edgeProbs

This function computes the relative frequencies of character state changes along edges from a sample of stochastically mapped character histories. This function assumes that all trees in the sample differ only in their mapped histories &amp; not at all in topology or branch lengths. Note that it only asks whether the starting and ending states of the edge differ in a particular way, and thus ignores multiple-hits along a single edge.

phylogenetics

plotting

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)

edgeProbs function

<dl>	<dt>trees</dt>
<dd>an object of class <code>"multiSimmap"</code> containing a sample of trees that are identical in topology &amp; branch lengths with different stochastically mapped character histories.</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

Compute the relative frequencies of state changes along edges — edgeProbs

<dl>

	<dt>trees</dt>
<dd>an object of class <code>"multiSimmap"</code> containing a sample of trees that are identical in topology &amp; branch lengths with different stochastically mapped character histories.</dd>

</dl>

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

edgeProbs: Compute the relative frequencies of state changes along edges

Description

Usage

Value

Arguments

Author

References

See Also