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<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/master/R/data.R'><code>R/data.R</code></a></small>
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<div class="hidden name"><code>rsi_translation.Rd</code></div>
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<div class="ref-description">
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<p>Data set to interpret MIC and disk diffusion to R/SI values. Included guidelines are CLSI (2011-2019) and EUCAST (2011-2020). 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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<pre class="usage"><span class='no'>rsi_translation</span></pre>
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<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
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<p>A <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with 18,650 observations and 10 variables:</p><ul>
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<li><p><code>guideline</code><br /> Name of the guideline</p></li>
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<li><p><code>method</code><br /> Either "MIC" or "DISK"</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>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 logical 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>
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<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</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/master/data-raw/rsi_translation.txt'>https://github.com/msberends/AMR/blob/master/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.</p>
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<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>
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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 analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
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