evol.vcv {phytools}  R Documentation 
This function takes a modified "phylo"
object with a mapped binary or multistate trait and data for an arbitrary number of continuously valued character. It then fits the multiple evolutionary variancecovariance matrix (rate matrix) model of Revell & Collar (2009; Evolution).
evol.vcv(tree, X, maxit=2000, vars=FALSE, ...)
tree 
a phylogenetic tree in modified 
X 
an 
maxit 
an optional integer value indicating the maximum number of iterations for optimization  may need to be increased for large trees. 
vars 
an optional logical value indicating whether or not to estimate the variances of the parameter estimates from the Hessian matrix. 
... 
optional arguments. 
This function performs optimization by first optimizing the likelihood with respect to the Cholesky matrices using optim
. Optimization is by method="NelderMead"
. Using box constraints does not make sense here as they would be applied to the Cholesky matrix rather than the target parameters. May have to increase maxit
for large trees and more than 2 traits.
A list with the following components:
R.single 
vcv matrix for the single rate matrix model. 
vars.single 
optionally, a matrix containing the variances of the elements of 
logL1 
loglikelihood for single matrix model. 
k1 
number of parameters in the single marix model. 
R.multiple 

vars.multiple 
optionally, an array containing the variances of the parameter estimates in 
logL.multiple 
loglikelihood of the multimatrix model. 
k2 
number of parameters estimated in this model. 
P.chisq 
Pvalue of the χ^2 test on the likelihood ratio. 
convergence 
logical value indicating whether or not the optimization has converged. 
Liam Revell liam.revell@umb.edu
Revell, L. J., and D. C. Collar (2009) Phylogenetic analysis of the evolutionary correlation using likelihood. Evolution, 63, 10901100.
Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217223.