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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!
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 |
public DemographicLikelihoodValue(SitePattern sp)
Method Detail |
public double compute()
compute
in class LikelihoodValue
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