PermuTest

class.pmt

<p>Abstract class for permutation tests.</p>

Implements non-parametric tests from Higgins (2004, ISBN:0534387756), including tests for one sample, two samples, k samples, paired comparisons, blocked designs, trends and association. Built with 'Rcpp' for efficiency and 'R6' for flexible, object-oriented design, the package provides a unified framework for performing or creating custom permutation tests.

Yan Du

LearnNonparam

'R6'-Based Flexible Framework for Permutation Tests

PermuTest function

<p><div class="r6-active-bindings"></div></p><dl>
<dt><code>type</code></dt>
<dd><p>The way to calculate the p-value.</p></dd><p></p><p>
<dt><code>method</code></dt>
<dd><p>The method used.</p></dd></p><p>
<dt><code>scoring</code></dt>
<dd><p>The scoring system used.</p></dd></p><p>
<dt><code>alternative</code></dt>
<dd><p>The alternative hypothesis.</p></dd></p><p>
<dt><code>null_value</code></dt>
<dd><p>The hypothesized value of the parameter in the null hypothesis.</p></dd></p><p>
<dt><code>conf_level</code></dt>
<dd><p>The confidence level of the interval.</p></dd></p><p>
<dt><code>n_permu</code></dt>
<dd><p>The number of permutations used.</p></dd></p><p>
<dt><code>data</code></dt>
<dd><p>The data.</p></dd></p><p>
<dt><code>statistic</code></dt>
<dd><p>The test statistic.</p></dd></p><p>
<dt><code>p_value</code></dt>
<dd><p>The p-value.</p></dd></p><p>
<dt><code>estimate</code></dt>
<dd><p>The estimated value of the parameter.</p></dd></p><p>
<dt><code>conf_int</code></dt>
<dd><p>The confidence interval of the parameter.</p></dd></p><p>
</p></dl><p></p>

Active bindings


<div class="section" id="public-methods">
<h3>Public methods</h3><p></p><p><ul>
<li><p><a href="/link/PermuTest%24test()?package=LearnNonparam&version=1.2.7" data-mini-rdoc="LearnNonparam::PermuTest$test()"><code>PermuTest$test()</code></a></p></li>
<li><p><a href="/link/PermuTest%24print()?package=LearnNonparam&version=1.2.7" data-mini-rdoc="LearnNonparam::PermuTest$print()"><code>PermuTest$print()</code></a></p></li>
<li><p><a href="/link/PermuTest%24plot()?package=LearnNonparam&version=1.2.7" data-mini-rdoc="LearnNonparam::PermuTest$plot()"><code>PermuTest$plot()</code></a></p></li>
</ul></p><p></p></div><p><hr>
<a id="method-PermuTest-test"></a></p><div class="section" id="method-test-">
<h3>Method <code>test()</code></h3>
<p>Perform test on sample(s).</p><div class="section" id="usage">
<h4>Usage</h4>
<p><div class="r"></div></p><pre><code>PermuTest$test(...)</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>...</code></dt>
<dd><p>sample(s). Can be numeric vector(s) or a <code>data.frame</code> or <code>list</code> containing them.</p></dd></dl></div></p><p>
</p><p></p>

<div class="section" id="details">
<h4>Details</h4>
<p>A progress bar is shown by default. Use <code>options(LearnNonparam.pmt_progress = FALSE)</code> to disable it.</p>
</div><p></p><p><div class="section" id="returns">
<h4>Returns</h4>
<p>The object itself (invisibly).</p>
</div></p><p></p><p><hr>
<a id="method-PermuTest-print"></a></p><div class="section" id="method-print-">
<h3>Method <code><a href="/link/print()?package=LearnNonparam&version=1.2.7" data-mini-rdoc="LearnNonparam::print()">print()</a></code></h3>
<p>Print the results of the test.</p><div class="section" id="usage">
<h4>Usage</h4>
<p><div class="r"></div></p><pre><code>PermuTest$print()</code></pre><p></p></div><p></p>
</div><p></p><p><div class="section" id="returns">
<h4>Returns</h4>
<p>The object itself (invisibly).</p>
</div></p><p></p><p><hr>
<a id="method-PermuTest-plot"></a></p><div class="section" id="method-plot-">
<h3>Method <code><a href="/link/plot()?package=LearnNonparam&version=1.2.7" data-mini-rdoc="LearnNonparam::plot()">plot()</a></code></h3>
<p>Plot histogram(s) of the permutation distribution. Note that this method only works if <code>type</code> is set to <code>"permu"</code>.</p><div class="section" id="usage">
<h4>Usage</h4>
<p><div class="r"></div></p><pre><code>PermuTest$plot(style = c("graphics", "ggplot2"), ...)</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>style</code></dt>
<dd><p>a character string specifying which package to use.</p></dd></dl></div></p><p>
<dt><code>...</code></dt>
<dd><p>passed to <code><a href="/link/graphics%3A%3Ahist.default()?package=LearnNonparam&version=1.2.7" data-mini-rdoc="LearnNonparam::graphics::hist.default()">graphics::hist.default()</a></code> or <code><a href="https://ggplot2.tidyverse.org/reference/geom_histogram.html">ggplot2::stat_bin()</a></code>.</p></dd></p><p>
</p><p></p>

