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<h1>Transform Input to Disk Diffusion Diameters</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/disk.R'><code>R/disk.R</code></a></small>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/disk.R" class="external-link"><code>R/disk.R</code></a></small>
<div class="hidden name"><code>as.disk.Rd</code></div>
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@ -238,97 +161,95 @@
<p>This transforms a vector to a new class <code>disk</code>, which is a disk diffusion growth zone size (around an antibiotic disk) in millimetres between 6 and 50.</p>
</div>
<pre class="usage"><span class='fu'>as.disk</span><span class='op'>(</span><span class='va'>x</span>, na.rm <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">as.disk</span><span class="op">(</span><span class="va">x</span>, na.rm <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>
<span class='va'>NA_disk_</span>
<span class="va">NA_disk_</span>
<span class='fu'>is.disk</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span></pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>x</th>
<td><p>vector</p></td>
</tr>
<tr>
<th>na.rm</th>
<td><p>a <a href='https://rdrr.io/r/base/logical.html'>logical</a> indicating whether missing values should be removed</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
<span class="fu">is.disk</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></code></pre></div></div>
<div id="format">
<h2>Format</h2>
<p>An object of class <code>disk</code> (inherits from <code>integer</code>) of length 1.</p>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>An <a href='https://rdrr.io/r/base/integer.html'>integer</a> with additional class <code>disk</code></p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>Interpret disk values as RSI values with <code><a href='as.rsi.html'>as.rsi()</a></code>. It supports guidelines from EUCAST and CLSI.</p>
</div>
<div id="arguments">
<h2>Arguments</h2>
<dl><dt>x</dt>
<dd><p>vector</p></dd>
<dt>na.rm</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> indicating whether missing values should be removed</p></dd>
</dl></div>
<div id="value">
<h2>Value</h2>
<p>An <a href="https://rdrr.io/r/base/integer.html" class="external-link">integer</a> with additional class <code>disk</code></p>
</div>
<div id="details">
<h2>Details</h2>
<p>Interpret disk values as RSI values with <code><a href="as.rsi.html">as.rsi()</a></code>. It supports guidelines from EUCAST and CLSI.</p>
<p><code>NA_disk_</code> is a missing value of the new <code>&lt;disk&gt;</code> class.</p>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable Lifecycle</h2>
</div>
<div id="stable-lifecycle">
<h2>Stable Lifecycle</h2>
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on Our Website!</h2>
<p><img src="figures/lifecycle_stable.svg" style="margin-bottom:5px"><br>
The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
</div>
<div id="read-more-on-our-website-">
<h2>Read more on Our Website!</h2>
<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<p>On our website <a href="https://msberends.github.io/AMR/">https://msberends.github.io/AMR/</a> you can find <a href="https://msberends.github.io/AMR/articles/AMR.html">a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href="https://msberends.github.io/AMR/reference/">complete documentation of all functions</a> and <a href="https://msberends.github.io/AMR/articles/WHONET.html">an example analysis using WHONET data</a>.</p>
</div>
<div id="see-also">
<h2>See also</h2>
<div class="dont-index"><p><code><a href="as.rsi.html">as.rsi()</a></code></p></div>
</div>
<div class='dont-index'><p><code><a href='as.rsi.html'>as.rsi()</a></code></p></div>
<div id="ref-examples">
<h2>Examples</h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="co"># \donttest{</span>
<span class="co"># transform existing disk zones to the `disk` class</span>
<span class="va">df</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>microorganism <span class="op">=</span> <span class="st">"E. coli"</span>,
AMP <span class="op">=</span> <span class="fl">20</span>,
CIP <span class="op">=</span> <span class="fl">14</span>,
GEN <span class="op">=</span> <span class="fl">18</span>,
TOB <span class="op">=</span> <span class="fl">16</span><span class="op">)</span>
<span class="va">df</span><span class="op">[</span>, <span class="fl">2</span><span class="op">:</span><span class="fl">5</span><span class="op">]</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">df</span><span class="op">[</span>, <span class="fl">2</span><span class="op">:</span><span class="fl">5</span><span class="op">]</span>, <span class="va">as.disk</span><span class="op">)</span>
<span class="co"># same with dplyr:</span>
<span class="co"># df %&gt;% mutate(across(AMP:TOB, as.disk))</span>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># \donttest{</span>
<span class='co'># transform existing disk zones to the `disk` class</span>
<span class='va'>df</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span>microorganism <span class='op'>=</span> <span class='st'>"E. coli"</span>,
AMP <span class='op'>=</span> <span class='fl'>20</span>,
CIP <span class='op'>=</span> <span class='fl'>14</span>,
GEN <span class='op'>=</span> <span class='fl'>18</span>,
TOB <span class='op'>=</span> <span class='fl'>16</span><span class='op'>)</span>
<span class='va'>df</span><span class='op'>[</span>, <span class='fl'>2</span><span class='op'>:</span><span class='fl'>5</span><span class='op'>]</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>df</span><span class='op'>[</span>, <span class='fl'>2</span><span class='op'>:</span><span class='fl'>5</span><span class='op'>]</span>, <span class='va'>as.disk</span><span class='op'>)</span>
<span class='co'># same with dplyr:</span>
<span class='co'># df %&gt;% mutate(across(AMP:TOB, as.disk))</span>
<span class='co'># interpret disk values, see ?as.rsi</span>
<span class='fu'><a href='as.rsi.html'>as.rsi</a></span><span class='op'>(</span>x <span class='op'>=</span> <span class='fu'>as.disk</span><span class='op'>(</span><span class='fl'>18</span><span class='op'>)</span>,
mo <span class='op'>=</span> <span class='st'>"Strep pneu"</span>, <span class='co'># `mo` will be coerced with as.mo()</span>
ab <span class='op'>=</span> <span class='st'>"ampicillin"</span>, <span class='co'># and `ab` with as.ab()</span>
guideline <span class='op'>=</span> <span class='st'>"EUCAST"</span><span class='op'>)</span>
<span class="co"># interpret disk values, see ?as.rsi</span>
<span class="fu"><a href="as.rsi.html">as.rsi</a></span><span class="op">(</span>x <span class="op">=</span> <span class="fu">as.disk</span><span class="op">(</span><span class="fl">18</span><span class="op">)</span>,
mo <span class="op">=</span> <span class="st">"Strep pneu"</span>, <span class="co"># `mo` will be coerced with as.mo()</span>
ab <span class="op">=</span> <span class="st">"ampicillin"</span>, <span class="co"># and `ab` with as.ab()</span>
guideline <span class="op">=</span> <span class="st">"EUCAST"</span><span class="op">)</span>
<span class='fu'><a href='as.rsi.html'>as.rsi</a></span><span class='op'>(</span><span class='va'>df</span><span class='op'>)</span>
<span class='co'># }</span>
</pre>
<span class="fu"><a href="as.rsi.html">as.rsi</a></span><span class="op">(</span><span class="va">df</span><span class="op">)</span>
<span class="co"># }</span>
</code></pre></div>
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