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@ -38,7 +38,7 @@
<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="">1.8.2.9111</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -176,7 +176,7 @@
<main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
<h4 data-toc-skip class="date">08 February 2023</h4>
<h4 data-toc-skip class="date">10 February 2023</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<div class="d-none name"><code>datasets.Rmd</code></div>
@ -197,7 +197,7 @@ of the data sets look like.</p>
<h2 id="microorganisms-full-microbial-taxonomy">
<code>microorganisms</code>: Full Microbial Taxonomy<a class="anchor" aria-label="anchor" href="#microorganisms-full-microbial-taxonomy"></a>
</h2>
<p>A data set with 52,142 rows and 22 columns, containing the following
<p>A data set with 52 142 rows and 22 columns, containing the following
column names:<br><em>mo</em>, <em>fullname</em>, <em>status</em>, <em>kingdom</em>,
<em>phylum</em>, <em>class</em>, <em>order</em>, <em>family</em>,
<em>genus</em>, <em>species</em>, <em>subspecies</em>, <em>rank</em>,
@ -275,23 +275,23 @@ Set Name ‘Microoganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href
</tr>
<tr class="even">
<td align="center">Animalia</td>
<td align="center">1,379</td>
<td align="center">1 379</td>
</tr>
<tr class="odd">
<td align="center">Archaea</td>
<td align="center">1,314</td>
<td align="center">1 314</td>
</tr>
<tr class="even">
<td align="center">Bacteria</td>
<td align="center">36,476</td>
<td align="center">36 476</td>
</tr>
<tr class="odd">
<td align="center">Fungi</td>
<td align="center">7,901</td>
<td align="center">7 901</td>
</tr>
<tr class="even">
<td align="center">Protozoa</td>
<td align="center">5,071</td>
<td align="center">5 071</td>
</tr>
</tbody>
</table>
@ -877,7 +877,7 @@ inhibitors</td>
<code>clinical_breakpoints</code>: Interpretation from MIC values
&amp; disk diameters to SIR<a class="anchor" aria-label="anchor" href="#clinical_breakpoints-interpretation-from-mic-values-disk-diameters-to-sir"></a>
</h2>
<p>A data set with 18,308 rows and 11 columns, containing the following
<p>A data set with 18 308 rows and 11 columns, containing the following
column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>,
<em>rank_index</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</em>,
<em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
@ -1052,7 +1052,7 @@ diffusion diameters. Included guidelines are CLSI (2013-2022) and EUCAST
<code>intrinsic_resistant</code>: Intrinsic Bacterial
Resistance<a class="anchor" aria-label="anchor" href="#intrinsic_resistant-intrinsic-bacterial-resistance"></a>
</h2>
<p>A data set with 134,634 rows and 2 columns, containing the following
<p>A data set with 134 634 rows and 2 columns, containing the following
column names:<br><em>mo</em> and <em>ab</em>.</p>
<p>This data set is in R available as <code>intrinsic_resistant</code>,
after you load the <code>AMR</code> package.</p>
@ -1482,7 +1482,7 @@ Breakpoint Tables’ v12.0</a> (2022).</p>
<h2 id="example_isolates-example-data-for-practice">
<code>example_isolates</code>: Example Data for Practice<a class="anchor" aria-label="anchor" href="#example_isolates-example-data-for-practice"></a>
</h2>
<p>A data set with 2,000 rows and 46 columns, containing the following
<p>A data set with 2 000 rows and 46 columns, containing the following
column names:<br><em>date</em>, <em>patient</em>, <em>age</em>, <em>gender</em>,
<em>ward</em>, <em>mo</em>, <em>PEN</em>, <em>OXA</em>, <em>FLC</em>,
<em>AMX</em>, <em>AMC</em>, <em>AMP</em>, <em>TZP</em>, <em>CZO</em>,
@ -1901,7 +1901,7 @@ reality and can be used to practise AMR data analysis.</p>
<code>example_isolates_unclean</code>: Example Data for
Practice<a class="anchor" aria-label="anchor" href="#example_isolates_unclean-example-data-for-practice"></a>
</h2>
<p>A data set with 3,000 rows and 8 columns, containing the following
<p>A data set with 3 000 rows and 8 columns, containing the following
column names:<br><em>patient_id</em>, <em>hospital</em>, <em>date</em>,
<em>bacteria</em>, <em>AMX</em>, <em>AMC</em>, <em>CIP</em> and
<em>GEN</em>.</p>