phytools (version 0.1-9)

fitDiversityModel: Fit diversity-dependent phenotypic evolution model

Description

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

Usage

fitDiversityModel(tree,x,d=NULL,showTree=TRUE)

Arguments

tree

is a phylogenetic tree in "phylo" format.

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.

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).
• convergence
  a logical value indicating whether or not R thinks that the optimization has converged.

Details

The optimization is performed using optim with method="L-BFGS-B", but box constraints are only used for the change parameter (psi).

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.

See Also

brownie.lite, estDiversity, evol.rate.mcmc