posterior.evolrate

Analyzes posterior sample from <code>evol.rate.mcmc</code>.

phylogenetics

comparative method

Bayesian

continuous character

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)

posterior.evolrate function

<dl>	<dt>tree</dt>
<dd>a phylogenetic tree in <code>"phylo"</code> format.</dd>	<dt>ave.shift</dt>
<dd>mean or median shift-point from the posterior sample (see <code>minSplit</code>.</dd>	<dt>mcmc</dt>
<dd>matrix <code>$mcmc</code> from <code>evol.rate.mcmc</code> (probably with burn-in excluded).</dd>	<dt>tips</dt>
<dd>list of tips in state $\sigma_1^2$ for each sampled generation of MCMC.</dd>	<dt>showTree</dt>
<dd>optional logical value indicating whether or not to plot the stretched and shrunken tree generated by the pre-processing algorithm implemented in this function (default is <code>FALSE</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

Analysis of the posterior sample from evol.rate.mcmc — posterior.evolrate

<dl>

	<dt>tree</dt>
<dd>a phylogenetic tree in <code>"phylo"</code> format.</dd>

	<dt>ave.shift</dt>
<dd>mean or median shift-point from the posterior sample (see <code>minSplit</code>.</dd>

	<dt>mcmc</dt>
<dd>matrix <code>$mcmc</code> from <code>evol.rate.mcmc</code> (probably with burn-in excluded).</dd>

	<dt>tips</dt>
<dd>list of tips in state $\sigma_1^2$ for each sampled generation of MCMC.</dd>

	<dt>showTree</dt>
<dd>optional logical value indicating whether or not to plot the stretched and shrunken tree generated by the pre-processing algorithm implemented in this function (default is <code>FALSE</code>).</dd>

</dl>

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

posterior.evolrate: Analysis of the posterior sample from evol.rate.mcmc

Description

Usage

Value

Arguments

Author

Details

References

See Also