sumstat_class

<p>If you want to create additional summary statistics for coala, create
<span class="pkg">R6</span> classes that inherit from this object.</p>

internal

Coalescent simulators can rapidly simulate biological sequences
evolving according to a given model of evolution.
You can use this package to specify such models, to conduct the simulations
and to calculate additional statistics from the results (Staab, Metzler,
2016 <doi:10.1093/bioinformatics/btw098>).
It relies on existing simulators for doing the simulation, and currently
supports the programs 'ms', 'msms' and 'scrm'. It also supports finite-sites
mutation models by combining the simulators with the program 'seq-gen'.
Coala provides functions for calculating certain summary statistics, which
can also be applied to actual biological data.
One possibility to import data is through the 'PopGenome' package
(<https://github.com/pievos101/PopGenome>).

Dirk Metzler

coala

A Framework for Coalescent Simulation

Paul Staab

Jorge E. Amaya Romero

sumstat_class function

<p><code>coala::coalmodelpart</code> -&gt; <code>sumstat</code></p>

Super class


<div class="section" id="public-methods">
<h3>Public methods</h3><p></p><p><ul>
<li><p><a href="/link/sumstat_class%24new()?package=coala&version=0.7.1" data-mini-rdoc="coala::sumstat_class$new()"><code>sumstat_class$new()</code></a></p></li>
<li><p><a href="/link/sumstat_class%24calculate()?package=coala&version=0.7.1" data-mini-rdoc="coala::sumstat_class$calculate()"><code>sumstat_class$calculate()</code></a></p></li>
<li><p><a href="/link/sumstat_class%24check()?package=coala&version=0.7.1" data-mini-rdoc="coala::sumstat_class$check()"><code>sumstat_class$check()</code></a></p></li>
<li><p><a href="/link/sumstat_class%24get_name()?package=coala&version=0.7.1" data-mini-rdoc="coala::sumstat_class$get_name()"><code>sumstat_class$get_name()</code></a></p></li>
<li><p><a href="/link/sumstat_class%24requires_files()?package=coala&version=0.7.1" data-mini-rdoc="coala::sumstat_class$requires_files()"><code>sumstat_class$requires_files()</code></a></p></li>
<li><p><a href="/link/sumstat_class%24requires_segsites()?package=coala&version=0.7.1" data-mini-rdoc="coala::sumstat_class$requires_segsites()"><code>sumstat_class$requires_segsites()</code></a></p></li>
<li><p><a href="/link/sumstat_class%24requires_trees()?package=coala&version=0.7.1" data-mini-rdoc="coala::sumstat_class$requires_trees()"><code>sumstat_class$requires_trees()</code></a></p></li>
<li><p><a href="/link/sumstat_class%24print()?package=coala&version=0.7.1" data-mini-rdoc="coala::sumstat_class$print()"><code>sumstat_class$print()</code></a></p></li>
<li><p><a href="/link/sumstat_class%24transform()?package=coala&version=0.7.1" data-mini-rdoc="coala::sumstat_class$transform()"><code>sumstat_class$transform()</code></a></p></li>
<li><p><a href="/link/sumstat_class%24clone()?package=coala&version=0.7.1" data-mini-rdoc="coala::sumstat_class$clone()"><code>sumstat_class$clone()</code></a></p></li>
</ul></p><p></p></div><p><hr>
<a id="method-sumstat-new"></a></p><div class="section" id="method-new-">
<h3>Method <code>new()</code></h3><p></p><p><div class="section" id="usage">
<h4>Usage</h4>
<p><div class="r"></div></p><pre><code>sumstat_class$new(name, transformation)</code></pre><p></p></div></p>
</div><p></p><p>
</p><p><hr>
<a id="method-sumstat-calculate"></a></p><div class="section" id="method-calculate-">
<h3>Method <code>calculate()</code></h3><p></p><p><div class="section" id="usage">
<h4>Usage</h4>
<p><div class="r"></div></p><pre><code>sumstat_class$calculate(seg_sites, trees, files, model)</code></pre><p></p></div></p>
</div><p></p><p>
</p><p><hr>
<a id="method-sumstat-check"></a></p><div class="section" id="method-check-">
<h3>Method <code>check()</code></h3><p></p><p><div class="section" id="usage">
<h4>Usage</h4>
<p><div class="r"></div></p><pre><code>sumstat_class$check(model)</code></pre><p></p></div></p>
</div><p></p><p>
</p><p><hr>
<a id="method-sumstat-get_name"></a></p><div class="section" id="method-get-name-">
<h3>Method <code>get_name()</code></h3><p></p><p><div class="section" id="usage">
<h4>Usage</h4>
<p><div class="r"></div></p><pre><code>sumstat_class$get_name()</code></pre><p></p></div></p>
</div><p></p><p>
</p><p><hr>
<a id="method-sumstat-requires_files"></a></p><div class="section" id="method-requires-files-">
<h3>Method <code>requires_files()</code></h3><p></p><p><div class="section" id="usage">
<h4>Usage</h4>
<p><div class="r"></div></p><pre><code>sumstat_class$requires_files()</code></pre><p></p></div></p>
</div><p></p><p>
</p><p><hr>
<a id="method-sumstat-requires_segsites"></a></p><div class="section" id="method-requires-segsites-">
<h3>Method <code>requires_segsites()</code></h3><p></p><p><div class="section" id="usage">
<h4>Usage</h4>
<p><div class="r"></div></p><pre><code>sumstat_class$requires_segsites()</code></pre><p></p></div></p>
</div><p></p><p>
</p><p><hr>
<a id="method-sumstat-requires_trees"></a></p><div class="section" id="method-requires-trees-">
<h3>Method <code>requires_trees()</code></h3><p></p><p><div class="section" id="usage">
<h4>Usage</h4>
<p><div class="r"></div></p><pre><code>sumstat_class$requires_trees()</code></pre><p></p></div></p>
</div><p></p><p>
</p><p><hr>
<a id="method-sumstat-print"></a></p><div class="section" id="method-print-">
<h3>Method <code><a href="/link/print()?package=coala&version=0.7.1" data-mini-rdoc="coala::print()">print()</a></code></h3><p></p><p><div class="section" id="usage">
<h4>Usage</h4>
<p><div class="r"></div></p><pre><code>sumstat_class$print()</code></pre><p></p></div></p>
</div><p></p><p>
</p><p><hr>
<a id="method-sumstat-transform"></a></p><div class="section" id="method-transform-">
<h3>Method <code><a href="/link/transform()?package=coala&version=0.7.1" data-mini-rdoc="coala::transform()">transform()</a></code></h3><p></p><p><div class="section" id="usage">
<h4>Usage</h4>
<p><div class="r"></div></p><pre><code>sumstat_class$transform(x)</code></pre><p></p></div></p>
</div><p></p><p>
</p><p><hr>
<a id="method-sumstat-clone"></a></p><div class="section" id="method-clone-">
<h3>Method <code>clone()</code></h3>
<p>The objects of this class are cloneable with this method.</p><div class="section" id="usage">
<h4>Usage</h4>
<p><div class="r"></div></p><pre><code>sumstat_class$clone(deep = FALSE)</code></pre><p></p></div><p></p>
</div><p></p><p><div class="section" id="arguments">
<h4>Arguments</h4>
<p><div class="arguments"></div></p><dl>
<dt><code>deep</code></dt>
<dd><p>Whether to make a deep clone.</p></dd></dl></div></p><p>
</p><p></p>
<p></p><p>
</p>

