fitDiversityModel {phytools}

Fit diversity-dependent phenotypic evolution model

Description

Fits a diversity-dependent phenotypic evolution model (similar to 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 elements:

logL

log-likelihood of the fitted model.

sig0

estimated starting value for the rate at the root of the tree, \sigma_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 [e-mail]

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. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.

See Also

brownie.lite, estDiversity, evol.rate.mcmc