Uses of Class
edu.cmu.tetrad.util.Matrix
Packages that use Matrix
Package
Description
Contains classes for searching for (mostly structural) causal models given data.
Contains classes for various various sorts of scores for running score-based algorithms.
Contains classes for running conditional independence tests for various sorts of data.
Contains some utility classes for search algorithms.
Contains some classes that aren't ready for prime time.
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Uses of Matrix in edu.cmu.tetrad.cluster
Methods in edu.cmu.tetrad.cluster with parameters of type Matrix -
Uses of Matrix in edu.cmu.tetrad.data
Methods in edu.cmu.tetrad.data that return MatrixModifier and TypeMethodDescriptionstatic Matrix
DataTransforms.centerData
(Matrix data) static Matrix
DataTransforms.concatenate
(Matrix... dataSets) static Matrix
static Matrix
DataTransforms.getBootstrapSample
(Matrix data, int sampleSize) BoxDataSet.getCorrelationMatrix()
DataSet.getCorrelationMatrix()
If this is a continuous data set, returns the correlation matrix.NumberObjectDataSet.getCorrelationMatrix()
BoxDataSet.getCovarianceMatrix()
DataSet.getCovarianceMatrix()
If this is a continuous data set, returns the covariance matrix.NumberObjectDataSet.getCovarianceMatrix()
TimeSeriesData.getData()
BoxDataSet.getDoubleData()
DataSet.getDoubleData()
NumberObjectDataSet.getDoubleData()
final Matrix
CorrelationMatrixOnTheFly.getMatrix()
final Matrix
CovarianceMatrix.getMatrix()
final Matrix
CovarianceMatrixOnTheFly.getMatrix()
final Matrix
CovarianceMatrixOnTheFly.getMatrix
(int[] rows) ICovarianceMatrix.getMatrix()
CorrelationMatrix.getSelection
(int[] rows, int[] cols) CorrelationMatrixOnTheFly.getSelection
(int[] rows, int[] cols) CovarianceMatrix.getSelection
(int[] rows, int[] cols) CovarianceMatrixOnTheFly.getSelection
(int[] rows, int[] cols) CovarianceMatrixOnTheFly.getSelection
(int[] rows, int[] cols, int[] dataRows) ICovarianceMatrix.getSelection
(int[] rows, int[] cols) static Matrix
DataTransforms.standardizeData
(Matrix data) static Matrix
static Matrix
static Matrix
static Matrix
Methods in edu.cmu.tetrad.data with parameters of type MatrixModifier and TypeMethodDescriptionstatic Matrix
DataTransforms.centerData
(Matrix data) static Matrix
DataTransforms.concatenate
(Matrix... dataSets) static boolean
DataUtils.containsMissingValue
(Matrix data) static Matrix
static Matrix
DataTransforms.getBootstrapSample
(Matrix data, int sampleSize) static Vector
static Vector
void
void
void
void
void
static Matrix
DataTransforms.standardizeData
(Matrix data) static Matrix
static Matrix
Constructors in edu.cmu.tetrad.data with parameters of type MatrixModifierConstructorDescriptionCorrelationMatrix
(List<Node> variables, Matrix matrix, int sampleSize) Constructs a correlation matrix data set using the given information.CovarianceMatrix
(List<Node> variables, Matrix matrix, int sampleSize) Protected constructor to construct a new covariance matrix using the supplied continuous variables and the the given symmetric, positive definite matrix and sample size.TimeSeriesData
(Matrix matrix, List<String> varNames) Constructs a new time series data contains for the given row-major data array and the given list of variables. -
Uses of Matrix in edu.cmu.tetrad.regression
Constructors in edu.cmu.tetrad.regression with parameters of type Matrix -
Uses of Matrix in edu.cmu.tetrad.search
Methods in edu.cmu.tetrad.search that return MatrixModifier and TypeMethodDescriptionstatic Matrix
Estimates the W matrix using FastICA.Fits an ICA-LiNGAM model to the given dataset using a default method for estimating W.Searches given a W matrix is that is provided by the user (where WX = e).FastIca.IcaResult.getK()
FactorAnalysis.getResidual()
Returns the matrix of residuals.FastIca.IcaResult.getS()
static Matrix
IcaLingD.getScaledBHat
(PermutationMatrixPair pair, double bThreshold) Returns the BHat matrix, permuted to the variable order of the original data and scaled so that the diagonal consists only of 1's.FastIca.IcaResult.getW()
FastIca.IcaResult.getX()
static Matrix
