getExtant

getExtinct

a phylogeny stored as an object of class <code>"phylo"</code> with some tips that are non-contemporaneous (i.e., end before the present).

tree

a tolerance value to account for numerical imprecision.

The function <code>getExtant</code> takes a tree as input and returns a vector containing the names of all the tips that have a height above the root that is equal (to a degree of numerical precision determined by <code>tol</code>) to the height of the highest tip.	
<code>getExtinct</code> returns the complement.

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)

getExtant function

<dl>	<dt>tree</dt>
<dd>a phylogeny stored as an object of class <code>"phylo"</code> with some tips that are non-contemporaneous (i.e., end before the present).</dd>	<dt>tol</dt>
<dd>a tolerance value to account for numerical imprecision.</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

Returns a list of the extant or extinct lineages in a tree containing non-contemporaneous tips — getExtant

<dl>

	<dt>tree</dt>
<dd>a phylogeny stored as an object of class <code>"phylo"</code> with some tips that are non-contemporaneous (i.e., end before the present).</dd>

	<dt>tol</dt>
<dd>a tolerance value to account for numerical imprecision.</dd>

</dl>

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

getExtant: Returns a list of the extant or extinct lineages in a tree containing non-contemporaneous tips

Description

Usage

Value

Arguments

Author

References

See Also