map.overlap

Map.Overlap

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

tree1

tree2

for <code>Map.Overlap</code>, a logical value indicating whether or not to standardize overlap by dividing by the summed branch length of the tree.

standardize

optional arguments, such as <code>check.equal</code>, a logical value indicating whether or not to check if <code>tree1</code> and <code>tree2</code> match in underlying topology and branch lengths (they should). This value is <code>TRUE</code> by default, but can be set to <code>FALSE</code> if <code>tree1</code> and <code>tree2</code> are known to be equal to speed up calculation.

This function computes the fraction of a stochastic character mapping that is shared between two differently mapped trees. In <code>map.overlap</code> it will compute a single quantity giving the overall similarity of the maps, consequently this measure only makes sense of some or all of the states are shared between the two mapped tress. In <code>Map.Overlap</code> what is computed instead is a matrix in which the rows correspond to the states observed in <code>tree1</code> and the columns give the states for <code>tree2</code>, with the numerical values of the matrix showing the total overlap between each pair of mapped states on the two trees.

phylogenetics

comparative method

discrete character

ancestral states

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)

map.overlap function

<dl>	<dt>tree1</dt>
<dd>an object of class <code>"simmap"</code>.</dd>	<dt>tree2</dt>
<dd>an object of class <code>"simmap"</code>.</dd>	<dt>tol</dt>
<dd>an optional tolerance value.</dd>	<dt>standardize</dt>
<dd>for <code>Map.Overlap</code>, a logical value indicating whether or not to standardize overlap by dividing by the summed branch length of the tree.</dd>	<dt>...</dt>
<dd>optional arguments, such as <code>check.equal</code>, a logical value indicating whether or not to check if <code>tree1</code> and <code>tree2</code> match in underlying topology and branch lengths (they should). This value is <code>TRUE</code> by default, but can be set to <code>FALSE</code> if <code>tree1</code> and <code>tree2</code> are known to be equal to speed up calculation.</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

Proportional overlap between two mapped character histories on a tree — map.overlap

<dl>

	<dt>tree1</dt>
<dd>an object of class <code>"simmap"</code>.</dd>

	<dt>tree2</dt>
<dd>an object of class <code>"simmap"</code>.</dd>

	<dt>tol</dt>
<dd>an optional tolerance value.</dd>

	<dt>standardize</dt>
<dd>for <code>Map.Overlap</code>, a logical value indicating whether or not to standardize overlap by dividing by the summed branch length of the tree.</dd>

	<dt>...</dt>
<dd>optional arguments, such as <code>check.equal</code>, a logical value indicating whether or not to check if <code>tree1</code> and <code>tree2</code> match in underlying topology and branch lengths (they should). This value is <code>TRUE</code> by default, but can be set to <code>FALSE</code> if <code>tree1</code> and <code>tree2</code> are known to be equal to speed up calculation.</dd>

</dl>

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

map.overlap: Proportional overlap between two mapped character histories on a tree

Description

Usage

Value

Arguments

Author

References

See Also