phytools (version 0.3-72.1)

anc.ML: Ancestral character estimation using likelihood

Description

This function estimates the evolutionary parameters and ancestral states for Brownian evolution using likelihood.

Usage

anc.ML(tree, x, maxit=2000)

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.

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.

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