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java.lang.Objectpal.statistics.KishinoHasegawaTest
public class KishinoHasegawaTest
Kishino-Hasegawa-(Templeton)-Test (1989, 1983) to compare a set of evolutionary hypotheses
Field Summary | |
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int |
bestH
number of maximum likelihood hypothesis |
double[] |
delta
log-likelihood difference to maximum likelihood hypothesis |
double[] |
deltaSE
estimated error of log-likelihood differences |
double[] |
pval
corresponding p-value (two-sided test on normal distribution) |
Constructor Summary | |
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KishinoHasegawaTest()
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Method Summary | |
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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) |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public int bestH
public double[] delta
public double[] deltaSE
public double[] pval
Constructor Detail |
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public KishinoHasegawaTest()
Method Detail |
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public void compare(double[][] sLogL)
sLogL
- log-likelihoods of each sitepublic void compare(double[][] pLogL, int[] alias)
pLogL
- log-likelihoods of each patternalias
- map of patterns to sites in sequencepublic void report(java.io.PrintWriter out)
Report
report
in interface Report
out
- output stream
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