R: Ancestral character estimation using likelihood

anc.ML {phytools}

R Documentation

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.

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.

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).

Author(s)

Liam Revell liam.revell@umb.edu

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.

Examples

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

[Package phytools version 0.4-60 Index]