Uses of Interface
edu.cmu.tetrad.data.DataModel

Packages that use DataModel

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.independence
edu.cmu.tetrad.algcomparison.score
edu.cmu.tetrad.algcomparison.simulation
edu.cmu.tetrad.algcomparison.statistic
edu.cmu.tetrad.bayes
edu.cmu.tetrad.data
edu.cmu.tetrad.data.simulation
edu.cmu.tetrad.search	Contains classes for searching for (mostly structural) causal models given data.
edu.cmu.tetrad.search.score	Contains classes for various 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.util
edu.pitt.dbmi.algo.resampling.task

Uses of DataModel in edu.cmu.tetrad.algcomparison

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

Modifier and Type	Method	Description
static String	CompareTwoGraphs.getStatsListTable(Graph trueGraph, Graph targetGraph, DataModel dataModel)	Returns a string representing a table of statistics that can be printed.

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

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

Modifier and Type	Method	Description
abstract long	ExternalAlgorithm.getElapsedTime(DataModel dataSet, Parameters parameters)
int	ExternalAlgorithm.getIndex(DataModel dataSet)
Graph	Algorithm.search(DataModel dataSet, Parameters parameters)	Runs the search.
Graph	FirstInflection.search(DataModel dataSet, Parameters parameters)
Graph	StabilitySelection.search(DataModel dataSet, Parameters parameters)
Graph	StARS.search(DataModel dataSet, Parameters parameters)

Method parameters in edu.cmu.tetrad.algcomparison.algorithm with type arguments of type DataModel

Modifier and Type	Method	Description
Graph	MultiDataSetAlgorithm.search(List<DataModel> dataSets, Parameters parameters)	Runs the search.

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

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

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

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

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

Modifier and Type	Method	Description
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)

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

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

Modifier and Type	Method	Description
long	ExternalAlgorithmBnlearnMmhc.getElapsedTime(DataModel dataSet, Parameters parameters)
long	ExternalAlgorithmBNTPc.getElapsedTime(DataModel dataSet, Parameters parameters)
long	ExternalAlgorithmIntersection.getElapsedTime(DataModel dataSet, Parameters parameters)
long	ExternalAlgorithmPcalgGes.getElapsedTime(DataModel dataSet, Parameters parameters)
long	ExternalAlgorithmPcalgPc.getElapsedTime(DataModel dataSet, Parameters parameters)
long	ExternalAlgorithmTetrad.getElapsedTime(DataModel dataSet, Parameters parameters)
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.

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

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

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

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

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

Modifier and Type	Method	Description
Graph	Fask.search(DataModel dataSet, Parameters parameters)
Graph	FaskConcatenated.search(DataModel dataSet, Parameters parameters)
Graph	FaskLofsConcatenated.search(DataModel dataSet, Parameters parameters)
Graph	FaskVote.search(DataModel dataSet, Parameters parameters)
Graph	FasLofs.search(DataModel dataSet, Parameters parameters)
Graph	FciIod.search(DataModel dataSet, Parameters parameters)
Graph	FgesConcatenated.search(DataModel dataSet, Parameters parameters)
Graph	Images.search(DataModel dataSet, Parameters parameters)

Method parameters in edu.cmu.tetrad.algcomparison.algorithm.multi with type arguments of type DataModel

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

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

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

Modifier and Type	Method	Description
Graph	Boss.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	PcLingam.search(DataModel dataModel, 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)

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

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

Modifier and Type	Method	Description
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)

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

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

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

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

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

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

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

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

Modifier and Type	Method	Description
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)

