locate.fossil

an object of class <code>"phylo"</code>.

tree

a matrix with continuous character data.

optional arguments including <code>time.constraint</code> which can be a scalar (positive height above the root of the fossil or negative time before present) or a vector (age range of fossil, either positive or negative); <code>edge.constraint</code>, which is equivalent to <code>constraint</code> in <code><a rd-options="" href="/link/locate.yeti?package=phytools&version=1.0-3" data-mini-rdoc="phytools::locate.yeti">locate.yeti</a></code>; <code>plot</code>, <code>rotate</code>, and <code>quiet</code>, which have the same interpretation (and defaults) as the equivalent arguments in <code><a rd-options="" href="/link/locate.yeti?package=phytools&version=1.0-3" data-mini-rdoc="phytools::locate.yeti">locate.yeti</a></code>.

This function uses ML to place a fossil lineage into a tree using continuous traits.

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.fossil 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>time.constraint</code> which can be a scalar (positive height above the root of the fossil or negative time before present) or a vector (age range of fossil, either positive or negative); <code>edge.constraint</code>, which is equivalent to <code>constraint</code> in <code>locate.yeti</code>; <code>plot</code>, <code>rotate</code>, and <code>quiet</code>, which have the same interpretation (and defaults) as the equivalent arguments in <code>locate.yeti</code>.</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

Locate a fossil lineage in a tree using continuous characters — locate.fossil

<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>time.constraint</code> which can be a scalar (positive height above the root of the fossil or negative time before present) or a vector (age range of fossil, either positive or negative); <code>edge.constraint</code>, which is equivalent to <code>constraint</code> in <code>locate.yeti</code>; <code>plot</code>, <code>rotate</code>, and <code>quiet</code>, which have the same interpretation (and defaults) as the equivalent arguments in <code>locate.yeti</code>.</dd>

</dl>

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

locate.fossil: Locate a fossil lineage in a tree using continuous characters

Description

Usage

Value

Arguments

Author

References