Scales the given matrix M by diving each entry (i, j) by M(j, j)FactorAnalysis.successiveFactorVarimax
(Matrix factorLoadingMatrix) Returns the matrix result for the varimax algorithm.FactorAnalysis.successiveResidual()
Successive method with residual matrix.static Matrix
Thresholds the given matrix, sending any small entries in absolute value to zero.Methods in edu.cmu.tetrad.search that return types with arguments of type MatrixModifier and TypeMethodDescriptionFits a LiNG-D model to the given dataset using a default method for estimating W.Performs the LiNG-D algorithm given a W matrix, which needs to be discovered elsewhere.Methods in edu.cmu.tetrad.search with parameters of type MatrixModifier and TypeMethodDescriptionSearches given a W matrix is that is provided by the user (where WX = e).Performs the LiNG-D algorithm given a W matrix, which needs to be discovered elsewhere.static PermutationMatrixPair
IcaLingD.hungarianDiagonal
(Matrix W) Finds a column permutation of the W matrix that maximizes the sum of 1 / |Wii| for diagonal elements Wii in W.static boolean
Determines whether a BHat matrix parses to an acyclic graph.static boolean
Whether the BHat matrix represents a stable model.static @NotNull Graph
Returns a graph given a coefficient matrix and a list of variables.static Matrix
Scales the given matrix M by diving each entry (i, j) by M(j, j)double
void
Sets the initial un-mixing matrix of dimension (n.comp,n.comp).FactorAnalysis.successiveFactorVarimax
(Matrix factorLoadingMatrix) Returns the matrix result for the varimax algorithm.static Matrix
Thresholds the given matrix, sending any small entries in absolute value to zero.Constructors in edu.cmu.tetrad.search with parameters of type MatrixModifierConstructorDescriptionConstructs an instance of the Fast ICA algorithm, taking as arguments the two arguments that cannot be defaulted: the data matrix itself and the number of components to be extracted. -
Uses of Matrix in edu.cmu.tetrad.search.score
Methods in edu.cmu.tetrad.search.score that return MatrixMethods in edu.cmu.tetrad.search.score with parameters of type Matrix -
Uses of Matrix in edu.cmu.tetrad.search.test
Methods in edu.cmu.tetrad.search.test with parameters of type MatrixModifier and TypeMethodDescriptiondouble
IndTestHsic.empiricalHSIC
(Matrix Ky, Matrix Kx, int m) Empirical unconditional Hilbert-Schmidt Dependence Measure for X and Ydouble
IndTestHsic.empiricalHSICincompleteCholesky
(Matrix Gy, Matrix Gx, int m) Empirical unconditional Hilbert-Schmidt Dependence Measure for X and Y using incomplete Cholesky decomposition to approximate Gram matricesdouble
IndTestHsic.empiricalHSICincompleteCholesky
(Matrix Gy, Matrix Gx, Matrix Gz, int m) Empirical unconditional Hilbert-Schmidt Dependence Measure for X and Y given Z using incomplete Cholesky decomposition to approximate Gram matricesConstructors in edu.cmu.tetrad.search.test with parameters of type MatrixModifierConstructorDescriptionIndTestFisherZ
(Matrix data, List<Node> variables, double alpha) Constructs a new Fisher Z independence test with the listed arguments.IndTestHsic
(Matrix data, List<Node> variables, double alpha) Constructs a new HSIC Independence test. -
Uses of Matrix in edu.cmu.tetrad.search.utils
Methods in edu.cmu.tetrad.search.utils that return MatrixModifier and TypeMethodDescriptionstatic Matrix
Constructs the centralized Gram matrix for a given vector valued sample.static Matrix
Constructs Gram matrix for a given vector valued sample.static Matrix
KernelUtils.constructH
(int m) Constructs the projection matrix on 1/mPermutationMatrixPair.getPermutedMatrix()
Returns W, permuted rowwise by the permutation passed in through the constructor.static Matrix
KernelUtils.incompleteCholeskyGramMatrix
(List<Kernel> kernels, DataSet dataset, List<Node> nodes, double precision) Approximates Gram matrix using incomplete Cholesky factorizationMethods in edu.cmu.tetrad.search.utils with parameters of type MatrixModifier and TypeMethodDescriptionstatic boolean
TsUtils.allEigenvaluesAreSmallerThanOneInModulus
