ouch-package

The ouch package provides facilities for Ornstein-Uhlenbeck based methods of phylogenetic comparative analysis.

models

Fit and compare Ornstein-Uhlenbeck models for evolution along a phylogenetic tree.

Aaron King

ouch

Ornstein-Uhlenbeck Models for Phylogenetic Comparative
Hypotheses

ouch-package function

The basic class, <code>ouchtree</code>, is provided to encode a phylogenetic tree.
 Plot and print methods are provided.
The class <code>browntree</code> derives from class <code>ouchtree</code> and encodes the results of fitting a Brownian Motion model to data.
The class <code>hansentree</code> derives from class <code>ouchtree</code> and encodes the results of fitting a Hansen model to data.

Classes

<dl class="dl-horizontal">
 <dt>ouchtree</dt><dd><code><a rd-options="" href="/link/ouchtree?package=ouch&version=2.14-1" data-mini-rdoc="ouch::ouchtree">ouchtree</a></code></dd>
 <dt>Brownian motion methods</dt><dd><code><a rd-options="" href="/link/brown?package=ouch&version=2.14-1" data-mini-rdoc="ouch::brown">brown</a></code>,
 <code><a rd-options="" href="/link/browntree-class?package=ouch&version=2.14-1" data-mini-rdoc="ouch::browntree-class">browntree-class</a></code></dd>
 <dt>Ornstein-Uhlenbeck methods</dt><dd><code><a rd-options="" href="/link/hansen?package=ouch&version=2.14-1" data-mini-rdoc="ouch::hansen">hansen</a></code>,
 <code><a rd-options="" href="/link/hansentree-class?package=ouch&version=2.14-1" data-mini-rdoc="ouch::hansentree-class">hansentree-class</a></code></dd>
 <dt>simulate methods</dt><dd><code><a rd-options="" href="/link/simulate-browntree?package=ouch&version=2.14-1" data-mini-rdoc="ouch::simulate-browntree">simulate-browntree</a></code>,
 <code><a rd-options="" href="/link/simulate-hansentree?package=ouch&version=2.14-1" data-mini-rdoc="ouch::simulate-hansentree">simulate-hansentree</a></code></dd>
 <dt>plot methods</dt><dd><code><a rd-options="" href="/link/plot-browntree?package=ouch&version=2.14-1" data-mini-rdoc="ouch::plot-browntree">plot-browntree</a></code>,
 <code><a rd-options="" href="/link/plot-hansentree?package=ouch&version=2.14-1" data-mini-rdoc="ouch::plot-hansentree">plot-hansentree</a></code></dd>
 <dt><code>ape2ouch</code></dt><dd>Convert a tree in ape format to ouch format.
 See <code><a rd-options="" href="/link/ape2ouch?package=ouch&version=2.14-1" data-mini-rdoc="ouch::ape2ouch">ape2ouch</a></code></dd>
 </dl>

Detailed Documentation

Ornstein-Uhlenbeck methods for comparative phylogenetic hypotheses — ouch-package

<dl class='dl-horizontal'>
 <dt>ouchtree</dt><dd><code><a rd-options='' href='ouchtree'>ouchtree</a></code></dd>
 <dt>Brownian motion methods</dt><dd><code><a rd-options='' href='brown'>brown</a></code>,
 <code><a rd-options='' href='browntree-class'>browntree-class</a></code></dd>
 <dt>Ornstein-Uhlenbeck methods</dt><dd><code><a rd-options='' href='hansen'>hansen</a></code>,
 <code><a rd-options='' href='hansentree-class'>hansentree-class</a></code></dd>
 <dt>simulate methods</dt><dd><code><a rd-options='' href='simulate-browntree'>simulate-browntree</a></code>,
 <code><a rd-options='' href='simulate-hansentree'>simulate-hansentree</a></code></dd>
 <dt>plot methods</dt><dd><code><a rd-options='' href='plot-browntree'>plot-browntree</a></code>,
 <code><a rd-options='' href='plot-hansentree'>plot-hansentree</a></code></dd>
 <dt><code>ape2ouch</code></dt><dd>Convert a tree in ape format to ouch format.
 See <code><a rd-options='' href='ape2ouch'>ape2ouch</a></code></dd>
 </dl>

ouch-package: Ornstein-Uhlenbeck methods for comparative phylogenetic hypotheses

Description

Arguments

Classes

Detailed Documentation

References