Package edu.cmu.tetrad.search

Class IndTestProbabilistic

java.lang.Object

edu.cmu.tetrad.search.IndTestProbabilistic

All Implemented Interfaces:

IndependenceTest

public class IndTestProbabilistic
extends Object
implements IndependenceTest

Uses BCInference by Cooper and Bui to calculate probabilistic conditional independence judgments.

Author:

Joseph Ramsey 3/2014

Constructor Summary

Constructors

Constructor	Description
IndTestProbabilistic(DataSet dataSet)	Initializes the test using a discrete data sets.

Method Summary

Modifier and Type	Method	Description
IndependenceResult	checkIndependence(Node x, Node y, Node... z)
IndependenceResult	checkIndependence(Node x, Node y, List<Node> z)
boolean	determines(List<Node> z, Node y)
double	getAlpha()
ICovarianceMatrix	getCov()
List<Matrix>	getCovMatrices()
DataModel	getData()
List<DataSet>	getDataSets()
Map<IndependenceFact,Double>	getH()
double	getPosterior()
int	getSampleSize()
double	getScore()	A score that is higher with more likely models.
Node	getVariable(String name)
List<String>	getVariableNames()
List<Node>	getVariables()
IndependenceTest	indTestSubset(List<Node> vars)
boolean	isVerbose()
double	probConstraint(BCInference bci, BCInference.OP op, Node x, Node y, Node[] z, Map<Node,Integer> indices)
void	setAlpha(double alpha)	Sets the significance level.
void	setCutoff(double cutoff)
void	setPriorEquivalentSampleSize(double priorEquivalentSampleSize)
void	setThreshold(boolean noRandomizedGeneratingConstraints)
void	setVerbose(boolean verbose)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface edu.cmu.tetrad.search.IndependenceTest

toString

Constructor Details

IndTestProbabilistic

public IndTestProbabilistic(DataSet dataSet)

Initializes the test using a discrete data sets.

Method Details

indTestSubset

public IndependenceTest indTestSubset(List<Node> vars)

Specified by:

indTestSubset in interface IndependenceTest

Returns:

an Independence test for a subset of the variables.

checkIndependence

public IndependenceResult checkIndependence(Node x,
 Node y,
 List<Node> z)

Specified by:

checkIndependence in interface IndependenceTest

Returns:

true if the given independence question is judged true, false if not. The independence question is of the form x _||_ y | z, z = <z1,...,zn>, where x, y, z1,...,zn are variables in the list returned by getVariableNames().

checkIndependence

public IndependenceResult checkIndependence(Node x,
 Node y,
 Node... z)

Specified by:

checkIndependence in interface IndependenceTest

Returns:

true if the given independence question is judged true, false if not. The independence question is of the form x _||_ y | z, z = <z1,...,zn>, where x, y, z1,...,zn are variables in the list returned by getVariableNames().

probConstraint

public double probConstraint(BCInference bci,
 BCInference.OP op,
 Node x,
 Node y,
 Node[] z,
 Map<Node,Integer> indices)

getVariables

public List<Node> getVariables()

Specified by:

getVariables in interface IndependenceTest

Returns:

the list of variables over which this independence checker is capable of determinining independence relations.

getVariable

public Node getVariable(String name)

Specified by:

getVariable in interface IndependenceTest

Returns:

the variable by the given name.

getVariableNames

public List<String> getVariableNames()

Specified by:

getVariableNames in interface IndependenceTest

Returns:

the list of names for the variables in getNodesInEvidence.

determines

public boolean determines(List<Node> z,
 Node y)

Specified by:

determines in interface IndependenceTest

Returns:

true if y is determined the variable in z.

getAlpha

public double getAlpha()

Specified by:

getAlpha in interface IndependenceTest

Returns:

the significance level of the independence test.

setAlpha

public void setAlpha(double alpha)

Description copied from interface: IndependenceTest

Sets the significance level.

Specified by:

setAlpha in interface IndependenceTest

getData

public DataModel getData()

Specified by:

getData in interface IndependenceTest

Returns:

The data model for the independence test.

getCov

public ICovarianceMatrix getCov()

Specified by:

getCov in interface IndependenceTest

getDataSets

public List<DataSet> getDataSets()

Specified by:

getDataSets in interface IndependenceTest

getSampleSize

public int getSampleSize()

Specified by:

getSampleSize in interface IndependenceTest

getCovMatrices

public List<Matrix> getCovMatrices()

Specified by:

getCovMatrices in interface IndependenceTest

getScore

public double getScore()

Description copied from interface: IndependenceTest

A score that is higher with more likely models.

Specified by:

getScore in interface IndependenceTest

getH

public Map<IndependenceFact,Double> getH()

getPosterior

public double getPosterior()

isVerbose

public boolean isVerbose()

Specified by:

isVerbose in interface IndependenceTest

setVerbose

public void setVerbose(boolean verbose)

Specified by:

setVerbose in interface IndependenceTest

setThreshold

public void setThreshold(boolean noRandomizedGeneratingConstraints)

setCutoff

public void setCutoff(double cutoff)

setPriorEquivalentSampleSize

public void setPriorEquivalentSampleSize(double priorEquivalentSampleSize)