plotThresh

tree

a named vector containing discrete character states; or a matrix containing the tip species, in rows, and probabilities of being in each state, in columns.

list object returned by <code><a rd-options="" href="/link/ancThresh?package=phytools&version=1.0-3" data-mini-rdoc="phytools::ancThresh">ancThresh</a></code>.

mcmc

number of generations (not samples) to exclude as burn in; if <code>NULL</code> then 20 percent of generations are excluded as burn-in.

burnin

a named vector containing the colors for the posterior probabilities plotted as pie charts at internal nodes.

piecol

a string indicating whether the tip colors should be based on the input data (<code>"input"</code>) or sampled tip liabilities (<code>"estimated"</code>). These will only differ if there is uncertainty in the tip states.

tipcol

logical value or text to be plotted in the legend.

legend

other arguments to be passed to <code><a rd-options="" href="/link/plot.phylo?package=phytools&version=1.0-3" data-mini-rdoc="phytools::plot.phylo">plot.phylo</a></code> - <code>label.offset</code> should be &gt;0 so that tip labels and species names do not overlap.

This function uses the object returned by <code>ancThresh</code> to plot the posterior probabilities of ancestral states under the threshold model. It is also called internally by <code>ancThresh</code>.

phylogenetics

comparative method

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)

plotThresh function

<dl>	<dt>tree</dt>
<dd>phylogenetic tree.</dd>	<dt>x</dt>
<dd>a named vector containing discrete character states; or a matrix containing the tip species, in rows, and probabilities of being in each state, in columns.</dd>	<dt>mcmc</dt>
<dd>list object returned by <code>ancThresh</code>.</dd>	<dt>burnin</dt>
<dd>number of generations (not samples) to exclude as burn in; if <code>NULL</code> then 20 percent of generations are excluded as burn-in.</dd>	<dt>piecol</dt>
<dd>a named vector containing the colors for the posterior probabilities plotted as pie charts at internal nodes.</dd>	<dt>tipcol</dt>
<dd>a string indicating whether the tip colors should be based on the input data (<code>"input"</code>) or sampled tip liabilities (<code>"estimated"</code>). These will only differ if there is uncertainty in the tip states.</dd>	<dt>legend</dt>
<dd>logical value or text to be plotted in the legend.</dd>	<dt>...</dt>
<dd>other arguments to be passed to <code>plot.phylo</code> - <code>label.offset</code> should be &gt;0 so that tip labels and species names do not overlap.</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

Tree plotting with posterior probabilities of ancestral states from the threshold model — plotThresh

<dl>

	<dt>tree</dt>
<dd>phylogenetic tree.</dd>

	<dt>x</dt>
<dd>a named vector containing discrete character states; or a matrix containing the tip species, in rows, and probabilities of being in each state, in columns.</dd>

	<dt>mcmc</dt>
<dd>list object returned by <code>ancThresh</code>.</dd>

	<dt>burnin</dt>
<dd>number of generations (not samples) to exclude as burn in; if <code>NULL</code> then 20 percent of generations are excluded as burn-in.</dd>

	<dt>piecol</dt>
<dd>a named vector containing the colors for the posterior probabilities plotted as pie charts at internal nodes.</dd>

	<dt>tipcol</dt>
<dd>a string indicating whether the tip colors should be based on the input data (<code>"input"</code>) or sampled tip liabilities (<code>"estimated"</code>). These will only differ if there is uncertainty in the tip states.</dd>

	<dt>legend</dt>
<dd>logical value or text to be plotted in the legend.</dd>

	<dt>...</dt>
<dd>other arguments to be passed to <code>plot.phylo</code> - <code>label.offset</code> should be &gt;0 so that tip labels and species names do not overlap.</dd>

</dl>

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

plotThresh: Tree plotting with posterior probabilities of ancestral states from the threshold model

Description

Usage

Value

Arguments

Author

References

See Also