likelihood.discrete {geiger}R Documentation

Likelihood for discrete character evolution

Description

Calculates the likelihood score for a set of discrete character data under a specified model

Usage

likelihood.discrete(phy, tip.data, q, delta=1, lambda=1, endf=1, break.point=0, f=1, rtt.rescale=0, total.rescale=F)

Arguments

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?

Details

Value

-loglnL

Note

Author(s)

Luke J. Harmon

References

Felsenstein pruning

See Also

Examples

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)



[Package geiger version 0.2-6 Index]