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

Packages that use ICovarianceMatrix

Package	Description
edu.cmu.tetrad.data
edu.cmu.tetrad.regression
edu.cmu.tetrad.search
edu.cmu.tetrad.sem
edu.pitt.csb.mgm

Uses of ICovarianceMatrix in edu.cmu.tetrad.data

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

Modifier and Type	Class	Description
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.

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

Modifier and Type	Method	Description
static ICovarianceMatrix	DataUtils.covarianceNonparanormalDrton(DataSet dataSet)
static @NotNull ICovarianceMatrix	SimpleDataLoader.getCorrelationMatrix(DataSet dataSet)
static ICovarianceMatrix	SimpleDataLoader.getCovarianceMatrix(DataModel dataModel)	Returns the model cast to ICovarianceMatrix if already a covariance matric, or else returns the covariance matrix for a dataset.
static @NotNull ICovarianceMatrix	SimpleDataLoader.getCovarianceMatrix(DataSet dataSet)
final ICovarianceMatrix	CorrelationMatrixOnTheFly.getSubmatrix(int[] indices)
final ICovarianceMatrix	CorrelationMatrixOnTheFly.getSubmatrix(List<String> submatrixVarNames)
final ICovarianceMatrix	CovarianceMatrix.getSubmatrix(int[] indices)
final ICovarianceMatrix	CovarianceMatrix.getSubmatrix(List<String> submatrixVarNames)
final ICovarianceMatrix	CovarianceMatrixOnTheFly.getSubmatrix(int[] indices)
final ICovarianceMatrix	CovarianceMatrixOnTheFly.getSubmatrix(int[] indices, int[] dataRows)
final ICovarianceMatrix	CovarianceMatrixOnTheFly.getSubmatrix(List<String> submatrixVarNames)
ICovarianceMatrix	ICovarianceMatrix.getSubmatrix(int[] indices)
ICovarianceMatrix	ICovarianceMatrix.getSubmatrix(String[] submatrixVarNames)
ICovarianceMatrix	ICovarianceMatrix.getSubmatrix(List<String> submatrixVarNames)
static ICovarianceMatrix	SimpleDataLoader.loadCovarianceMatrix(char[] chars, String commentMarker, DelimiterType delimiterType, char quoteChar, String missingValueMarker)	Parses a covariance matrix from a char[] array.
static ICovarianceMatrix	SimpleDataLoader.loadCovarianceMatrix(File file, String commentMarker, DelimiterType delimiter, char quoteCharacter, String missingValueMarker)	Parses the given files for a tabular data set, returning a RectangularDataSet if successful.
static ICovarianceMatrix	CorrelationMatrixOnTheFly.serializableInstance()	Generates a simple exemplar of this class to test serialization.
static ICovarianceMatrix	CovarianceMatrix.serializableInstance()	Generates a simple exemplar of this class to test serialization.
static ICovarianceMatrix	CovarianceMatrixOnTheFly.serializableInstance()	Generates a simple exemplar of this class to test serialization.

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

Modifier and Type	Method	Description
static double	DataUtils.getEss(ICovarianceMatrix covariances)	Returns the equivalent sample size, assuming all units are equally correlated and all unit variances are equal.
static Matrix	DataUtils.subMatrix(ICovarianceMatrix m, Node x, Node y, List<Node> z)
static Matrix	DataUtils.subMatrix(ICovarianceMatrix m, Map<Node,Integer> indexMap, Node x, Node y, List<Node> z)
static void	DataWriter.writeCovMatrix(ICovarianceMatrix covMatrix, PrintWriter out, NumberFormat nf)	Writes the lower triangle of a covariance matrix to file.

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

Modifier	Constructor	Description
	CorrelationMatrix(ICovarianceMatrix matrix)	Constructs a new correlation matrix using the covariances in the given covariance matrix.
	CorrelationMatrixOnTheFly(ICovarianceMatrix cov)	Constructs a new covariance matrix from the given data set.
	CovarianceMatrix(ICovarianceMatrix covMatrix)

Uses of ICovarianceMatrix in edu.cmu.tetrad.regression

Constructors in edu.cmu.tetrad.regression with parameters of type ICovarianceMatrix

Modifier	Constructor	Description
	RegressionCovariance(ICovarianceMatrix covariances)	Constructs a covariance-based regression model using the given covariance matrix, assuming that no means are specified.

