeAncestors.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	NumCompatiblePossiblyDirectedEdgeNonAncestors.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	NumCompatibleVisibleAncestors.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	NumCompatibleVisibleNonancestors.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	NumCorrectDDAncestors.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	NumCorrectPDAncestors.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	NumCorrectVisibleAncestors.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	NumDefinitelyDirected.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	NumDefinitelyNotDirectedPaths.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	NumDirectedEdgeAncestors.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	NumDirectedEdgeBnaMeasuredCounfounded.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	NumDirectedEdgeNoMeasureAncestors.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	NumDirectedEdgeNotAncNotRev.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	NumDirectedEdgeReversed.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	NumDirectedEdges.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	NumDirectedEdgeVisible.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	NumDirectedPathsEst.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	NumDirectedPathsTrue.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	NumDirectedShouldBePartiallyDirected.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	NumIncorrectDDAncestors.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	NumIncorrectPDAncestors.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	NumIncorrectVisibleAncestors.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	NumLatentCommonAncestorBidirected.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	NumNondirectedEdges.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	NumParametersEst.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	NumPartiallyOrientedEdges.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	NumPossiblyDirected.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	NumUndirectedEdges.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	NumVisibleEst.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	OrientationPrecision.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	OrientationRecall.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	PagAdjacencyPrecision.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	PagAdjacencyRecall.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	ParameterColumn.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	PercentAmbiguous.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	PercentBidirectedEdges.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	ProportionSemidirectedPathsNotReversedEst.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	ProportionSemidirectedPathsNotReversedTrue.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	PvalueDistanceToAlpha.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	PvalueUniformityUnderNull.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	SemidirectedPathF1.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	SemidirectedPrecision.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	SemidirectedRecall.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	Statistic.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)	Returns the value of this statistic, given the true graph and the estimated graph.
double	StructuralHammingDistance.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	TailPrecision.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	TailRecall.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	TrueDagFalseNegativesArrows.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	TrueDagFalseNegativesTails.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	TrueDagFalsePositiveArrow.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	TrueDagFalsePositiveTails.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	TrueDagPrecisionArrow.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	TrueDagPrecisionTails.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	TrueDagRecallArrows.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	TrueDagRecallTails.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	TrueDagTruePositiveArrow.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	TrueDagTruePositiveDirectedPathNonancestor.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	TrueDagTruePositiveTails.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	TwoCycleFalseNegative.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	TwoCycleFalsePositive.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	TwoCyclePrecision.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	TwoCycleRecall.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	TwoCycleTruePositive.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)

Uses of Graph in edu.cmu.tetrad.algcomparison.statistic.utils

Constructors in edu.cmu.tetrad.algcomparison.statistic.utils with parameters of type Graph

Modifier	Constructor	Description
	AdjacencyConfusion(Graph truth, Graph est)	Constructs a new AdjacencyConfusion object from the given graphs.
	ArrowConfusion(Graph truth, Graph est)	Constructs a new ArrowConfusion object.
	ArrowConfusion(Graph truth, Graph est, boolean truthAdj)	Constructs a new ArrowConfusion object.
	BidirectedConfusion(Graph truth, Graph est)	Constructs a new confusion matrix for bidirected edges.
	OrientationConfusion(Graph truth, Graph est)
	TailConfusion(Graph truth, Graph est)

Uses of Graph in edu.cmu.tetrad.bayes

Methods in edu.cmu.tetrad.bayes that return Graph

Modifier and Type	Method	Description
Graph	BayesIm.getDag()	$Description
Graph	BayesPm.getDag()	Returns the DAG.
Graph	DirichletBayesIm.getDag()
Graph	MlBayesIm.getDag()
Graph	MlBayesImObs.getDag()
Graph	UpdatedBayesIm.getDag()
Graph	ApproximateUpdater.getManipulatedGraph()
Graph	CptInvariantUpdater.getManipulatedGraph()
Graph	Identifiability.getManipulatedGraph()
Graph	JunctionTreeUpdater.getManipulatedGraph()
Graph	ManipulatingBayesUpdater.getManipulatedGraph()	Returns the manipulated graph.
Graph	RowSummingExactUpdater.getManipulatedGraph()
static Graph	GraphTools.moralize(Graph graph)	Create a moral graph.

Methods in edu.cmu.tetrad.bayes that return types with arguments of type Graph

Modifier and Type	Method	Description
static List<Graph>	ModelGenerator.generate(Graph graph)	This method takes an acyclic graph as input and returns a list of graphs each of which is a modification of the original graph with either an edge deleted, added or reversed.

Methods in edu.cmu.tetrad.bayes with parameters of type Graph

Modifier and Type	Method	Description
static void	GraphTools.fillIn(Graph graph, Node[] ordering)	Apply Tarjan and Yannakakis (1984) fill in algorithm for graph triangulation.
static List<Graph>	ModelGenerator.generate(Graph graph)	This method takes an acyclic graph as input and returns a list of graphs each of which is a modification of the original graph with either an edge deleted, added or reversed.
static Map<Node,Set<Node>>	GraphTools.getCliques(Node[] ordering, Graph graph)	Get cliques in a decomposable graph.
BayesProperties.LikelihoodRet	BayesProperties.getLikelihoodRatioP(Graph graph)	Calculates the p-value of the graph with respect to the given data.
static Node[]	GraphTools.getMaximumCardinalityOrdering(Graph graph)	Perform Tarjan and Yannakakis (1984) maximum cardinality search (MCS) to get the maximum cardinality ordering.
static Graph	GraphTools.moralize(Graph graph)	Create a moral graph.
void	EmBayesProperties.setGraph(Graph graph)

Constructors in edu.cmu.tetrad.bayes with parameters of type Graph

Modifier	Constructor	Description
	BayesPm(Graph graph)	Construct a new BayesPm using the given DAG, assigning each variable two values named "value1" and "value2" unless nodes are discrete variables with categories already defined.
	BayesPm(Graph graph, int lowerBound, int upperBound)	Constructs a new BayesPm from the given DAG, assigning each variable a random number of values between lowerBound and upperBound.
	BayesPm(Graph graph, BayesPm oldBayesPm)	Constructs a new BayesPm using a given DAG, using as much information from the old BayesPm as possible.
	BayesPm(Graph graph, BayesPm oldBayesPm, int lowerBound, int upperBound)	Constructs a new BayesPm from the given DAG, using as much information from the old BayesPm as possible.
	EmBayesProperties(DataSet dataSet, Graph graph)
	JunctionTreeAlgorithm(Graph graph, DataModel dataModel)

Uses of Graph in edu.cmu.tetrad.calibration

Methods in edu.cmu.tetrad.calibration that return Graph

Modifier and Type	Method	Description
Graph	DataForCalibrationRfci.learnBNRFCI(DataSet bootstrapSample, int depth, Graph truePag)
Graph	DataForCalibrationRfci.makeDAG(int numVars, double edgesPerNode, int numLatentConfounders)

Methods in edu.cmu.tetrad.calibration with parameters of type Graph

Modifier and Type	Method	Description
Graph	DataForCalibrationRfci.learnBNRFCI(DataSet bootstrapSample, int depth, Graph truePag)

Uses of Graph in edu.cmu.tetrad.data

Methods in edu.cmu.tetrad.data that return Graph

Modifier and Type	Method	Description
Graph	KnowledgeBoxInput.getResultGraph()
Graph	KnowledgeBoxInput.getSourceGraph()
static Graph	DataGraphUtils.randomBifactorModel(int numStructuralNodes, int numStructuralEdges, int numMeasurementsPerLatent, int numLatentMeasuredImpureParents, int numMeasuredMeasuredImpureParents, int numMeasuredMeasuredImpureAssociations)	First a random single factor model is created with the specified number of latent nodes and latent edges, and impurity structure.
static Graph	DataGraphUtils.randomMim(Graph graph, int numMeasurementsPerLatent, int numLatentMeasuredImpureParents, int numMeasuredMeasuredImpureParents, int numMeasuredMeasuredImpureAssociations, boolean arrangeGraph)
static Graph	DataGraphUtils.randomSingleFactorModel(int numStructuralNodes, int numStructuralEdges, int numMeasurementsPerLatent, int numLatentMeasuredImpureParents, int numMeasuredMeasuredImpureParents, int numMeasuredMeasuredImpureAssociations)

