Package pal.statistics
Class ShimodairaHasegawaTest
- java.lang.Object
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- pal.statistics.ShimodairaHasegawaTest
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- 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
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Field Summary
Fields Modifier and Type Field Description int
bestH
number of maximum likelihood hypothesisdouble[]
delta
log-likelihood difference to maximum likelihood hypothesisint
numBootstraps
number of bootstrap replicatesdouble[]
pval
corresponding p-value
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Constructor Summary
Constructors Constructor Description ShimodairaHasegawaTest()
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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)
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Method Detail
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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 sitenumBoot
- number of bootstraps
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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 patternalias
- map of patterns to sites in sequencenumBoot
- number of bootstraps
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