orderMappedEdge

This function takes a modified object of class <code>"multiPhylo"</code> with a mapped discrete character (e.g., see <code>read.simmap</code> and sorts the columns of each <code>tree$mapped.edge</code> to have the same state ordering. This is handy if we want to, for instance, run <code>brownie.lite</code> on a set of mapped trees, and then average the fitted parameter values across trees. The function also works for a single tree.

utilities

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)

orderMappedEdge function

<dl>	<dt>trees</dt>
<dd>object of class <code>"phylo"</code> or <code>"multiPhylo"</code>.</dd>	<dt>ordering</dt>
<dd>ordering for the columns of <code>$mapped.edge</code>. If <code>NULL</code>, then an alphabetical order is assumed. Options are <code>"alphabetical"</code>, <code>"numerical"</code>, or any specific ordering of the mapped traits (e.g., <code>c("A","B","C")</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

Order the columns of mapped.edge to match across trees — orderMappedEdge

<dl>

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

	<dt>ordering</dt>
<dd>ordering for the columns of <code>$mapped.edge</code>. If <code>NULL</code>, then an alphabetical order is assumed. Options are <code>"alphabetical"</code>, <code>"numerical"</code>, or any specific ordering of the mapped traits (e.g., <code>c("A","B","C")</code>.</dd>

</dl>

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

orderMappedEdge: Order the columns of mapped.edge to match across trees

Description

Usage

Value

Arguments

Author

References