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	This package contains classes for causal graph search algorithms.
edu.cmu.tetrad.search.score	This package contains classes for scoring causal graph models.
edu.cmu.tetrad.search.test	This package contains classes for testing causal graph search algorithms.
edu.cmu.tetrad.search.utils	This package contains utility classes for causal graph search algorithms.
edu.cmu.tetrad.search.work_in_progress	A package for algorithms that are not ready for prime time.
edu.cmu.tetrad.sem

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	DataTransforms.covarianceNonparanormalDrton(DataSet dataSet)	covarianceNonparanormalDrton.
static @NotNull ICovarianceMatrix	SimpleDataLoader.getCorrelationMatrix(DataSet dataSet)	getCorrelationMatrix.
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 @NotNull ICovarianceMatrix	SimpleDataLoader.getCovarianceMatrix(DataSet dataSet, boolean precomputeCovariances)	getCovarianceMatrix.
final ICovarianceMatrix	CorrelationMatrixOnTheFly.getSubmatrix(int[] indices)	getSubmatrix.
final ICovarianceMatrix	CorrelationMatrixOnTheFly.getSubmatrix(List<String> submatrixVarNames)	getSubmatrix.
final ICovarianceMatrix	CovarianceMatrix.getSubmatrix(int[] indices)	getSubmatrix.
final ICovarianceMatrix	CovarianceMatrix.getSubmatrix(List<String> submatrixVarNames)	getSubmatrix.
final ICovarianceMatrix	CovarianceMatrixOnTheFly.getSubmatrix(int[] indices)	getSubmatrix.
final ICovarianceMatrix	CovarianceMatrixOnTheFly.getSubmatrix(int[] indices, int[] dataRows)	getSubmatrix.
final ICovarianceMatrix	CovarianceMatrixOnTheFly.getSubmatrix(List<String> submatrixVarNames)	getSubmatrix.
ICovarianceMatrix	ICovarianceMatrix.getSubmatrix(int[] indices)	Returns a submatrix of the covariance matrix, including only the specified variables.
ICovarianceMatrix	ICovarianceMatrix.getSubmatrix(String[] submatrixVarNames)	Returns a submatrix of the covariance matrix, including only the specified variables.
ICovarianceMatrix	ICovarianceMatrix.getSubmatrix(List<String> submatrixVarNames)	Returns a submatrix of the covariance matrix, including only the specified variables.
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 List<Node>	DataUtils.getExampleNonsingular(ICovarianceMatrix covarianceMatrix, int depth)	getExampleNonsingular.
static Matrix	DataUtils.subMatrix(ICovarianceMatrix m, Node x, Node y, List<Node> z)	subMatrix.
static Matrix	DataUtils.subMatrix(ICovarianceMatrix m, Map<Node,Integer> indexMap, Node x, Node y, List<Node> z)	subMatrix.
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)	Constructor for CovarianceMatrix.

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	IsGFci.getCovarianceMatrix()	Retrieves the current covariance matrix object used by the IGFci algorithm.
ICovarianceMatrix	IsGFci.getCovMatrix()	Retrieves the current covariance matrix object used by the IGFci algorithm.
ICovarianceMatrix	MimbuildTrek.getLatentsCov()	Deprecated. The covariance matrix over the latents that is implied by the clustering.
ICovarianceMatrix	MimbuildBollen.getLatentsCovariance()	Retrieves the latent covariance matrix associated with the MimbuildBollen instance.
ICovarianceMatrix	MimbuildPca.getLatentsCovariance()	Retrieves the latent covariance matrix, which encapsulates the covariances between the latent variables associated with the specified blocks in the PCA analysis.

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

Modifier and Type	Method	Description
Graph	MimbuildTrek.search(List<List<Node>> clustering, List<String> latentNames, ICovarianceMatrix measuresCov)	Deprecated. Does the search and returns the graph.
void	IsGFci.setCovarianceMatrix(ICovarianceMatrix covarianceMatrix)	Sets the covariance matrix to be used in the IGFci algorithm.

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

Modifier	Constructor	Description
	FactorAnalysis(ICovarianceMatrix covarianceMatrix)	Constructor.

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

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

Modifier and Type	Method	Description
ICovarianceMatrix	GicScores.getCovariances()	Returns the sample size.
ICovarianceMatrix	PoissonPriorScore.getCovariances()	Returns the covariance matrix.
ICovarianceMatrix	SemBicScore.getCovariances()	Returns the covariance matrix.
ICovarianceMatrix	ZsbScore.getCovariances()	Returns the covariance matrix.

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

Modifier and Type	Method	Description
static SemBicScore.CovAndCoefs	SemBicScore.getCovAndCoefs(int i, int[] parents, Matrix data, ICovarianceMatrix covariances, boolean calculateRowSubsets, double lambda)	Returns the covariance matrix of the regression of the ith variable on its parents and the regression coefficients.
static @NotNull SemBicScore.CovAndCoefs	SemBicScore.getCovAndCoefs(int i, int[] parents, Matrix data, ICovarianceMatrix covariances, double lambda, List<Integer> rows)	Returns the covariance matrix of the regression of the ith variable on its parents and the regression
static double	SemBicScore.getResidualVariance(int i, int[] parents, Matrix data, ICovarianceMatrix covariances, boolean calculateRowSubsets, double lambda)	Returns the variance of the residual of the regression of the ith variable on its parents.

