sim.ctt

sim.multiCtt

This function generates a 'changes through time' plot in the style of a lineage-through-time (LTT) plot. It shows the mean rate or the mean number of changes per unit time from a set of stochastic character map trees.

phylogenetics

comparative method

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)

ctt function

<dl>	<dt>trees</dt>
<dd>an object of class <code>"multiSimmap"</code>.</dd>	<dt>segments</dt>
<dd>number of segments to break up the history of the tree.</dd>	<dt>tree</dt>
<dd>for <code>sim.ctt</code>, an object of class <code>"phylo"</code>.</dd>	<dt>Q</dt>
<dd>for <code>sim.ctt</code>, a transition matrix to use for simulation.</dd>	<dt>anc</dt>
<dd>ancestral state at the root node for simulation.</dd>	<dt>nmaps</dt>
<dd>number of stochastic maps per simulation.</dd>	<dt>nsim</dt>
<dd>for <code>sim.multiCtt</code> only, the number of simulations to run.</dd>	<dt>...</dt>
<dd>optional arguments.</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

Generates (or simulates) a 'changes through time' plot from a set of stochastic map character histories — ctt

<dl>

	<dt>trees</dt>
<dd>an object of class <code>"multiSimmap"</code>.</dd>

	<dt>segments</dt>
<dd>number of segments to break up the history of the tree.</dd>

	<dt>tree</dt>
<dd>for <code>sim.ctt</code>, an object of class <code>"phylo"</code>.</dd>

	<dt>Q</dt>
<dd>for <code>sim.ctt</code>, a transition matrix to use for simulation.</dd>

	<dt>anc</dt>
<dd>ancestral state at the root node for simulation.</dd>

	<dt>nmaps</dt>
<dd>number of stochastic maps per simulation.</dd>

	<dt>nsim</dt>
<dd>for <code>sim.multiCtt</code> only, the number of simulations to run.</dd>

	<dt>...</dt>
<dd>optional arguments.</dd>

</dl>

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

ctt: Generates (or simulates) a 'changes through time' plot from a set of stochastic map character histories

Description

Usage

Value

Arguments

Author

References

See Also