brownieREML: REML version of brownie.lite

Description Usage Arguments Value Author(s) References See Also

View source: R/brownieREML.R


This function takes 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, ...)



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


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.


An object of class "brownieREML" containing the following components:


is the rate 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 from the multi-rate model.


log-likelihood of the multi-rate model.


numerical value from optim.


Liam Revell


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.

See Also

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

phytools documentation built on May 20, 2017, 2:22 a.m.
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