locate.yeti

This function uses ML (or REML) to place a recently extinct, cryptic, or missing taxon on an ultrametric (i.e., time-calibrated) phylogeny.

phylogenetics

maximum likelihood

continuous character

phylogeny inference

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)

locate.yeti function

<dl>	<dt>tree</dt>
<dd>an object of class <code>"phylo"</code>.</dd>	<dt>X</dt>
<dd>a matrix with continuous character data.</dd>	<dt>...</dt>
<dd>optional arguments including: <code>method</code> (<code>"ML"</code> or <code>"REML"</code>, defaults to <code>"ML"</code>); <code>search</code> (<code>"heuristic"</code> or <code>"exhaustive"</code>, defaults to <code>"heuristic"</code>); <code>constraint</code>, a vector containing the daughter node numbers from <code>tree$edge</code> for each edge to try; <code>plot</code> a logical argument specifying whether or not to plot the likelihood profile on edges (defaults to <code>FALSE</code>); <code>rotate</code> a logical indicating whether or not to rotate the data based on the input tree; and <code>quiet</code>, which is logical and has an obvious interpretation.</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

Locate a cryptic, recently extinct, or missing taxon on a tree — locate.yeti

<dl>

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

	<dt>X</dt>
<dd>a matrix with continuous character data.</dd>

	<dt>...</dt>
<dd>optional arguments including: <code>method</code> (<code>"ML"</code> or <code>"REML"</code>, defaults to <code>"ML"</code>); <code>search</code> (<code>"heuristic"</code> or <code>"exhaustive"</code>, defaults to <code>"heuristic"</code>); <code>constraint</code>, a vector containing the daughter node numbers from <code>tree$edge</code> for each edge to try; <code>plot</code> a logical argument specifying whether or not to plot the likelihood profile on edges (defaults to <code>FALSE</code>); <code>rotate</code> a logical indicating whether or not to rotate the data based on the input tree; and <code>quiet</code>, which is logical and has an obvious interpretation.</dd>

</dl>

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

locate.yeti: Locate a cryptic, recently extinct, or missing taxon on a tree

Description

Usage

Value

Arguments

Author

References