tree.grow

This function simulates a birth-death tree under user-defined conditions and then creates an animation of that tree growing from left-to-right in the plotting device, or upwards.

Simulation

phylogenetics

comparative method

plotting

diversification

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)

tree.grow function

<dl>	<dt>...</dt>
<dd>arguments to pass to <code>pbtree</code>.</dd>	<dt>res</dt>
<dd>number of steps (the resolution of the animation). This also corresponds to the number of frames that will be created if the animation is to be converted to a .gif file.</dd>	<dt>direction</dt>
<dd>the direction to plot the tree. Only <code>direction="rightwards"</code> (the default) and <code>direction="upwards"</code> are supported.</dd>	<dt>ladderize</dt>
<dd>logical value indicating whether or not to 'ladderize' the plotted tree. (Defaults to <code>TRUE</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 an animation of a tree growing from left-to-right or upwards — tree.grow

<dl>

	<dt>...</dt>
<dd>arguments to pass to <code>pbtree</code>.</dd>

	<dt>res</dt>
<dd>number of steps (the resolution of the animation). This also corresponds to the number of frames that will be created if the animation is to be converted to a .gif file.</dd>

	<dt>direction</dt>
<dd>the direction to plot the tree. Only <code>direction="rightwards"</code> (the default) and <code>direction="upwards"</code> are supported.</dd>

	<dt>ladderize</dt>
<dd>logical value indicating whether or not to 'ladderize' the plotted tree. (Defaults to <code>TRUE</code>.)</dd>

</dl>

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

tree.grow: Creates an animation of a tree growing from left-to-right or upwards

Description

Usage

Value

Arguments

Author

References

See Also