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Predict antimicrobial resistance
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Determine multi-drug resistance (MDR)
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Work with WHONET data
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Get properties of a microorganism
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Get properties of an antibiotic
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Other: benchmarks
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Manual
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<h1>Data set with unclean data</h1>
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<div class="hidden name"><code>example_isolates_unclean.Rd</code></div>
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</div>
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<div class="ref-description">
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<p>A data set containing 3,000 microbial isolates that are not cleaned up and consequently not really for AMR analysis. This data set can be used for practice.</p>
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</div>
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<pre class="usage"><span class='no'>example_isolates_unclean</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 3,000 observations and 8 variables:</p><ul>
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<li><p><code>patient_id</code><br /> ID of the patient</p></li>
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<li><p><code>date</code><br /> date of receipt at the laboratory</p></li>
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<li><p><code>hospital</code><br /> ID of the hospital, from A to C</p></li>
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<li><p><code>bacteria</code><br /> info about microorganism that can be transformed with <code><a href='as.mo.html'>as.mo()</a></code>, see also <a href='microorganisms.html'>microorganisms</a></p></li>
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<li><p><code>AMX:GEN</code><br /> 4 different antibiotics that have to be transformed with <code><a href='as.rsi.html'>as.rsi()</a></code></p></li>
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</ul>
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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.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
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<h2>Contents</h2>
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<li><a href="#format">Format</a></li>
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<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
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</ul>
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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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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
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