(Matrix mat) Constructors in edu.cmu.tetrad.search.utils with parameters of type MatrixModifierConstructorDescriptionPartialCorrelation
(List<Node> nodes, Matrix cov, int sampleSize) Constructor.PermutationMatrixPair
(Matrix M, int[] rowPerm, int[] colPerm) Constructs with a given matrix M and a row and column permutation (which may be null). -
Uses of Matrix in edu.cmu.tetrad.search.work_in_progress
Methods in edu.cmu.tetrad.search.work_in_progress that return MatrixConstructors in edu.cmu.tetrad.search.work_in_progress with parameters of type Matrix -
Uses of Matrix in edu.cmu.tetrad.sem
Methods in edu.cmu.tetrad.sem that return MatrixModifier and TypeMethodDescriptionSemEstimatorGibbs.getDataSet()
DagScorer.getEdgeCoef()
Scorer.getEdgeCoef()
SemIm.getEdgeCoef()
SemIm.getErrCovar()
DagScorer.getErrorCovar()
Scorer.getErrorCovar()
ISemIm.getImplCovar
(boolean recalculate) SemIm.getImplCovar
(boolean recalculate) SemIm.getImplCovar
(List<Node> nodes) StandardizedSemIm.getImplCovar()
ISemIm.getImplCovarMeas()
SemIm.getImplCovarMeas()
StandardizedSemIm.getImplCovarMeas()
DagScorer.getSampleCovar()
Scorer.getSampleCovar()
SemIm.getSampleCovar()
Methods in edu.cmu.tetrad.sem with parameters of type MatrixModifier and TypeMethodDescriptiondouble
double
double
ISemIm.getVariance
(Node nodeA, Matrix implCovar) double
SemIm.getVariance
(Node node, Matrix implCovar) Constructors in edu.cmu.tetrad.sem with parameters of type Matrix -
Uses of Matrix in edu.cmu.tetrad.util
Methods in edu.cmu.tetrad.util that return MatrixModifier and TypeMethodDescriptionstatic Matrix
static Matrix
MatrixUtils.convertCovToCorr
(Matrix m) Converts a covariance matrix to a correlation matrix in place; the same matrix is returned for convenience, but m is modified in the process.Matrix.copy()
Vector.diag()
Matrix.getPart
(int i, int j, int k, int l) Matrix.getSelection
(int[] rows, int[] cols) Matrix.ginverse()
static Matrix
Matrix.identity
(int rows) static Matrix
TetradAlgebra.identity
(int rows) static Matrix
MatrixUtils.impliedCovar
(Matrix edgeCoef, Matrix errCovar) static Matrix
MatrixUtils.impliedCovar2
(Matrix edgeCoef, Matrix errCovar) Matrix.inverse()
Matrix.like()
static Matrix
Matrix.scalarMult
(double scalar) static Matrix
Matrix.serializableInstance()
Generates a simple exemplar of this class to test serialization.static Matrix
static Matrix
Matrix.sparseMatrix
(int m, int n) Matrix.sqrt()
Matrix.symmetricInverse()
Matrix.transpose()
Methods in edu.cmu.tetrad.util with parameters of type MatrixModifier and TypeMethodDescriptionvoid
static Matrix
static Matrix
MatrixUtils.convertCovToCorr
(Matrix m) Converts a covariance matrix to a correlation matrix in place; the same matrix is returned for convenience, but m is modified in the process.boolean
static Matrix
MatrixUtils.impliedCovar
(Matrix edgeCoef, Matrix errCovar) static Matrix
MatrixUtils.impliedCovar2
(Matrix edgeCoef, Matrix errCovar) static boolean
MatrixUtils.isPositiveDefinite
(Matrix matrix) Return true if the given matrix is symmetric positive definite--that is, if it would make a valid covariance matrix.static double
StatUtils.partialCorrelation
(Matrix submatrix) Assumes that the given covariance matrix was extracted in such a way that the order of the variables (in either direction) is X, Y, Z1, ..., Zn, where the partial correlation one wants is correlation(X, Y | Z1,...,Zn).static double
StatUtils.partialCorrelation
(Matrix covariance, int x, int y, int... z) static double
StatUtils.partialCorrelationPrecisionMatrix
(Matrix submatrix) static double
StatUtils.partialCovarianceWhittaker
(Matrix submatrix) Assumes that the given covariance matrix was extracted in such a way that the order of the variables (in either direction) is X, Y, Z1, ..., Zn, where the partial covariance one wants is covariance(X, Y | Z1,...,Zn).static double
StatUtils.partialCovarianceWhittaker
(Matrix covariance, int x, int y, int... z) static double
StatUtils.partialStandardDeviation
(Matrix covariance, int x, int... z) static double
StatUtils.partialVariance
(Matrix covariance, int x, int... z) static Vector
static Matrix
Constructors in edu.cmu.tetrad.util with parameters of type Matrix