drop.tip.simmap

extract.clade.simmap

a modified object of class <code>"phylo"</code> (see <code><a rd-options="" href="/link/read.simmap?package=phytools&version=1.0-3" data-mini-rdoc="phytools::read.simmap">read.simmap</a></code>).

tree

name or names of species to be dropped.

node number for the root node of the clade to be extracted.

node

optional arguments. Currently the logical argument <code>untangle</code> which if set to <code>TRUE</code> will call <code><a rd-options="" href="/link/untangle?package=phytools&version=1.0-3" data-mini-rdoc="phytools::untangle">untangle</a></code> before returning the <code>"simmap"</code> object to the user.

This function drops one or multiple tips from the modified <code>"phylo"</code> object with a mapped binary or multistate trait (see <code>read.simmap</code>) while maintaining the matrix <code>$mapped.edge</code> and list of mappings by branch <code>maps</code>. This function is equivalent to <code>drop.tip</code> but for a tree with a mapped discrete character.
<code>extract.clade.simmap</code> is functionally equivalent to <code>extract.clade</code> but preserves discrete character mappings on the tree.

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)

drop.tip.simmap function

<dl>	<dt>tree</dt>
<dd>a modified object of class <code>"phylo"</code> (see <code>read.simmap</code>).</dd>	<dt>tip</dt>
<dd>name or names of species to be dropped.</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></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

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

<dl>

	<dt>tree</dt>
<dd>a modified object of class <code>"phylo"</code> (see <code>read.simmap</code>).</dd>

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

</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

References

See Also