This function takes an object of class "phylo" or an object of class "simmap" 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.
brownieREML(tree, x, maxit=2000, ...)An object of class "brownieREML" containing the following components:
is the rate, \(\sigma^2\), for a single rate model - this is usually the "null" model.
log-likelihood of the single-rate model.
is a length p (for p rates) vector of BM rates (\(\sigma_1^2\), \(\sigma_2^2\), and so on) from the multi-rate model.
log-likelihood of the multi-rate model.
numerical value from optim.
an object of class "phylo" or "simmap". (See read.simmap and make.simmap for more information about the latter object class.)
a vector of tip values for species. names(x) should be the species names.
an optional integer value indicating the maximum number of iterations for optimization - may need to be increased for large trees.
optional arguments.
Liam Revell liam.revell@umb.edu
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.
Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.
brownie.lite, evol.vcv, evol.rate.mcmc, ratebytree