phytools: sim.rates – R documentation

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sim.rates

Brownian or OU simulation with multiple evolutionary regimes

The function sim.rates conducts BM simulation on a tree with multiple rates.

The function multiOU conducts multi-regime OU simulations on the tree under a range of conditions.

sim.rates(tree, sig2, anc=0, nsim=1, internal=FALSE, plot=FALSE)
multiOU(tree, alpha, sig2, theta=NULL, a0=NULL, nsim=1, internal=FALSE, ...)

`tree`	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`.
`alpha`	single value or vector of values of the OU α parameter.
`theta`	single value or vector of values of the OU θ parameter.
`a0`	optional value of the root state. Defaults to zero.
`...`	optional arguments.

multiOU uses a difference equation approximation of the OU process.

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.