phytools: fastBM – R documentation

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fastBM

(Reasonably) fast quantitative trait simulation on phylogenies

Description

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.

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, 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.

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.

Author(s)

Liam Revell liam.revell@umb.edu

References

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

Examples

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

phytools

Phylogenetic Tools for Comparative Biology (and Other Things)

v0.7-70

GPL (>= 2)

Authors

Liam J. Revell

Initial release

2020-9-19