Class ShimodairaHasegawaTest

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

public class ShimodairaHasegawaTest extends 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
    number of maximum likelihood hypothesis
    double[]
    log-likelihood difference to maximum likelihood hypothesis
    int
    number of bootstrap replicates
    double[]
    corresponding p-value
  • Constructor Summary

    Constructors
    Constructor
    Description
     
  • Method Summary

    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
    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

    • 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 Details

    • ShimodairaHasegawaTest

      public ShimodairaHasegawaTest()
  • Method Details

    • 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(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