di2multi.simmap

multi2di.simmap

di2multi.multiSimmap

multi2di.multiSimmap

di2multi.contMap

multi2di.contMap

di2multi.densityMap

multi2di.densityMap

object of class <code>"simmap"</code>, <code>"multiSimmap"</code>, <code>"contMap"</code>, or <code>"densityMap"</code> containing a character mapped onto the edges of a tree or set of trees.

optional arguments: <code>tol</code>, length below which edges should be treated as having zero length; and <code>random</code>, specifying whether to resolve polytomies randomly (if <code>TRUE</code>) or in the order in which they are encountered.

The method <code>di2multi</code> collapses branches of zero length (or, more specifically, branches with length shorter than <code>tol</code>) to create a polytomy in a tree or set of trees.
	The method <code>multi2di</code> resolves polytomies by adding branches of zero length (while preserving the mappings) in a tree or set of trees.

utilities

phylogenetics

comparative method

A wide range of functions for phylogenetic analysis. Functionality is concentrated in phylogenetic comparative biology, but also includes a diverse array of 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)

di2multi.simmap function

Collapse or resolve polytomies in a tree with a character painted on the edges — di2multi.simmap

Collapse or resolve polytomies in a tree with a character painted on the edges

di2multi.simmap: Collapse or resolve polytomies in a tree with a character painted on the edges

Description

Usage

Arguments

Value

Details

References

See Also