<div class="section" id="returns">
<h4>Returns</h4>
<p>The object itself (invisibly).</p>
</div><p></p><p>
</p>

Methods

PermuTest Class — PermuTest

<p><div class="r6-active-bindings"></p><dl>
<dt><code>type</code></dt>
<dd><p>The way to calculate the p-value.</p></dd>


<dt><code>method</code></dt>
<dd><p>The method used.</p></dd>


<dt><code>scoring</code></dt>
<dd><p>The scoring system used.</p></dd>


<dt><code>alternative</code></dt>
<dd><p>The alternative hypothesis.</p></dd>


<dt><code>null_value</code></dt>
<dd><p>The hypothesized value of the parameter in the null hypothesis.</p></dd>


<dt><code>conf_level</code></dt>
<dd><p>The confidence level of the interval.</p></dd>


<dt><code>n_permu</code></dt>
<dd><p>The number of permutations used.</p></dd>


<dt><code>data</code></dt>
<dd><p>The data.</p></dd>


<dt><code>statistic</code></dt>
<dd><p>The test statistic.</p></dd>


<dt><code>p_value</code></dt>
<dd><p>The p-value.</p></dd>


<dt><code>estimate</code></dt>
<dd><p>The estimated value of the parameter.</p></dd>


<dt><code>conf_int</code></dt>
<dd><p>The confidence interval of the parameter.</p></dd>


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


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

<ul>
<li><p><a href='#method-PermuTest-test'><code>PermuTest$test()</code></a></p></li>
<li><p><a href='#method-PermuTest-print'><code>PermuTest$print()</code></a></p></li>
<li><p><a href='#method-PermuTest-plot'><code>PermuTest$plot()</code></a></p></li>
</ul>

</div><p><hr>
<a id="method-PermuTest-test"></a></p><div class='section' id='method-test-'>
<h3>Method <code>test()</code></h3>
<p>Perform test on sample(s).</p><div class='section' id='usage'>
<h4>Usage</h4>
<p><div class="r"></p><pre><code>PermuTest$test(...)</code></pre><p></div></p>
</div>

<div class='section' id='arguments'>
<h4>Arguments</h4>
<p><div class="arguments"></p><dl>
<dt><code>...</code></dt>
<dd><p>sample(s). Can be numeric vector(s) or a <code>data.frame</code> or <code>list</code> containing them.</p></dd>


</dl><p></div></p>
</div>
<div class='section' id='details'>
<h4>Details</h4>
<p>A progress bar is shown by default. Use <code>options(LearnNonparam.pmt_progress = FALSE)</code> to disable it.</p>
</div>

<div class='section' id='returns'>
<h4>Returns</h4>
<p>The object itself (invisibly).</p>
</div>

</div><p><hr>
<a id="method-PermuTest-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>
<p>Print the results of the test.</p><div class='section' id='usage'>
<h4>Usage</h4>
<p><div class="r"></p><pre><code>PermuTest$print()</code></pre><p></div></p>
</div>

<div class='section' id='returns'>
<h4>Returns</h4>
<p>The object itself (invisibly).</p>
</div>

</div><p><hr>
<a id="method-PermuTest-plot"></a></p><div class='section' id='method-plot-'>
<h3>Method <code><a href='https://rdrr.io/r/graphics/plot.default.html'>plot()</a></code></h3>
<p>Plot histogram(s) of the permutation distribution. Note that this method only works if <code>type</code> is set to <code>"permu"</code>.</p><div class='section' id='usage'>
<h4>Usage</h4>
<p><div class="r"></p><pre><code>PermuTest$plot(style = c("graphics", "ggplot2"), ...)</code></pre><p></div></p>
</div>

<div class='section' id='arguments'>
<h4>Arguments</h4>
<p><div class="arguments"></p><dl>
<dt><code>style</code></dt>
<dd><p>a character string specifying which package to use.</p></dd>


<dt><code>...</code></dt>
<dd><p>passed to <code><a href='https://rdrr.io/r/graphics/hist.html'>graphics::hist.default()</a></code> or <code><a href='https://ggplot2.tidyverse.org/reference/geom_histogram.html'>ggplot2::stat_bin()</a></code>.</p></dd>


</dl><p></div></p>
</div>
<div class='section' id='returns'>
<h4>Returns</h4>
<p>The object itself (invisibly).</p>
</div>

</div>


PermuTest: PermuTest Class

Description

Arguments

Active bindings

Methods

Public methods

Method `test()`

Usage

Arguments

Details

Returns

Method `print()`

Usage

Returns

Method `plot()`

Usage

Arguments

Returns

Description

Arguments

Active bindings

Methods

Public methods

Method test()

Usage

Arguments

Details

Returns

Method print()

Usage

Returns

Method plot()

Usage

Arguments

Returns

Method `test()`

Method `print()`

Method `plot()`