drop.tip.simmap

keep.tip.simmap

extract.clade.simmap

This function drops one or multiple tips from an object of class <code>"simmap"</code>.

utilities

phylogenetics

A wide range of methods for phylogenetic analysis - concentrated in phylogenetic comparative biology, but also including numerous techniques for visualizing, analyzing, 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 trait data. 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 phenotype space or a onto a geographic map, and for visualizing correlated speciation between trees. Lastly, numerous functions are designed for reading, writing, analyzing, inferring, simulating, and manipulating phylogenetic trees and comparative data. For instance, there are functions for computing consensus phylogenies from a set, for simulating phylogenetic trees and data under a range of models, for randomly or non-randomly attaching species or clades to a tree, as well as for a wide range 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)

drop.tip.simmap function

<dl>	<dt>phy</dt>
<dd>an object of class <code>"simmap"</code>.</dd>	<dt>tip</dt>
<dd>name or names of species to be dropped (or kept).</dd>	<dt>node</dt>
<dd>node number for the root node of the clade to be extracted.</dd>	<dt>...</dt>
<dd>optional arguments. Currently the logical argument <code>untangle</code> which if set to <code>TRUE</code> will call <code>untangle</code> before returning the <code>"simmap"</code> object to the user.</dd>	<dt>tree</dt>
<dd>for <code>extract.clade.simmap</code>, an object of class <code>"simmap"</code>.</dd></dl>

Arguments

Liam Revell <a href="/link/liam.revell%40umb.edu?package=phytools&version=2.1-1" data-mini-rdoc="phytools::liam.revell@umb.edu">liam.revell@umb.edu</a>

Author

Drop tips or extract clade from tree with mapped discrete character — drop.tip.simmap

<dl>

	<dt>phy</dt>
<dd>an object of class <code>"simmap"</code>.</dd>

	<dt>tip</dt>
<dd>name or names of species to be dropped (or kept).</dd>

	<dt>node</dt>
<dd>node number for the root node of the clade to be extracted.</dd>

	<dt>...</dt>
<dd>optional arguments. Currently the logical argument <code>untangle</code> which if set to <code>TRUE</code> will call <code>untangle</code> before returning the <code>"simmap"</code> object to the user.</dd>

	<dt>tree</dt>
<dd>for <code>extract.clade.simmap</code>, an object of class <code>"simmap"</code>.</dd>

</dl>

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

drop.tip.simmap: Drop tips or extract clade from tree with mapped discrete character

Description

Usage

Value

Arguments

Author

Details

References

See Also