Package pal.statistics

Class ModelSupport

  • All Implemented Interfaces:
    Report
    public class ModelSupport
extends java.lang.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[] deltaL
      log-likelihood differences to the best tree
      int[] likelihoodOrder
      likelhood order of the tree hypotheses
      int numBootstraps
      number of bootstrap replicates
      double[] posterior
      posterior probabilities for each hypothesis
      double[] support
      support in each hypothesis
      int[] supportOrder
      support order of the tree hypotheses

    • Constructor Summary

      Constructors 
      Constructor Description
      ModelSupport()  

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      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 report​(java.io.PrintWriter out)
      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 Detail

      • 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 Detail

      • ModelSupport

        public ModelSupport()

    • Method Detail

      • 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​(java.io.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