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

Version:

$Id: ShimodairaHasegawaTest.java,v 1.4 2001/07/13 14:39:13 korbinian Exp $

Author:

Korbinian Strimmer

Field Summary

Fields
Modifier and Type	Field	Description
`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 Summary

Constructors
Constructor Description

ShimodairaHasegawaTest()

Constructors
Constructor	Description
`ShimodairaHasegawaTest()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`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

- Field Detail
  - 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
- Constructor Detail
  - ShimodairaHasegawaTest
```
public ShimodairaHasegawaTest()
```
- Method Detail
  - 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 site
    
    numBoot - 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 pattern
    
    alias - map of patterns to sites in sequence
    
    numBoot - 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
    
    Parameters:
    
    out - output stream

Class ShimodairaHasegawaTest

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

bestH

delta

pval

numBootstraps

Constructor Detail

ShimodairaHasegawaTest

Method Detail

compare

compare

report