R: Likelihood test for a shift in the evolutionary correlation...

evolvcv.lite {phytools}

R Documentation

Likelihood test for a shift in the evolutionary correlation between traits

Description

This function takes a modified "phylo" object with a mapped binary or multistate trait and data for two and only two continuously valued character. It then fits four different evolutionary models: common rates and correlation; different rates, common correlation; different correlations, common rates; no common structure.

Usage

evolvcv.lite(tree, X, maxit=2000, tol=1e-10)

Arguments

`tree`	a phylogenetic tree in modified `"phylo"` format (see `read.simmap`).
`X`	an `n` x `m` matrix of tip values for `m` continuously valued traits in `n` species - row names should be species names.
`maxit`	an optional integer value indicating the maximum number of iterations for optimization - may need to be increased for large trees.
`tol`	tolerance value for `"L-BFGS-B"` optimization.

Value

A list with the results summarized for each model.

Author(s)

Liam Revell liam.revell@umb.edu

References

Revell, L. J., and D. C. Collar (2009) Phylogenetic analysis of the evolutionary correlation using likelihood. Evolution, 63, 1090-1100.

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