phytools (version 0.0-8)

evol.vcv: Likelihood test for variation in the evolutionary VCV matrix

Description

This function takes a modified "phylo" object with a mapped binary or multistate trait and data for an arbitrary number of continuously valued character. It then fits the multiple evolutionary variance-covariance matrix (rate matrix) model of Revell & Collar (2009; Evolution.

Usage

evol.vcv(scm.tre,dat,maxit=2000)

Arguments

scm.tre

a phylogenetic tree in modified "phylo" format (see read.simmap).

dat

an n x m matrix of tip values for m continuously valued traits in n species - row names should be species names.

maxit

an optional integer value indicating the maximum number of iterations for optimization - may need to be increased for large trees.

Value

• a list with the following components:
• R.single
  vcv matrix for the single rate matrix model.
• logL1
  log-likelihood for single matrix model.
• k1
  number of parameters in the single marix model.
• R.multiple
  m x m x p array containing the p estimated vcv matrices for the p regimes painted on the tree.
• logL.multiple
  log-likelihood of the multi-matrix model.
• k2
  number of parameters estimated in this model.
• P.chisq
  P-value of the X^2 test on the likelihood ratio.
• convergence
  logical value indicating whether or not the optimization has converged.

Details

May have to increase maxit for large trees and more than 2 traits.

References

Revell, L. J., and D. C. Collar. 2009. Phylogenetic analysis of the evolutionary correlation using likelihood. Evolution, 63, 1090-1100.

See Also

evol.rate.mcmc, brownie.lite