Uses of Interface
edu.cmu.tetrad.search.IndependenceTest

Packages that use IndependenceTest

Package	Description
edu.cmu.tetrad.algcomparison.independence
edu.cmu.tetrad.graph
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.pitt.csb.mgm

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

Methods in edu.cmu.tetrad.algcomparison.independence that return IndependenceTest

Modifier and Type	Method	Description
IndependenceTest	BasisFunctionBicTest.getTest(DataModel dataSet, Parameters parameters)	Returns an instance of IndependenceTest for the Basis Function BIC test.
IndependenceTest	BdeuTest.getTest(DataModel dataSet, Parameters parameters)	Returns true iff x and y are independent conditional on z for the given data set.
IndependenceTest	CciTest.getTest(DataModel dataSet, Parameters parameters)	Returns true iff x and y are independent conditional on z for the given data set.
IndependenceTest	ChiSquare.getTest(DataModel dataSet, Parameters parameters)	Retrieves an instance of the IndependenceTest interface that performs a Chi Square Test for independence.
IndependenceTest	ConditionalGaussianLRT.getTest(DataModel dataSet, Parameters parameters)	Returns true iff x and y are independent conditional on z for the given data set.
IndependenceTest	DegenerateGaussianLRT.getTest(DataModel dataSet, Parameters parameters)	Returns true iff x and y are independent conditional on z for the given data set.
IndependenceTest	DiscreteBicTest.getTest(DataModel dataSet, Parameters parameters)	Returns true iff x and y are independent conditional on z for the given data set.
IndependenceTest	FisherZ.getTest(DataModel dataModel, Parameters parameters)	Gets an independence test based on the given data model and parameters.
IndependenceTest	GICScoreTests.getTest(DataModel dataSet, Parameters parameters)	Returns true iff x and y are independent conditional on z for the given data set.
IndependenceTest	GSquare.getTest(DataModel dataSet, Parameters parameters)	Returns true iff x and y are independent conditional on z for the given data set.
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)	Returns true iff x and y are independent conditional on z for the given data set.
IndependenceTest	MagSemBicTest.getTest(DataModel dataSet, Parameters parameters)	Returns true iff x and y are independent conditional on z for the given data set.
IndependenceTest	Mnlrlrt.getTest(DataModel dataSet, Parameters parameters)	Returns true iff x and y are independent conditional on z for the given data set.
IndependenceTest	MSeparationTest.getTest(DataModel dataSet, Parameters parameters)	Returns true iff x and y are independent conditional on z for the given data set.
IndependenceTest	MultinomialLogisticRegressionWald.getTest(DataModel dataSet, Parameters parameters)	Returns true iff x and y are independent conditional on z for the given data set.
IndependenceTest	Mvplrt.getTest(DataModel dataSet, Parameters parameters)	Returns true iff x and y are independent conditional on z for the given data set.
IndependenceTest	PoissonPriorTest.getTest(DataModel dataSet, Parameters parameters)	Returns an instance of IndependenceTest for the Poisson Prior test.
IndependenceTest	PositiveCorr.getTest(DataModel dataSet, Parameters parameters)	Returns true iff x and y are independent conditional on z for the given data set.
IndependenceTest	ProbabilisticTest.getTest(DataModel dataSet, Parameters parameters)	Returns true iff x and y are independent conditional on z for the given data set.
IndependenceTest	SemBicDTest.getTest(DataModel dataSet, Parameters parameters)	Retrieves an IndependenceTest object for testing independence against a given data set and parameters.
IndependenceTest	SemBicTest.getTest(DataModel dataSet, Parameters parameters)	Returns an instance of IndependenceTest for the SEM BIC test.

