AMR/reference/example_isolates_unclean.html

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      <img src="../logo.svg" class="logo" alt=""><h1>Data Set with Unclean Data</h1>
      <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>
      <div class="d-none name"><code>example_isolates_unclean.Rd</code></div>
    </div>

    <div class="ref-description section level2">
    <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>
    </div>

    <div class="section level2">
    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">example_isolates_unclean</span></span></code></pre></div>
    </div>

    <div class="section level2">
    <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
    <p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 3 000 observations and 8 variables:</p><ul><li><p><code>patient_id</code><br> ID of the patient</p></li>
<li><p><code>date</code><br> date of receipt at the laboratory</p></li>
<li><p><code>hospital</code><br> ID of the hospital, from A to C</p></li>
<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>
<li><p><code>AMX:GEN</code><br> 4 different antibiotics that have to be transformed with <code><a href="as.sir.html">as.sir()</a></code></p></li>
</ul></div>
    <div class="section level2">
    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
    <p>Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. Please visit <a href="https://msberends.github.io/AMR/articles/datasets.html">our website for the download links</a>. The actual files are of course available on <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>.</p>
    </div>

    <div class="section level2">
    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">example_isolates_unclean</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3,000 × 8</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span>    patient_id hospital date       bacteria      AMX   AMC   CIP   GEN  </span>
<span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>      <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;date&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> J3         A        2012-11-21 E. coli       R     I     S     S    </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> R7         A        2018-04-03 K. pneumoniae R     I     S     S    </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> P3         A        2014-09-19 E. coli       R     S     S     S    </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> P10        A        2015-12-10 E. coli       S     I     S     S    </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> B7         A        2015-03-02 E. coli       S     S     S     S    </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> W3         A        2018-03-31 S. aureus     R     S     R     S    </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> J8         A        2016-06-14 E. coli       R     S     S     S    </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> M3         A        2015-10-25 E. coli       R     S     S     S    </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> J3         A        2019-06-19 E. coli       S     S     S     S    </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> G6         A        2015-04-27 S. aureus     S     S     S     S    </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 2,990 more rows</span></span>
</code></pre></div>
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