pal.statistics
Class ShimodairaHasegawaTest

java.lang.Object
  extended by 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