Package edu.cmu.tetrad.search

Class SemBicScore

java.lang.Object
edu.cmu.tetrad.search.SemBicScore
All Implemented Interfaces:
Score
public class SemBicScore extends Object implements Score
Implements the continuous BIC score for FGES.
Author:
Joseph Ramsey

  • Constructor Details

    • SemBicScore

      public SemBicScore(ICovarianceMatrix covariances)
      Constructs the score using a covariance matrix.

    • SemBicScore

      public SemBicScore(DataSet dataSet)
      Constructs the score using a covariance matrix.

  • Method Details

    • getVarRy

      public static double getVarRy(int i, int[] parents, Matrix data, ICovarianceMatrix covariances, boolean calculateRowSubsets) throws org.apache.commons.math3.linear.SingularMatrixException
      Throws:
      org.apache.commons.math3.linear.SingularMatrixException

    • bStar

      @NotNull public static @NotNull Matrix bStar(Matrix b)

    • localScoreDiff

      public double localScoreDiff(int x, int y, int[] z)
      Specified by:
      localScoreDiff in interface Score

    • nandyBic

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

    • localScoreDiff

      public double localScoreDiff(int x, int y)
      Specified by:
      localScoreDiff in interface Score

    • localScore

      public double localScore(int i, int... parents)
      Specified by:
      localScore in interface Score
      Parameters:
      i - The index of the node.
      parents - The indices of the node's parents.
      Returns:
      The score, or NaN if the score cannot be calculated.

    • 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

    • localScore

      public double localScore(int i)
      Specialized scoring method for no parents. Used to speed up the effect edges search.
      Specified by:
      localScore in interface Score

    • getPenaltyDiscount

      public double getPenaltyDiscount()

    • setPenaltyDiscount

      public void setPenaltyDiscount(double penaltyDiscount)

    • getStructurePrior

      public double getStructurePrior()

    • setStructurePrior

      public void setStructurePrior(double structurePrior)

    • getCovariances

      public ICovarianceMatrix getCovariances()

    • getSampleSize

      public int getSampleSize()
      Specified by:
      getSampleSize in interface Score

    • isEffectEdge

      public boolean isEffectEdge(double bump)
      Specified by:
      isEffectEdge in interface Score

    • getDataModel

      public DataModel getDataModel()

    • isVerbose

      public boolean isVerbose()

    • setVerbose

      public void setVerbose(boolean verbose)

    • getVariables

      public List<Node> getVariables()
      Specified by:
      getVariables in interface Score

    • setVariables

      public void setVariables(List<Node> variables)

    • getVariable

      public Node getVariable(String targetName)
      Specified by:
      getVariable in interface Score

    • getMaxDegree

      public int getMaxDegree()
      Specified by:
      getMaxDegree in interface Score

    • determines

      public boolean determines(List<Node> z, Node y)
      Specified by:
      determines in interface Score

    • getData

      public DataModel getData()

    • setRuleType

      public void setRuleType(SemBicScore.RuleType ruleType)

    • subset

      public SemBicScore subset(List<Node> pi2)