markChanges

This function adds the reconstructed changes to a plotted tree with a stochastically mapped discrete character.

phylogenetics

plotting

Bayesian

discrete character

ancestral states

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)

markChanges function

<dl>	<dt>tree</dt>
<dd>an object of class <code>"simmap"</code>.</dd>	<dt>colors</dt>
<dd>a named vector of colors used to plot the stochastically mapped character on the tree.</dd>	<dt>cex</dt>
<dd>expansion factor for line height.</dd>	<dt>lwd</dt>
<dd>line width.</dd>	<dt>plot</dt>
<dd>logical value indicating whether the changes should be plotted or not.</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

Add marked changes to a plotted tree with mapped discrete character — markChanges

<dl>

	<dt>tree</dt>
<dd>an object of class <code>"simmap"</code>.</dd>

	<dt>colors</dt>
<dd>a named vector of colors used to plot the stochastically mapped character on the tree.</dd>

	<dt>cex</dt>
<dd>expansion factor for line height.</dd>

	<dt>lwd</dt>
<dd>line width.</dd>

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

</dl>

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

markChanges: Add marked changes to a plotted tree with mapped discrete character

Description

Usage

Value

Arguments

Author

References

See Also