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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 containing reference data to interpret MIC and disk diffusion to R/SI values, according to international guidelines. Currently implemented guidelines are EUCAST (2011-2021) and CLSI (2010-2020). 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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<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='va'>rsi_translation</span></code></pre></div>
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<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
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<p>A <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 22,000 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 "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>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'>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>
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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="reference-data-publicly-available"><a class="anchor" href="#reference-data-publicly-available"></a>Reference Data Publicly Available</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 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 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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<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
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<div class='dont-index'><p><a href='intrinsic_resistant.html'>intrinsic_resistant</a></p></div>
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<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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