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<img src="../logo.svg" class="logo" alt=""><h1>Data Set for R/SI 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>rsi_translation.Rd</code></div>
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<div class="ref-description section level2">
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<p>Data set containing reference data to interpret MIC and disk diffusion to R/SI values, according to international guidelines. Currently implemented guidelines are EUCAST (2011-2022) and CLSI (2011-2022). Use <code><a href="as.rsi.html">as.rsi()</a></code> to transform MICs or disks measurements to R/SI values.</p>
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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="va">rsi_translation</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>A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with 20,369 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>
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<li><p><code>site</code><br> Body site, e.g. "Oral" or "Respiratory"</p></li>
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<li><p><code>mo</code><br> Microbial ID, see <code><a href="as.mo.html">as.mo()</a></code></p></li>
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<li><p><code>rank_index</code><br> Taxonomic rank index of <code>mo</code> from 1 (subspecies/infraspecies) to 5 (unknown microorganism)</p></li>
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<li><p><code>ab</code><br> Antibiotic ID, see <code><a href="as.ab.html">as.ab()</a></code></p></li>
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<li><p><code>ref_tbl</code><br> Info about where the guideline rule can be found</p></li>
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<li><p><code>disk_dose</code><br> Dose of the used disk diffusion method</p></li>
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<li><p><code>breakpoint_S</code><br> Lowest MIC value or highest number of millimetres that leads to "S"</p></li>
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<li><p><code>breakpoint_R</code><br> Highest MIC value or lowest number of millimetres that leads to "R"</p></li>
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<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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</ul></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>The repository of this <code>AMR</code> package contains a file comprising this exact data set: <a href="https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt" class="external-link">https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt</a>. This file <strong>allows for machine reading EUCAST and CLSI guidelines</strong>, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. The file is updated automatically and the <code>mo</code> and <code>ab</code> columns have been transformed to contain the full official names instead of codes.</p>
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<div class="section level2">
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<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2>
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<p>All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find <a href="https://msberends.github.io/AMR/articles/datasets.html">all download links on our website</a>, which is automatically updated with every code change.</p>
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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><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="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">rsi_translation</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> guideline method site mo rank_index ab ref_tbl disk_dose</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 EUCAST 2022 MIC <NA> F_ASPRG_MGTS 2 AMB Aspergillus <NA></span>
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<span class="r-out co"><span class="r-pr">#></span> 2 EUCAST 2022 MIC <NA> F_ASPRG_NIGR 2 AMB Aspergillus <NA></span>
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<span class="r-out co"><span class="r-pr">#></span> 3 EUCAST 2022 MIC <NA> F_CANDD 3 AMB Candida <NA></span>
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<span class="r-out co"><span class="r-pr">#></span> 4 EUCAST 2022 MIC <NA> F_CANDD_ALBC 2 AMB Candida <NA></span>
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<span class="r-out co"><span class="r-pr">#></span> 5 EUCAST 2022 MIC <NA> F_CANDD_DBLN 2 AMB Candida <NA></span>
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<span class="r-out co"><span class="r-pr">#></span> 6 EUCAST 2022 MIC <NA> F_CANDD_KRUS 2 AMB Candida <NA></span>
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<span class="r-out co"><span class="r-pr">#></span> breakpoint_S breakpoint_R uti</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 1 1 FALSE</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 1 1 FALSE</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 1 1 FALSE</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 1 1 FALSE</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 1 1 FALSE</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 1 1 FALSE</span>
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</code></pre></div>
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<p></p><p><code>AMR</code> (for R). Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> in collaboration with non-profit organisations<br><a target="_blank" href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p>
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