Methods in edu.cmu.tetrad.data with parameters of type Graph

Modifier and Type	Method	Description
boolean	Knowledge.isViolatedBy(Graph graph)
static Graph	DataGraphUtils.randomMim(Graph graph, int numMeasurementsPerLatent, int numLatentMeasuredImpureParents, int numMeasuredMeasuredImpureParents, int numMeasuredMeasuredImpureAssociations, boolean arrangeGraph)

Constructors in edu.cmu.tetrad.data with parameters of type Graph

Modifier	Constructor	Description
	IndependenceFacts(Graph graph)

Uses of Graph in edu.cmu.tetrad.data.simulation

Methods in edu.cmu.tetrad.data.simulation that return Graph

Modifier and Type	Method	Description
Graph	LoadContinuousDataAndGraphs.getTrueGraph(int index)
Graph	LoadContinuousDataAndSingleGraph.getTrueGraph(int index)
Graph	LoadContinuousDataSmithSim.getTrueGraph(int index)
Graph	LoadDataAndGraphs.getTrueGraph(int index)
Graph	LoadDataFromFileWithoutGraph.getTrueGraph(int index)
Graph	LoadContinuousDataSmithSim.readGraph(File file)

Uses of Graph in edu.cmu.tetrad.graph

Classes in edu.cmu.tetrad.graph that implement Graph

Modifier and Type	Class	Description
final class	Dag	Represents a directed acyclic graph--that is, a graph containing only directed edges, with no cycles.
class	EdgeListGraph	Stores a graph a list of lists of edges adjacent to each node in the graph, with an additional list storing all of the edges in the graph.
class	LagGraph	Implements a graph allowing nodes in the getModel time lag to have parents taken from previous time lags.
final class	SemGraph	Represents the graphical structure of a structural equation model.
class	TimeLagGraph	Represents a time series graph--that is, a graph with a fixed number S of lags, with edges into initial lags only--that is, into nodes in the first R lags, for some R.

Methods in edu.cmu.tetrad.graph that return Graph

Modifier and Type	Method	Description
static Graph	GraphUtils.bidirectedToUndirected(Graph graph)
static Graph	GraphUtils.completeGraph(Graph graph)
static Graph	GraphUtils.convert(String spec)	Converts a string spec of a graph--for example, "X1-->X2, X1---X3, X2o->X4, X3<->X4" to a Graph.
static Graph	GraphTransforms.cpdagForDag(Graph dag)
static Graph	GraphTransforms.dagFromCpdag(Graph graph)
static Graph	GraphTransforms.dagFromCpdag(Graph graph, Knowledge knowledge)	Returns a DAG from the given CPDAG.
static @NotNull Graph	GraphTransforms.dagToPag(Graph trueGraph)
static Graph	GraphUtils.emptyGraph(int numNodes)
static Graph	GraphUtils.getComparisonGraph(Graph graph, Parameters params)
Graph	RandomGraph.UniformGraphGenerator.getDag()
Graph	RandomGraph.UniformGraphGenerator.getDag(List<Node> nodes)
static Graph	GraphSaveLoadUtils.loadGraph(File file)
static Graph	GraphSaveLoadUtils.loadGraphBNTPcMatrix(List<Node> vars, DataSet dataSet)
static Graph	GraphSaveLoadUtils.loadGraphJson(File file)
static Graph	GraphSaveLoadUtils.loadGraphPcalg(File file)
static Graph	GraphSaveLoadUtils.loadGraphRuben(File file)
static Graph	GraphSaveLoadUtils.loadGraphTxt(File file)
static Graph	GraphSaveLoadUtils.loadRSpecial(File file)
static Graph	GraphUtils.markovBlanketSubgraph(Node target, Graph graph)	Calculates the subgraph over the Markov blanket of a target node in a given DAG, CPDAG, MAG, or PAG.
static Graph	GraphTransforms.pagToMag(Graph pag)
static Graph	GraphSaveLoadUtils.parseGraphXml(nu.xom.Element graphElement, Map<String,Node> nodes)
static Graph	RandomGraph.randomCyclicGraph2(int numNodes, int numEdges, int maxDegree)	Makes a cyclic graph by repeatedly adding cycles of length of 3, 4, or 5 to the graph, then finally adding two cycles.
static Graph	RandomGraph.randomCyclicGraph3(int numNodes, int numEdges, int maxDegree, double probCycle, double probTwoCycle)	Makes a cyclic graph by repeatedly adding cycles of length of 3, 4, or 5 to the graph, then finally adding two cycles.
static Graph	RandomGraph.randomDag(int numNodes, int numLatentConfounders, int maxNumEdges, int maxDegree, int maxIndegree, int maxOutdegree, boolean connected)
static Graph	RandomGraph.randomGraph(int numNodes, int numLatentConfounders, int numEdges, int maxDegree, int maxIndegree, int maxOutdegree, boolean connected)
static Graph	RandomGraph.randomGraph(List<Node> nodes, int numLatentConfounders, int maxNumEdges, int maxDegree, int maxIndegree, int maxOutdegree, boolean connected)	Defaults to random forward graphs.
static Graph	RandomGraph.randomGraphRandomForwardEdges(int numNodes, int numLatentConfounders, int numEdges, int maxDegree, int maxIndegree, int maxOutdegree, boolean connected)
static Graph	RandomGraph.randomGraphRandomForwardEdges(List<Node> nodes, int numLatentConfounders, int numEdges, int maxDegree, int maxIndegree, int maxOutdegree, boolean connected)
static Graph	RandomGraph.randomGraphRandomForwardEdges(List<Node> nodes, int numLatentConfounders, int numEdges, int maxDegree, int maxIndegree, int maxOutdegree, boolean connected, boolean layoutAsCircle)
static Graph	RandomGraph.randomGraphUniform(List<Node> nodes, int numLatentConfounders, int maxNumEdges, int maxDegree, int maxIndegree, int maxOutdegree, boolean connected, int numIterations)
static Graph	RandomGraph.randomScaleFreeGraph(int numNodes, int numLatentConfounders, double alpha, double beta, double delta_in, double delta_out)
static Graph	GraphSaveLoadUtils.readerToGraphJson(Reader reader)
static Graph	GraphSaveLoadUtils.readerToGraphRuben(Reader reader)
static Graph	GraphSaveLoadUtils.readerToGraphTxt(Reader reader)
static Graph	GraphSaveLoadUtils.readerToGraphTxt(String graphString)
static Graph	GraphUtils.removeBidirectedOrientations(Graph estCpdag)
static Graph	GraphUtils.replaceNodes(Graph originalGraph, List<Node> newVariables)	Converts the given graph, originalGraph, to use the new variables (with the same names as the old).
static Graph	GraphUtils.restrictToMeasured(Graph graph)
Graph	Dag.subgraph(List<Node> nodes)
Graph	EdgeListGraph.subgraph(List<Node> nodes)
Graph	Graph.subgraph(List<Node> nodes)	Constructs and returns a subgraph consisting of a given subset of the nodes of this graph together with the edges between them.
Graph	LagGraph.subgraph(List<Node> nodes)
Graph	SemGraph.subgraph(List<Node> nodes)
Graph	TimeLagGraph.subgraph(List<Node> nodes)
static Graph	GraphUtils.trimGraph(List<Node> targets, Graph graph, int trimmingStyle)
static Graph	GraphUtils.undirectedGraph(Graph graph)
static Graph	GraphUtils.undirectedToBidirected(Graph graph)

Methods in edu.cmu.tetrad.graph that return types with arguments of type Graph

Modifier and Type	Method	Description
static List<Graph>	GraphTransforms.generateCpdagDags(Graph cpdag, boolean orientBidirectedEdges)	Generates the list of DAGs in the given cpdag.
static List<Graph>	GraphTransforms.getAllGraphsByDirectingUndirectedEdges(Graph skeleton)
static List<Graph>	GraphTransforms.getDagsInCpdagMeek(Graph cpdag, Knowledge knowledge)

