pal.statistics
Class ModelSupport

java.lang.Object
  extended by 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