Uses of ICovarianceMatrix in edu.cmu.tetrad.search

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

Modifier and Type	Method	Description
ICovarianceMatrix	IndependenceTest.getCov()
ICovarianceMatrix	IndTestChiSquare.getCov()
ICovarianceMatrix	IndTestCodec.getCov()
ICovarianceMatrix	IndTestConditionalCorrelation.getCov()
ICovarianceMatrix	IndTestConditionalCorrelationLingam.getCov()
ICovarianceMatrix	IndTestConditionalGaussianLRT.getCov()
ICovarianceMatrix	IndTestCramerT.getCov()
ICovarianceMatrix	IndTestDegenerateGaussianLRT.getCov()
ICovarianceMatrix	IndTestDSep.getCov()
ICovarianceMatrix	IndTestFisherZ.getCov()
ICovarianceMatrix	IndTestFisherZConcatenateResiduals.getCov()
ICovarianceMatrix	IndTestFisherZFisherPValue.getCov()
ICovarianceMatrix	IndTestFisherZGeneralizedInverse.getCov()
ICovarianceMatrix	IndTestFisherZPercentIndependent.getCov()
ICovarianceMatrix	IndTestFisherZRecursive.getCov()
ICovarianceMatrix	IndTestGSquare.getCov()
ICovarianceMatrix	IndTestHsic.getCov()
ICovarianceMatrix	IndTestIndependenceFacts.getCov()
ICovarianceMatrix	IndTestMixedMultipleTTest.getCov()
ICovarianceMatrix	IndTestMNLRLRT.getCov()
ICovarianceMatrix	IndTestMulti.getCov()
ICovarianceMatrix	IndTestMultinomialLogisticRegression.getCov()
ICovarianceMatrix	IndTestMVPLRT.getCov()
ICovarianceMatrix	IndTestPositiveCorr.getCov()
ICovarianceMatrix	IndTestProbabilistic.getCov()
ICovarianceMatrix	IndTestRegression.getCov()
ICovarianceMatrix	IndTestScore.getCov()
ICovarianceMatrix	IndTestSepset.getCov()
ICovarianceMatrix	IndTestTeyssier.getCov()
ICovarianceMatrix	IndTestTrekSep.getCov()
ICovarianceMatrix	Kci.getCov()
ICovarianceMatrix	ProbabilisticMAPIndependence.getCov()
ICovarianceMatrix	SampleVcpc.getCov()
ICovarianceMatrix	SampleVcpcFast.getCov()
ICovarianceMatrix	BFci.getCovarianceMatrix()
ICovarianceMatrix	BfciFoo.getCovarianceMatrix()
ICovarianceMatrix	BfciTr.getCovarianceMatrix()
ICovarianceMatrix	BuildPureClusters.getCovarianceMatrix()	Data storage
ICovarianceMatrix	GFci.getCovarianceMatrix()
ICovarianceMatrix	GraspFci.getCovarianceMatrix()
ICovarianceMatrix	SpFci.getCovarianceMatrix()
ICovarianceMatrix	SvarGFci.getCovarianceMatrix()
ICovarianceMatrix	EbicScore.getCovariances()
ICovarianceMatrix	KimEtAlScores.getCovariances()
ICovarianceMatrix	PoissonPriorScore.getCovariances()
ICovarianceMatrix	SemBicScore.getCovariances()
ICovarianceMatrix	SemBicScoreDeterministic.getCovariances()
ICovarianceMatrix	ZhangShenBoundScore.getCovariances()
ICovarianceMatrix	ZhangShenBoundTest.getCovariances()
ICovarianceMatrix	BFci.getCovMatrix()
ICovarianceMatrix	BfciFoo.getCovMatrix()
ICovarianceMatrix	BfciTr.getCovMatrix()
ICovarianceMatrix	ContinuousTetradTest.getCovMatrix()
ICovarianceMatrix	DiscreteTetradTest.getCovMatrix()
ICovarianceMatrix	GFci.getCovMatrix()
ICovarianceMatrix	GraspFci.getCovMatrix()
ICovarianceMatrix	PopulationTetradTest.getCovMatrix()
ICovarianceMatrix	SpFci.getCovMatrix()
ICovarianceMatrix	SvarGFci.getCovMatrix()
ICovarianceMatrix	TetradTest.getCovMatrix()
ICovarianceMatrix	Mimbuild.getLatentsCov()
ICovarianceMatrix	MimbuildTrek.getLatentsCov()

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

Modifier and Type	Method	Description
static double	SemBicScore.getVarRy(int i, int[] parents, Matrix data, ICovarianceMatrix covariances, boolean calculateRowSubsets)
static double	ZhangShenBoundTest.getVarRy(int i, int[] parents, Matrix data, ICovarianceMatrix covariances, boolean calculateRowSubsets, boolean calculateSquareEuclideanNorms)
Graph	Mimbuild.search(List<List<Node>> clustering, List<String> latentNames, ICovarianceMatrix measuresCov)
Graph	MimbuildTrek.search(List<List<Node>> clustering, List<String> latentNames, ICovarianceMatrix measuresCov)
void	BFci.setCovarianceMatrix(ICovarianceMatrix covarianceMatrix)
void	BfciFoo.setCovarianceMatrix(ICovarianceMatrix covarianceMatrix)
void	BfciTr.setCovarianceMatrix(ICovarianceMatrix covarianceMatrix)
void	GFci.setCovarianceMatrix(ICovarianceMatrix covarianceMatrix)
void	GraspFci.setCovarianceMatrix(ICovarianceMatrix covarianceMatrix)
void	LvSwap.setCovarianceMatrix(ICovarianceMatrix covarianceMatrix)
void	SpFci.setCovarianceMatrix(ICovarianceMatrix covarianceMatrix)
void	SvarGFci.setCovarianceMatrix(ICovarianceMatrix covarianceMatrix)
void	ContinuousTetradTest.setCovMatrix(ICovarianceMatrix covMatrix)

