phytools: brownieREML – R documentation

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brownieREML

REML version of brownie.lite

Description

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.

Usage

brownieREML(tree, x, maxit=2000, ...)

Arguments

`tree`	an object of class `"phylo"` or `"simmap"`. (See `read.simmap` and `make.simmap` for more information about the latter object class.)
`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.
`...`	optional arguments.

Value

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

`sig2.single`	is the rate, σ^2, 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 (σ_1^2, σ_2^2, and so on) from the multi-rate model.
`logL2`	log-likelihood of the multi-rate model.
`convergence`	numerical value from `optim`.

Author(s)

Liam Revell liam.revell@umb.edu

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.

Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.