phytools: simBMphylo – R documentation

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simBMphylo

Creates a graphical illustration of Brownian motion evolution on a phylogeny

Description

The function simulates a discrete-time pure-birth phylogeny (for fixed N and t using rejection sampling) and then discrete-time Brownian motion on that tree. It then proceeds to generating a plot of the results.

Usage

simBMphylo(n, t, sig2, plot=TRUE, ...)
## S3 method for class 'simBMphylo'
plot(x, ...)

Arguments

`n`	number of taxa to simulate in the output tree.
`t`	total time for the simulation.
`sig2`	the rate of evolution under Brownian motion, σ^2, or a vector of rates. If the latter the length of the vector must exactly match `t`, otherwise the first element of `sig2` will just be duplicated `t` times.
`plot`	optional logical value indicating whether or not the simulated object should be plotted.
`...`	optional arguments to be passed to the `plot` method.
`x`	in `plot` method, object of class `"simBMphylo"`.

Value

An object of class "simBMphylo" or a plot.

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

set.seed(777)
simBMphylo(n=6,t=100,sig2=0.01)
## reset par to defaults
par(mfrow=c(1,1))
par(mar=c(5.1,4.1,4.1,2.1))

phytools

Phylogenetic Tools for Comparative Biology (and Other Things)

v0.7-70

GPL (>= 2)

Authors

Liam J. Revell

Initial release

2020-9-19