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.

Version:

$Id: $Id

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()	Returns the data set.
int	getMaxDegree()	Returns the max degree, by default 1000.
int	getSampleSize()	Returns the sample size.
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()	Returns true if verbose output should be sent to out.
double	localScore(int i)	Returns the local score of the gien node in the graph.
double	localScore(int i, int parent)	localScore.
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)	Sets whether verbose output should be sent to out.

Methods inherited from class java.lang.Object

equals, 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.

Parameters:

test - The independence test.

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 index of the variable.

parents - The indices of the parents of i.

Returns:

a double

localScoreDiff

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

Returns the score difference of the graph.

Returns a "score difference", which amounts to a conditional local scoring criterion results. Only difference methods is implemented, since the other methods don't make sense here.

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)

localScore.

Specified by:

localScore in interface Score

Parameters:

i - a int

parent - a int

Returns:

a double

Throws:

UnsupportedOperationException - if called.

localScore

public double localScore(int i)

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)

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

Returns true if the edge with the given bump 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()

Returns the data set.

Returns:

The data set.

isVerbose

public boolean isVerbose()

Returns true if verbose output should be sent to out.

Returns:

True if verbose output should be sent to out.

setVerbose

public void setVerbose(boolean verbose)

Sets whether verbose output should be sent to out.

Parameters:

verbose - True if verbose output should be sent to out.

getVariables

public List<Node> getVariables()

The variables of the score.

Returns the list of variables.

Specified by:

getVariables in interface Score

Returns:

This list.

getSampleSize

public int getSampleSize()

Returns the sample size.

Specified by:

getSampleSize in interface Score

Returns:

The sample size.

getMaxDegree

public int getMaxDegree()

Returns the max degree, by default 1000.

Returns the maximum degree, which is set to 1000.

Specified by:

getMaxDegree in interface Score

Returns:

The max degree.

determines

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

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

Returns the 'determines' judgment from the first score.

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.