Package pal.statistics

Class ShimodairaHasegawaTest

  • All Implemented Interfaces:
    Report
    public class ShimodairaHasegawaTest
extends java.lang.Object
implements Report
    Shimodaira-Hasegawa-Test (1999) to compare a set of evolutionary hypotheses
    Version:
    $Id: ShimodairaHasegawaTest.java,v 1.4 2001/07/13 14:39:13 korbinian Exp $
    Author:
    Korbinian Strimmer

    • Field Summary

      Fields 
      Modifier and Type Field Description
      int bestH
      number of maximum likelihood hypothesis
      double[] delta
      log-likelihood difference to maximum likelihood hypothesis
      int numBootstraps
      number of bootstrap replicates
      double[] pval
      corresponding p-value

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void compare​(double[][] sLogL, int numBoot)
      Compare all given hypotheses to the best (ML) hypothesis and store results in public arrays delta, pval (which will automatically be created by this procedure).
      void compare​(double[][] pLogL, int[] alias, int numBoot)
      Compare all given hypotheses to the best (ML) hypothesis and store results in public arrays delta, pval (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

      • bestH

        public int bestH
        number of maximum likelihood hypothesis

      • delta

        public double[] delta
        log-likelihood difference to maximum likelihood hypothesis

      • pval

        public double[] pval
        corresponding p-value

      • numBootstraps

        public int numBootstraps
        number of bootstrap replicates

    • Constructor Detail

      • ShimodairaHasegawaTest

        public ShimodairaHasegawaTest()

    • Method Detail

      • compare

        public void compare​(double[][] sLogL,
                    int numBoot)
        Compare all given hypotheses to the best (ML) hypothesis and store results in public arrays delta, pval (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)
        Compare all given hypotheses to the best (ML) hypothesis and store results in public arrays delta, pval (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