map.to.singleton

plotTree.singletons

drop.tip.singleton

rootedge.to.singleton

an object of class <code>"simmap"</code> (for <code>map.to.singleton</code>, or a tree with one or more singleton nodes (for <code>plotTree.singletons</code>, <code>drop.tip.singleton</code>, and <code>rootedge.to.singleton</code>).

tree

for <code>drop.tip.singleton</code>, a tip label or vector of tip labels.

The function <code>map.to.singleton</code> takes an object of class <code>"simmap"</code> with a mapped discrete character and converts it to a tree with singleton nodes, in which edge has only one state. The states for each edge are stored in <code>names(tree$edge.length)</code>. In a sense this is just an alternative way to use the general structure of the <code>"phylo"</code> object to encode a tree with a mapped character.	
<code>plotTree.singletons</code> plots a tree with singleton nodes. Note that <code>plotTree</code> and <code>plot.phylo</code> now have no trouble graphing trees with singleton nodes - but they do this by just ignoring the singletons. <code>plotTree.singletons</code> marks the singletons as nodes on the plotted phylogeny.	
<code>drop.tip.singleton</code> drops tips from the tree leaving ancestral nodes for all remaining tips as singletons.	
Finally, <code>rootedge.to.singleton</code> converts a tree with a root edge to a tree with a singleton node instead.

utilities

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)

map.to.singleton function

<dl>	<dt>tree</dt>
<dd>an object of class <code>"simmap"</code> (for <code>map.to.singleton</code>, or a tree with one or more singleton nodes (for <code>plotTree.singletons</code>, <code>drop.tip.singleton</code>, and <code>rootedge.to.singleton</code>).</dd>	<dt>tip</dt>
<dd>for <code>drop.tip.singleton</code>, a tip label or vector of tip labels.</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 a tree without singletons to a tree with singleton nodes — map.to.singleton

<dl>

	<dt>tree</dt>
<dd>an object of class <code>"simmap"</code> (for <code>map.to.singleton</code>, or a tree with one or more singleton nodes (for <code>plotTree.singletons</code>, <code>drop.tip.singleton</code>, and <code>rootedge.to.singleton</code>).</dd>

	<dt>tip</dt>
<dd>for <code>drop.tip.singleton</code>, a tip label or vector of tip labels.</dd>

</dl>

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

map.to.singleton: Converts a tree without singletons to a tree with singleton nodes

Description

Usage

Value

Arguments

Author

References

See Also