geo.legend

geo.palette

a matrix with the starting &amp; ending point of each plotted era in rows, &amp; names of the time periods as rownames.

a vector of colors for the time periods of the rows in <code>leg</code>.

colors

transparency level to apply to <code>colors</code>.

alpha

The function <code>geo.legend</code> adds a geological (or other temporal) legend to a plotted tree.	
The function <code>geo.palette</code> returns a geological time color palette to the user.

phylogenetics

plotting

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)

geo.legend function

<dl>	<dt>leg</dt>
<dd>a matrix with the starting &amp; ending point of each plotted era in rows, &amp; names of the time periods as rownames.</dd>	<dt>colors</dt>
<dd>a vector of colors for the time periods of the rows in <code>leg</code>.</dd>	<dt>alpha</dt>
<dd>transparency level to apply to <code>colors</code>.</dd>	<dt>...</dt>
<dd>optional arguments.</dd></dl>

Arguments

Liam Revell <a href="/link/liam.revell%40umb.edu?package=phytools&version=1.0-3" data-mini-rdoc="phytools::liam.revell@umb.edu">liam.revell@umb.edu</a>

Author

Adds a geological (or other temporal) legend to a plotted tree — geo.legend

<dl>

	<dt>leg</dt>
<dd>a matrix with the starting &amp; ending point of each plotted era in rows, &amp; names of the time periods as rownames.</dd>

	<dt>colors</dt>
<dd>a vector of colors for the time periods of the rows in <code>leg</code>.</dd>

	<dt>alpha</dt>
<dd>transparency level to apply to <code>colors</code>.</dd>

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

</dl>

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

geo.legend: Adds a geological (or other temporal) legend to a plotted tree

Description

Usage

Value

Arguments

Author

References