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 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:

    • 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:

    • toString

      public String toString()

      toString.

      Specified by:
      toString in interface Score
      Overrides:
      toString in class Object
      Returns:
      a String object