Methods in edu.cmu.tetrad.graph with parameters of type Graph

Modifier and Type	Method	Description
static void	GraphUtils.addForbiddenReverseEdgesForDirectedEdges(Graph graph, Knowledge knowledge)
static void	GraphUtils.addPagColoring(Graph graph)
static void	RandomGraph.addTwoCycles(Graph graph, int numTwoCycles)
boolean	Triple.alongPathIn(Graph graph)
static void	LayoutUtil.arrangeByLayout(Graph graph, HashMap<String,PointXy> layout)
static boolean	LayoutUtil.arrangeBySourceGraph(Graph resultGraph, Graph sourceGraph)	Arranges the nodes in the result graph according to their positions in the source graph.
static Graph	GraphUtils.bidirectedToUndirected(Graph graph)
static void	LayoutUtil.circleLayout(Graph graph)	Arranges the nodes in the graph in a circle.
static Graph	GraphUtils.completeGraph(Graph graph)
static boolean	GraphUtils.containsBidirectedEdge(Graph graph)
static nu.xom.Element	GraphSaveLoadUtils.convertToXml(Graph graph)
static int	GraphUtils.countAdjErrors(Graph graph1, Graph graph2)	Counts the adjacencies that are in graph1 but not in graph2.
static int	GraphUtils.countArrowptErrors(Graph graph1, Graph graph2)	Counts the arrowheads that are in graph1 but not in graph2.
static Graph	GraphTransforms.cpdagForDag(Graph dag)
static Graph	GraphTransforms.dagFromCpdag(Graph graph)
static Graph	GraphTransforms.dagFromCpdag(Graph graph, Knowledge knowledge)	Returns a DAG from the given CPDAG.
static @NotNull Graph	GraphTransforms.dagToPag(Graph trueGraph)
static void	LayoutUtil.defaultLayout(Graph graph)	Arranges the nodes in the graph in a circle if there are 20 or fewer nodes, otherwise arranges them in a square.
static int	GraphUtils.degree(Graph graph)
static Set<Node>	GraphUtils.district(Node x, Graph G)
static int[][]	GraphUtils.edgeMisclassificationCounts(Graph leftGraph, Graph topGraph, boolean print)
static String	MisclassificationUtils.edgeMisclassifications(Graph estGraph, Graph refGraph)
static String	MisclassificationUtils.endpointMisclassification(Graph estGraph, Graph refGraph)
static void	GraphUtils.fciOrientbk(Knowledge knowledge, Graph graph, List<Node> variables)	Orients according to background knowledge
static void	RandomGraph.fixLatents1(int numLatentConfounders, Graph graph)
static void	RandomGraph.fixLatents4(int numLatentConfounders, Graph graph)
static void	LayoutUtil.fruchtermanReingoldLayout(Graph graph)
static List<Graph>	GraphTransforms.generateCpdagDags(Graph cpdag, boolean orientBidirectedEdges)	Generates the list of DAGs in the given cpdag.
static List<Graph>	GraphTransforms.getAllGraphsByDirectingUndirectedEdges(Graph skeleton)
static List<Triple>	GraphUtils.getAmbiguousTriplesFromGraph(Node node, Graph graph)
static Node	GraphUtils.getAssociatedNode(Node errorNode, Graph graph)
static List<Triple>	GraphSaveLoadUtils.getCollidersFromGraph(Node node, Graph graph)
static Graph	GraphUtils.getComparisonGraph(Graph graph, Parameters params)
static List<Graph>	GraphTransforms.getDagsInCpdagMeek(Graph cpdag, Knowledge knowledge)
static int	GraphUtils.getDegree(Graph graph)
static List<Triple>	GraphUtils.getDottedUnderlinedTriplesFromGraph(Node node, Graph graph)
static int	GraphUtils.getIndegree(Graph graph)
static int	GraphUtils.getNumCorrectArrowpts(Graph correct, Graph estimated)
static GraphUtils.TwoCycleErrors	GraphUtils.getTwoCycleErrors(Graph trueGraph, Graph estGraph)
static List<Triple>	GraphUtils.getUnderlinedTriplesFromGraph(Node node, Graph graph)
static void	GraphUtils.gfciExtraEdgeRemovalStep(Graph graph, Graph referenceCpdag, List<Node> nodes, SepsetProducer sepsets)	The extra edge removal step for GFCI.
static void	GraphUtils.gfciR0(Graph graph, Graph referenceCpdag, SepsetProducer sepsets, Knowledge knowledge)
static String	GraphUtils.graphAttributesToText(Graph graph, String title)
static String	GraphUtils.graphEdgesToText(Graph graph, String title)
static String	GraphUtils.graphNodeAttributesToText(Graph graph, String title, char delimiter)
static String	GraphUtils.graphNodesToText(Graph graph, String title, char delimiter)
static String	GraphSaveLoadUtils.graphRMatrixTxt(Graph graph)
static String	GraphSaveLoadUtils.graphToDot(Graph graph)	Converts a graph to a Graphviz .dot file
static void	GraphSaveLoadUtils.graphToDot(Graph graph, File file)
static String	GraphSaveLoadUtils.graphToLavaan(Graph g)
static String	GraphSaveLoadUtils.graphToPcalg(Graph g)
static String	GraphUtils.graphToText(Graph graph, boolean doPagColoring)
static String	GraphSaveLoadUtils.graphToXml(Graph graph)
static boolean	GraphUtils.isClique(Collection<Node> set, Graph graph)
static boolean	GraphUtils.isDag(Graph graph)
boolean	Paths.isSatisfyBackDoorCriterion(Graph graph, Node x, Node y, Set<Node> z)	Check to see if a set of variables Z satisfies the back-door criterion relative to node x and node y.
static void	LayoutUtil.kamadaKawaiLayout(Graph graph, boolean randomlyInitialized, double naturalEdgeLength, double springConstant, double stopEnergy)
static void	LayoutUtil.layoutByCausalOrder(Graph graph)
static LinkedList<Triple>	GraphUtils.listColliderTriples(Graph graph)
static String	GraphSaveLoadUtils.loadGraphRMatrix(Graph graph)
static Set<Node>	GraphUtils.markovBlanket(Node x, Graph G)	Returns a Markov blanket of a node for a DAG, CPDAG, MAG, or PAG.
static Graph	GraphUtils.markovBlanketSubgraph(Node target, Graph graph)	Calculates the subgraph over the Markov blanket of a target node in a given DAG, CPDAG, MAG, or PAG.
static Set<Set<Node>>	GraphUtils.maximalCliques(Graph graph, List<Node> nodes)
static Graph	GraphTransforms.pagToMag(Graph pag)
static String	GraphUtils.pathString(Graph graph, Node... x)
static String	GraphUtils.pathString(Graph graph, List<Node> path)
static String	Triple.pathString(Graph graph, Node x, Node y, Node z)
static Graph	GraphUtils.removeBidirectedOrientations(Graph estCpdag)
static void	GraphUtils.removeNonSkeletonEdges(Graph graph, Knowledge knowledge)
static Graph	GraphUtils.replaceNodes(Graph originalGraph, List<Node> newVariables)	Converts the given graph, originalGraph, to use the new variables (with the same names as the old).
static List<Node>	GraphUtils.replaceNodes(List<Node> originalNodes, Graph graph)	Converts the given list of nodes, originalNodes, to use the replacement nodes for them by the same name in the given graph.
static Graph	GraphUtils.restrictToMeasured(Graph graph)
static PrintWriter	GraphSaveLoadUtils.saveGraph(Graph graph, File file, boolean xml)
static void	LayoutUtil.squareLayout(Graph graph)
void	Dag.transferAttributes(Graph graph)
void	EdgeListGraph.transferAttributes(Graph graph)
void	Graph.transferAttributes(Graph graph)
void	LagGraph.transferAttributes(Graph graph)
void	SemGraph.transferAttributes(Graph graph)
void	TimeLagGraph.transferAttributes(Graph graph)
void	Dag.transferNodesAndEdges(Graph graph)
void	EdgeListGraph.transferNodesAndEdges(Graph graph)	Transfers nodes and edges from one graph to another.
void	Graph.transferNodesAndEdges(Graph graph)	Transfers nodes and edges from one graph to another.
void	LagGraph.transferNodesAndEdges(Graph graph)
void	SemGraph.transferNodesAndEdges(Graph graph)
void	TimeLagGraph.transferNodesAndEdges(Graph graph)
static Graph	GraphUtils.trimGraph(List<Node> targets, Graph graph, int trimmingStyle)
static Graph	GraphUtils.undirectedGraph(Graph graph)
static Graph	GraphUtils.undirectedToBidirected(Graph graph)

Method parameters in edu.cmu.tetrad.graph with type arguments of type Graph

Modifier and Type	Method	Description
static String	GraphUtils.getIntersectionComparisonString(List<Graph> graphs)

