Package 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
Constructors Constructor Description DemographicLikelihoodValue(SitePattern sp)
Parameter taking a site pattern.
-
Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description 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
-
-
-
-
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 classLikelihoodValue
-
-