phytools: evolvcv.lite – R documentation

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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`.
`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.

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.

Examples

## 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)

phytools

Phylogenetic Tools for Comparative Biology (and Other Things)

v0.7-70

GPL (>= 2)

Authors

Liam J. Revell

Initial release

2020-9-19