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<h1>Transform Input to Disk Diffusion Diameters</h1>
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<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>
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<div class="hidden name"><code>as.disk.Rd</code></div>
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</div>
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<div class="ref-description">
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<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>
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</div>
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<div id="ref-usage">
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<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>
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<span class="va">NA_disk_</span>
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<span class="fu">is.disk</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></code></pre></div>
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</div>
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<div id="format">
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<h2>Format</h2>
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<p>An object of class <code>disk</code> (inherits from <code>integer</code>) of length 1.</p>
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</div>
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<div id="arguments">
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<h2>Arguments</h2>
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<dl><dt>x</dt>
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<dd><p>vector</p></dd>
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<dt>na.rm</dt>
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<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>
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</dl></div>
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<div id="value">
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<h2>Value</h2>
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<p>An <a href="https://rdrr.io/r/base/integer.html" class="external-link">integer</a> with additional class <code>disk</code></p>
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</div>
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<div id="details">
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<h2>Details</h2>
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<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>
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<p><code>NA_disk_</code> is a missing value of the new <code><disk></code> class.</p>
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</div>
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<div id="stable-lifecycle">
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<h2>Stable Lifecycle</h2>
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<p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><br>
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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>
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<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 a 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>
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</div>
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<div id="read-more-on-our-website-">
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<h2>Read more on Our Website!</h2>
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<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>
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</div>
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<div id="see-also">
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<h2>See also</h2>
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<div class="dont-index"><p><code><a href="as.rsi.html">as.rsi()</a></code></p></div>
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</div>
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<div id="ref-examples">
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<h2>Examples</h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="co"># \donttest{</span>
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<span class="co"># transform existing disk zones to the `disk` class</span>
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<span class="va">df</span> <span class="op"><-</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>,
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AMP <span class="op">=</span> <span class="fl">20</span>,
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CIP <span class="op">=</span> <span class="fl">14</span>,
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GEN <span class="op">=</span> <span class="fl">18</span>,
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TOB <span class="op">=</span> <span class="fl">16</span><span class="op">)</span>
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<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"><-</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>
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<span class="co"># same with dplyr:</span>
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<span class="co"># df %>% mutate(across(AMP:TOB, as.disk))</span>
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<span class="co"># interpret disk values, see ?as.rsi</span>
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<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>,
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mo <span class="op">=</span> <span class="st">"Strep pneu"</span>, <span class="co"># `mo` will be coerced with as.mo()</span>
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ab <span class="op">=</span> <span class="st">"ampicillin"</span>, <span class="co"># and `ab` with as.ab()</span>
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guideline <span class="op">=</span> <span class="st">"EUCAST"</span><span class="op">)</span>
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<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>
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<span class="co"># }</span>
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</code></pre></div>
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