Package pal.statistics
Class ShimodairaHasegawaTest
java.lang.Object
pal.statistics.ShimodairaHasegawaTest
- All Implemented Interfaces:
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
FieldsModifier and TypeFieldDescriptionint
number of maximum likelihood hypothesisdouble[]
log-likelihood difference to maximum likelihood hypothesisint
number of bootstrap replicatesdouble[]
corresponding p-value -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
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
(PrintWriter out) print human readable report (e.g., on parameters and associated model)
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Field Details
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bestH
public int bestHnumber of maximum likelihood hypothesis -
delta
public double[] deltalog-likelihood difference to maximum likelihood hypothesis -
pval
public double[] pvalcorresponding p-value -
numBootstraps
public int numBootstrapsnumber of bootstrap replicates
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Constructor Details
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ShimodairaHasegawaTest
public ShimodairaHasegawaTest()
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Method Details
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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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report
Description copied from interface:Report
print human readable report (e.g., on parameters and associated model)
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