phylo.toBackbone

backbone.toPhylo

an object of class <code>"phylo"</code> (for the function <code>phylo.toBackbone</code>), or an object of the special class <code>"backbonePhylo"</code> (for <code>backbone.toPhylo</code>).

data frame containing the attributes necessary to translate a backbone tree to an object of class <code>"backbonePhylo"</code>. The data frame should contain the following variables: <code>tip.label</code>: the tip labels in the input tree (not all need be included); <code>clade.label</code>: labels for the unobserved subtrees; <code>N</code>: number of species in each subtree; and <code>depth</code>: desired depth of each subtree. <code>depth</code> for each terminal taxon in <code>x</code> cannot be greater than the terminal edge length for that taxon.

trans

Converts between <code>"phylo"</code> and <code>"backbonePhylo"</code>.

phylogenetics

plotting

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)

phylo.toBackbone function

<dl>	<dt>x</dt>
<dd>an object of class <code>"phylo"</code> (for the function <code>phylo.toBackbone</code>), or an object of the special class <code>"backbonePhylo"</code> (for <code>backbone.toPhylo</code>).</dd>	<dt>trans</dt>
<dd>data frame containing the attributes necessary to translate a backbone tree to an object of class <code>"backbonePhylo"</code>. The data frame should contain the following variables: <code>tip.label</code>: the tip labels in the input tree (not all need be included); <code>clade.label</code>: labels for the unobserved subtrees; <code>N</code>: number of species in each subtree; and <code>depth</code>: desired depth of each subtree. <code>depth</code> for each terminal taxon in <code>x</code> cannot be greater than the terminal edge length for that taxon.</dd>	<dt>...</dt>
<dd>optional arguments.</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

Converts tree to backbone or vice versa — phylo.toBackbone

<dl>

	<dt>x</dt>
<dd>an object of class <code>"phylo"</code> (for the function <code>phylo.toBackbone</code>), or an object of the special class <code>"backbonePhylo"</code> (for <code>backbone.toPhylo</code>).</dd>

	<dt>trans</dt>
<dd>data frame containing the attributes necessary to translate a backbone tree to an object of class <code>"backbonePhylo"</code>. The data frame should contain the following variables: <code>tip.label</code>: the tip labels in the input tree (not all need be included); <code>clade.label</code>: labels for the unobserved subtrees; <code>N</code>: number of species in each subtree; and <code>depth</code>: desired depth of each subtree. <code>depth</code> for each terminal taxon in <code>x</code> cannot be greater than the terminal edge length for that taxon.</dd>

	<dt>...</dt>
<dd>optional arguments.</dd>

</dl>

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

phylo.toBackbone: Converts tree to backbone or vice versa

Description

Usage

Value

Arguments

Author

References

See Also