Package pal.statistics
Class KishinoHasegawaTest
java.lang.Object
pal.statistics.KishinoHasegawaTest
- All Implemented Interfaces:
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
-
Field Summary
Fields -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
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
(PrintWriter out) print human readable report (e.g., on parameters and associated model)
-
Field Details
-
bestH
public int bestHnumber of maximum likelihood hypothesis -
delta
public double[] deltalog-likelihood difference to maximum likelihood hypothesis -
deltaSE
public double[] deltaSEestimated error of log-likelihood differences -
pval
public double[] pvalcorresponding p-value (two-sided test on normal distribution)
-
-
Constructor Details
-
KishinoHasegawaTest
public KishinoHasegawaTest()
-
-
Method Details
-
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
-
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
-
report
Description copied from interface:Report
print human readable report (e.g., on parameters and associated model)
-