Package edu.cmu.tetrad.search.work_in_progress

Class MagSemBicScore

java.lang.Object

edu.cmu.tetrad.search.work_in_progress.MagSemBicScore

All Implemented Interfaces:

Score

@Experimental
public class MagSemBicScore
extends Object
implements Score

Gives a BIC score for a linear, Gaussian MAG (Mixed Ancestral Graph). It will perform the same as SemBicScore for DAGs.

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

Version:

$Id: $Id

Author:

Bryan Andrews

Constructor Summary

Constructors

Constructor	Description
MagSemBicScore(DataSet dataSet, boolean precomputeCovariances)	Constructor.
MagSemBicScore(ICovarianceMatrix covariances)	Constructor.

Method Summary

Modifier and Type	Method	Description
Graph	getMag()	Returns the wrapped MAG.
int	getMaxDegree()	Returns the max degree, by default 1000.
List<Node>	getOrder()	Returns the order.
double	getPenaltyDiscount()	getPenaltyDiscount.
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.
double	localScore(int i, int... js)	The score of a node given its parents.
double	localScoreDiff(int x, int y, int[] z)	Returns the score difference of the graph.
void	resetMag()	Sets the MAG to null.
void	resetOrder()	Sets the order ot null.
void	setMag(Graph mag)	Sets the MAG to wrap.
void	setOrder(List<Node> order)	Sets the order.
void	setPenaltyDiscount(double penaltyDiscount)	Seets the penalty discount.
String	toString()	toString.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface edu.cmu.tetrad.search.score.Score

append, determines, getVariable, localScore, localScore, localScoreDiff

Constructor Details

MagSemBicScore

public MagSemBicScore(ICovarianceMatrix covariances)

Constructor.

Parameters:

covariances - The covarainces to analyze.

MagSemBicScore

public MagSemBicScore(DataSet dataSet,
 boolean precomputeCovariances)

Constructor.

Parameters:

dataSet - The continuous dataset to analyze.

precomputeCovariances - a boolean

Method Details

getMag

public Graph getMag()

Returns the wrapped MAG.

Returns:

This MAG.

setMag

public void setMag(Graph mag)

Sets the MAG to wrap.

Parameters:

mag - This MAG.

resetMag

public void resetMag()

Sets the MAG to null.

getOrder

public List<Node> getOrder()

Returns the order.

Returns:

The order of variables, a list.

setOrder

public void setOrder(List<Node> order)

Sets the order.

Parameters:

order - The order of variables, a list.

resetOrder

public void resetOrder()

Sets the order ot null.

localScore

public double localScore(int i,
 int... js)

The score of a node given its parents.

Return the BIC score for a node given its parents.

Specified by:

localScore in interface Score

Parameters:

i - The node.

js - The parents.

Returns:

The score.

getPenaltyDiscount

public double getPenaltyDiscount()

getPenaltyDiscount.

Returns:

The penalty discount, a multiplier on the penalty term of BIC.

setPenaltyDiscount

public void setPenaltyDiscount(double penaltyDiscount)

Seets the penalty discount.

Parameters:

penaltyDiscount - This number, a multiplier on the penalty term of BIC.

localScoreDiff

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

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.

getSampleSize

public int getSampleSize()

The sample size of the data.

Returns the sample size.

Specified by:

getSampleSize in interface Score

Returns:

This size.

getVariables

public List<Node> getVariables()

The variables of the score.

Returns the list of variables.

Specified by:

getVariables in interface Score

Returns:

This list.

isEffectEdge

public boolean isEffectEdge(double bump)

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

Returns a judgment for FGES as to whether an edges with this bump (for this score) counts as 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.

See Also:

• Fges

getMaxDegree

public int getMaxDegree()

Returns the max degree, by default 1000.

Returns a judgment of the max degree needed for this score.

Specified by:

getMaxDegree in interface Score

Returns:

The max degree.

See Also:

• Fges

toString

public String toString()

toString.

Specified by:

toString in interface Score

Overrides:

toString in class Object

Returns:

a String object