Methods

Base Class for Summary Statistics — sumstat_class


<div class='section' id='public-methods'>
<h3>Public methods</h3>

<ul>
<li><p><a href='#method-sumstat-new'><code>sumstat_class$new()</code></a></p></li>
<li><p><a href='#method-sumstat-calculate'><code>sumstat_class$calculate()</code></a></p></li>
<li><p><a href='#method-sumstat-check'><code>sumstat_class$check()</code></a></p></li>
<li><p><a href='#method-sumstat-get_name'><code>sumstat_class$get_name()</code></a></p></li>
<li><p><a href='#method-sumstat-requires_files'><code>sumstat_class$requires_files()</code></a></p></li>
<li><p><a href='#method-sumstat-requires_segsites'><code>sumstat_class$requires_segsites()</code></a></p></li>
<li><p><a href='#method-sumstat-requires_trees'><code>sumstat_class$requires_trees()</code></a></p></li>
<li><p><a href='#method-sumstat-print'><code>sumstat_class$print()</code></a></p></li>
<li><p><a href='#method-sumstat-transform'><code>sumstat_class$transform()</code></a></p></li>
<li><p><a href='#method-sumstat-clone'><code>sumstat_class$clone()</code></a></p></li>
</ul>

</div><p><hr>
<a id="method-sumstat-new"></a></p><div class='section' id='method-new-'>
<h3>Method <code>new()</code></h3>

<div class='section' id='usage'>
<h4>Usage</h4>
<p><div class="r"></p><pre><code>sumstat_class$new(name, transformation)</code></pre><p></div></p>
</div>