Constructors in edu.cmu.tetrad.graph with parameters of type Graph

Modifier	Constructor	Description
	Dag(Graph graph)	Constructs a new directed acyclic graph from the given graph object.
	EdgeListGraph(Graph graph)	Constructs a EdgeListGraph using the nodes and edges of the given graph.
	FruchtermanReingoldLayout(Graph graph)
	KamadaKawaiLayout(Graph graph)
	Paths(Graph graph)
	SemGraph(Graph graph)	Constructs a new SemGraph from the nodes and edges of the given graph.
	Underlines(Graph graph)

Uses of Graph in edu.cmu.tetrad.regression

Methods in edu.cmu.tetrad.regression that return Graph

Modifier and Type	Method	Description
Graph	Regression.getGraph()
Graph	RegressionCovariance.getGraph()
Graph	RegressionDataset.getGraph()

Methods in edu.cmu.tetrad.regression with parameters of type Graph

Modifier and Type	Method	Description
static DataSet	RegressionUtils.residuals(DataSet dataSet, Graph graph)

Uses of Graph in edu.cmu.tetrad.search

Methods in edu.cmu.tetrad.search that return Graph

Modifier and Type	Method	Description
Graph	SvarFges.getAdjacencies()
Graph	SvarFges.getExternalGraph()
Graph	Mimbuild.getFullGraph()	The full graph inferred, including the edges from latents to measures.
Graph	MimbuildTrek.getFullGraph()	The full graph discovered.
Graph	Cpc.getGraph()	The graph that's constructed during the search.
@NotNull Graph	Grasp.getGraph(boolean cpDag)	Returns the graph implied by the discovered permutation.
static Graph	PermutationSearch.getGraph(List<Node> nodes, Map<Node,Set<Node>> parents, boolean cpDag)	Construct a graph given a specification of the parents for each node.
static Graph	PermutationSearch.getGraph(List<Node> nodes, Map<Node,Set<Node>> parents, Knowledge knowledge, boolean cpDag)	Construct a graph given a specification of the parents for each node.
Graph	Cstar.makeGraph(List<Cstar.Record> records)	Makes a graph of the estimated predictors to the effect.
static @NotNull Graph	IcaLingD.makeGraph(Matrix B, List<Node> variables)	Returns a graph given a coefficient matrix and a list of variables.
Graph	Lofs.orient()	Orients the graph and returns the oriented graph.
Graph	PcMb.resultGraph()	Returns the result graph.
Graph	BFci.search()	Does the search and returns a PAG.
Graph	BossLingam.search()	Runs the search and returns the result graph.
Graph	Bpc.search()	Runs the search and returns the graph, or null if there is no model.
Graph	Ccd.search()	The search method assumes that the IndependenceTest provided to the constructor is a conditional independence oracle for the SEM (or Bayes network) which describes the causal structure of the population.
Graph	Cfci.search()	Performs the search and returns the PAG.
Graph	Cpc.search()	Runs CPC starting with a fully connected graph over all the variables in the domain of the independence test.
Graph	Dagma.search()	NEEDS DOCUMENTATION
Graph	DirectLingam.search()	Performs the search.
Graph	Fas.search()	Runs the search and returns the resulting (undirected) graph.
Graph	Fas.search(List<Node> nodes)	Discovers all adjacencies in data.
Graph	Fasd.search()	Discovers all adjacencies in data.
Graph	Fask.search()	Runs the search on the concatenated data, returning a graph, possibly cyclic, possibly with two-cycles.
Graph	Fci.search()	Performs the search.
Graph	FciMax.search()	Performs the search and returns the PAG.
Graph	Fges.search()	Greedy equivalence search: Start from the empty graph, add edges till the model is significant.
Graph	FgesMb.search(List<Node> targets)	Greedy equivalence search: Start from the empty graph, add edges till the model is significant.
Graph	Fofc.search()	Runs the search and returns a graph of clusters with the ir respective latent parents.
Graph	Ftfc.search()	Runs the search and returns a graph of clusters, each of which has two common latent parents.
Graph	GFci.search()	Runs the graph and returns the search PAG.
Graph	GraspFci.search()	Run the search and return s a PAG.
Graph	IGraphSearch.search()	Runs the search and returns a graph.
Graph	Mimbuild.search(List<List<Node>> clustering, List<String> latentNames, ICovarianceMatrix measuresCov)	Does a Mimbuild search.
Graph	MimbuildTrek.search(List<List<Node>> clustering, List<String> latentNames, ICovarianceMatrix measuresCov)	Does the search and returns the graph.
Graph	Pc.search()	Runs PC starting with a complete graph over all nodes of the given conditional independence test, using the given independence test and knowledge and returns the resultant graph.
Graph	Pc.search(IFas fas, Set<Node> nodes)	Runs the search using a particular implementation of the fast adjacency search (FAS), over the given sublist of nodes.
Graph	Pc.search(Set<Node> nodes)	Runs PC starting with a complete graph over the given list of nodes, using the given independence test and knowledge and returns the resultant graph.
Graph	Pcd.search()	Runs PC starting with a complete graph over all nodes of the given conditional independence test, using the given independence test and knowledge and returns the resultant graph.
Graph	Pcd.search(IFas fas, List<Node> nodes)
Graph	Pcd.search(List<Node> nodes)	Runs PC starting with a complete graph over the given list of nodes, using the given independence test and knowledge and returns the resultant graph.
Graph	PcMb.search()	Does the search.
Graph	PcMb.search(List<Node> targets)	Searches for the MB CPDAG for the given targets.
Graph	PermutationSearch.search()	Performe the search and return a CPDAG.
Graph	Rfci.search()	Runs the search and returns the RFCI PAG.
Graph	Rfci.search(IFas fas, List<Node> nodes)	Runs the search and returns the RFCI PAG.
Graph	Rfci.search(List<Node> nodes)	Searches of a specific sublist of nodes.
Graph	SpFci.search()	Runs the search and returns the discovered PAG.
Graph	SvarFas.search()	Discovers all adjacencies in data.
Graph	SvarFci.search()	Runs the search and returns the PAG.
Graph	SvarFci.search(IFas fas)	Runs the search using a particular implementation of FAS.
Graph	SvarFges.search()	Greedy equivalence search: Start from the empty graph, add edges till the model is significant.
Graph	SvarGfci.search()	Runs the search and returns a PAG.

Methods in edu.cmu.tetrad.search with parameters of type Graph

Modifier and Type	Method	Description
static List<Edge>	CheckKnowledge.forbiddenViolations(Graph graph, Knowledge knowledge)	Returns a sorted list of edges that violate the given knowledge.
double	SvarFges.getScore(Graph dag)	Returns the score of the given DAG.
static List<Edge>	CheckKnowledge.requiredViolations(Graph graph, Knowledge knowledge)	Returns a sorted list of edges that are required by knowledge but which do not appear in the graph.
double	Fges.scoreDag(Graph dag)
double	FgesMb.scoreDag(Graph dag)
double	SvarFges.scoreDag(Graph dag)	Scores the given DAG, up to a constant.
void	SvarFges.setAdjacencies(Graph adjacencies)	Sets the set of preset adjacencies for the algorithm; edges not in this adjacencies graph will not be added.
void	Fges.setBoundGraph(Graph boundGraph)	If non-null, edges not adjacent in this graph will not be added.
void	FgesMb.setBoundGraph(Graph boundGraph)	If non-null, edges not adjacent in this graph will not be added.
void	Fasd.setExternalGraph(Graph externalGraph)	Sets the external graph.
void	Fask.setExternalGraph(Graph externalGraph)	Sets the external graph to use.
void	SvarFas.setExternalGraph(Graph externalGraph)	Sets an external graph.
void	SvarFges.setExternalGraph(Graph externalGraph)	Sets the initial graph.
void	Fges.setInitialGraph(Graph initialGraph)
void	FgesMb.setInitialGraph(Graph initialGraph)
void	SvarFges.setTrueGraph(Graph trueGraph)	Sets the true graph, which will result in some edges in output graphs being marked with asterisks.
double	Ida.trueEffect(Node x, Node y, Graph trueDag)	Calculates the true effect of (x, y) given the true DAG (which must be provided).

Constructors in edu.cmu.tetrad.search with parameters of type Graph

Modifier	Constructor	Description
	BossLingam(Graph cpdag, DataSet dataSet)	Constructor.
	Ida(DataSet dataSet, Graph cpdag, List<Node> possibleCauses)	Constructor.
	Lofs(Graph graph, List<DataSet> dataSets)	Constructor.
	MarkovCheck(Graph graph, IndependenceTest independenceTest, ConditioningSetType setType)	Constructor.

