simBMphylo

plot.simBMphylo

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.

phylogenetics

comparative method

plotting

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)

simBMphylo function

<dl>	<dt>n</dt>
<dd>number of taxa to simulate in the output tree.</dd>	<dt>t</dt>
<dd>total time for the simulation.</dd>	<dt>sig2</dt>
<dd>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 <code>t</code>, otherwise the first element of <code>sig2</code> will just be duplicated <code>t</code> times.</dd>	<dt>plot</dt>
<dd>optional logical value indicating whether or not the simulated object should be plotted.</dd>	<dt>...</dt>
<dd>optional arguments to be passed to the <code>plot</code> method.</dd>	<dt>x</dt>
<dd>in <code>plot</code> method, object of class <code>"simBMphylo"</code>.</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

Creates a graphical illustration of Brownian motion evolution on a phylogeny — simBMphylo

<dl>

	<dt>n</dt>
<dd>number of taxa to simulate in the output tree.</dd>

	<dt>t</dt>
<dd>total time for the simulation.</dd>

	<dt>sig2</dt>
<dd>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 <code>t</code>, otherwise the first element of <code>sig2</code> will just be duplicated <code>t</code> times.</dd>

	<dt>plot</dt>
<dd>optional logical value indicating whether or not the simulated object should be plotted.</dd>

	<dt>...</dt>
<dd>optional arguments to be passed to the <code>plot</code> method.</dd>

	<dt>x</dt>
<dd>in <code>plot</code> method, object of class <code>"simBMphylo"</code>.</dd>

</dl>

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

simBMphylo: Creates a graphical illustration of Brownian motion evolution on a phylogeny

Description

Usage

Value

Arguments

Author

References

See Also

Examples