fit.discrete {geiger}R Documentation

Model fitting for discrete comparative data

Description

Fits macroevolutionary models to phylogenetic trees

Usage

fit.discrete(tip.data, phy, lambda=FALSE, delta=FALSE, start=1.0)

Arguments

tip.data Character states for tip data; names should match, and data should be a factor with levels
phy Phylogenetic tree in ape format
lambda Estimate lambda?
delta Estimate delta?
start Starting guess for q

Details

Value

Returns maximum likelihood value for q and selected parameters, along with the likelihood score Sometimes, parameters are confounded!

Note

Author(s)

Luke J. Harmon and R. E. Glor

References

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)

fit.discrete(gb, g.tree)
fit.discrete(gb, g.tree, lambda=TRUE)
fit.discrete(gb, g.tree, delta=TRUE)


[Package geiger version 0.2-6 Index]