public class ShimodairaHasegawaTest extends java.lang.Object implements Report
Modifier and Type | Field and Description |
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int |
bestH
number of maximum likelihood hypothesis
|
double[] |
delta
log-likelihood difference to maximum likelihood hypothesis
|
int |
numBootstraps
number of bootstrap replicates
|
double[] |
pval
corresponding p-value
|
Constructor and Description |
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ShimodairaHasegawaTest() |
Modifier and Type | Method and Description |
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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)
|
public int bestH
public double[] delta
public double[] pval
public int numBootstraps
public void compare(double[][] sLogL, int numBoot)
sLogL
- log-likelihoods of each sitenumBoot
- number of bootstrapspublic void compare(double[][] pLogL, int[] alias, int numBoot)
pLogL
- log-likelihoods of each patternalias
- map of patterns to sites in sequencenumBoot
- number of bootstraps