phytools (version 0.4-45)

anc.ML: Ancestral character estimation using likelihood

Description

This function estimates the evolutionary parameters and ancestral states for Brownian evolution using likelihood. It is also possible (for model="BM") to allow for missing data for some tip taxa.

Usage

anc.ML(tree, x, maxit=2000, model=c("BM","OU"), ...)

Arguments

tree

an object of class "phylo".

x

a vector of tip values for species; names(x) should be the species names.

maxit

an optional integer value indicating the maximum number of iterations for optimization.

model

model of continuous character evolution ont he tree. It's possible that only model="BM" works in the present version as model="OU" has not be thoroughly tested & some bugs were reported for an earlier version.

...

other arguments.

Value

• A list with the following components:
• sig2
  the variance of the BM process.
• ace
  a vector with the ancestral states.
• logLik
  the log-likelihood.
• convergence
  the value of $convergence returned by optim() (0 is good).

Details

Because this function relies on a high dimensional numerical optimization of the likelihood function, fastAnc should probably be preferred for most purposes. If using anc.ML, users should be cautious to ensure convergence. This has been ameliorated in phytools>=0.2-48 by seeding the ML optimization with the result from fastAnc.

References

Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223. Schluter, D., Price, T., Mooers, A. O., and Ludwig, D. (1997) Likelihood of ancestor states in adaptive radiation. Evolution 51, 1699-1711.

See Also

ace, anc.Bayes, fastAnc, optim

Examples

tree<-pbtree(n=50)
x<-fastBM(tree) # simulate using fastBM
anc.ML(tree,x) # fit model & estimate ancestral states