Class KishinoHasegawaTest

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

public class KishinoHasegawaTest extends Object implements Report
Kishino-Hasegawa-(Templeton)-Test (1989, 1983) to compare a set of evolutionary hypotheses
Version:
$Id: KishinoHasegawaTest.java,v 1.6 2004/02/25 02:55:55 matt 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
    double[]
    estimated error of log-likelihood differences
    double[]
    corresponding p-value (two-sided test on normal distribution)
  • Constructor Summary

    Constructors
    Constructor
    Description
     
  • Method Summary

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

      public double[] deltaSE
      estimated error of log-likelihood differences
    • pval

      public double[] pval
      corresponding p-value (two-sided test on normal distribution)
  • Constructor Details

    • KishinoHasegawaTest

      public KishinoHasegawaTest()
  • Method Details

    • compare

      public void compare(double[][] sLogL)
      Compare all given hypotheses to the best (ML) hypothesis and store results in public arrays delta, deltaSE, pval (which will automatically be created by this procedure).
      Parameters:
      sLogL - log-likelihoods of each site
    • compare

      public void compare(double[][] pLogL, int[] alias)
      Compare all given hypotheses to the best (ML) hypothesis and store results in public arrays delta, deltaSE, pval (which will automatically be created by this procedure).
      Parameters:
      pLogL - log-likelihoods of each pattern
      alias - map of patterns to sites in sequence
    • 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