Uses of Graph in edu.cmu.tetrad.search.score

Methods in edu.cmu.tetrad.search.score that return Graph

Modifier and Type	Method	Description
Graph	GraphScore.getDag()	Returns a copy of the DAG being searched over.
Graph	ScoredGraph.getGraph()	Returns the graph.

Methods in edu.cmu.tetrad.search.score with parameters of type Graph

Modifier and Type	Method	Description
static double	SemBicScorer.scoreDag(Graph dag, DataModel data, boolean precomputeCovariances)	Scores the given DAG using the given data model, usimg a BIC score.
static double	SemBicScorer.scoreDag(Graph dag, DataModel data, double penaltyDiscount, boolean precomputeCovariances)	Scores the given DAG using the given data model, usimg a BIC score.

Constructors in edu.cmu.tetrad.search.score with parameters of type Graph

Modifier	Constructor	Description
	GraphScore(Graph dag)	Constructs a GraphScore from a DAG.
	ScoredGraph(Graph graph, Double score)	Constructs a scored graph.

Uses of Graph in edu.cmu.tetrad.search.test

Methods in edu.cmu.tetrad.search.test that return Graph

Modifier and Type	Method	Description
Graph	MsepTest.getGraph()	Returns the underlying graph that is being used to calculate d-separation relationships.

Constructors in edu.cmu.tetrad.search.test with parameters of type Graph

Modifier	Constructor	Description
	MsepTest(Graph graph)	Constructor.
	MsepTest(Graph graph, boolean keepLatents)	Constructor.

Uses of Graph in edu.cmu.tetrad.search.utils

Methods in edu.cmu.tetrad.search.utils that return Graph

Modifier and Type	Method	Description
Graph	DagToPag.convert()	This method does the convertion of DAG to PAG.
Graph	TsDagToPag.convert()
static Graph	ClusterUtils.convertSearchGraph(List<int[]> clusters, String[] varNames)	Converts a list of indices into a list of Nodes representing a cluster.
static Graph	Purify.convertSearchGraph(SemGraph input)
Graph	FgesOrienter.getAdjacencies()
Graph	TsUtils.VarResult.getCollapsedVarGraph()
Graph	DagSepsets.getDag()	Returns the DAG being analyzed.
Graph	SepsetsGreedy.getDag()
Graph	FgesOrienter.getExternalGraph()
Graph	TeyssierScorer.getGraph(boolean cpDag)	Returns the DAG build for the current permutation, or its CPDAG.
static Graph	MbUtils.getOneMbDag(Graph mbCpdag)	Returns an example DAG from the given MB CPDAG.
Graph	PossibleMConnectingPath.getPag()
Graph	FciOrient.getTruePag()	The true PAG if available.
Graph	SvarFciOrient.getTruePag()	The true PAG if available.
Graph	TsDagToPag.getTruePag()
Graph	DagInCpcagIterator.next()	Successive calls to this method return successive DAGs in the CPDAG, in a more or less natural enumeration of them in which an arbitrary undirected edge is picked, oriented one way, Meek rules applied, then a remaining unoriented edge is picked, oriented one way, and so on, until a DAG is obtained, and then by backtracking the other orientation of each chosen edge is tried.
Graph	DagIterator.next()	Successive calls to this method return successive DAGs in the CPDAG, in a more or less natural enumeration of them in which an arbitrary undirected edge is picked, oriented one way, Meek rules applied, then a remaining unoriented edge is picked, oriented one way, and so on, until a DAG is obtained, and then by backtracking the other orientation of each chosen edge is tried.
Graph	FciOrient.orient(Graph graph)	Performs final FCI orientation on the given graph.
Graph	SvarFciOrient.orient(Graph graph)
Graph	FgesOrienter.search()	Greedy equivalence search: Start from the empty graph, add edges till model is significant.
Graph	PcCommon.search()	Runs the search and returns the search graph.
Graph	PcCommon.search(List<Node> nodes)	Runs the search over the given list of nodes only, returning the serach graph.
Graph	Purify.search()	****************************************************** SEARCH INTERFACE *******************************************************

Methods in edu.cmu.tetrad.search.utils that return types with arguments of type Graph

Modifier and Type	Method	Description
static List<Graph>	MbUtils.generateMbDags(Graph mbCPDAG, boolean orientBidirectedEdges, IndependenceTest test, int depth, Node target)	Generates the list of MB DAGs consistent with the MB CPDAG returned by the previous search.

