branching.diffusion

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

Simulation

phylogenetics

plotting

animation

continuous character

A wide range of functions for phylogenetic analysis - concentrated in phylogenetic comparative biology, but also including numerous methods for visualizing, manipulating, reading or writing, and even inferring phylogenetic trees. Included among the functions in phylogenetic comparative biology are various for ancestral state reconstruction, model-fitting, and simulation of phylogenies and data, for continuous, discrete, and multivariate characters. A broad range of plotting methods for phylogenies and comparative data include, but are not restricted to, methods for mapping trait evolution on trees, for projecting trees into phenotypic space or a geographic map, and for visualizing correlated speciation between trees. Finally, numerous functions are designed for reading, writing, analyzing, inferring, simulating, and manipulating phylogenetic trees and comparative data. For instance, there are functions for randomly or non-randomly attaching species or clades to a phylogeny, for computing consensus phylogenies from a set, for simulating trees and phylogenetic data under a range of models, and for a wide variety of other manipulations and analyses that phylogenetic biologists might find useful in their research.

Liam Revell

phytools

Phylogenetic Tools for Comparative Biology (and Other Things)

branching.diffusion function

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

Arguments

Liam Revell <a href="/link/liam.revell%40umb.edu?package=phytools&version=1.2-0" data-mini-rdoc="phytools::liam.revell@umb.edu">liam.revell@umb.edu</a>

Author

Animation of branching random diffusion — branching.diffusion

<dl>

	<dt>sig2</dt>
<dd>variance of BM process, \(\sigma^2\).</dd>

	<dt>b</dt>
<dd>birthrate for branching process.</dd>

	<dt>time.stop</dt>
<dd>number of generations to run.</dd>

	<dt>ylim</dt>
<dd>y limits (for plotting).</dd>

	<dt>smooth</dt>
<dd>no longer used.</dd>

	<dt>pause</dt>
<dd>pause (in s) between generations.</dd>

	<dt>record</dt>
<dd>filename for video file output (no video if <code>NULL</code>).</dd>

	<dt>path</dt>
<dd>full path to file for video rendering. (By default <code>branching.diffusion</code> will look for the executable <code>ffmpeg.exe</code> in the directory <code>C:/Program Files/ffmpeg/bin</code>, even though this will not make sense on non-Windows machines.)</dd>

	<dt>...</dt>
<dd>optional arguments.</dd>

</dl>

Liam Revell <a href='mailto:liam.revell@umb.edu'>liam.revell@umb.edu</a>

branching.diffusion: Animation of branching random diffusion

Description

Usage

Value

Arguments

Author

References

See Also