Package edu.cmu.tetrad.search.score

Class BasisFunctionBicScore

java.lang.Object

edu.cmu.tetrad.search.score.BasisFunctionBicScore

All Implemented Interfaces:

Score

public class BasisFunctionBicScore
extends Object
implements Score

Calculates the basis function BIC score for a given dataset. This is a modification of the Degenerate Gaussian score by adding basis functions of the continuous variables and retains the function of the degenerate Gaussian for discrete variables by adding indicator variables per category.

Author:

bandrews, josephramsey

See Also:

• DegenerateGaussianScore

Constructor Summary

Constructors

Constructor	Description
BasisFunctionBicScore(DataSet dataSet, boolean precomputeCovariances, int truncationLimit, int basisType, double basisScale)	Constructs a BasisFunctionBicScore object with the specified parameters.

Method Summary

Modifier and Type	Method	Description
int	getMaxDegree()	Retrieves the maximum degree from the underlying BIC score component.
int	getSampleSize()	Retrieves the sample size from the underlying BIC score component.
List<Node>	getVariables()	Retrieves the list of nodes representing the variables in the basis function score.
boolean	isEffectEdge(double bump)	Determines if the given bump value represents an effect edge.
double	localScore(int i, int... parents)	Calculates the local score for a given node and its parent nodes.
double	localScoreDiff(int x, int y, int[] z)	Returns the score difference of the graph.
void	setPenaltyDiscount(double penaltyDiscount)	Sets the penalty discount value, which is used to adjust the penalty term in the BIC score calculation.
String	toString()	Returns a string representation of the BasisFunctionBicScore object.

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

BasisFunctionBicScore

public BasisFunctionBicScore(DataSet dataSet,
 boolean precomputeCovariances,
 int truncationLimit,
 int basisType,
 double basisScale)

Constructs a BasisFunctionBicScore object with the specified parameters.

Parameters:

dataSet - the data set on which the score is to be calculated.

precomputeCovariances - flag indicating whether covariances should be precomputed.

truncationLimit - the truncation limit of the basis.

basisType - the type of basis function used in the BIC score computation.

basisScale - the basisScale factor used in the calculation of the BIC score for basis functions. All variables are scaled to [-basisScale, basisScale], or standardized if 0.

See Also:

• StatUtils.basisFunctionValue(int, int, double)

Method Details

localScore

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

Calculates the local score for a given node and its parent nodes.

Specified by:

localScore in interface Score

Parameters:

i - The index of the node whose score is being calculated.

parents - The indices for the parent nodes of the given node.

Returns:

The calculated local score as a double value.

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.

getVariables

public List<Node> getVariables()

Retrieves the list of nodes representing the variables in the basis function score.

Specified by:

getVariables in interface Score

Returns:

a list containing the nodes that represent the variables in the basis function score.

isEffectEdge

public boolean isEffectEdge(double bump)

Determines if the given bump value represents an effect edge.

Specified by:

isEffectEdge in interface Score

Parameters:

bump - the bump value to be evaluated.

Returns:

true if the bump is an effect edge, false otherwise.

getSampleSize

public int getSampleSize()

Retrieves the sample size from the underlying BIC score component.

Specified by:

getSampleSize in interface Score

Returns:

the sample size as an integer

getMaxDegree

public int getMaxDegree()

Retrieves the maximum degree from the underlying BIC score component.

Specified by:

getMaxDegree in interface Score

Returns:

the maximum degree as an integer.

toString

public String toString()

Returns a string representation of the BasisFunctionBicScore object.

Specified by:

toString in interface Score

Overrides:

toString in class Object

Returns:

A string detailing the degenerate Gaussian score penalty with the penalty discount formatted to two decimal places.

setPenaltyDiscount

public void setPenaltyDiscount(double penaltyDiscount)

Sets the penalty discount value, which is used to adjust the penalty term in the BIC score calculation.

Parameters:

penaltyDiscount - The multiplier on the penalty term for this score.