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<img src="../logo.svg" class="logo" alt=""><h1>Data Set with Unclean Data</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>example_isolates_unclean.Rd</code></div>
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<div class="ref-description section level2">
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<p>A data set containing 3,000 microbial isolates that are not cleaned up and consequently not ready for AMR data analysis. This data set can be used for practice.</p>
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</div>
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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">example_isolates_unclean</span></span></code></pre></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 3,000 observations and 8 variables:</p><ul><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></div>
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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="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">example_isolates_unclean</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> patient_id hospital date bacteria AMX AMC CIP GEN</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 J3 A 2012-11-21 E. coli R I S S</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 R7 A 2018-04-03 K. pneumoniae R I S S</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 P3 A 2014-09-19 E. coli R S S S</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 P10 A 2015-12-10 E. coli S I S S</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 B7 A 2015-03-02 E. coli S S S S</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 W3 A 2018-03-31 S. aureus R S R S</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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