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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -138,14 +138,12 @@
<div class="section level2">
<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
<p>A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with 5,604 observations and 2 variables:</p><ul><li><p><code>code</code><br> Commonly used code of a microorganism</p></li>
<p>A [tibble<a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble::tibble</a> with 5,604 observations and 2 variables:</p><ul><li><p><code>code</code><br> Commonly used code of a microorganism</p></li>
<li><p><code>mo</code><br> ID of the microorganism in the <a href="microorganisms.html">microorganisms</a> data set</p></li>
</ul></div>
<div class="section level2">
<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2>
<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>
<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="catalogue-of-life">Catalogue of Life<a class="anchor" aria-label="anchor" href="#catalogue-of-life"></a></h2>
@ -162,14 +160,21 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<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="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">microorganisms.codes</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> code mo</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 _FAM_A- B_GRAMN</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 _FAM_A+ B_GRAMP</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 _FAM_AC B_GRAMP</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 _FAM_AE B_GRAMN</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 _FAM_AN B_GRAMN</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 _FAM_AO B_GRAMP</span>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">microorganisms.codes</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 5,604 × 2</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> code mo </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;mo&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> _FAM_A- B_GRAMN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> _FAM_A+ B_GRAMP </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> _FAM_AC B_GRAMP </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> _FAM_AE B_GRAMN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> _FAM_AN B_GRAMN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> _FAM_AO B_GRAMP </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> _FAM_AP UNKNOWN</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> _FAM_AS F_FUNGUS </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> _FAM_AT UNKNOWN</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> _FAM_AV UNKNOWN</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 5,594 more rows</span></span>
</code></pre></div>
</div>
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