Package pal.statistics
Class KishinoHasegawaTest
- java.lang.Object
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- pal.statistics.KishinoHasegawaTest
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- All Implemented Interfaces:
Report
public class KishinoHasegawaTest extends java.lang.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
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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 hypothesisdouble[]
deltaSE
estimated error of log-likelihood differencesdouble[]
pval
corresponding p-value (two-sided test on normal distribution)
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Constructor Summary
Constructors Constructor Description KishinoHasegawaTest()
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Method Summary
All Methods Instance Methods Concrete Methods 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
report(java.io.PrintWriter out)
print human readable report (e.g., on parameters and associated model)
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Field Detail
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bestH
public int bestH
number of maximum likelihood hypothesis
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delta
public double[] delta
log-likelihood difference to maximum likelihood hypothesis
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deltaSE
public double[] deltaSE
estimated error of log-likelihood differences
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pval
public double[] pval
corresponding p-value (two-sided test on normal distribution)
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Method Detail
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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
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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 patternalias
- map of patterns to sites in sequence
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