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

Modifier	Constructor	Description
	EbicScore(ICovarianceMatrix covariances)	Constructs the score using a covariance matrix.
	GicScores(ICovarianceMatrix covariances)	Constructs the score using a covariance matrix.
	InstanceAugmentedSemBicScore(ICovarianceMatrix cov, double[] instanceRowCentered)	Constructs an `InstanceAugmentedSemBicScore` object using a covariance matrix and a fully centered row of instance data.
	InstanceAugmentedSemBicScore(ICovarianceMatrix cov, double[] instanceRowRaw, double[] populationMeans)	Constructs an `InstanceAugmentedSemBicScore` object using a covariance matrix, a raw row of instance data, and the population mean values.
	PoissonPriorScore(ICovarianceMatrix covariances)	Constructs the score using a covariance matrix.
	SemBicScore(ICovarianceMatrix covariances)	Constructs the score using a covariance matrix.
	SemBicScore(ICovarianceMatrix covariances, double penaltyDiscount)	Constructs the score using a covariance matrix.
	ZsbScore(ICovarianceMatrix covMatrix)	Constructs the score using a covariance matrix.

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

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

Modifier and Type	Method	Description
default ICovarianceMatrix	IndependenceTest.getCov()	Returns the covariance matrix.
ICovarianceMatrix	IndTestFisherZ.getCov()	Retrieves the covariance matrix used by this instance.
ICovarianceMatrix	IndTestFisherZConcatenateResiduals.getCov()	Deprecated. Returns the covariance matrix for the data sets.
ICovarianceMatrix	IndTestFisherZFisherPValue.getCov()	Returns the covariance matrix of the concatenated data.
ICovarianceMatrix	IndTestTrekSep.getCov()	Deprecated. Returns the covariance matrix.
ICovarianceMatrix	ScoreIndTest.getCov()	Returns the covariance matrix.

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

Modifier	Constructor	Description
	IndTestFisherZ(ICovarianceMatrix covMatrix, double alpha)	Constructs an instance of IndTestFisherZ using the given covariance matrix and significance level.
	IndTestFisherZ(ICovarianceMatrix covMatrix, double alpha, double ridge)	Constructor for the IndTestFisherZ class.
	IndTestTrekSep(ICovarianceMatrix covMatrix, double alpha, List<List<Node>> clustering, List<Node> latents)	Deprecated. Constructs a new independence test that will determine conditional independence facts using the given correlation matrix and the given significance level.

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

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

Modifier and Type	Method	Description
ICovarianceMatrix	TetradTest.getCovMatrix()	getCovMatrix.
ICovarianceMatrix	TetradTestContinuous.getCovMatrix()	getCovMatrix.
ICovarianceMatrix	TetradTestDiscrete.getCovMatrix()	getCovMatrix.
ICovarianceMatrix	TetradTestPopulation.getCovMatrix()	getCovMatrix.

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

Modifier and Type	Method	Description
void	TetradTestContinuous.setCovMatrix(ICovarianceMatrix covMatrix)	Setter for the field covMatrix.

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

Modifier	Constructor	Description
	DeltaSextadTest(ICovarianceMatrix cov)	Constructs a test using the given covariance matrix.
	DeltaTetradTest(ICovarianceMatrix covarianceMatrix)	Constructor for a covariance matrix.
	DeltaTetradTest2(ICovarianceMatrix cov)	Constructs a test using the given covariance matrix.
	DeltaTetradTest3(ICovarianceMatrix covarianceMatrix)	Constructor for a covariance matrix.
	PartialCorrelation(ICovarianceMatrix cov)	Constructor

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

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

Modifier and Type	Method	Description
ICovarianceMatrix	IndTestFisherZPercentIndependent.getCov()	Deprecated. Retrieves the covariance matrix.
ICovarianceMatrix	IndTestFisherZRecursive.getCov()	Deprecated. getCov.
ICovarianceMatrix	IndTestPositiveCorr.getCov()	Deprecated. getCov.
ICovarianceMatrix	SampleVcpc.getCov()	getCov.
ICovarianceMatrix	SampleVcpcFast.getCov()	getCov.
ICovarianceMatrix	SemBicScoreDeterministic.getCovariances()	Getter for the field covariances.

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

Modifier	Constructor	Description
	IndTestCramerT(ICovarianceMatrix covMatrix, double alpha)	Deprecated. 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)	Deprecated. Constructs a new independence test that will determine conditional independence facts using the given correlation matrix and the given significance level.
	MagSemBicScore(ICovarianceMatrix covariances)	Constructor.
	SemBicScoreDeterministic(ICovarianceMatrix covariances)	Constructs the score using a covariance matrix.
	Washdown(ICovarianceMatrix cov, double alpha)	Constructor.

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()	Getter for the field covMatrix.
ICovarianceMatrix	Scorer.getCovMatrix()	getCovMatrix.
ICovarianceMatrix	SemEstimator.getCovMatrix()	Getter for the field covMatrix.

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

Modifier and Type	Method	Description
static double	Ricf.logLikMAG(cern.colt.matrix.DoubleMatrix2D B, cern.colt.matrix.DoubleMatrix2D Omega, cern.colt.matrix.DoubleMatrix2D Lambda, int[] ug, ICovarianceMatrix covMatrix)	Calculates the log-likelihood for a Mixed Ancestral Graph (MAG) model given the input matrices and provides a measure of model fit.
Ricf.RicfResult	Ricf.ricf(SemGraph mag, ICovarianceMatrix covMatrix, double tolerance)	Calculates the Restricted Information Criterion Fusion (RICF) for a given SemGraph.
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)	The result.
	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.