R: Function to test for correlated evolution of binary traits

fitPagel {phytools}

R Documentation

Function to test for correlated evolution of binary traits

Description

This function fit's Pagel's (1994) model for the correlated evolution of two binary characters.

Usage

fitPagel(tree, x, y, ...)

Arguments

`tree`	an object of class `"phylo"`.
`x`	a vector of phenotypic values for a binary trait for the species in `tree`.
`y`	a second binary character for the species in `tree`.
`...`	optional arguments. Currently includes `method`, which can be set to `"ace"` to use the `ace` function in ape for optimization, or to `"fitDiscrete"` (if the geiger package is installed) to use geiger's `fitDiscrete` for optimization.

Value

An object of class "fitPagel" which contains the optimized matrices under an independence & a dependence model, log-likelihoods, a likelihood ratio, and a P-value for the independence model based on a chi-squared test.

Author(s)

Liam Revell liam.revell@umb.edu

References

Pagel, M. (1994) Detecting correlated evolution on phylogenies: A general method for the comparative analysis fo discrete characters. Proceedings of the Royal Society B, 255, 37-45.

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