R: Fit diversity-dependent phenotypic evolution model

fitDiversityModel {phytools}

R Documentation

Fit diversity-dependent phenotypic evolution model

Description

This function fits a diversity-dependent phenotypic evolution model (based on Mahler et al. 2010).

Usage

fitDiversityModel(tree, x, d=NULL, showTree=TRUE, tol=1e-6)

Arguments

`tree`	an object of class `"phylo"`.
`x`	a vector with tip values for a continuously distributed trait.
`d`	a vector containing the inferred historical diversity at each node in the tree - if `d=NULL` (the default) function will treat the diversification as if it occurred in a single geographic area.
`showTree`	optional logical value indicating whether to plot the tree transformation implied by the model.
`tol`	some small value by which `d` is incremented during rescaling of `psi` for optimization. If R thinks your matrices are singular during optimization, try increasing `tol` slightly.

Value

A list with the following components:

`logL`	log-likelihood of the fitted model.
`sig0`	estimated starting value for the rate at the root of the tree.
`psi`	the estimated rate of change in the rate associated with the addition of a lineage.
`vcv`	a matrix with the variances and covariance of the estimated parameters (from the Hessian).

Author(s)

Liam Revell liam.revell@umb.edu

References

Mahler, D. L, L. J. Revell, R. E. Glor, and J. B. Losos. 2010. Ecological opportunity and the rate of morphological evolution in the diversification of Greater Antillean anoles. Evolution, 64, 2731-2745.

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