Methods in edu.cmu.tetrad.search.utils with parameters of type Graph

Modifier and Type	Method	Description
static void	GraphSearchUtils.arrangeByKnowledgeTiers(Graph graph)
static void	GraphSearchUtils.arrangeByKnowledgeTiers(Graph graph, Knowledge knowledge)
static void	GraphSearchUtils.basicCpdag(Graph graph)	Get a graph and direct only the unshielded colliders.
static void	GraphSearchUtils.basicCpdagRestricted2(Graph graph, Node node)
void	Bes.bes(Graph graph, List<Node> variables)	Runs BES for a graph over the given list of variables
void	BesPermutation.bes(Graph graph, List<Node> order, List<Node> suborder)	Runs BES.
static Clusters	MimUtils.convertToClusters(Graph clusterGraph)
static Clusters	MimUtils.convertToClusters(Graph clusterGraph, List<Node> measuredVariables)	Converts a disconnected multiple indicator model into a set of clusters.
static List<List<Node>>	MimUtils.convertToClusters2(Graph clusterGraph)
void	FciOrient.ddpOrient(Node a, Node b, Node c, Graph graph)	a method to search "back from a" to find a DDP.
void	SvarFciOrient.ddpOrient(Node a, Node b, Node c, Graph graph)	a method to search "back from a" to find a DDP.
boolean	FciOrient.doDdpOrientation(Node d, Node a, Node b, Node c, Graph graph)	Orients the edges inside the definte discriminating path triangle.
void	FciOrient.doFinalOrientation(Graph graph)	Orients the graph according to rules in the graph (FCI step D).
void	SvarFciOrient.doFinalOrientation(Graph graph)	Orients the graph according to rules in the graph (FCI step D).
static boolean	DagToPag.existsInducingPathInto(Node x, Node y, Graph graph)
static boolean	TsDagToPag.existsInducingPathInto(Node x, Node y, Graph graph, Knowledge knowledge)
static boolean	TsDagToPag.existsInducingPathVisitts(Graph graph, Node a, Node b, Node x, Node y, LinkedList<Node> path, Knowledge knowledge)
void	FciOrient.fciOrientbk(Knowledge bk, Graph graph, List<Node> variables)	Orients according to background knowledge
static List<PossibleMConnectingPath>	PossibleMConnectingPath.findMConnectingPaths(Graph pag, Node x, Node y, Collection<Node> z)	Finds all possible D-connection undirectedPaths as sub-graphs of the pag given at construction time from x to y given z.
static List<PossibleMConnectingPath>	PossibleMConnectingPath.findMConnectingPathsOfLength(Graph pag, Node x, Node y, Collection<Node> z, Integer length)	Finds all possible D-connection undirectedPaths as sub-graphs of the pag given at construction time from x to y given z for a particular path length.
static List<Graph>	MbUtils.generateMbDags(Graph mbCPDAG, boolean orientBidirectedEdges, IndependenceTest test, int depth, Node target)	Generates the list of MB DAGs consistent with the MB CPDAG returned by the previous search.
static GraphSearchUtils.CpcTripleType	GraphSearchUtils.getCpcTripleType(Node x, Node y, Node z, IndependenceTest test, int depth, Graph graph)
static String	GraphSearchUtils.getEdgewiseComparisonString(String trueGraphName, Graph trueGraph, String targetGraphName, Graph targetGraph)
static GraphUtils.GraphComparison	GraphSearchUtils.getGraphComparison(Graph trueGraph, Graph targetGraph)	Just counts arrowhead errors--for cyclic edges counts an arrowhead at each node.
static Knowledge	TsUtils.getKnowledge(Graph graph)
static Graph	MbUtils.getOneMbDag(Graph mbCpdag)	Returns an example DAG from the given MB CPDAG.
static Set<Node>	GraphSearchUtils.getReachableNodes(List<Node> initialNodes, LegalPairs legalPairs, List<Node> c, List<Node> d, Graph graph, int maxPathLength)
double	FgesOrienter.getScore(Graph dag)
static List<List<Node>>	FciOrient.getUcCirclePaths(Node n1, Node n2, Graph graph)	Gets a list of every uncovered circle path between two nodes in the graph by iterating through the uncovered partially directed undirectedPaths and only keeping the circle undirectedPaths.
static List<List<Node>>	FciOrient.getUcPdPaths(Node n1, Node n2, Graph graph)	Gets a list of every uncovered partially directed path between two nodes in the graph.
static int[][]	GraphSearchUtils.graphComparison(Graph trueCpdag, Graph estCpdag, PrintStream out)
static boolean	GraphInPag.graphInPagStep0(Graph pag, Graph dag)	This method implements step (1) of the definition.
static boolean	GraphInPag.graphInPagStep1(Graph pag, Graph dag)
static boolean	GraphInPag.graphInPagStep2(Graph pag, Graph dag)
static boolean	GraphInPag.graphInPagStep3(Graph pag, Graph dag)
static boolean	GraphInPag.graphInPagStep4(Graph pag, Graph dag)
static boolean	GraphInPag.graphInPagStep5(Graph pag, Graph dag)
static TimeLagGraph	TsUtils.graphToLagGraph(Graph _graph, int numLags)
static boolean	FciOrient.isArrowheadAllowed(Node x, Node y, Graph graph, Knowledge knowledge)
static GraphSearchUtils.LegalPagRet	GraphSearchUtils.isLegalPag(Graph pag)
static boolean	GraphSearchUtils.isPdag(Graph graph)	Returns true just in case the given graph is a CPDAG.
static Clusters	ClusterUtils.mimClusters(Graph mim)	Converts a list of indices into a list of Nodes representing a cluster.
Graph	FciOrient.orient(Graph graph)	Performs final FCI orientation on the given graph.
void	FgesOrienter.orient(Graph graph)
void	MaxP.orient(Graph graph)	Adds colliders to the given graph using the max P rule.
Graph	SvarFciOrient.orient(Graph graph)
static void	PcCommon.orientCollider(Node x, Node y, Node z, PcCommon.ConflictRule conflictRule, Graph graph)	Orient a single unshielded triple, x*-*y*-*z, in a graph.
static void	GraphSearchUtils.orientCollidersUsingSepsets(SepsetMap set, Knowledge knowledge, Graph graph, boolean verbose, boolean enforceCpdag)	Step C of PC; orients colliders using specified sepset.
Set<Node>	MeekRules.orientImplied(Graph graph)	Uses the Meek rules to do as many orientations in the given graph as possible.
void	FciOrient.orientTailPath(List<Node> path, Graph graph)	Orients every edge on a path as undirected (i.e.
static void	GraphSearchUtils.pcdOrientC(IndependenceTest test, Knowledge knowledge, Graph graph)	Performs step C of the algorithm, as indicated on page xxx of CPS, with the modification that X--W--Y is oriented as X-->W<--Y if W is *determined by* the sepset of (X, Y), rather than W just being *in* the sepset of (X, Y).
static void	GraphSearchUtils.pcOrientbk(Knowledge bk, Graph graph, List<Node> nodes)	Orients according to background knowledge.
void	FciOrient.ruleR0(Graph graph)	Orients colliders in the graph.
void	SvarFciOrient.ruleR0(Graph graph)	Orients colliders in the graph.
void	FciOrient.ruleR1(Node a, Node b, Node c, Graph graph)
void	FciOrient.ruleR10(Node a, Node c, Graph graph)	Tries to apply Zhang's rule R10 to a pair of nodes A and C which are assumed to be such that Ao->C.
void	FciOrient.ruleR2(Node a, Node b, Node c, Graph graph)
void	FciOrient.ruleR3(Graph graph)	Implements the double-triangle orientation rule, which states that if D*-oB, A*->B<-*C and A*-oDo-*C, and !adj(a, c), D*-oB, then D*->B.
void	SvarFciOrient.ruleR3(Graph graph)	Implements the double-triangle orientation rule, which states that if D*-oB, A*->B<-*C and A*-oDo-*C, then D*->B.
void	FciOrient.ruleR4B(Graph graph)	The triangles that must be oriented this way (won't be done by another rule) all look like the ones below, where the dots are a collider path from L to A with each node on the path (except L) a parent of C.
void	SvarFciOrient.ruleR4B(Graph graph)	The triangles that must be oriented this way (won't be done by another rule) all look like the ones below, where the dots are a collider path from L to A with each node on the path (except L) a parent of C.
void	FciOrient.ruleR5(Graph graph)	Implements Zhang's rule R5, orient circle undirectedPaths: for any Ao-oB, if there is an uncovered circle path u = [A,C,...,D,B] such that A,D nonadjacent and B,C nonadjacent, then A---B and orient every edge on u undirected.
void	SvarFciOrient.ruleR5(Graph graph)	Implements Zhang's rule R5, orient circle undirectedPaths: for any Ao-oB, if there is an uncovered circle path u = [A,C,...,D,B] such that A,D nonadjacent and B,C nonadjacent, then A---B and orient every edge on u undirected.
void	FciOrient.ruleR6R7(Graph graph)	Implements Zhang's rules R6 and R7, applies them over the graph once.
void	SvarFciOrient.ruleR6R7(Graph graph)	Implements Zhang's rules R6 and R7, applies them over the graph once.
boolean	FciOrient.ruleR8(Node a, Node c, Graph graph)	Tries to apply Zhang's rule R8 to a pair of nodes A and C which are assumed to be such that Ao->C.
boolean	FciOrient.ruleR9(Node a, Node c, Graph graph)	Tries to apply Zhang's rule R9 to a pair of nodes A and C which are assumed to be such that Ao->C.
void	FciOrient.rulesR1R2cycle(Graph graph)
void	SvarFciOrient.rulesR1R2cycle(Graph graph)
void	FciOrient.rulesR8R9R10(Graph graph)	Implements Zhang's rules R8, R9, R10, applies them over the graph once.
void	SvarFciOrient.rulesR8R9R10(Graph graph)	Implements Zhang's rules R8, R9, R10, applies them over the graph once.
double	DagScorer.scoreDag(Graph dag)
double	FgesOrienter.scoreDag(Graph dag)	Scores the given DAG, up to a constant.
void	FgesOrienter.setAdjacencies(Graph adjacencies)	Sets the set of preset adjacenies for the algorithm; edges not in this adjacencies graph will not be added.
void	FgesOrienter.setExternalGraph(Graph externalGraph)	Sets the initial graph.
void	FgesOrienter.setTrueGraph(Graph trueGraph)	If the true graph is set, askterisks will be printed in log output for the true edges.
void	IPurify.setTrueGraph(Graph mim)
void	PurifyScoreBased.setTrueGraph(Graph mim)
void	PurifyTetradBased.setTrueGraph(Graph mim)
void	FciOrient.setTruePag(Graph truePag)	Sets the true PAG for comparison.
void	SvarFciOrient.setTruePag(Graph truePag)
void	TsDagToPag.setTruePag(Graph truePag)
void	FciOrient.spirtesFinalOrientation(Graph graph)
static void	LogUtilsSearch.stampWithBic(Graph graph, DataModel dataModel)
static void	LogUtilsSearch.stampWithScore(Graph graph, Score score)
static int	GraphSearchUtils.structuralHammingDistance(Graph trueGraph, Graph estGraph)	Tsamardinos, I., Brown, L.
static void	MbUtils.trimEdgesAmongParents(Graph graph, Node target)	Removes edges among the parents of the target.
static void	MbUtils.trimEdgesAmongParentsOfChildren(Graph graph, Node target)	Removes edges among the parents of children of the target.
static void	MbUtils.trimToAdjacents(Graph graph, Node target)	Trims the graph to just the adjacents of the target.
static void	MbUtils.trimToMbNodes(Graph graph, Node target, boolean includeBidirected)	Trims the graph to the target, the parents and children of the target, and the parents of the children of the target.
void	FciOrient.zhangFinalOrientation(Graph graph)