Uses of IndependenceTest in edu.cmu.tetrad.graph

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

Modifier and Type	Method	Description
Set<Node>	Dag.getSepset(Node n1, Node n2, IndependenceTest test)	Returns the sepset between two given nodes in the graph.
Set<Node>	EdgeListGraph.getSepset(Node x, Node y, IndependenceTest test)	Returns the set of nodes that form the separating set between two given nodes.
Set<Node>	Graph.getSepset(Node n1, Node n2, IndependenceTest test)	Returns the set of nodes that form the separating set between two given nodes.
Set<Node>	LagGraph.getSepset(Node n1, Node n2, IndependenceTest test)	Returns the set of nodes that form the separating set between two given nodes.
Set<Node>	Paths.getSepset(Node x, Node y, boolean allowSelectionBias, IndependenceTest test, int depth)	Finds a sepset for x and y, if there is one; otherwise, returns null.
Set<Node>	SemGraph.getSepset(Node n1, Node n2, IndependenceTest test)	Returns the set of nodes that form the separating set between two given nodes.
Set<Node>	TimeLagGraph.getSepset(Node n1, Node n2, IndependenceTest test)	Retrieves the sepset of two nodes in the graph.
static double	GraphUtils.localMarkovInitializePValues(Graph dag, boolean ensureMarkov, IndependenceTest test, Map<org.apache.commons.lang3.tuple.Pair<Node,Node>,Set<Double>> pValues)	Initializes and evaluates p-values for local Markov properties in a given graph.
void	Paths.removeByPossibleMsep(IndependenceTest test, SepsetMap sepsets)	Remove edges by the possible m-separation rule.

Uses of IndependenceTest in edu.cmu.tetrad.search

Classes in edu.cmu.tetrad.search that implement IndependenceTest

Modifier and Type	Class	Description
class	CompositeIndependenceTest	CompositeIndependenceTest class.
class	IndTestIod	Checks independence results by listing all tests with those variables, testing each one, and returning the resolution of these test results.

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

Modifier and Type	Method	Description
IndependenceTest	BFci.getIndependenceTest()	The independence test being used for some steps in final orientation.
IndependenceTest	Cpc.getIndependenceTest()	Rreturn the independence test used in the search, set in the constructor.
IndependenceTest	Fci.getIndependenceTest()	Returns the independence test used in search.
IndependenceTest	FciMax.getIndependenceTest()	Returns the independence test used in search.
IndependenceTest	GFci.getIndependenceTest()	Returns the independence test used in search.
IndependenceTest	MarkovCheck.getIndependenceTest()	Returns the independence test being used.
IndependenceTest	Pc.getIndependenceTest()	Returns the independence test being used in the search.
IndependenceTest	Pcd.getIndependenceTest()	Retrieves the IndependenceTest used by this method.
IndependenceTest	Rfci.getIndependenceTest()	Returns the independence test.
IndependenceTest	SpFci.getIndependenceTest()	Returns the independence test used in search.
IndependenceTest	SvarFci.getIndependenceTest()	Returns independence test.
IndependenceTest	PcMb.getTest()	Returns the test used in search.
default IndependenceTest	IndependenceTest.indTestSubset(List<Node> vars)	Returns an Independence test for a sublist of the variables.
IndependenceTest	IndTestIod.indTestSubset(List<Node> vars)	Calculates the independence test for a subset of variables.

