Package pal.eval
Class DemographicLikelihoodValue
java.lang.Object
pal.eval.LikelihoodValue
pal.eval.DemographicLikelihoodValue
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
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Field Summary
Fields inherited from class pal.eval.LikelihoodValue
logL, rateAtSite, siteLogL
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptiondouble
compute()
compute log-likelihood for current branch lengths and model return negative log-likelihoodMethods inherited from class pal.eval.LikelihoodValue
getModel, getSitePattern, getTree, optimiseParameters, optimiseParameters, renewSitePattern, setModel, setTree
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Constructor Details
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DemographicLikelihoodValue
Parameter taking a site pattern.
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Method Details
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compute
public double compute()compute log-likelihood for current branch lengths and model return negative log-likelihood- Overrides:
compute
in classLikelihoodValue
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