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<img src="../logo.svg" class="logo" alt=""><h1>Data Set with Clinical Breakpoints for SIR Interpretation</h1>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/data.R" class="external-link"><code>R/data.R</code></a></small>
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<div class="d-none name"><code>clinical_breakpoints.Rd</code></div>
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<p>Data set containing clinical breakpoints to interpret MIC and disk diffusion to SIR values, according to international guidelines. Currently implemented guidelines are EUCAST (2013-2022) and CLSI (2013-2022). Use <code><a href="as.sir.html">as.sir()</a></code> to transform MICs or disks measurements to SIR values.</p>
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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="va">clinical_breakpoints</span></span></code></pre></div>
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<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
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<p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 18,308 observations and 11 variables:</p><ul><li><p><code>guideline</code><br> Name of the guideline</p></li>
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<li><p><code>method</code><br> Either "DISK" or "MIC"</p></li>
<li><p><code>site</code><br> Body site, e.g. "Oral" or "Respiratory"</p></li>
<li><p><code>mo</code><br> Microbial ID, see <code><a href="as.mo.html">as.mo()</a></code></p></li>
<li><p><code>rank_index</code><br> Taxonomic rank index of <code>mo</code> from 1 (subspecies/infraspecies) to 5 (unknown microorganism)</p></li>
<li><p><code>ab</code><br> Antibiotic ID, see <code><a href="as.ab.html">as.ab()</a></code></p></li>
<li><p><code>ref_tbl</code><br> Info about where the guideline rule can be found</p></li>
<li><p><code>disk_dose</code><br> Dose of the used disk diffusion method</p></li>
<li><p><code>breakpoint_S</code><br> Lowest MIC value or highest number of millimetres that leads to "S"</p></li>
<li><p><code>breakpoint_R</code><br> Highest MIC value or lowest number of millimetres that leads to "R"</p></li>
<li><p><code>uti</code><br> A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> value (<code>TRUE</code>/<code>FALSE</code>) to indicate whether the rule applies to a urinary tract infection (UTI)</p></li>
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<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
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<p>Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. Please visit <a href="https://msberends.github.io/AMR/articles/datasets.html">our website for the download links</a>. The actual files are of course available on <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>.</p>
<p>They <strong>allow for machine reading EUCAST and CLSI guidelines</strong>, which is almost impossible with the MS Excel and PDF files distributed by EUCAST and CLSI.</p>
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<h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
<div class="dont-index"><p><a href="intrinsic_resistant.html">intrinsic_resistant</a></p></div>
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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="va">clinical_breakpoints</span></span></span>
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<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 18,308 × 11</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> guideline method site mo rank_…¹ ab ref_tbl disk_…² break…³</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> EUCAST 2… MIC <span style="color: #BB0000;">NA</span> F_ASPRG_MGTS 2 AMB Aspergi… <span style="color: #BB0000;">NA</span> 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> EUCAST 2… MIC <span style="color: #BB0000;">NA</span> F_ASPRG_NIGR 2 AMB Aspergi… <span style="color: #BB0000;">NA</span> 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> EUCAST 2… MIC <span style="color: #BB0000;">NA</span> F_CANDD_ALBC 2 AMB Candida <span style="color: #BB0000;">NA</span> 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> EUCAST 2… MIC <span style="color: #BB0000;">NA</span> F_CANDD_DBLN 2 AMB Candida <span style="color: #BB0000;">NA</span> 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> EUCAST 2… MIC <span style="color: #BB0000;">NA</span> F_CANDD_GLBR 2 AMB Candida <span style="color: #BB0000;">NA</span> 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> EUCAST 2… MIC <span style="color: #BB0000;">NA</span> F_CANDD_KRUS 2 AMB Candida <span style="color: #BB0000;">NA</span> 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> EUCAST 2… MIC <span style="color: #BB0000;">NA</span> F_CANDD_PRPS 2 AMB Candida <span style="color: #BB0000;">NA</span> 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> EUCAST 2… MIC <span style="color: #BB0000;">NA</span> F_CANDD_TRPC 2 AMB Candida <span style="color: #BB0000;">NA</span> 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> EUCAST 2… MIC <span style="color: #BB0000;">NA</span> F_CRYPT_NFRM 2 AMB Candida <span style="color: #BB0000;">NA</span> 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> EUCAST 2… DISK <span style="color: #BB0000;">NA</span> B_[ORD]_ENTRBCTR 5 AMC Enterob… 20ug/1… 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 18,298 more rows, 2 more variables: breakpoint_R &lt;dbl&gt;, uti &lt;lgl&gt;, and</span></span>
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<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># abbreviated variable names ¹​rank_index, ²​disk_dose, ³​breakpoint_S</span></span>
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