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

Modifier and Type	Method	Description
List<List<Node>>	MarkovCheck.getAndersonDarlingTestAcceptsRejectsNodesForAllNodes(IndependenceTest independenceTest, Graph graph, Double threshold, Double shuffleThreshold)	Calculates the Anderson-Darling test and classifies nodes as accepted or rejected based on the given threshold.
List<List<Node>>	MarkovCheck.getAndersonDarlingTestAcceptsRejectsNodesForAllNodesPlotData(IndependenceTest independenceTest, Graph estimatedCpdag, Graph trueGraph, Double threshold, Double shuffleThreshold, Double lowRecallBound)	Get accepts and rejects nodes for all nodes from Anderson-Darling test and generate the plot data for confusion statistics.
List<List<Node>>	MarkovCheck.getAndersonDarlingTestAcceptsRejectsNodesForAllNodesPlotData2(IndependenceTest independenceTest, Graph estimatedCpdag, Graph trueGraph, Double threshold, Double shuffleThreshold, Double lowRecallBound)	Get accepts and rejects nodes for all nodes from Anderson-Darling test and generate the plot data for confusion statistics.
List<Double>	MarkovCheck.getLocalPValues(IndependenceTest independenceTest, List<IndependenceFact> facts)	Calculates the local p-values for a given independence test and a list of independence facts.
List<List<Double>>	MarkovCheck.getLocalPValues(IndependenceTest independenceTest, List<IndependenceFact> facts, Double shuffleThreshold)	Get Local P values with shuffle threshold provided.
static Set<Node>	SepsetFinder.getSepsetContainingGreedy(Graph graph, Node x, Node y, Set<Node> containing, IndependenceTest test, int depth)	Returns the sepset that contains the greedy test for variables x and y in the given graph.
static Set<Node>	SepsetFinder.getSepsetContainingMaxPHybrid(Graph graph, Node x, Node y, Set<Node> containing, IndependenceTest test, int depth)	Returns the set of nodes that act as a separating set between two given nodes (x and y) in a graph.
static Set<Node>	SepsetFinder.getSepsetContainingMinPHybrid(Graph graph, Node x, Node y, Set<Node> containing, IndependenceTest test, int depth)	Returns the sepset containing the minimum p-value for the given variables x and y.
static Set<Node>	SepsetFinder.getSepsetPathBlockingOutOfX(Graph mpdag, Node x, Node y, IndependenceTest test, int maxLength, int depth, boolean allowSelectionBias, Set<Node> blacklist)	Calculates the sepset path blocking out-of operation for a given pair of nodes in a graph.
void	MarkovCheck.setIndependenceTest(IndependenceTest test)	Sets the independence test to be used for determining independence between variables.

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

Modifier	Constructor	Description
	BFci(IndependenceTest test, Score score)	Constructor.
	Ccd(IndependenceTest test)	Construct a CCD algorithm with the given independence test.
	Cfci(IndependenceTest independenceTest)	Constructs a new FCI search for the given independence test and background knowledge.
	CompositeIndependenceTest(IndependenceTest[] independenceTests)	Constructor for CompositeIndependenceTest.
	Cpc(IndependenceTest independenceTest)	Constructs a CPC algorithm that uses the given independence test as oracle.
	Fas(IndependenceTest test)	Constructor.
	Fasd(IndependenceTest test)	Constructs a new FastAdjacencySearch.
	FaskOrig(DataSet dataSet, Score score, IndependenceTest test)	Constructor.
	Fci(IndependenceTest independenceTest)	Constructor.
	Fci(IndependenceTest independenceTest, List<Node> searchVars)	Constructor.
	FciMax(IndependenceTest independenceTest)	Constructor.
	GFci(IndependenceTest test, Score score)	Constructs a new GFci algorithm with the given independence test and score.
	Grasp(@NotNull IndependenceTest test)	Constructor for a test.
	Grasp(IndependenceTest test, Score score)	Constructor that takes both a test and a score; only one is used-- the parameter setting will decide which.
	GraspFci(IndependenceTest test, Score score)	Constructs a new GraspFci object.
	GrowShrink(IndependenceTest test)	Constructs a new search.
	LvLite(Graph cpdag, IndependenceTest test)	Alternative LV-Lite constructor.
	LvLite(IndependenceTest test, Score score)	LV-Lite constructor.
	MarkovCheck(Graph graph, IndependenceTest independenceTest, ConditioningSetType setType)	Constructor.
	Pc(IndependenceTest independenceTest)	Constructs a new PC search using the given independence test as oracle.
	Pcd(IndependenceTest independenceTest)	Constructs a new PC search using the given independence test as oracle.
	PcMb(IndependenceTest test, int depth)	Constructs a new search.
	Rfci(IndependenceTest independenceTest)	Constructs a new RFCI search for the given independence test and background knowledge.
	Rfci(IndependenceTest independenceTest, List<Node> searchVars)	Constructs a new RFCI search for the given independence test and background knowledge and a list of variables to search over.
	SpFci(IndependenceTest test, Score score)	Constructor; requires by ta test and a score, over the same variables.
	SvarFas(IndependenceTest test)	Constructs a new FastAdjacencySearch.
	SvarFci(IndependenceTest independenceTest)	Constructs a new FCI search for the given independence test and background knowledge.
	SvarGfci(IndependenceTest test, Score score)	Constructs a new GFCI search for the given independence test and background knowledge.

