Class ModelSupport

java.lang.Object
pal.statistics.ModelSupport
All Implemented Interfaces:
Report

public class ModelSupport extends Object implements Report
Computes Akaike weights and expected Akaike weights (relative evidence, expected relative evidence) for a set of models and computes corresponding confidence sets
Version:
$Id: ModelSupport.java,v 1.3 2001/07/13 14:39:13 korbinian Exp $
Author:
Korbinian Strimmer
  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    double[]
    log-likelihood differences to the best tree
    int[]
    likelhood order of the tree hypotheses
    int
    number of bootstrap replicates
    double[]
    posterior probabilities for each hypothesis
    double[]
    support in each hypothesis
    int[]
    support order of the tree hypotheses
  • Constructor Summary

    Constructors
    Constructor
    Description
     
  • Method Summary

    Modifier and Type
    Method
    Description
    void
    compare(double[][] sLogL, int numBoot)
    Determine posterior probabilties and support values for each hypothesis and store results in public arrays posterior, support etc which will automatically be created by this procedure.
    void
    compare(double[][] pLogL, int[] alias, int numBoot)
    Determine posterior probabilties and support values for each hypothesis and store results in public arrays posterior, support etc which will automatically be created by this procedure.
    void
    print human readable report (e.g., on parameters and associated model)

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
  • Field Details

    • likelihoodOrder

      public int[] likelihoodOrder
      likelhood order of the tree hypotheses
    • supportOrder

      public int[] supportOrder
      support order of the tree hypotheses
    • deltaL

      public double[] deltaL
      log-likelihood differences to the best tree
    • posterior

      public double[] posterior
      posterior probabilities for each hypothesis
    • support

      public double[] support
      support in each hypothesis
    • numBootstraps

      public int numBootstraps
      number of bootstrap replicates
  • Constructor Details

    • ModelSupport

      public ModelSupport()
  • Method Details

    • compare

      public void compare(double[][] sLogL, int numBoot)
      Determine posterior probabilties and support values for each hypothesis and store results in public arrays posterior, support etc which will automatically be created by this procedure.
      Parameters:
      sLogL - log-likelihoods of each site
      numBoot - number of bootstraps
    • compare

      public void compare(double[][] pLogL, int[] alias, int numBoot)
      Determine posterior probabilties and support values for each hypothesis and store results in public arrays posterior, support etc which will automatically be created by this procedure.
      Parameters:
      pLogL - log-likelihoods of each pattern
      alias - map of patterns to sites in sequence
      numBoot - number of bootstraps
    • report

      public void report(PrintWriter out)
      Description copied from interface: Report
      print human readable report (e.g., on parameters and associated model)
      Specified by:
      report in interface Report
      Parameters:
      out - output stream