AMR/reference/intrinsic_resistant.html

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      <img src="../logo.svg" class="logo" alt=""><h1>Data Set with Bacterial Intrinsic Resistance</h1>
      <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>
      <div class="d-none name"><code>intrinsic_resistant.Rd</code></div>
    </div>

    <div class="ref-description section level2">
    <p>Data set containing defined intrinsic resistance by EUCAST of all bug-drug combinations.</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">intrinsic_resistant</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 301 583 observations and 2 variables:</p><ul><li><p><code>mo</code><br> Microorganism ID</p></li>
<li><p><code>ab</code><br> Antibiotic ID</p></li>
</ul></div>
    <div class="section level2">
    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
    <p>This data set is based on <a href="https://www.eucast.org/expert_rules_and_expected_phenotypes" class="external-link">'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3</a> (2021).</p><div class="section">
<h3 id="direct-download">Direct download<a class="anchor" aria-label="anchor" href="#direct-download"></a></h3>


<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, 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>
<p>They <strong>allow for machine reading EUCAST and CLSI guidelines</strong>, which is almost impossible with the MS Excel and PDF files distributed by EUCAST and CLSI.</p>
</div>

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    <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">intrinsic_resistant</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 301,583 × 2</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span>    mo          ab  </span>
<span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span>        <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> B_GRAMP     ATM </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> B_GRAMP     COL </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> B_GRAMP     NAL </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> B_GRAMP     PLB </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> B_GRAMP     TEM </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> B_ANAER-POS ATM </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> B_ANAER-POS COL </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> B_ANAER-POS NAL </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> B_ANAER-POS PLB </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> B_ANAER-POS TEM </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 301,573 more rows</span></span>
</code></pre></div>
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