evolvcv.lite: Likelihood test for a shift in the evolutionary correlation between traits

Description

This function takes an object of class "simmap" 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

an object of class "simmap". If tree is an object of class "phylo" then a simple multivariate Brownian motion model will be fit to the data in X.

an n x m matrix of tip values for m continuously valued traits in n species - row names should be species names. If X is supplied as a data frame it will be coerced into a matrix without warning.

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.

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.

Examples

Run this code

# NOT RUN {
## load data from Revell & Collar (2009)
data(sunfish.tree)
data(sunfish.data)
## fit heirarchical common-structure models
sunfish.fit<-evolvcv.lite(sunfish.tree,sunfish.data[,2:3])
print(sunfish.fit)
# }