branching.diffusion {phytools}

Animation of branching random diffusion

Description

This function creates an animation of branching random diffusion (i.e., Brownian motion evolution 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, \sigma^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.

Details

For animation to be recorded to file, the function requires the package animation as well as a video renderer.

Value

An animated plot and (optionally) a recorded video file.

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