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

Modifier	Constructor	Description
	IndTestIod(List<IndependenceTest> tests)	Constructs a new pooled independence test from the given list of independence tests.

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

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

Modifier	Constructor	Description
	IndTestScore(IndependenceTest test)	Constructs the score using a covariance matrix.

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

Classes in edu.cmu.tetrad.search.test that implement IndependenceTest

Modifier and Type	Class	Description
final class	IndTestChiSquare	Checks the conditional independence X _||_ Y | S, where S is a set of discrete variable, and X and Y are discrete variable not in S, by applying a conditional Chi Square test.
final class	IndTestConditionalCorrelation	Checks conditional independence of variable in a continuous data set using a conditional correlation test for the nonlinear nonGaussian with the additive error case.
class	IndTestConditionalGaussianLrt	Performs a test of conditional independence X _||_ Y | Z1...Zn where all searchVariables are either continuous or discrete.
class	IndTestDegenerateGaussianLrt	Implements a degenerate Gaussian score as a LRT.
final class	IndTestFisherZ	Checks conditional independence of variable in a continuous data set using Fisher's Z test.
final class	IndTestFisherZConcatenateResiduals	Calculates independence from pooled residuals using the Fisher Z method.
final class	IndTestFisherZFisherPValue	Calculates independence from multiple datasets from using the Fisher method of pooling independence results.
final class	IndTestGSquare	Checks the conditional independence X _||_ Y | S, where S is a set of discrete variable, and X and Y are discrete variable not in S, by applying a conditional G Square test.
final class	IndTestHsic	Checks the conditional independence X _||_ Y | S, where S is a set of continuous variable, and X and Y are discrete variable not in S, using the Hilbert-Schmidth Independence Criterion (HSIC), a kernel based nonparametric test for conditional independence.
final class	IndTestIndependenceFacts	Checks conditional independence against a list of conditional independence facts, manually entered.
final class	IndTestMulti	A class that represents a pooled independence test for multiple data sets.
class	IndTestMvpLrt	Performs a test of conditional independence X _||_ Y | Z1...Zn where all variables are either continuous or discrete.
class	IndTestProbabilistic	Uses BCInference by Cooper and Bui to calculate probabilistic conditional independence judgments.
final class	IndTestRegression	Checks independence of X _||_ Y | Z for variables X and Y and list Z of variables by regressing X on {Y} U Z and testing whether the coefficient for Y is zero.
final class	IndTestTrekSep	Checks d-separations in a structural model using t-separations over indicators.
class	Kci	Gives an implementation of the Kernel Independence Test (KCI) by Kun Zhang, which is a general test of conditional independence.
class	MsepTest	Checks independence facts for variables associated with the nodes in a given graph by checking m-separation facts on the underlying nodes.
class	ScoreIndTest	Gives a way of interpreting a score as an independence test.

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

Modifier and Type	Method	Description
IndependenceTest	IndTestChiSquare.indTestSubset(List<Node> nodes)	Checks conditional independence between variables in a subset.
IndependenceTest	IndTestConditionalCorrelation.indTestSubset(List<Node> vars)	Constructs a new Independence test which checks independence facts based on the correlation data implied by the given data set (must be continuous).
IndependenceTest	IndTestConditionalGaussianLrt.indTestSubset(List<Node> vars)	This method returns an instance of the IndependenceTest interface that can test the independence of a subset of variables.
IndependenceTest	IndTestDegenerateGaussianLrt.indTestSubset(List<Node> vars)	Subsets the variables used in the independence test.
IndependenceTest	IndTestFisherZ.indTestSubset(List<Node> vars)	Creates a new independence test instance for a subset of the variables.
IndependenceTest	IndTestFisherZConcatenateResiduals.indTestSubset(List<Node> vars)	Returns an Independence test for a sublist of the variables.
IndependenceTest	IndTestFisherZFisherPValue.indTestSubset(List<Node> vars)	Returns an Independence test for a sublist of the variables.
IndependenceTest	IndTestGSquare.indTestSubset(List<Node> vars)	Performs an independence test on a subset of variables.
IndependenceTest	IndTestHsic.indTestSubset(List<Node> vars)	Subset of variables for independence testing.
IndependenceTest	IndTestIndependenceFacts.indTestSubset(List<Node> vars)	Returns an IndependenceTest object for a sublist of variables.
IndependenceTest	IndTestMulti.indTestSubset(List<Node> vars)	Returns an Independence test for a sublist of the variables.
IndependenceTest	IndTestMvpLrt.indTestSubset(List<Node> vars)	Returns an Independence test for a sublist of the variables.
IndependenceTest	IndTestProbabilistic.indTestSubset(List<Node> vars)	Returns an Independence test for a sublist of the variables.
IndependenceTest	IndTestRegression.indTestSubset(List<Node> vars)	Performs an independence test for a sublist of variables.
IndependenceTest	IndTestTrekSep.indTestSubset(List<Node> vars)	Determines independence between variables in a given subset.
IndependenceTest	Kci.indTestSubset(List<Node> vars)
IndependenceTest	MsepTest.indTestSubset(List<Node> vars)	Conducts an independence test on a subset of variables.

