orderMappedEdge

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

trees

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>.

ordering

This function takes a modified object of class <code>"multiPhylo"</code> with a mapped discrete character (e.g., see <code><a rd-options="" href="/link/read.simmap?package=phytools&version=0.7-70" data-mini-rdoc="phytools::read.simmap">read.simmap</a></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. Functionality is concentrated in phylogenetic comparative biology, but also includes numerous methods for visualizing, manipulating, reading or writing, and even inferring phylogenetic trees and data. Included among the functions in phylogenetic comparative biology are various for ancestral state reconstruction, model-fitting, simulation of phylogenies and data, and multivariate analysis. There are a broad range of plotting methods for phylogenies and comparative data which 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, there are a number of functions for reading, writing, analyzing, inferring, simulating, and manipulating phylogenetic trees and comparative data not covered by other packages. For instance, there are functions for randomly or non-randomly attaching species or clades to a phylogeny, for estimating supertrees or 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

This function takes a modified object of class <code>"multiPhylo"</code> with a mapped discrete character (e.g., see <code><a rd-options='' href='read.simmap'>read.simmap</a></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.

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

Description

Usage

Arguments

Value

References