add.random

This function adds new tips at random to a tree with branch lengths. If no edge lengths are provided, and the tree is ultrametric, then edge lengths are assigned to keep the tree ultrametric. The probability that at new tip is added along any branch is directly proportional to the length of the branch.

utilities

phylogenetics

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)

add.random function

<dl>	<dt>tree</dt>
<dd>an object of class <code>"phylo"</code>.</dd>	<dt>n</dt>
<dd>a number of tips to add to the tree. If <code>NULL</code>, will use <code>length(tips)</code>. If <code>tips</code> is specified, then <code>n</code> is also ignored, regardless of its value.</dd>	<dt>tips</dt>
<dd>a set of tip names for the added tips. If <code>NULL</code>, names will be supplied</dd>	<dt>edge.length</dt>
<dd>terminal edge length for the added tips. If <code>NULL</code>, and <code>is.ultrametric(tree)</code> <code>==TRUE</code>, then edge lengths will be assigned to keep the tree ultrametric. Note that if edge lengths are assigned and <code>n&gt;1</code>, then the asssigned terminal edge lengths are not guaranteed as subsequent random tip addition could occur along the new terminal edge.</dd>	<dt>order</dt>
<dd>addition order for the new tips.</dd></dl>

Arguments

Liam Revell <a href="/link/liam.revell%40umb.edu?package=phytools&version=1.2-0" data-mini-rdoc="phytools::liam.revell@umb.edu">liam.revell@umb.edu</a>

Author

Add tips at random to the tree — add.random

<dl>

	<dt>tree</dt>
<dd>an object of class <code>"phylo"</code>.</dd>

	<dt>n</dt>
<dd>a number of tips to add to the tree. If <code>NULL</code>, will use <code>length(tips)</code>. If <code>tips</code> is specified, then <code>n</code> is also ignored, regardless of its value.</dd>

	<dt>tips</dt>
<dd>a set of tip names for the added tips. If <code>NULL</code>, names will be supplied</dd>

	<dt>edge.length</dt>
<dd>terminal edge length for the added tips. If <code>NULL</code>, and <code>is.ultrametric(tree)</code> <code>==TRUE</code>, then edge lengths will be assigned to keep the tree ultrametric. Note that if edge lengths are assigned and <code>n&gt;1</code>, then the asssigned terminal edge lengths are not guaranteed as subsequent random tip addition could occur along the new terminal edge.</dd>

	<dt>order</dt>
<dd>addition order for the new tips.</dd>

</dl>

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

add.random: Add tips at random to the tree

Description

Usage

Value

Arguments

Author

Details

References

See Also