Dtest

Conducts the 'D-test' of Huelsenbeck et al. (2003).

Simulation

phylogenetics

comparative method

Bayesian

discrete character

A wide range of methods for phylogenetic analysis - concentrated in phylogenetic comparative biology, but also including numerous techniques for visualizing, analyzing, 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 trait data. 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 phenotype space or a onto a geographic map, and for visualizing correlated speciation between trees. Lastly, numerous functions are designed for reading, writing, analyzing, inferring, simulating, and manipulating phylogenetic trees and comparative data. For instance, there are functions for computing consensus phylogenies from a set, for simulating phylogenetic trees and data under a range of models, for randomly or non-randomly attaching species or clades to a tree, as well as for a wide range 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)

Dtest function

<dl>	<dt>t1</dt>
<dd>set of stochastic map trees (i.e., object of class <code>"multiSimmap"</code> for character 1. Note that <code>t1</code> and <code>t2</code> should be of the same length.</dd>	<dt>t2</dt>
<dd>set of stochastic map trees (i.e., object of class <code>"multiSimmap"</code> for character 2. Note that <code>t1</code> and <code>t2</code> should be of the same length.</dd>	<dt>nsim</dt>
<dd>number of simulations to use in the test.</dd>	<dt>...</dt>
<dd>arguments to be passed internally to <code>make.simmap</code>. Note that (for now) these must be the same for both <code>t1</code> and <code>t2</code> (that is to say, we are not able to assume different trait evolution models for each tree).</dd></dl>

Arguments

Liam Revell <a href="/link/liam.revell%40umb.edu?package=phytools&version=2.1-1" data-mini-rdoc="phytools::liam.revell@umb.edu">liam.revell@umb.edu</a>

Author

Conducts correlational D-test from stochastic mapping — Dtest

<dl>

	<dt>t1</dt>
<dd>set of stochastic map trees (i.e., object of class <code>"multiSimmap"</code> for character 1. Note that <code>t1</code> and <code>t2</code> should be of the same length.</dd>

	<dt>t2</dt>
<dd>set of stochastic map trees (i.e., object of class <code>"multiSimmap"</code> for character 2. Note that <code>t1</code> and <code>t2</code> should be of the same length.</dd>

	<dt>nsim</dt>
<dd>number of simulations to use in the test.</dd>

	<dt>...</dt>
<dd>arguments to be passed internally to <code>make.simmap</code>. Note that (for now) these must be the same for both <code>t1</code> and <code>t2</code> (that is to say, we are not able to assume different trait evolution models for each tree).</dd>

</dl>

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

Dtest: Conducts correlational D-test from stochastic mapping

Description

Usage

Value

Arguments

Author

Details

References

See Also