Constructor parameters in edu.cmu.tetrad.search.test with type arguments of type IndependenceTest

Modifier	Constructor	Description
	IndTestMulti(List<IndependenceTest> independenceTests, ResolveSepsets.Method method)	Constructs a new pooled independence test for the given data sets.

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

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

Modifier and Type	Method	Description
IndependenceTest	PcCommon.getIndependenceTest()	Getter for the field independenceTest.
IndependenceTest	R0R4StrategyTestBased.getTest()	Retrieves the IndependenceTest object used by the strategy.

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

Modifier and Type	Method	Description
static R0R4Strategy	R0R4StrategyTestBased.defaultConfiguration(IndependenceTest test, Knowledge knowledge)	Returns a default configuration of the FciOrientDataExaminationStrategy object.
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)	getCpcTripleType.
Set<Node>	PossibleMsepFci.getSepset(IndependenceTest test, Node node1, Node node2)	Getter for the field sepset.
static Map<org.apache.commons.lang3.tuple.Pair<Node,Node>,Set<Double>>	EnsureMarkov.localMarkovAdjustPValues(Graph cpdag, boolean ensureMarkov, IndependenceTest test, Map<org.apache.commons.lang3.tuple.Pair<Node,Node>,Set<Double>> pValues, org.apache.commons.lang3.tuple.Pair<Node,Node> withoutPair)	Adjusts the p-values for a local Markov condition in a given constraint-based partially directed acyclic graph (CPDAG).
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 R0R4Strategy	R0R4StrategyTestBased.specialConfiguration(IndependenceTest test, Knowledge knowledge, boolean verbose)	Provides a special configuration for creating an instance of FciOrientDataExaminationStrategy.

Method parameters in edu.cmu.tetrad.search.utils with type arguments of type IndependenceTest

Modifier and Type	Method	Description
static boolean	ResolveSepsets.isIndependentPooled(ResolveSepsets.Method method, List<IndependenceTest> independenceTests, Node x, Node y, Set<Node> condSet)	Tests for independence using one of the pooled methods
static boolean	ResolveSepsets.isIndependentPooledAverage(List<IndependenceTest> independenceTests, Node x, Node y, Set<Node> condSet)	Checks independence from pooled samples by taking the average p value
static boolean	ResolveSepsets.isIndependentPooledAverageTest(List<IndependenceTest> independenceTests, Node x, Node y, Set<Node> condSet)	Checks independence from pooled samples by taking the average test statistic CURRENTLY ONLY WORKS FOR CHISQUARE TEST
static boolean	ResolveSepsets.isIndependentPooledFisher(List<IndependenceTest> independenceTests, Node x, Node y, Set<Node> condSet)	Checks independence from pooled samples using Fisher's method.
static boolean	ResolveSepsets.isIndependentPooledFisher2(List<IndependenceTest> independenceTests, Node x, Node y, Set<Node> condSet)	Eliminates from considerations independence tests that cannot be evaluated (due to missing variables mainly).
static boolean	ResolveSepsets.isIndependentPooledMudholkerGeorge(List<IndependenceTest> independenceTests, Node x, Node y, Set<Node> condSet)	Checks independence from pooled samples using Mudholker and George's method
static boolean	ResolveSepsets.isIndependentPooledMudholkerGeorge2(List<IndependenceTest> independenceTests, Node x, Node y, Set<Node> condSet)	The same as isIndepenentPooledMudholkerGeoerge, except that only available independence tests are used.
static boolean	ResolveSepsets.isIndependentPooledRandom(List<IndependenceTest> independenceTests, Node x, Node y, Set<Node> condSet)	Checks independence from pooled samples by randomly selecting a p value
static boolean	ResolveSepsets.isIndependentPooledStouffer(List<IndependenceTest> independenceTests, Node x, Node y, Set<Node> condSet)	Checks independence from pooled samples using Stouffer et al.'s method
static boolean	ResolveSepsets.isIndependentPooledTippett(List<IndependenceTest> independenceTests, Node x, Node y, Set<Node> condSet)	Checks independence from pooled samples using Tippett's method
static boolean	ResolveSepsets.isIndependentPooledWilkinson(List<IndependenceTest> independenceTests, Node x, Node y, Set<Node> condSet, int r)	Checks independence from pooled samples using Wilkinson's method
static boolean	ResolveSepsets.isIndependentPooledWorsleyFriston(List<IndependenceTest> independenceTests, Node x, Node y, Set<Node> condSet)	Checks independence from pooled samples using Worsley and Friston's method

