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<img src="../logo.svg" class="logo" alt=""><h1>Data Set with 500 ESBL Isolates</h1>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/data.R" class="external-link"><code>R/data.R</code></a></small>
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<div class="d-none name"><code>esbl_isolates.Rd</code></div>
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<div class="ref-description section level2">
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<p>A data set containing 500 microbial isolates with MIC values of common antibiotics and a binary <code>esbl</code> column for extended-spectrum beta-lactamase (ESBL) production. This data set contains randomised fictitious data but reflects reality and can be used to practise AMR-related machine learning, e.g., classification modelling with <a href="https://amr-for-r.org/articles/AMR_with_tidymodels.html">tidymodels</a>.</p>
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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">esbl_isolates</span></span></code></pre></div>
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</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://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 500 observations and 19 variables:</p><ul><li><p><code>esbl</code><br> Logical indicator if the isolate is ESBL-producing</p></li>
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<li><p><code>genus</code><br> Genus of the microorganism</p></li>
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<li><p><code>AMC:COL</code><br> MIC values for 17 antimicrobial agents, transformed to class <code><a href="as.mic.html">mic</a></code> (see <code><a href="as.mic.html">as.mic()</a></code>)</p></li>
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</ul></div>
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<div class="section level2">
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<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
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<p>See our <a href="amr-tidymodels.html">tidymodels integration</a> for an example using this data set.</p>
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<div class="section level2">
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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="va">esbl_isolates</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 500 × 19</span></span>
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<span class="r-out co"><span class="r-pr">#></span> esbl genus AMC AMP TZP CXM FOX CTX CAZ GEN TOB TMP SXT</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><lgl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mic></span> <span style="color: #949494; font-style: italic;"><mic></span> <span style="color: #949494; font-style: italic;"><mic></span> <span style="color: #949494; font-style: italic;"><mic></span> <span style="color: #949494; font-style: italic;"><mic></span> <span style="color: #949494; font-style: italic;"><mic></span> <span style="color: #949494; font-style: italic;"><mic></span> <span style="color: #949494; font-style: italic;"><mic></span> <span style="color: #949494; font-style: italic;"><mic></span> <span style="color: #949494; font-style: italic;"><mic></span> <span style="color: #949494; font-style: italic;"><mic></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> FALSE Esch… 32 32 4 64 64 8<span style="color: #BBBBBB;">.00</span> 8<span style="color: #BBBBBB;">.00</span> 1 1 16<span style="color: #BBBBBB;">.0</span> 20</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> FALSE Esch… 32 32 4 64 64 4<span style="color: #BBBBBB;">.00</span> 8<span style="color: #BBBBBB;">.00</span> 1 1 16<span style="color: #BBBBBB;">.0</span> 320</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> FALSE Esch… 4 2 64 8 4 8<span style="color: #BBBBBB;">.00</span> 0.12 16 16 0.5 20</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> FALSE Kleb… 32 32 16 64 64 8<span style="color: #BBBBBB;">.00</span> 8<span style="color: #BBBBBB;">.00</span> 1 1 0.5 20</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> FALSE Esch… 32 32 4 4 4 0.25 2<span style="color: #BBBBBB;">.00</span> 1 1 16<span style="color: #BBBBBB;">.0</span> 320</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> FALSE Citr… 32 32 16 64 64 64<span style="color: #BBBBBB;">.00</span> 32<span style="color: #BBBBBB;">.00</span> 1 1 0.5 20</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> FALSE Morg… 32 32 4 64 64 16<span style="color: #BBBBBB;">.00</span> 2<span style="color: #BBBBBB;">.00</span> 1 1 0.5 20</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> FALSE Prot… 16 32 4 1 4 8<span style="color: #BBBBBB;">.00</span> 0.12 1 1 16<span style="color: #BBBBBB;">.0</span> 320</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> FALSE Ente… 32 32 8 64 64 32<span style="color: #BBBBBB;">.00</span> 4<span style="color: #BBBBBB;">.00</span> 1 1 0.5 20</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> FALSE Citr… 32 32 32 64 64 8<span style="color: #BBBBBB;">.00</span> 64<span style="color: #BBBBBB;">.00</span> 1 1 16<span style="color: #BBBBBB;">.0</span> 320</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 490 more rows</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 6 more variables: NIT <mic>, FOS <mic>, CIP <mic>, IPM <mic>, MEM <mic>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># COL <mic></span></span>
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</code></pre></div>
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