phytools: fitDiversityModel – R documentation

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phytools

fitDiversityModel

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)
## S3 method for class 'fitDiversityModel'
logLik(object, ...)
## S3 method for class 'fitDiversityModel'
print(x, ...)

Arguments

`tree`	an object of class `"phylo"`.
`x`	a vector with tip values for a continuously distributed trait. For `print` method, an object of class `"fitDiversityModel"`.
`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.
`object`	for `logLik` method, an object of class `"fitDiversityModel"`.
`...`	optional arguments for `logLik` and `print` methods. Note that for the `logLik` method the number of fitted parameters (`"df"`) is assumed to be 3 for the diversity dependent model (that is, if `psi` is estimated) and 2 for the diversity independent model, unless otherwise specified (using the argument `df`).

Value

An object of class "fitDiversityModel" consisting of the following components:

`logL`	log-likelihood of the fitted model.
`sig0`	estimated starting value for the rate at the root of the tree, σ_0^2.
`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.