pal.eval
Class DemographicLikelihoodValue

java.lang.Object
  pal.eval.LikelihoodValue
      pal.eval.DemographicLikelihoodValue

public class DemographicLikelihoodValue
extends LikelihoodValue

Estimates the likelihood for a tree using a specified model of sequence evolution and a sequence alignment and a specific demographic model as a prior on coalescent intervals. Must be used in conjunction with DemographicClockTree!

Version:

$Id: DemographicLikelihoodValue.java,v 1.2 2001/07/13 14:39:13 korbinian Exp $

Author:

Alexei Drummond

Field Summary

Fields inherited from class pal.eval.LikelihoodValue

logL, rateAtSite, siteLogL

Constructor Summary

DemographicLikelihoodValue(SitePattern sp)
Parameter taking a site pattern.

Method Summary

double

compute() compute log-likelihood for current branch lengths and model return negative log-likelihood

Methods inherited from class pal.eval.LikelihoodValue

getModel, getSitePattern, getTree, optimiseParameters, optimiseParameters, renewSitePattern, setModel, setTree

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

DemographicLikelihoodValue

public DemographicLikelihoodValue(SitePattern sp)

Parameter taking a site pattern.

Method Detail

compute

public double compute()

compute log-likelihood for current branch lengths and model return negative log-likelihood

Overrides:

compute in class LikelihoodValue