phytools (version 0.2-40)

brownieREML: REML version of brownie.lite

Description

This function takes a modified "phylo" object with a mapped binary or multistate trait (see read.simmap) and data for a single continuously valued character. It then uses restricted maximum likelihood (REML) to fit the Brownian rate variation ("noncensored") model of O'Meara et al. (2006; Evolution). This function is similar to brownie.lite but uses REML (which is faster and unbiased) instead of ML. REML optimization takes advantage of Felsenstein's (1985) contrasts algorithm.

Usage

brownieREML(tree, x, maxit=2000)

Arguments

tree

a phylogenetic tree in modified "phylo" format (see read.simmap and make.simmap).

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 - may need to be increased for large trees.

Value

• a list with the following components:
• sig2.single
  is the rate for a single rate model - this is usually the "null" model.
• logL1
  log-likelihood of the single-rate model.
• sig2.multiple
  is a length p (for p rates) vector of BM rates from the multi-rate model.
• logL2
  log-likelihood of the multi-rate model.
• convergence
  numerical value from optim.

References

Felsenstein, J. 1985. Phylogenies and the comparative method. American Naturalist, 125, 1--15. O'Meara, B. C., C. Ane, M. J. Sanderson, and P. C. Wainwright. 2006. Testing for different rates of continuous trait evolution using likelihood. Evolution, 60, 922--933.

See Also

brownie.lite, evol.vcv, evol.rate.mcmc