</div><p><hr>
<a id="method-sumstat-calculate"></a></p><div class='section' id='method-calculate-'>
<h3>Method <code>calculate()</code></h3>

<div class='section' id='usage'>
<h4>Usage</h4>
<p><div class="r"></p><pre><code>sumstat_class$calculate(seg_sites, trees, files, model)</code></pre><p></div></p>
</div>


</div><p><hr>
<a id="method-sumstat-check"></a></p><div class='section' id='method-check-'>
<h3>Method <code>check()</code></h3>

<div class='section' id='usage'>
<h4>Usage</h4>
<p><div class="r"></p><pre><code>sumstat_class$check(model)</code></pre><p></div></p>
</div>


</div><p><hr>
<a id="method-sumstat-get_name"></a></p><div class='section' id='method-get-name-'>
<h3>Method <code>get_name()</code></h3>

<div class='section' id='usage'>
<h4>Usage</h4>
<p><div class="r"></p><pre><code>sumstat_class$get_name()</code></pre><p></div></p>
</div>


</div><p><hr>
<a id="method-sumstat-requires_files"></a></p><div class='section' id='method-requires-files-'>
<h3>Method <code>requires_files()</code></h3>

<div class='section' id='usage'>
<h4>Usage</h4>
<p><div class="r"></p><pre><code>sumstat_class$requires_files()</code></pre><p></div></p>
</div>


</div><p><hr>
<a id="method-sumstat-requires_segsites"></a></p><div class='section' id='method-requires-segsites-'>
<h3>Method <code>requires_segsites()</code></h3>

<div class='section' id='usage'>
<h4>Usage</h4>
<p><div class="r"></p><pre><code>sumstat_class$requires_segsites()</code></pre><p></div></p>
</div>


</div><p><hr>
<a id="method-sumstat-requires_trees"></a></p><div class='section' id='method-requires-trees-'>
<h3>Method <code>requires_trees()</code></h3>

<div class='section' id='usage'>
<h4>Usage</h4>
<p><div class="r"></p><pre><code>sumstat_class$requires_trees()</code></pre><p></div></p>
</div>


</div><p><hr>
<a id="method-sumstat-print"></a></p><div class='section' id='method-print-'>
<h3>Method <code><a href='https://rdrr.io/r/base/print.html'>print()</a></code></h3>

<div class='section' id='usage'>
<h4>Usage</h4>
<p><div class="r"></p><pre><code>sumstat_class$print()</code></pre><p></div></p>
</div>


</div><p><hr>
<a id="method-sumstat-transform"></a></p><div class='section' id='method-transform-'>
<h3>Method <code><a href='https://rdrr.io/r/base/transform.html'>transform()</a></code></h3>

<div class='section' id='usage'>
<h4>Usage</h4>
<p><div class="r"></p><pre><code>sumstat_class$transform(x)</code></pre><p></div></p>
</div>


</div><p><hr>
<a id="method-sumstat-clone"></a></p><div class='section' id='method-clone-'>
<h3>Method <code>clone()</code></h3>
<p>The objects of this class are cloneable with this method.</p><div class='section' id='usage'>
<h4>Usage</h4>
<p><div class="r"></p><pre><code>sumstat_class$clone(deep = FALSE)</code></pre><p></div></p>
</div>

<div class='section' id='arguments'>
<h4>Arguments</h4>
<p><div class="arguments"></p><dl>
<dt><code>deep</code></dt>
<dd><p>Whether to make a deep clone.</p></dd>


</dl><p></div></p>
</div>

</div>


sumstat_class: Base Class for Summary Statistics

Description

Arguments

Super class

Methods

Public methods

Method `new()`

Usage

Method `calculate()`

Usage

Method `check()`

Usage

Method `get_name()`

Usage

Method `requires_files()`

Usage

Method `requires_segsites()`

Usage

Method `requires_trees()`

Usage

Method `print()`

Usage

Method `transform()`

Usage

Method `clone()`

Usage

Arguments

Description

Arguments

Super class

Methods

Public methods

Method new()

Usage

Method calculate()

Usage

Method check()

Usage

Method get_name()

Usage

Method requires_files()

Usage

Method requires_segsites()

Usage

Method requires_trees()

Usage

Method print()

Usage

Method transform()

Usage

Method clone()

Usage

Arguments

Method `new()`

Method `calculate()`

Method `check()`

Method `get_name()`

Method `requires_files()`

Method `requires_segsites()`

Method `requires_trees()`

Method `print()`

Method `transform()`

Method `clone()`