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

Modifier	Constructor	Description
	EnsureMarkov(Graph dag, IndependenceTest test)	Constructs an EnsureMarkov class for a given Markov dag.
	MaxP(IndependenceTest test)	Constructor.
	PcCommon(IndependenceTest independenceTest)	Constructs a CPC algorithm that uses the given independence test as oracle.
	PossibleMsepFci(Graph graph, IndependenceTest test)	Creates a new SepSet and assumes that none of the variables have yet been checked.
	R0R4StrategyTestBased(IndependenceTest test)	Creates a new instance of FciOrientDataExaminationStrategyTestBased.
	SepsetsGreedy(Graph graph, IndependenceTest independenceTest, int depth)	Constructor for Sepsets.
	SepsetsMaxP(Graph graph, IndependenceTest independenceTest, int depth)	Constructs a SepsetsMaxP object with the given graph, independence test, and depth.
	SepsetsMinP(Graph graph, IndependenceTest independenceTest, int depth)	Initializes a new instance of the SepsetsMinP class.
	SepsetsPossibleMsep(Graph graph, IndependenceTest test, Knowledge knowledge, int depth, int maxDiscriminatingPathLength)	Constructor for SepsetsPossibleMsep.
	SepsetsSet(SepsetMap sepsets, IndependenceTest test)	Constructor for SepsetsSet.
	SvarSetEndpointStrategy(IndependenceTest independenceTest, Knowledge knowledge)	Creates a new instance of SvarSetEndpointStrategy with the given IndependenceTest and Knowledge.
	TeyssierScorer(IndependenceTest test, Score score)	Constructor that takes both a test or a score.

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

Classes in edu.cmu.tetrad.search.work_in_progress that implement IndependenceTest

Modifier and Type	Class	Description
final class	IndTestCramerT	Checks conditional independence for continuous variables using Cramer's T-test formula (Cramer, Mathematical Methods of Statistics (1951), page 413).
final class	IndTestFisherZPercentIndependent	Calculates independence from pooled residuals.
final class	IndTestFisherZRecursive	Checks conditional independence of variable in a continuous data set using Fisher's Z test.
class	IndTestMixedMultipleTTest	Performs a test of conditional independence X _||_ Y | Z1...Zn where all searchVariables are either continuous or discrete.
class	IndTestMnlrLr	Performs a test of conditional independence X _||_ Y | Z1...Zn where all searchVariables are either continuous or discrete.
class	IndTestMultinomialLogisticRegression	Performs a test of conditional independence X _||_ Y | Z1...Zn where all searchVariables are either continuous or discrete.
final class	IndTestPositiveCorr	Checks conditional independence of variable in a continuous data set using Fisher's Z test.
class	IndTestSepsetDci	Checks independence facts for variables associated with a sepset by simply querying the sepset
class	ProbabilisticMapIndependence	Uses BCInference by Cooper and Bui to calculate probabilistic conditional independence judgments.

