REML version of brownie.lite

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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

1
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.

...

optional arguments.

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.

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.

See Also

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

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