Package edu.cmu.tetrad.search.score

Class IndTestScore

java.lang.Object

edu.cmu.tetrad.search.score.IndTestScore

All Implemented Interfaces:

Score

public class IndTestScore
extends Object
implements Score

Gives a method of interpreting a test as a score. Various independence tests will calculate p-values; they simply report alpha - p as a score, which will be higher for greater dependence. This class wraps such an independence test and returns the score reported by that test.

As for all scores in Tetrad, higher scores mean more dependence, and negative scores indicate independence.

Author:

josephramsey

See Also:

• IndependenceTest

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
boolean	determines(List<Node> z, Node y)	Returns true iff the score determines the edge between x and y.
DataSet	getDataSet()
int	getMaxDegree()	Returns the max degree, by default 1000.
int	getSampleSize()	The sample size of the data.
List<Node>	getVariables()	The variables of the score.
boolean	isEffectEdge(double bump)	Returns true iff the edge between x and y is an effect edge.
boolean	isVerbose()
double	localScore(int i)	Returns the local score of the gien node in the graph.
double	localScore(int i, int parent)	Specialized scoring method for a single parent.
double	localScore(int i, int[] parents)	Calculates the sample likelihood and BIC score for i, given its parents in a simple SEM model
double	localScoreDiff(int x, int y, int[] z)	Returns the score difference of the graph.
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.score.Score

append, getVariable, localScoreDiff, toString

Constructor Details

IndTestScore

public IndTestScore(IndependenceTest test)

Constructs the score using a covariance matrix.

Method Details

localScore

public double localScore(int i,
 int[] parents)

Calculates the sample likelihood and BIC score for i, given its parents in a simple SEM model

Specified by:

localScore in interface Score

Parameters:

i - The node.

parents - The parents.

Returns:

The score.

localScoreDiff

public double localScoreDiff(int x,
 int y,
 int[] z)

Description copied from interface: Score

Returns the score difference of the graph.

Specified by:

localScoreDiff in interface Score

Parameters:

x - A node.

y - TAhe node.

z - A set of nodes.

Returns:

The score difference.

localScore

public double localScore(int i,
 int parent)

Specialized scoring method for a single parent. Used to speed up the effect edges search.

Specified by:

localScore in interface Score

Parameters:

i - A node.

parent - A parent.

Returns:

The local score.

localScore

public double localScore(int i)

Description copied from interface: Score

Returns the local score of the gien node in the graph.

Specified by:

localScore in interface Score

Parameters:

i - A node.

Returns:

The local score.

isEffectEdge

public boolean isEffectEdge(double bump)

Description copied from interface: Score

Returns true iff the edge between x and y is an effect edge.

Specified by:

isEffectEdge in interface Score

Parameters:

bump - The bump.

Returns:

True iff the edge between x and y is an effect edge.

getDataSet

public DataSet getDataSet()

isVerbose

public boolean isVerbose()

setVerbose

public void setVerbose(boolean verbose)

getVariables

public List<Node> getVariables()

Description copied from interface: Score

The variables of the score.

Specified by:

getVariables in interface Score

Returns:

This list.

getSampleSize

public int getSampleSize()

Description copied from interface: Score

The sample size of the data.

Specified by:

getSampleSize in interface Score

Returns:

This size.

getMaxDegree

public int getMaxDegree()

Description copied from interface: Score

Returns the max degree, by default 1000.

Specified by:

getMaxDegree in interface Score

Returns:

The max degree.

determines

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

Description copied from interface: Score

Returns true iff the score determines the edge between x and y.

Specified by:

determines in interface Score

Parameters:

z - The set of nodes.

y - The node.

Returns:

True iff the score determines the edge between x and y.