fastBM: (Reasonably) fast quantitative trait simulation on phylogenies

Description

Simulates one or multiple continuous traits on the tree under various evolutionary models.

Usage

fastBM(tree, a=0, mu=0, sig2=1, bounds=c(-Inf,Inf), internal=FALSE, nsim=1, 
   ...)

Value

A vector (for nsim=1) or matrix containing the tip states for the n species in the tree, and (optionally) the ancestral states for internal nodes.

Arguments

tree: is a phylogenetic tree in "phylo" format.
a: a value for ancestral state at the root node.
mu: an optional value for the mean of random normal changes along branches of the tree - can be used to simulate a trend if mu!=0.
sig2: instantaneous variance of the BM process, $σ^{2}$ .
bounds: a vector with the lower and upper bounds (respectively) for bounded Brownian simulation - by default simulation is unbounded.
internal: logical value indicating whether or not to return states for internal nodes.
nsim: number of simulations.
...: optional arguments alpha and theta used for OU simulation. If alpha is set then mu and bounds are ignored with a warning.

Author

Liam Revell liam.revell@umb.edu

Details

This function conducts (reasonably) fast quantitative trait simulation on a phylogeny under several different models: Brownian motion (default), BM with a trend (for mu!=0), bounds (for bounds!=c(-Inf, Inf)), and OU.

References

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

Examples

Run this code

## simulate 10 characters on the Anolis tree 
## under Brownian motion
data(anoletree)
X<-fastBM(anoletree,nsim=10)
head(X)

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