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

Modifier	Constructor	Description
	BpcTetradPurifyWashdown(ICovarianceMatrix cov, TestType testType, double alpha)
	BuildPureClusters(ICovarianceMatrix covarianceMatrix, double alpha, TestType sigTestType)	Constructor BuildPureClusters
	ContinuousTetradTest(ICovarianceMatrix covMatrix, TestType sigTestType, double sig)
	DeltaSextadTest(ICovarianceMatrix cov)	Constructs a test using the given covariance matrix.
	DeltaTetradTest(ICovarianceMatrix cov)	Constructs a test using the given covariance matrix.
	EbicScore(ICovarianceMatrix covariances)	Constructs the score using a covariance matrix.
	FactorAnalysis(ICovarianceMatrix covarianceMatrix)
	FindOneFactorClusters(ICovarianceMatrix cov, TestType testType, FindOneFactorClusters.Algorithm algorithm, double alpha)
	FindTwoFactorClusters(ICovarianceMatrix cov, FindTwoFactorClusters.Algorithm algorithm, double alpha)
	IndTestCramerT(ICovarianceMatrix covMatrix, double alpha)	Constructs a new independence test that will determine conditional independence facts using the given correlation matrix and the given significance level.
	IndTestFisherZ(ICovarianceMatrix covMatrix, double alpha)	Constructs a new independence test that will determine conditional independence facts using the given correlation matrix and the given significance level.
	IndTestFisherZRecursive(ICovarianceMatrix covMatrix, double alpha)	Constructs a new independence test that will determine conditional independence facts using the given correlation matrix and the given significance level.
	IndTestTeyssier(ICovarianceMatrix covMatrix, double penaltyDiscount)	Constructs a new independence test that will determine conditional independence facts using the given correlation matrix and the given significance level.
	IndTestTrekSep(ICovarianceMatrix covMatrix, double alpha, List<List<Node>> clustering, List<Node> latents)	Constructs a new independence test that will determine conditional independence facts using the given correlation matrix and the given significance level.
	KimEtAlScores(ICovarianceMatrix covariances)	Constructs the score using a covariance matrix.
	MagSemBicScore(ICovarianceMatrix covariances)
	PoissonPriorScore(ICovarianceMatrix covariances)	Constructs the score using a covariance matrix.
	RecursivePartialCorrelation(ICovarianceMatrix cov)
	SemBicScore(ICovarianceMatrix covariances)	Constructs the score using a covariance matrix.
	SemBicScoreDeterministic(ICovarianceMatrix covariances)	Constructs the score using a covariance matrix.
	Washdown(ICovarianceMatrix cov, double alpha)
	ZhangShenBoundScore(ICovarianceMatrix covariances)	Constructs the score using a covariance matrix.
	ZhangShenBoundTest(ICovarianceMatrix covariances)	Constructs the score using a covariance matrix.

Uses of ICovarianceMatrix in edu.cmu.tetrad.sem

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

Modifier and Type	Method	Description
ICovarianceMatrix	DagScorer.getCovMatrix()
ICovarianceMatrix	Scorer.getCovMatrix()
ICovarianceMatrix	SemEstimator.getCovMatrix()

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

Modifier and Type	Method	Description
Ricf.RicfResult	Ricf.ricf(SemGraph mag, ICovarianceMatrix covMatrix, double tolerance)
Ricf.RicfResult	Ricf.ricf2(Graph mag, ICovarianceMatrix covMatrix, double tolerance)	same as above but takes a Graph instead of a SemGraph
void	SemIm.setCovMatrix(ICovarianceMatrix covMatrix)	Sets the sample covariance matrix for this Sem as a submatrix of the given matrix.

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

Modifier	Constructor	Description
	DagScorer(ICovarianceMatrix covMatrix)	Constructs a new SemEstimator that uses the specified optimizer.
	RicfResult(cern.colt.matrix.DoubleMatrix2D shat, cern.colt.matrix.DoubleMatrix2D lhat, cern.colt.matrix.DoubleMatrix2D bhat, cern.colt.matrix.DoubleMatrix2D ohat, int iterations, double diff, ICovarianceMatrix covMatrix)
	SemEstimator(ICovarianceMatrix covMatrix, SemPm semPm)	Constructs a SEM estimator that does default estimation.
	SemEstimator(ICovarianceMatrix covMatrix, SemPm semPm, SemOptimizer semOptimizer)	Constructs a new SemEstimator that uses the specified optimizer.
	SemIm(SemPm semPm, ICovarianceMatrix covMatrix)	Constructs a SEM model using the given SEM PM and sample covariance matrix.

Uses of ICovarianceMatrix in edu.pitt.csb.mgm

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

Modifier and Type	Method	Description
ICovarianceMatrix	IndTestMultinomialLogisticRegressionWald.getCov()