tree.grow

Animates a birth-death tree simulation.

Simulation

phylogenetics

comparative method

plotting

diversification

A wide range of methods for phylogenetic analysis - concentrated in phylogenetic comparative biology, but also including numerous techniques for visualizing, analyzing, 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 trait data. 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 phenotype space or a onto a geographic map, and for visualizing correlated speciation between trees. Lastly, numerous functions are designed for reading, writing, analyzing, inferring, simulating, and manipulating phylogenetic trees and comparative data. For instance, there are functions for computing consensus phylogenies from a set, for simulating phylogenetic trees and data under a range of models, for randomly or non-randomly attaching species or clades to a tree, as well as for a wide range 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=2.1-1" 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

Details

References

See Also