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!


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