phytools: branching.diffusion – R documentation

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Documentation

phytools

branching.diffusion

Animation of branching random diffusion

Description

This function creates an animation of branching random diffusion (i.e., BM with speciation).

Usage

branching.diffusion(sig2=1, b=0.0023, time.stop=1000, ylim=NULL, 
   smooth=TRUE, pause=0.02, record=NULL, path=NULL, ...)

Arguments

`sig2`	variance of BM process, σ^2.
`b`	birthrate for branching process.
`time.stop`	number of generations to run.
`ylim`	y limits (for plotting).
`smooth`	no longer used.
`pause`	pause (in s) between generations.
`record`	filename for video file output (no video if `NULL`).
`path`	full path to file for video rendering. (By default `branching.diffusion` will look for the executable `ffmpeg.exe` in the directory `C:/Program Files/ffmpeg/bin`, even though this will not make sense on non-Windows machines.)
`...`	optional arguments.

Value

An animated plot and (optionally) a recorded video file. For animation to be recorded to file, the function requires the package animation as well as a video renderer.

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.