Constructors in edu.cmu.tetrad.search.utils with parameters of type Graph

Modifier	Constructor	Description
	DagInCpcagIterator(Graph CPDAG)	The given CPDAG must be a CPDAG.
	DagInCpcagIterator(Graph CPDAG, Knowledge knowledge)	The given CPDAG must be a CPDAG.
	DagInCpcagIterator(Graph CPDAG, Knowledge knowledge, boolean allowArbitraryOrientations, boolean allowNewColliders)	The given CPDAG must be a CPDAG.
	DagIterator(Graph CPDAG)	The given CPDAG must be a CPDAG.
	DagSepsets(Graph dag)	Constructs a new DagSepsets object for the given DAG.
	DagToPag(Graph dag)	Constructs a new FCI search for the given independence test and background knowledge.
	PossibleMsepFci(Graph graph, IndependenceTest test)	Creates a new SepSet and assumes that none of the variables have yet been checked.
	SepsetsConservative(Graph graph, IndependenceTest independenceTest, SepsetMap extraSepsets, int depth)
	SepsetsGreedy(Graph graph, IndependenceTest independenceTest, SepsetMap extraSepsets, int depth, Knowledge knowledge)
	SepsetsPossibleMsep(Graph graph, IndependenceTest test, Knowledge knowledge, int depth, int maxPathLength)
	TsDagToPag(Graph dag)	Constructs a new FCI search for the given independence test and background knowledge.
	VarResult(DataSet dataSet, Graph collapsedVarGraph)

Uses of Graph in edu.cmu.tetrad.search.work_in_progress

Methods in edu.cmu.tetrad.search.work_in_progress that return Graph

Modifier and Type	Method	Description
Graph	GraphChange.applyTo(Graph graph)	Outputs a new PAG, a copy of the input excepting the applied changes of this object.
@NotNull Graph	GraspTol.getGraph(boolean cpDag)
Graph	HbsmsBeam.getGraph()
Graph	HbsmsGes.getGraph()
Graph	HbsmsGes.GraphWithPValue.getGraph()
@NotNull Graph	OtherPermAlgs.getGraph(boolean cpDag)
Graph	SampleVcpc.getGraph()	The graph that's constructed during the search.
Graph	SampleVcpcFast.getGraph()	The graph that's constructed during the search.
Graph	VcPc.getGraph()	The graph that's constructed during the search.
Graph	VcPcAlt.getGraph()	The graph that's constructed during the search.
Graph	VcPcFast.getGraph()	The graph that's constructed during the search.
Graph	MagSemBicScore.getMag()	Returns the wrapped MAG.
Graph	DMSearch.LatentStructure.latentStructToEdgeListGraph(DMSearch.LatentStructure structure)
Graph	HbsmsBeam.removeZeroEdges(Graph bestGraph)
Graph	BpcTetradPurifyWashdown.search()	Runs the search and returns a graph.
Graph	DMSearch.search()
Graph	FasFdr.search()	Discovers all adjacencies in data.
Graph	FaskVote.search(Parameters parameters)	Does the search.
Graph	FasLofs.search()	Runs the search on the concatenated data, returning a graph, possibly cyclic, possibly with two-cycles.
Graph	Hbsms.search()
Graph	HbsmsBeam.search()
Graph	HbsmsGes.search()
Graph	InverseCorrelation.search()
Graph	Kpc.search()	Runs PC starting with a complete graph over all nodes of the given conditional independence test, using the given independence test and knowledge and returns the resultant graph.
Graph	Kpc.search(List<Node> nodes)	Runs PC starting with a commplete graph over the given list of nodes, using the given independence test and knowledge and returns the resultant graph.
Graph	Mmhc.search()	Runs PC starting with a fully connected graph over all of the variables in the domain of the independence test.
Graph	SampleVcpc.search()
Graph	SampleVcpcFast.search()
Graph	VcFas.search()	Discovers all adjacencies in data.
Graph	VcPc.search()
Graph	VcPcAlt.search()
Graph	VcPcFast.search()
Graph	Washdown.search()	Runs the Washdown algorithm and return a graph.

Methods in edu.cmu.tetrad.search.work_in_progress that return types with arguments of type Graph

Modifier and Type	Method	Description
List<Graph>	Dci.search()	Begins the DCI search procedure, described at each step
List<Graph>	Ion.search()	Runs the ION search and returns a list of compatible graphs.

Methods in edu.cmu.tetrad.search.work_in_progress with parameters of type Graph

Modifier and Type	Method	Description
DMSearch.LatentStructure	DMSearch.applyDmSearch(Graph pattern, Set<String> inputString, double penalty)
Graph	GraphChange.applyTo(Graph graph)	Outputs a new PAG, a copy of the input excepting the applied changes of this object.
static void	SampleVcpc.futureNodeVisit(Graph graph, Node b, LinkedList<Node> path, Set<Node> futureNodes)
static void	SampleVcpcFast.futureNodeVisit(Graph graph, Node b, LinkedList<Node> path, Set<Node> futureNodes)
static void	VcPc.futureNodeVisit(Graph graph, Node b, LinkedList<Node> path, Set<Node> futureNodes)
static void	VcPcAlt.futureNodeVisit(Graph graph, Node b, LinkedList<Node> path, Set<Node> futureNodes)
static void	VcPcFast.futureNodeVisit(Graph graph, Node b, LinkedList<Node> path, Set<Node> futureNodes)
VcPc.CpcTripleType	VcPc.getPopulationTripleType(Node x, Node y, Node z, IndependenceTest test, int depth, Graph graph, boolean verbose)
VcPcFast.CpcTripleType	VcPcFast.getPopulationTripleType(Node x, Node y, Node z, IndependenceTest test, int depth, Graph graph, boolean verbose)
Graph	HbsmsBeam.removeZeroEdges(Graph bestGraph)
HbsmsGes.Score	HbsmsGes.scoreDag(Graph dag)
HbsmsBeam.Score	HbsmsBeam.scoreGraph(Graph graph)
HbsmsGes.Score	HbsmsGes.scoreGraph(Graph graph)
void	VcFas.setExternalGraph(Graph externalGraph)
void	SampleVcpc.setGraph(Graph graph)
void	SampleVcpcFast.setGraph(Graph graph)
void	VcPc.setGraph(Graph graph)
void	VcPcAlt.setGraph(Graph graph)
void	VcPcFast.setGraph(Graph graph)
void	MagSemBicScore.setMag(Graph mag)	Sets the MAG to wrap.
static List<List<Node>>	Ion.treks(Graph graph, Node node1, Node node2)

Constructors in edu.cmu.tetrad.search.work_in_progress with parameters of type Graph

Modifier	Constructor	Description
	FasDci(Graph graph, IndependenceTest independenceTest)	Constructs a new FastAdjacencySearch for DCI.
	FasDci(Graph graph, IndependenceTest independenceTest, ResolveSepsets.Method method, List<Set<Node>> marginalVars, List<IndependenceTest> independenceTests, SepsetMapDci knownIndependencies, SepsetMapDci knownAssociations)	Constructs a new FastAdjacencySearch for DCI with independence test pooling to resolve inconsistencies.
	GraphWithPValue(Graph graph, double pValue)
	HbsmsBeam(Graph graph, CovarianceMatrix cov, Knowledge knowledge)
	HbsmsBeam(Graph graph, DataSet data, Knowledge knowledge)
	HbsmsGes(Graph graph, DataSet data)

Constructor parameters in edu.cmu.tetrad.search.work_in_progress with type arguments of type Graph

Modifier	Constructor	Description
	Ion(List<Graph> pags)	Constructs a new instance of the ION search from the input PAGs

Uses of Graph in edu.cmu.tetrad.sem

Methods in edu.cmu.tetrad.sem that return Graph

Modifier and Type	Method	Description
Graph	LargeScaleSimulation.getGraph()
Graph	SemUpdater.getManipulatedGraph()

Methods in edu.cmu.tetrad.sem with parameters of type Graph

Modifier and Type	Method	Description
List<List<Node>>	Ricf.cliques(Graph graph)
Knowledge	LargeScaleSimulation.getKnowledge(Graph graph)
static List<Node>	ReidentifyVariables.getLatents(Graph graph)
static List<String>	ReidentifyVariables.reidentifyVariables1(List<List<Node>> partition, Graph trueGraph)
static List<String>	ReidentifyVariables.reidentifyVariables2(List<List<Node>> clusters, Graph trueGraph, DataSet data)
Ricf.RicfResult	Ricf.ricf2(Graph mag, ICovarianceMatrix covMatrix, double tolerance)	same as above but takes a Graph instead of a SemGraph
double	DagScorer.score(Graph dag)	Runs the estimator on the data and SemPm passed in through the constructor.
double	Scorer.score(Graph dag)

Constructors in edu.cmu.tetrad.sem with parameters of type Graph

Modifier	Constructor	Description
	GeneralizedSemPm(Graph graph)	Constructs a BayesPm from the given Graph, which must be convertible first into a ProtoSemGraph and then into a SemGraph.
	LargeScaleSimulation(Graph graph)
	LargeScaleSimulation(Graph graph, List<Node> nodes, int[] tierIndices)
	SemPm(Graph graph)	Constructs a BayesPm from the given Graph, which must be convertible first into a ProtoSemGraph and then into a SemGraph.

