phytools (version 0.1-9)

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), and bounds (for bounds!=c(-Inf,Inf)).

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

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.

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.

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.

See Also

branching.diffusion

Examples

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