threshDIC

tree

a named vector containing discrete character states; or a matrix containing the tip species, in rows, and probabilities of being in each state, in columns.

list object returned by <code><a rd-options="" href="/link/ancThresh?package=phytools&version=1.0-3" data-mini-rdoc="phytools::ancThresh">ancThresh</a></code>.

mcmc

number of generations (not samples) to exclude as burn in; if not supplied then 20 percent of generations are excluded.

burnin

assumed ordering of the discrete character state. If not supplied and <code>x</code> is a vector then numerical-alphabetical order is assumed; if not supplied and <code>x</code> is a matrix, then the column order of <code>x</code> is used.

sequence

method for computing the effective number of parameters (options are <code>"pD"</code> and <code>"pV"</code>).

method

This function computes the Deviance Information Criterion from the MCMC object returned by <code>ancThresh</code>.

Statistics

phylogenetics

comparative method

information criteria

Bayesian

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)

threshDIC function

<dl>	<dt>tree</dt>
<dd>phylogenetic tree.</dd>	<dt>x</dt>
<dd>a named vector containing discrete character states; or a matrix containing the tip species, in rows, and probabilities of being in each state, in columns.</dd>	<dt>mcmc</dt>
<dd>list object returned by <code>ancThresh</code>.</dd>	<dt>burnin</dt>
<dd>number of generations (not samples) to exclude as burn in; if not supplied then 20 percent of generations are excluded.</dd>	<dt>sequence</dt>
<dd>assumed ordering of the discrete character state. If not supplied and <code>x</code> is a vector then numerical-alphabetical order is assumed; if not supplied and <code>x</code> is a matrix, then the column order of <code>x</code> is used.</dd>	<dt>method</dt>
<dd>method for computing the effective number of parameters (options are <code>"pD"</code> and <code>"pV"</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

Deviance Information Criterion from the threshold model — threshDIC

<dl>

	<dt>tree</dt>
<dd>phylogenetic tree.</dd>

	<dt>x</dt>
<dd>a named vector containing discrete character states; or a matrix containing the tip species, in rows, and probabilities of being in each state, in columns.</dd>

	<dt>mcmc</dt>
<dd>list object returned by <code>ancThresh</code>.</dd>

	<dt>burnin</dt>
<dd>number of generations (not samples) to exclude as burn in; if not supplied then 20 percent of generations are excluded.</dd>

	<dt>sequence</dt>
<dd>assumed ordering of the discrete character state. If not supplied and <code>x</code> is a vector then numerical-alphabetical order is assumed; if not supplied and <code>x</code> is a matrix, then the column order of <code>x</code> is used.</dd>

	<dt>method</dt>
<dd>method for computing the effective number of parameters (options are <code>"pD"</code> and <code>"pV"</code>).</dd>

</dl>

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

threshDIC: Deviance Information Criterion from the threshold model

Description

Usage

Value

Arguments

Author

References

See Also