parmap.W

These functions calculate weight matrices from regimes specified by a bayou formatted parameter list
<code>parmap.W</code> calculates the weight matrix for a set of regimes from a phylogeny
with a stored regime history. <code>.parmap.W</code> calculates the same matrix, but without checks and is
generally run internally.

Fits and simulates multi-optima Ornstein-Uhlenbeck models to phylogenetic comparative data using
Bayesian reversible-jump methods. See Uyeda and Harmon (2014) <DOI:10.1093/sysbio/syu057>.

Josef Uyeda

bayou

Bayesian Fitting of Ornstein-Uhlenbeck Models to Phylogenies

Josef C. Uyeda

Jon Eastman

Luke Harmon

Abhishek Hari

parmap.W function

<dl><dt>tree</dt>
<dd>either a tree of class "phylo" or a cache object produced by bayOU's internal
functions. Must include list element 'maps' which is a simmap reconstruction of regime history.</dd>
<dt>pars</dt>
<dd>a list of the parameters used to calculate the weight matrix. Only pars$alpha is
necessary to calculate the matrix, but others can be present.</dd></dl>

Arguments

Calculate the weight matrix of a set of regimes on a phylogeny — parmap.W

<dl>

<dt>tree</dt>
<dd>either a tree of class "phylo" or a cache object produced by bayOU's internal
functions. Must include list element 'maps' which is a simmap reconstruction of regime history.</dd>


<dt>pars</dt>
<dd>a list of the parameters used to calculate the weight matrix. Only pars$alpha is
necessary to calculate the matrix, but others can be present.</dd>

</dl>

parmap.W: Calculate the weight matrix of a set of regimes on a phylogeny

Description

Usage

Value

Arguments

Details