consensus.edges

Computes consensus edge lengths from a set of input trees using multiple methods.

utilities

phylogenetics

phylogeny inference

consensus tree

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)

consensus.edges function

<dl>	<dt>trees</dt>
<dd>object of class <code>"multiPhylo"</code> in which the trees must have edge lengths. This could be, for instance, a sample from the posterior distribution of trees in a Bayesian analysis.</dd>	<dt>method</dt>
<dd>method for computing the edge lengths. Could be the mean of all trees in which the edge is present, or it could be the least-squares edge lengths computed on the mean patristic distance matrices from the input phylogenies in <code>trees</code>. Note that in the latter case the phangorn function <code>nnls.tree</code> is used and the option <code>rooted</code> will be set to <code>is.rooted(tree)</code> for the consensus tree.</dd>	<dt>...</dt>
<dd>optional arguments, the most popular of which is <code>consensus.tree</code> - a user supplied consensus tree. Another optional argument for <code>method="mean.edge"</code> is <code>if.absent</code> which tells the function how to include absent edges in the computation of average edge lengths. Possible values are <code>"zero"</code> (the default) or <code>"ignore"</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

Compute consensus edges for a tree under some criterion — consensus.edges

<dl>

	<dt>trees</dt>
<dd>object of class <code>"multiPhylo"</code> in which the trees must have edge lengths. This could be, for instance, a sample from the posterior distribution of trees in a Bayesian analysis.</dd>

	<dt>method</dt>
<dd>method for computing the edge lengths. Could be the mean of all trees in which the edge is present, or it could be the least-squares edge lengths computed on the mean patristic distance matrices from the input phylogenies in <code>trees</code>. Note that in the latter case the phangorn function <code>nnls.tree</code> is used and the option <code>rooted</code> will be set to <code>is.rooted(tree)</code> for the consensus tree.</dd>

	<dt>...</dt>
<dd>optional arguments, the most popular of which is <code>consensus.tree</code> - a user supplied consensus tree. Another optional argument for <code>method="mean.edge"</code> is <code>if.absent</code> which tells the function how to include absent edges in the computation of average edge lengths. Possible values are <code>"zero"</code> (the default) or <code>"ignore"</code>.</dd>

</dl>

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

consensus.edges: Compute consensus edges for a tree under some criterion

Description

Usage

Value

Arguments

Author

References