fastBM: Fast Brownian simulation

Description

This function conducts 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.

Usage

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

Arguments

tree

is a phylogenetic tree in "phylo" format.

a value for ancestral state at the root node.

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.

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.

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.

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

tree<-pbtree(n=1000)
x<-fastBM(tree,sig2=0.1) # Brownian motion
y<-fastBM(tree,mu=1) # with a trend