likelihood.discrete {geiger} | R Documentation |
Calculates the likelihood score for a set of discrete character data under a specified model
likelihood.discrete(phy, tip.data, q, delta=1, lambda=1, endf=1, break.point=0, f=1, rtt.rescale=0, total.rescale=F)
phy |
Phylogenetic tree |
tip.data |
Tip data |
q |
Instantaneous rate of change |
delta |
Tree scaling parameter |
lambda |
Tree scaling parameter |
endf |
Tree scaling parameter |
break.point |
Tree scaling parameter |
f |
Tree scaling parameter |
rtt.rescale |
Rescale root-to-tip distance? |
total.rescale |
Rescale total tree length? |
-loglnL
Luke J. Harmon
Felsenstein pruning
data(geospiza) attach(geospiza) drop.tip(geospiza.tree, "olivacea")->g.tree gb<-as.factor(geospiza.data[,1]>4.2) names(gb)<-rownames(geospiza.data) likelihood.discrete(g.tree, gb, q=1) likelihood.discrete(g.tree, gb, q=1, delta=0.5) likelihood.discrete(g.tree, gb, q=1, lambda=0.5) likelihood.discrete(g.tree, gb, q=1, endf=0.5) likelihood.discrete(g.tree, gb, q=1, break.point=0.5, endf=0.2)