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

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

Modifier and Type	Method	Description
IndependenceTest	BdeuTest.getTest(DataModel dataSet, Parameters parameters)	Returns the test.
IndependenceTest	CciTest.getTest(DataModel dataSet, Parameters parameters)
IndependenceTest	ChiSquare.getTest(DataModel dataSet, Parameters parameters)
IndependenceTest	ConditionalGaussianLRT.getTest(DataModel dataSet, Parameters parameters)
IndependenceTest	DegenerateGaussianLRT.getTest(DataModel dataSet, Parameters parameters)
IndependenceTest	DiscreteBicTest.getTest(DataModel dataSet, Parameters parameters)
IndependenceTest	FisherZ.getTest(DataModel dataSet, Parameters parameters)
IndependenceTest	GICScoreTests.getTest(DataModel dataSet, Parameters parameters)
IndependenceTest	Gsquare.getTest(DataModel dataSet, Parameters parameters)
IndependenceTest	IndependenceWrapper.getTest(DataModel dataSet, Parameters parameters)	Returns true iff x and y are independent conditional on z for the given data set.
IndependenceTest	Kci.getTest(DataModel dataSet, Parameters parameters)
IndependenceTest	MagSemBicTest.getTest(DataModel dataSet, Parameters parameters)
IndependenceTest	Mnlrlrt.getTest(DataModel dataSet, Parameters parameters)
IndependenceTest	MSeparationTest.getTest(DataModel dataSet, Parameters parameters)
IndependenceTest	MultinomialLogisticRegressionWald.getTest(DataModel dataSet, Parameters parameters)
IndependenceTest	Mvplrt.getTest(DataModel dataSet, Parameters parameters)
IndependenceTest	PoissonScoreTest.getTest(DataModel dataSet, Parameters parameters)
IndependenceTest	PositiveCorr.getTest(DataModel dataSet, Parameters parameters)
IndependenceTest	ProbabilisticTest.getTest(DataModel dataSet, Parameters parameters)
IndependenceTest	SemBicDTest.getTest(DataModel dataSet, Parameters parameters)
IndependenceTest	SemBicTest.getTest(DataModel dataSet, Parameters parameters)
IndependenceTest	UniformScatterTest.getTest(DataModel dataSet, Parameters parameters)

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

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

Modifier and Type	Method	Description
Score	BdeuScore.getScore(DataModel dataSet, Parameters parameters)
Score	CciScore.getScore(DataModel dataSet, Parameters parameters)
Score	ConditionalGaussianBicScore.getScore(DataModel dataSet, Parameters parameters)
Score	DegenerateGaussianBicScore.getScore(DataModel dataSet, Parameters parameters)
Score	DiscreteBicScore.getScore(DataModel dataSet, Parameters parameters)
Score	EbicScore.getScore(DataModel dataSet, Parameters parameters)
Score	FisherZScore.getScore(DataModel dataSet, Parameters parameters)
Score	GicScores.getScore(DataModel dataSet, Parameters parameters)
Score	MagSemBicScore.getScore(DataModel dataSet, Parameters parameters)
Score	MSeparationScore.getScore(DataModel dataSet, Parameters parameters)
Score	MVPBicScore.getScore(DataModel dataSet, Parameters parameters)
Score	PoissonPriorScore.getScore(DataModel dataSet, Parameters parameters)
Score	PositiveCorrScore.getScore(DataModel dataSet, Parameters parameters)
Score	ScoreWrapper.getScore(DataModel dataSet, Parameters parameters)	Returns true iff x and y are independent conditional on z for the given data set.
Score	SemBicScore.getScore(DataModel dataSet, Parameters parameters)
Score	SemBicScoreDeterministic.getScore(DataModel dataSet, Parameters parameters)
Score	ZhangShenBoundScore.getScore(DataModel dataSet, Parameters parameters)

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

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

Modifier and Type	Method	Description
DataModel	BayesNetSimulation.getDataModel(int index)	Returns the simulated data set.
DataModel	BooleanGlassSimulation.getDataModel(int index)
DataModel	ConditionalGaussianSimulation.getDataModel(int index)
DataModel	GeneralSemSimulation.getDataModel(int index)
DataModel	GeneralSemSimulationSpecial1.getDataModel(int index)
DataModel	LeeHastieSimulation.getDataModel(int index)
DataModel	LinearFisherModel.getDataModel(int index)
DataModel	LinearSineSimulation.getDataModel(int index)
DataModel	NLSemSimulation.getDataModel(int index)
DataModel	SemSimulation.getDataModel(int index)
DataModel	SemThenDiscretize.getDataModel(int index)
DataModel	Simulation.getDataModel(int index)	Returns the number of data sets to simulate.
DataModel	StandardizedSemSimulation.getDataModel(int index)
DataModel	TimeSeriesSemSimulation.getDataModel(int index)

Constructor parameters in edu.cmu.tetrad.algcomparison.simulation with type arguments of type DataModel

Modifier	Constructor	Description
	LinearFisherModel(RandomGraph graph, List<DataModel> shocks)

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

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

Modifier and Type	Method	Description
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)
double	BicDiffPerRecord.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	BicEst.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
double	BicTrue.getValue(Graph trueGraph, Graph estGraph, DataModel dataModel)
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	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	MarkovAdequacyScore.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	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 DataModel in edu.cmu.tetrad.bayes

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

Modifier	Constructor	Description
	JunctionTreeAlgorithm(Graph graph, DataModel dataModel)

Uses of DataModel in edu.cmu.tetrad.data

Subinterfaces of DataModel in edu.cmu.tetrad.data

Modifier and Type	Interface	Description
interface	DataSet	Implements a rectangular data set, in the sense of being a dataset with a fixed number of columns and a fixed number of rows, the length of each column being constant.
interface	ICovarianceMatrix	Interface for covariance matrices.

Classes in edu.cmu.tetrad.data that implement DataModel

Modifier and Type	Class	Description
final class	BoxDataSet	Wraps a DataBox in such a way that mixed data sets can be stored.
final class	CorrelationMatrix	Stores a correlation matrix together with variable names and sample size; intended as a representation of a data set.
class	CorrelationMatrixOnTheFly	Stores a covariance matrix together with variable names and sample size, intended as a representation of a data set.
class	CovarianceMatrix	Stores a covariance matrix together with variable names and sample size, intended as a representation of a data set.
class	CovarianceMatrixOnTheFly	Stores a covariance matrix together with variable names and sample size, intended as a representation of a data set.
final class	DataModelList	Stores a list of data models and keeps track of which one is selected.
class	IndependenceFacts	Stores a list of independence facts.
final class	NumberObjectDataSet	Wraps a 2D array of Number objects in such a way that mixed data sets can be stored.
final class	TimeSeriesData	Stores time series data as a list of continuous columns.

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

Modifier and Type	Method	Description
DataModel	CorrelationMatrixOnTheFly.copy()
DataModel	CovarianceMatrix.copy()
DataModel	CovarianceMatrixOnTheFly.copy()
DataModel	DataModel.copy()
DataModel	DataModelList.copy()
DataModel	IndependenceFacts.copy()
DataModel	TimeSeriesData.copy()
DataModel	DataModelList.get(int index)
DataModel	DataModelList.getSelectedModel()
DataModel	DataModelList.remove(int index)	Removes the DataModel at the given index.

Methods in edu.cmu.tetrad.data that return types with arguments of type DataModel

Modifier and Type	Method	Description
List<DataModel>	DataModelList.getModelList()

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

Modifier and Type	Method	Description
void	DataModelList.add(int index, DataModel element)	Adds the given DataModel to the list at the given index.
static DataSet	SimpleDataLoader.getContinuousDataSet(DataModel dataSet)	Returns the datamodel case to DataSet if it is continuous.
static ICovarianceMatrix	SimpleDataLoader.getCovarianceMatrix(DataModel dataModel, boolean precomputeCovariances)	Returns the model cast to ICovarianceMatrix if already a covariance matric, or else returns the covariance matrix for a dataset.
static DataSet	SimpleDataLoader.getDiscreteDataSet(DataModel dataSet)	Returns the datamodel case to DataSet if it is discrete.
static DataSet	SimpleDataLoader.getMixedDataSet(DataModel dataSet)	Returns the datamodel case to DataSet if it is mixed.
void	DataModelList.setSelectedModel(DataModel model)

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

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

Modifier and Type	Method	Description
DataModel	LoadContinuousDataAndGraphs.getDataModel(int index)
DataModel	LoadContinuousDataAndSingleGraph.getDataModel(int index)
DataModel	LoadContinuousDataSmithSim.getDataModel(int index)
DataModel	LoadDataAndGraphs.getDataModel(int index)
DataModel	LoadDataFromFileWithoutGraph.getDataModel(int index)

Uses of DataModel in edu.cmu.tetrad.search

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

Modifier and Type	Method	Description
DataModel	IndependenceTest.getData()

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

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

Modifier and Type	Method	Description
DataModel	GraphScore.getData()
DataModel	PoissonPriorScore.getData()
DataModel	SemBicScore.getData()
DataModel	SemBicScore.getDataModel()

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

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.

