posterior.evolrate

This fucntion takes a phylogenetic tree, an average split position, and a raw MCMC output from <code>evol.rate.mcmc</code> and returns a posterior sample of evolutionary rates rootward ($\sigma_1^2$) and tipward ($\sigma_2^2$) from the average split.

phylogenetics

comparative method

Bayesian

continuous character

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)

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 burnin excluded).</dd>	<dt>tips</dt>
<dd>list of stips 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=1.2-0" 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 burnin excluded).</dd>

	<dt>tips</dt>
<dd>list of stips 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

References

See Also