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

Modifier and Type	Method	Description
IndependenceTest	IGFci.getIndependenceTest()	Retrieves the current independence test object being used.
IndependenceTest	Kpc.getIndependenceTest()	Getter for the field independenceTest.
IndependenceTest	Mmhc.getIndependenceTest()	Getter for the field independenceTest.
IndependenceTest	SampleVcpc.getIndependenceTest()	Getter for the field independenceTest.
IndependenceTest	SampleVcpcFast.getIndependenceTest()	Getter for the field independenceTest.
IndependenceTest	VcPc.getIndependenceTest()	Getter for the field independenceTest.
IndependenceTest	VcPcAlt.getIndependenceTest()	Getter for the field independenceTest.
IndependenceTest	VcPcFast.getIndependenceTest()	Getter for the field independenceTest.
IndependenceTest	IndTestCramerT.indTestSubset(List<Node> vars)	This method performs an independence test based on a given sublist of variables.
IndependenceTest	IndTestFisherZPercentIndependent.indTestSubset(List<Node> vars)	Performs an independence test on a subset of variables.
IndependenceTest	IndTestFisherZRecursive.indTestSubset(List<Node> vars)	Returns an Independence test for a sublist of the variables.
IndependenceTest	IndTestMixedMultipleTTest.indTestSubset(List<Node> vars)
IndependenceTest	IndTestMnlrLr.indTestSubset(List<Node> vars)	This method returns an independence test for a sublist of variables.
IndependenceTest	IndTestMultinomialLogisticRegression.indTestSubset(List<Node> vars)	Performs an independence test for a sublist of variables.
IndependenceTest	IndTestPositiveCorr.indTestSubset(List<Node> vars)	Performs an independence test on a subset of variables.
IndependenceTest	IndTestSepsetDci.indTestSubset(List<Node> vars)	Determines independence between a subset of variables.
IndependenceTest	ProbabilisticMapIndependence.indTestSubset(List<Node> vars)	Returns an Independence test for a sublist of the variables.

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

Modifier and Type	Method	Description
VcPc.CpcTripleType	VcPc.getPopulationTripleType(Node x, Node y, Node z, IndependenceTest test, int depth, Graph graph, boolean verbose)	getPopulationTripleType.
VcPcFast.CpcTripleType	VcPcFast.getPopulationTripleType(Node x, Node y, Node z, IndependenceTest test, int depth, Graph graph, boolean verbose)	getPopulationTripleType.
void	IGFci.setIndependenceTest(IndependenceTest independenceTest)	Sets the independence test for the IGFci algorithm.

Method parameters in edu.cmu.tetrad.search.work_in_progress with type arguments of type IndependenceTest

