pal.statistics
Class ShimodairaHasegawaTest
java.lang.Object
|
+--pal.statistics.ShimodairaHasegawaTest
- All Implemented Interfaces:
- Report
- public class ShimodairaHasegawaTest
- extends java.lang.Object
- implements Report
Shimodaira-Hasegawa-Test (1999) to
compare a set of evolutionary hypotheses
Field Summary |
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 |
Method Summary |
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) |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
bestH
public int bestH
- number of maximum likelihood hypothesis
delta
public double[] delta
- log-likelihood difference to maximum likelihood hypothesis
pval
public double[] pval
- corresponding p-value
numBootstraps
public int numBootstraps
- number of bootstrap replicates
ShimodairaHasegawaTest
public ShimodairaHasegawaTest()
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
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
report
public void report(java.io.PrintWriter out)
- Description copied from interface:
Report
- print human readable report (e.g., on parameters and associated model)
- Specified by:
report
in interface Report
- Following copied from interface:
pal.misc.Report
- Parameters:
out
- output stream