averageTree

ls.consensus

minTreeDist

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

trees

object of class <code>"phylo"</code>. For <code>minTreeDist</code> the tree on which to find the edge lengths that minimize the distance to the phylogenies in <code>trees</code>.

tree

start

distance criterion for minimization. Options are <code>"symmetric.difference"</code>, <code>"branch.score.difference"</code>, <code>"path.difference"</code>, and <code>"quadratic.path.difference"</code>.

method

logical value indicating whether to run "quietly" or not.

quiet

other arguments to be passed internally.

These functions compute average trees or consensus trees by various criteria.

phylogenetics

consensus tree

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)

averageTree function

<dl>	<dt>trees</dt>
<dd>object of class <code>"multiPhylo"</code>.</dd>	<dt>tree</dt>
<dd>object of class <code>"phylo"</code>. For <code>minTreeDist</code> the tree on which to find the edge lengths that minimize the distance to the phylogenies in <code>trees</code>.</dd>	<dt>start</dt>
<dd>starting tree for optimization.</dd>	<dt>method</dt>
<dd>distance criterion for minimization. Options are <code>"symmetric.difference"</code>, <code>"branch.score.difference"</code>, <code>"path.difference"</code>, and <code>"quadratic.path.difference"</code>.</dd>	<dt>tol</dt>
<dd>tolerance value for optimization.</dd>	<dt>quiet</dt>
<dd>logical value indicating whether to run "quietly" or not.</dd>	<dt>...</dt>
<dd>other arguments to be passed internally.</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

Compute an average tree from a set of trees and related operations — averageTree

<dl>

	<dt>trees</dt>
<dd>object of class <code>"multiPhylo"</code>.</dd>

	<dt>tree</dt>
<dd>object of class <code>"phylo"</code>. For <code>minTreeDist</code> the tree on which to find the edge lengths that minimize the distance to the phylogenies in <code>trees</code>.</dd>

	<dt>start</dt>
<dd>starting tree for optimization.</dd>

	<dt>method</dt>
<dd>distance criterion for minimization. Options are <code>"symmetric.difference"</code>, <code>"branch.score.difference"</code>, <code>"path.difference"</code>, and <code>"quadratic.path.difference"</code>.</dd>

	<dt>tol</dt>
<dd>tolerance value for optimization.</dd>

	<dt>quiet</dt>
<dd>logical value indicating whether to run "quietly" or not.</dd>

	<dt>...</dt>
<dd>other arguments to be passed internally.</dd>

</dl>

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

averageTree: Compute an average tree from a set of trees and related operations

Description

Usage

Value

Arguments

Author