brownieREML: REML version of brownie.lite

In phytools: Phylogenetic Tools for Comparative Biology (and Other Things)

REML version of brownie.lite

Description

Fits a multi-rate Brownian motion evolution model using REML. (See brownie.lite for more details.)

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.

Details

This function takes an object of class "phylo" or an object of class "simmap" with a mapped binary or multi-state 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.

Value

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

sig2.single	is the rate, \sigma^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 (\sigma_1^2, \sigma_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 [e-mail]

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. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.

See Also

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

Examples

## load data from Revell & Collar (2009)
data(sunfish.tree)
data(sunfish.data)
## extract character of interest
gape.width<-setNames(sunfish.data$gape.width,
    rownames(sunfish.data))
## fit model
multiBM.reml<-brownieREML(sunfish.tree,
	gape.width)
print(multiBM.reml)

phytools documentation built on June 22, 2024, 10:39 a.m.