reorderSimmap

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

tree

either <code>"cladewise"</code> or <code>"pruningwise"</code> (see <code><a rd-options="" href="/link/reorder.phylo?package=phytools&version=0.7-90" data-mini-rdoc="phytools::reorder.phylo">reorder.phylo</a></code>).

order

logical value indicating whether only an index should be returned.

index.only

Function returns a reordered modified <code>"phylo"</code> object by using <code>reorder.phylo</code> but then sorting the additional elements <code>$mapped.edge</code> and <code>$maps</code> to have the same order as <code>$edge</code>.

utilities

phylogenetics

comparative method

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. 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 numerous 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 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)

reorderSimmap function

either <code>"cladewise"</code> or <code>"pruningwise"</code> (see <code><a rd-options='' href='reorder.phylo'>reorder.phylo</a></code>).

reorderSimmap: Reorder edges of a simmap tree

Description

Usage

Arguments

Value

References

See Also