simBMphylo: Creates a graphical illustration of Brownian motion evolution...

In phytools: Phylogenetic Tools for Comparative Biology (and Other Things)

Creates a graphical illustration of Brownian motion evolution on a phylogeny

Description

Simulates a discrete time phylogeny and Brownian motion trait, and generates a plot.

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, \sigma^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".

Details

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.

Value

An object of class "simBMphylo" or a plot.

Author(s)

Liam Revell [e-mail]

References

Revell, L. J. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.

See Also

bmPlot, fastBM, pbtree

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 documentation built on June 22, 2024, 10:39 a.m.