vcvPhylo

object of class <code>"phylo"</code>.

tree

logical value indicating whether or not to include ancestral nodes.

anc.nodes

optional arguments including <code>internal</code> (synonym of <code>anc.nodes</code>) and <code>model</code> (can be <code>"BM"</code>, <code>"OU"</code>, or <code>"lambda"</code>.

This function returns a so-called phylogenetic variance covariance matrix (e.g., see <code>vcv.phylo</code>), but (optionally) including ancestral nodes and under different evolutionary models.

utilities

Statistics

phylogenetics

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)

vcvPhylo function

<dl>	<dt>tree</dt>
<dd>object of class <code>"phylo"</code>.</dd>	<dt>anc.nodes</dt>
<dd>logical value indicating whether or not to include ancestral nodes.</dd>	<dt>...</dt>
<dd>optional arguments including <code>internal</code> (synonym of <code>anc.nodes</code>) and <code>model</code> (can be <code>"BM"</code>, <code>"OU"</code>, or <code>"lambda"</code>.</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

Calculates cophenetic (i.e., phylogenetic VCV) matrix — vcvPhylo

<dl>

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

	<dt>anc.nodes</dt>
<dd>logical value indicating whether or not to include ancestral nodes.</dd>

	<dt>...</dt>
<dd>optional arguments including <code>internal</code> (synonym of <code>anc.nodes</code>) and <code>model</code> (can be <code>"BM"</code>, <code>"OU"</code>, or <code>"lambda"</code>.</dd>

</dl>

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

vcvPhylo: Calculates cophenetic (i.e., phylogenetic VCV) matrix

Description

Usage

Value

Arguments

Author

References