brownieREML {phytools} | R Documentation |
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.
brownieREML(tree, x, maxit=2000)
tree |
a phylogenetic tree in modified |
x |
a vector of tip values for species; |
maxit |
an optional integer value indicating the maximum number of iterations for optimization - may need to be increased for large trees. |
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 |
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