pal.statistics
Class ShimodairaHasegawaTest

java.lang.Object
  pal.statistics.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

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

Constructor Summary

ShimodairaHasegawaTest()

Method Summary

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