Uses of Graph in edu.cmu.tetrad.simulation

Methods in edu.cmu.tetrad.simulation that return Graph

Modifier and Type	Method	Description
static Graph	HsimUtils.evalEdges(Graph inputgraph, Set<Node> simnodes, Set<Node> realnodes)
static Graph	HsimUtils.mkRandSEMDAG(int numVars, int numEdges)

Methods in edu.cmu.tetrad.simulation with parameters of type Graph

Modifier and Type	Method	Description
List<Double>	Gdistance.distances(Graph graph1, Graph graph2)
static double[]	HsimUtils.errorEval(Graph estCPDAG, Graph truePattern)
static Graph	HsimUtils.evalEdges(Graph inputgraph, Set<Node> simnodes, Set<Node> realnodes)
static Set<Node>	HsimUtils.getAllParents(Graph inputgraph, Set<Node> inputnodes)

Uses of Graph in edu.cmu.tetrad.study.performance

Methods in edu.cmu.tetrad.study.performance that return Graph

Modifier and Type	Method	Description
Graph	ComparisonResult.getCorrectResult()
Graph	ComparisonResult.getResultGraph()
Graph	ComparisonResult.getTrueDag()

Methods in edu.cmu.tetrad.study.performance with parameters of type Graph

Modifier and Type	Method	Description
static String	PerformanceTests.endpointMisclassification(List<Node> _nodes, Graph estGraph, Graph refGraph)
static Knowledge	Comparison2.getKnowledge(Graph graph)
void	ComparisonResult.setCorrectResult(Graph correctResult)
void	ComparisonResult.setResultGraph(Graph graph)
void	ComparisonResult.setTrueDag(Graph trueDag)

Uses of Graph in edu.cmu.tetrad.util

Methods in edu.cmu.tetrad.util that return Graph

Modifier and Type	Method	Description
static Graph	GraphSampling.createDisplayGraph(Graph graph, ResamplingEdgeEnsemble ensemble)	Create a graph for displaying and print out.
static Graph	GraphSampling.createGraphWithHighProbabilityEdges(List<Graph> graphs)	Combine all the edges from the list of graphs onto one graph with the edge type that has the highest frequency probability.
static Graph	GraphSampling.createGraphWithHighProbabilityEdges(List<Graph> graphs, ResamplingEdgeEnsemble ensemble)
static Graph	GraphSampling.createGraphWithoutNullEdges(Graph graph)	Create a graph from the given graph that contains no null edges.
static Graph	JsonUtils.parseJSONObjectToTetradGraph(String jsonResponse)
static Graph	JsonUtils.parseJSONObjectToTetradGraph(org.json.JSONObject jObj)

Methods in edu.cmu.tetrad.util with parameters of type Graph

Modifier and Type	Method	Description
static Graph	GraphSampling.createDisplayGraph(Graph graph, ResamplingEdgeEnsemble ensemble)	Create a graph for displaying and print out.
static Graph	GraphSampling.createGraphWithoutNullEdges(Graph graph)	Create a graph from the given graph that contains no null edges.
static Set<Edge>	JsonUtils.parseJSONArrayToTetradEdges(Graph graph, org.json.JSONArray jArray)
static Edge	JsonUtils.parseJSONObjectToTetradEdge(Graph graph, org.json.JSONObject jObj)

Method parameters in edu.cmu.tetrad.util with type arguments of type Graph

Modifier and Type	Method	Description
static Graph	GraphSampling.createGraphWithHighProbabilityEdges(List<Graph> graphs)	Combine all the edges from the list of graphs onto one graph with the edge type that has the highest frequency probability.
static Graph	GraphSampling.createGraphWithHighProbabilityEdges(List<Graph> graphs, ResamplingEdgeEnsemble ensemble)
static Set<edu.cmu.tetrad.util.GraphSampling.NodePair>	GraphSampling.getEdgeNodePairs(List<Graph> graphs)

Uses of Graph in edu.pitt.csb.mgm

Methods in edu.pitt.csb.mgm that return Graph

Modifier and Type	Method	Description
Graph	Mgm.graphFromMGM()	Converts MGM object to Graph object with edges if edge parameters are non-zero.
static Graph	MixedUtils.makeMixedGraph(Graph g, Map<String,Integer> m)
Graph	Mgm.search()	Simple search command for GraphSearch implementation.

Methods in edu.pitt.csb.mgm with parameters of type Graph

Modifier and Type	Method	Description
static int[][]	MixedUtils.allEdgeStats(Graph pT, Graph pE)
static int[][]	MixedUtils.allEdgeStats(Graph pT, Graph pE, HashMap<String,String> nodeDists)
static GeneralizedSemPm	MixedUtils.GaussianCategoricalPm(Graph trueGraph, String paramTemplate)
static GeneralizedSemPm	MixedUtils.GaussianTrinaryPm(Graph trueGraph, HashMap<String,String> nodeDists, int maxSample, String paramTemplate)
static Map<String,Integer>	MixedUtils.getNodeDists(Graph g)
static cern.colt.matrix.DoubleMatrix2D	MixedUtils.graphToMatrix(Graph graph)
static cern.colt.matrix.DoubleMatrix2D	MixedUtils.graphToMatrix(Graph graph, double undirectedWeight, double directedWeight)
static Graph	MixedUtils.makeMixedGraph(Graph g, Map<String,Integer> m)
static cern.colt.matrix.DoubleMatrix2D	MixedUtils.skeletonToMatrix(Graph graph)

Uses of Graph in edu.pitt.csb.stability

Methods in edu.pitt.csb.stability that return Graph

Modifier and Type	Method	Description
abstract Graph	DataGraphSearch.search(DataSet data)
Graph	SearchWrappers.FgesWrapper.search(DataSet ds)
Graph	SearchWrappers.MGMWrapper.search(DataSet ds)
Graph	SearchWrappers.PcStableWrapper.search(DataSet ds)

Uses of Graph in edu.pitt.dbmi.algo.bayesian.constraint.search

Methods in edu.pitt.dbmi.algo.bayesian.constraint.search that return Graph

Modifier and Type	Method	Description
Graph	RfciBsc.getGraphRBD()	Returns the graph that was learned using the BSC-D method.
Graph	RfciBsc.getGraphRBI()	Returns the graph that was learned using the BSC-I method.
Graph	PagSamplingRfci.search()	Search for a PAG.
Graph	RfciBsc.search()	Performs the search.

Uses of Graph in edu.pitt.dbmi.algo.resampling

Methods in edu.pitt.dbmi.algo.resampling that return Graph

Modifier and Type	Method	Description
Graph	GeneralResamplingTest.search()	Runs the resampling test.

Methods in edu.pitt.dbmi.algo.resampling that return types with arguments of type Graph

Modifier and Type	Method	Description
List<Graph>	GeneralResamplingTest.getGraphs()	Returns the individual bootstrap result graphs.
List<Graph>	GeneralResamplingSearch.search()	Performs the search.

Methods in edu.pitt.dbmi.algo.resampling with parameters of type Graph

Modifier and Type	Method	Description
static int[][]	GeneralResamplingTest.getAdjConfusionMatrix(Graph truth, Graph estimate)	Constructor.
static int[][]	GeneralResamplingTest.getEdgeTypeConfusionMatrix(Graph truth, Graph estimate)	Constructor.
void	GeneralResamplingSearch.setExternalGraph(Graph externalGraph)	Sets the external graph.
void	GeneralResamplingTest.setExternalGraph(Graph externalGraph)	Sets the initial graph.

Uses of Graph in edu.pitt.dbmi.algo.resampling.task

Methods in edu.pitt.dbmi.algo.resampling.task that return Graph

Modifier and Type	Method	Description
Graph	GeneralResamplingSearchRunnable.call()
Graph	GeneralResamplingSearchRunnable.getExternalGraph()

Methods in edu.pitt.dbmi.algo.resampling.task with parameters of type Graph

Modifier and Type	Method	Description
void	GeneralResamplingSearchRunnable.setExternalGraph(Graph externalGraph)