Modifier and Type	Method	Description
static boolean	ResolveSepsetsDci.isIndependentPooled(ResolveSepsetsDci.Method method, List<IndependenceTest> independenceTests, Node x, Node y, Set<Node> condSet)	Tests for independence using one of the pooled methods
static boolean	ResolveSepsetsDci.isIndependentPooledAverage(List<IndependenceTest> independenceTests, Node x, Node y, Set<Node> condSet)	Checks independence from pooled samples by taking the average p value
static boolean	ResolveSepsetsDci.isIndependentPooledAverageTest(List<IndependenceTest> independenceTests, Node x, Node y, Set<Node> condSet)	Checks independence from pooled samples by taking the average test statistic CURRENTLY ONLY WORKS FOR CHISQUARE TEST
static boolean	ResolveSepsetsDci.isIndependentPooledFisher(List<IndependenceTest> independenceTests, Node x, Node y, Set<Node> condSet)	Checks independence from pooled samples using Fisher's method.
static boolean	ResolveSepsetsDci.isIndependentPooledFisher2(List<IndependenceTest> independenceTests, Node x, Node y, Set<Node> condSet)	Eliminates from considerations independence tests that cannot be evaluated (due to missing variables mainly).
static boolean	ResolveSepsetsDci.isIndependentPooledMudholkerGeorge(List<IndependenceTest> independenceTests, Node x, Node y, Set<Node> condSet)	Checks independence from pooled samples using Mudholker and George's method
static boolean	ResolveSepsetsDci.isIndependentPooledMudholkerGeorge2(List<IndependenceTest> independenceTests, Node x, Node y, Set<Node> condSet)	The same as isIndepenentPooledMudholkerGeoerge, except that only available independence tests are used.
static boolean	ResolveSepsetsDci.isIndependentPooledRandom(List<IndependenceTest> independenceTests, Node x, Node y, Set<Node> condSet)	Checks independence from pooled samples by randomly selecting a p value
static boolean	ResolveSepsetsDci.isIndependentPooledStouffer(List<IndependenceTest> independenceTests, Node x, Node y, Set<Node> condSet)	Checks independence from pooled samples using Stouffer et al.'s method
static boolean	ResolveSepsetsDci.isIndependentPooledTippett(List<IndependenceTest> independenceTests, Node x, Node y, Set<Node> condSet)	Checks independence from pooled samples using Tippett's method
static boolean	ResolveSepsetsDci.isIndependentPooledWilkinson(List<IndependenceTest> independenceTests, Node x, Node y, Set<Node> condSet, int r)	Checks independence from pooled samples using Wilkinson's method
static boolean	ResolveSepsetsDci.isIndependentPooledWorsleyFriston(List<IndependenceTest> independenceTests, Node x, Node y, Set<Node> condSet)	Checks independence from pooled samples using Worsley and Friston's method

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

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.
	FasFdr(IndependenceTest test, int numIndependenceTests)	Constructs a new FastAdjacencySearch.
	GraspTol(@NotNull IndependenceTest test)	Constructor for GraspTol.
	GraspTol(@NotNull IndependenceTest test, Score score)	Constructor for GraspTol.
	Iamb(IndependenceTest test)	Constructs a new search.
	IambnPc(IndependenceTest test)	Constructs a new search.
	IGFci(IndependenceTest test, ISScore score)	Constructs an instance of IGFci with the provided independence test and score.
	IGFci(IndependenceTest test, ISScore score, Graph populationGraph)	Constructs an instance of IGFci with the provided independence test, score, and population graph.
	InterIamb(IndependenceTest test)	Constructs a new search.
	Mmhc(IndependenceTest test, DataSet dataSet)	Constructor for Mmhc.
	Mmmb(IndependenceTest test, int depth, boolean symmetric)	Constructs.
	SampleVcpc(IndependenceTest independenceTest)	Constructs a CPC algorithm that uses the given independence test as oracle.
	SampleVcpcFast(IndependenceTest independenceTest)	Constructs a CPC algorithm that uses the given independence test as oracle.
	VcFas(IndependenceTest test)	Constructor for VcFas.
	VcPc(IndependenceTest independenceTest)	Constructs a CPC algorithm that uses the given independence test as oracle.
	VcPcAlt(IndependenceTest independenceTest)	Constructs a CPC algorithm that uses the given independence test as oracle.
	VcPcFast(IndependenceTest independenceTest)	Constructs a CPC algorithm that uses the given independence test as oracle.

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

Modifier	Constructor	Description
	Dci(List<IndependenceTest> tests)	Constructor for Dci.
	Dci(List<IndependenceTest> tests, ResolveSepsets.Method method)	Constructor for Dci.

Uses of IndependenceTest in edu.pitt.csb.mgm

Classes in edu.pitt.csb.mgm that implement IndependenceTest

Modifier and Type	Class	Description
class	IndTestMultinomialLogisticRegressionWald	Performs a test of conditional independence X _||_ Y | Z1...Zn where all searchVariables are either continuous or discrete.

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

Modifier and Type	Method	Description
static IndependenceTest	MixedUtils.IndTestFromString(String name, DataSet data, double alpha)	Returns independence tests by name located in edu.cmu.tetrad.search and edu.pitt.csb.mgm also supports shorthand for LRT ("lrt) and t-tests ("tlin" for prefer linear (fastest) or "tlog" for prefer logistic)
IndependenceTest	IndTestMultinomialLogisticRegressionWald.indTestSubset(List<Node> vars)	Tests the conditional independence between two variables given a sublist of variables.