|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectpal.eval.LikelihoodValue
pal.eval.DemographicLikelihoodValue
public class 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!
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 |
---|
public DemographicLikelihoodValue(SitePattern sp)
Method Detail |
---|
public double compute()
compute
in class LikelihoodValue
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |