treeSlice

is a phylogenetic tree in <code>"phylo"</code> format.

tree

a real number indicating the height above the root at which to slice the tree.

slice

a logical value indicating whether or not to return subtrees with a number of tips less than two (default is <code>FALSE</code>).

trivial

logical value indicating whether or not the height of the slice should be given interactively.

prompt

for <code>prompt=TRUE</code>, other arguments to be passed to <code><a rd-options="" href="/link/plotTree?package=phytools&version=1.0-3" data-mini-rdoc="phytools::plotTree">plotTree</a></code>. In addition, the argument <code>orientation</code> can be used to specify whether the <code>"tipwards"</code> subtrees or the <code>"rootwards"</code> phylogeny are/is to be returned by the function call (using those two argument values, respectively).

This function slices a tree at a particular height above the root and returns all subtrees or all non-trivial subtrees (i.e., subtrees with more than 1 taxon). Uses <code>extract.clade</code> in the "ape" package.	
It can also be used to crop the terminal fraction of a tree for <code>orientation="rootwards"</code>.

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)

treeSlice function

<dl>	<dt>tree</dt>
<dd>is a phylogenetic tree in <code>"phylo"</code> format.</dd>	<dt>slice</dt>
<dd>a real number indicating the height above the root at which to slice the tree.</dd>	<dt>trivial</dt>
<dd>a logical value indicating whether or not to return subtrees with a number of tips less than two (default is <code>FALSE</code>).</dd>	<dt>prompt</dt>
<dd>logical value indicating whether or not the height of the slice should be given interactively.</dd>	<dt>...</dt>
<dd>for <code>prompt=TRUE</code>, other arguments to be passed to <code>plotTree</code>. In addition, the argument <code>orientation</code> can be used to specify whether the <code>"tipwards"</code> subtrees or the <code>"rootwards"</code> phylogeny are/is to be returned by the function call (using those two argument values, respectively).</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

Slices the tree at a particular point and returns all subtrees, or the tree rootward of the point — treeSlice

<dl>

	<dt>tree</dt>
<dd>is a phylogenetic tree in <code>"phylo"</code> format.</dd>

	<dt>slice</dt>
<dd>a real number indicating the height above the root at which to slice the tree.</dd>

	<dt>trivial</dt>
<dd>a logical value indicating whether or not to return subtrees with a number of tips less than two (default is <code>FALSE</code>).</dd>

	<dt>prompt</dt>
<dd>logical value indicating whether or not the height of the slice should be given interactively.</dd>

	<dt>...</dt>
<dd>for <code>prompt=TRUE</code>, other arguments to be passed to <code>plotTree</code>. In addition, the argument <code>orientation</code> can be used to specify whether the <code>"tipwards"</code> subtrees or the <code>"rootwards"</code> phylogeny are/is to be returned by the function call (using those two argument values, respectively).</dd>

</dl>

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

treeSlice: Slices the tree at a particular point and returns all subtrees, or the tree rootward of the point

Description

Usage

Value

Arguments

Author

References

See Also