R: Brownian simulation with multiple evolutionary rates

sim.rates {phytools}

R Documentation

Brownian simulation with multiple evolutionary rates

This function conducts BM simulation on a tree with multiple rates.

sim.rates(mtree, sig2, anc=0, nsim=1, internal=F, plot=F)

`mtree`	is a stochastic map format phylogenetic tree in modified `"phylo"` format (e.g., see `make.simmap`).
`sig2`	a named vector containing the rates for each state; names should be states in `mtree`.
`anc`	optional value for the root state.
`nsim`	number of simulations.
`internal`	logical value indicating whether to return states at internal nodes.
`plot`	logical value indicating whether or not to visual the rate heterogeneity (default value is `FALSE`.

A vector (for nsim=1) or matrix containing the tip states for the n species in the tree.

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