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Conduct AMR Analysis
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Generate Antibiogram (Trad./Syndromic/WISCA)
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Get Properties of an Antibiotic Drug
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<main id="main" class="col-md-9"><div class="page-header">
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<img src="../logo.svg" class="logo" alt=""><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="d-none name"><code>as.disk.Rd</code></div>
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</div>
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<div class="ref-description section level2">
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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 class="section level2">
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<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><span><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>
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<span></span>
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<span><span class="va">NA_disk_</span></span>
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<span></span>
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<span><span class="fu">is.disk</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></code></pre></div>
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</div>
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<div class="section level2">
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<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></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 class="section level2">
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<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></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 class="section level2">
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<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></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 class="section level2">
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<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
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<p>Interpret disk values as SIR values with <code><a href="as.sir.html">as.sir()</a></code>. It supports guidelines from EUCAST and CLSI.</p>
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<p>Disk diffusion growth zone sizes must be between 6 and 50 millimetres. Values higher than 50 but lower than 100 will be maximised to 50. All others input values outside the 6-50 range will return <code>NA</code>.</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 class="section level2">
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<h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
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<div class="dont-index"><p><code><a href="as.sir.html">as.sir()</a></code></p></div>
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</div>
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<div class="section level2">
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<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># transform existing disk zones to the `disk` class (using base R)</span></span></span>
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<span class="r-in"><span><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></span></span>
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<span class="r-in"><span> microorganism <span class="op">=</span> <span class="st">"Escherichia coli"</span>,</span></span>
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<span class="r-in"><span> AMP <span class="op">=</span> <span class="fl">20</span>,</span></span>
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<span class="r-in"><span> CIP <span class="op">=</span> <span class="fl">14</span>,</span></span>
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<span class="r-in"><span> GEN <span class="op">=</span> <span class="fl">18</span>,</span></span>
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<span class="r-in"><span> TOB <span class="op">=</span> <span class="fl">16</span></span></span>
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<span class="r-in"><span><span class="op">)</span></span></span>
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<span class="r-in"><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"><-</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></span>
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<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/str.html" class="external-link">str</a></span><span class="op">(</span><span class="va">df</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> 'data.frame': 1 obs. of 5 variables:</span>
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<span class="r-out co"><span class="r-pr">#></span> $ microorganism: chr "Escherichia coli"</span>
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<span class="r-out co"><span class="r-pr">#></span> $ AMP : 'disk' int 20</span>
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<span class="r-out co"><span class="r-pr">#></span> $ CIP : 'disk' int 14</span>
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<span class="r-out co"><span class="r-pr">#></span> $ GEN : 'disk' int 18</span>
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<span class="r-out co"><span class="r-pr">#></span> $ TOB : 'disk' int 16</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
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<span class="r-in"><span><span class="co"># transforming is easier with dplyr:</span></span></span>
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<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
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<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="va">AMP</span><span class="op">:</span><span class="va">TOB</span>, <span class="va">as.disk</span><span class="op">)</span><span class="op">)</span></span></span>
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<span class="r-in"><span><span class="op">}</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> microorganism AMP CIP GEN TOB</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 Escherichia coli 20 14 18 16</span>
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<span class="r-in"><span><span class="co"># }</span></span></span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># interpret disk values, see ?as.sir</span></span></span>
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<span class="r-in"><span><span class="fu"><a href="as.sir.html">as.sir</a></span><span class="op">(</span></span></span>
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<span class="r-in"><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>,</span></span>
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<span class="r-in"><span> mo <span class="op">=</span> <span class="st">"Strep pneu"</span>, <span class="co"># `mo` will be coerced with as.mo()</span></span></span>
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<span class="r-in"><span> ab <span class="op">=</span> <span class="st">"ampicillin"</span>, <span class="co"># and `ab` with as.ab()</span></span></span>
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<span class="r-in"><span> guideline <span class="op">=</span> <span class="st">"EUCAST"</span></span></span>
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<span class="r-in"><span><span class="op">)</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
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<span class="r-msg co"><span class="r-pr">#></span> all the details of the breakpoint interpretations. Note that some</span>
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<span class="r-msg co"><span class="r-pr">#></span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
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<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2023.</span>
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<span class="r-msg co"><span class="r-pr">#></span> Interpreting disk diffusion zones: 'ampicillin' (AMP), EUCAST 2023...</span>
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<span class="r-msg co"><span class="r-pr">#></span> OK </span>
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<span class="r-out co"><span class="r-pr">#></span> Class 'sir'</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] R</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># interpret whole data set, pretend to be all from urinary tract infections:</span></span></span>
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<span class="r-in"><span><span class="fu"><a href="as.sir.html">as.sir</a></span><span class="op">(</span><span class="va">df</span>, uti <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> all the details of the breakpoint interpretations. Note that some</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2023.</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting disk diffusion zones: column 'AMP' (ampicillin), EUCAST</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> 2023...</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting disk diffusion zones: column 'CIP' (ciprofloxacin), EUCAST</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> 2023...</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting disk diffusion zones: column 'GEN' (gentamicin), EUCAST</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> 2023...</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting disk diffusion zones: column 'TOB' (tobramycin), EUCAST</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> 2023...</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> microorganism AMP CIP GEN TOB</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> 1 Escherichia coli S <NA> S S</span>
|
||
</code></pre></div>
|
||
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|
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