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

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

Modifier and Type	Method	Description
DataModel	IndTestIndependenceFacts.getData()	Returns the facts supplied in the constructor, which constutite a data model.
DataModel	IndTestProbabilistic.getData()
DataModel	Kci.getData()	Returns The data model for the independence test.
DataModel	ScoreIndTest.getData()

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

Modifier	Constructor	Description
	ScoreIndTest(Score score, DataModel data)

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

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

Modifier	Constructor	Description
	ClusterSignificance(List<Node> variables, DataModel dataModel)

Constructor parameters in edu.cmu.tetrad.search.utils with type arguments of type DataModel

Modifier	Constructor	Description
	ShiftSearch(List<DataModel> dataSets)

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

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

Modifier and Type	Method	Description
DataModel	IndTestUniformScatter.getData()
DataModel	ProbabilisticMapIndependence.getData()

Uses of DataModel in edu.cmu.tetrad.util

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

Modifier and Type	Method	Description
static DataModel	MultidataUtils.combineDataset(List<DataModel> dataModels)
static DataModel	DataConvertUtils.toContinuousDataModel(edu.pitt.dbmi.data.reader.ContinuousData dataset)
static DataModel	DataConvertUtils.toCovarianceMatrix(edu.pitt.dbmi.data.reader.covariance.CovarianceData dataset)
static DataModel	DataConvertUtils.toDataModel(edu.pitt.dbmi.data.reader.Data data)
static DataModel	DataConvertUtils.toDataModel(edu.pitt.dbmi.data.reader.Data data, edu.pitt.dbmi.data.reader.metadata.Metadata metadata)
static DataModel	DataConvertUtils.toMixedDataBox(edu.pitt.dbmi.data.reader.tabular.MixedTabularData dataset)
static DataModel	DataConvertUtils.toMixedDataBox(edu.pitt.dbmi.data.reader.tabular.MixedTabularData dataset, edu.pitt.dbmi.data.reader.metadata.Metadata metadata)	Converting using metadata
static DataModel	DataConvertUtils.toVerticalDiscreteDataModel(edu.pitt.dbmi.data.reader.tabular.VerticalDiscreteTabularData dataset)
static DataModel	DataConvertUtils.toVerticalDiscreteDataModel(edu.pitt.dbmi.data.reader.tabular.VerticalDiscreteTabularData dataset, edu.pitt.dbmi.data.reader.metadata.Metadata metatdata)	Converting using metadata

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

Modifier and Type	Method	Description
static int	MultidataUtils.getNumberOfColumns(DataModel dataModel)

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

Modifier and Type	Method	Description
static void	MultidataUtils.combineContinuousData(List<DataModel> dataModels, double[][] combinedData)
static DataModel	MultidataUtils.combineDataset(List<DataModel> dataModels)
static void	MultidataUtils.combineDiscreteDataToDiscreteVerticalData(List<DataModel> dataModels, List<Node> variables, int[][] combinedData, int numOfRows, int numOfColumns)
static void	MultidataUtils.combineMixedContinuousData(List<DataModel> dataModels, List<Node> variables, double[][] combinedData, int numOfRows, int numOfColumns)
static void	MultidataUtils.combineMixedDiscreteData(List<DataModel> dataModels, List<Node> variables, int[][] combinedData, int numOfRows, int numOfColumns)
static void	MultidataUtils.combineVariables(List<DataModel> dataModels, List<Node> variables)	Combine the list of variables from each of data model in the list into one variable list.
static int[]	MultidataUtils.getRowCounts(List<DataModel> dataModels)

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

Constructors in edu.pitt.dbmi.algo.resampling.task with parameters of type DataModel

Modifier	Constructor	Description
	GeneralResamplingSearchRunnable(DataModel dataModel, Algorithm algorithm, Parameters parameters, GeneralResamplingSearch resamplingAlgorithmSearch, boolean verbose)

Constructor parameters in edu.pitt.dbmi.algo.resampling.task with type arguments of type DataModel

Modifier	Constructor	Description
	GeneralResamplingSearchRunnable(List<DataModel> dataModel, MultiDataSetAlgorithm algorithm, Parameters parameters, GeneralResamplingSearch resamplingAlgorithmSearch, boolean verbose)