pal.statistics
Class ModelSupport

java.lang.Object
  pal.statistics.ModelSupport

All Implemented Interfaces:

Report

public class ModelSupport
extends java.lang.Object
implements Report

Computes Akaike weights and expected Akaike weights (relative evidence, expected relative evidence) for a set of models and computes corresponding confidence sets

Version:

$Id: ModelSupport.java,v 1.3 2001/07/13 14:39:13 korbinian Exp $

Author:

Korbinian Strimmer

Field Summary

double[]	deltaL log-likelihood differences to the best tree
int[]	likelihoodOrder likelhood order of the tree hypotheses
int	numBootstraps number of bootstrap replicates
double[]	posterior posterior probabilities for each hypothesis
double[]	support support in each hypothesis
int[]	supportOrder support order of the tree hypotheses

Constructor Summary

ModelSupport()

Method Summary

void	compare(double[][] sLogL, int numBoot) Determine posterior probabilties and support values for each hypothesis and store results in public arrays posterior, support etc which will automatically be created by this procedure.
void	compare(double[][] pLogL, int[] alias, int numBoot) Determine posterior probabilties and support values for each hypothesis and store results in public arrays posterior, support etc 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

likelihoodOrder

public int[] likelihoodOrder

likelhood order of the tree hypotheses

supportOrder

public int[] supportOrder

support order of the tree hypotheses

deltaL

public double[] deltaL

log-likelihood differences to the best tree

posterior

public double[] posterior

posterior probabilities for each hypothesis

support

public double[] support

support in each hypothesis

numBootstraps

public int numBootstraps

number of bootstrap replicates

Constructor Detail

ModelSupport

public ModelSupport()

Method Detail

compare

public void compare(double[][] sLogL,
                    int numBoot)

Determine posterior probabilties and support values for each hypothesis and store results in public arrays posterior, support etc 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)

Determine posterior probabilties and support values for each hypothesis and store results in public arrays posterior, support etc 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