Package edu.cmu.tetrad.search

Class IndTestFisherZPercentIndependent

java.lang.Object

edu.cmu.tetrad.search.IndTestFisherZPercentIndependent

All Implemented Interfaces:

IndependenceTest

public final class IndTestFisherZPercentIndependent
extends Object
implements IndependenceTest

Calculates independence from pooled residuals.

Author:

Joseph Ramsey

Constructor Summary

Constructors

Constructor	Description
IndTestFisherZPercentIndependent(List<DataSet> dataSets, double alpha)

Method Summary

Modifier and Type	Method	Description
IndependenceResult	checkIndependence(Node x, Node y, List<Node> z)
boolean	determines(List z, Node x)
double	getAlpha()	Gets the getModel significance level.
ICovarianceMatrix	getCov()
List<Matrix>	getCovMatrices()
DataSet	getData()
List<DataSet>	getDataSets()
double	getPercent()
double	getPValue()
int[]	getRows()
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()
void	setAlpha(double alpha)	Sets the significance level at which independence judgments should be made.
void	setFdr(boolean fdr)
void	setPercent(double percent)
void	setVerbose(boolean verbose)
String	toString()

Methods inherited from class java.lang.Object

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

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

checkIndependence

Constructor Details

IndTestFisherZPercentIndependent

public IndTestFisherZPercentIndependent(List<DataSet> dataSets,
 double alpha)

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().

getPValue

public double getPValue()

Returns:

the probability associated with the most recently computed independence test.

setAlpha

public void setAlpha(double alpha)

Sets the significance level at which independence judgments should be made. Affects the cutoff for partial correlations to be considered statistically equal to zero.

Specified by:

setAlpha in interface IndependenceTest

getAlpha

public double getAlpha()

Gets the getModel significance level.

Specified by:

getAlpha in interface IndependenceTest

Returns:

the significance level of the independence test.

getVariables

public List<Node> getVariables()

Specified by:

getVariables in interface IndependenceTest

Returns:

the list of variables over which this independence checker is capable of determinine independence relations-- that is, all the variables in the given graph or the given data set.

getVariable

public Node getVariable(String name)

Specified by:

getVariable in interface IndependenceTest

Returns:

the variable with the given name.

getVariableNames

public List<String> getVariableNames()

Specified by:

getVariableNames in interface IndependenceTest

Returns:

the list of variable varNames.

determines

public boolean determines(List z,
 Node x)
                   throws UnsupportedOperationException

Specified by:

determines in interface IndependenceTest

Returns:

true if y is determined the variable in z.

Throws:

UnsupportedOperationException

getData

public DataSet getData()

Specified by:

getData in interface IndependenceTest

Returns:

The data model for the independence test.

Throws:

UnsupportedOperationException

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

toString

public String toString()

Specified by:

toString in interface IndependenceTest

Overrides:

toString in class Object

Returns:

a string representation of this test.

getRows

public int[] getRows()

getPercent

public double getPercent()

setPercent

public void setPercent(double percent)

setFdr

public void setFdr(boolean fdr)

isVerbose

public boolean isVerbose()

Specified by:

isVerbose in interface IndependenceTest

setVerbose

public void setVerbose(boolean verbose)

Specified by:

setVerbose in interface IndependenceTest