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@ -44,7 +44,7 @@
<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">
@ -317,8 +317,8 @@
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span>
<span></span>
<span><span class="va">out</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="co"># group by hospital code:</span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="co"># group by ward:</span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">ward</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="co"># calculate AMR using resistance(), over all aminoglycosides</span></span>
<span> <span class="co"># and polymyxins:</span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="reference/antibiotic_class_selectors.html">polymyxins</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>,</span>
@ -326,45 +326,37 @@
<span><span class="va">out</span></span></code></pre></div>
<table class="table">
<thead><tr class="header">
<th align="left">hospital_id</th>
<th align="center">GEN</th>
<th align="center">TOB</th>
<th align="center">AMK</th>
<th align="center">KAN</th>
<th align="center">COL</th>
<th align="left">ward</th>
<th align="right">GEN</th>
<th align="right">TOB</th>
<th align="right">AMK</th>
<th align="right">KAN</th>
<th align="right">COL</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">A</td>
<td align="center">0.203</td>
<td align="center">0.328</td>
<td align="center">0.657</td>
<td align="center">1</td>
<td align="center">0.853</td>
<td align="left">Clinical</td>
<td align="right">0.229</td>
<td align="right">0.315</td>
<td align="right">0.626</td>
<td align="right">1</td>
<td align="right">0.780</td>
</tr>
<tr class="even">
<td align="left">B</td>
<td align="center">0.274</td>
<td align="center">0.367</td>
<td align="center">0.645</td>
<td align="center">1</td>
<td align="center">0.845</td>
<td align="left">ICU</td>
<td align="right">0.290</td>
<td align="right">0.400</td>
<td align="right">0.662</td>
<td align="right">1</td>
<td align="right">0.857</td>
</tr>
<tr class="odd">
<td align="left">C</td>
<td align="center">0.212</td>
<td align="center">0.342</td>
<td align="center">0.582</td>
<td align="center">1</td>
<td align="center">0.865</td>
</tr>
<tr class="even">
<td align="left">D</td>
<td align="center">0.251</td>
<td align="center">0.332</td>
<td align="center">0.642</td>
<td align="center">1</td>
<td align="center">0.745</td>
<td align="left">Outpatient</td>
<td align="right">0.200</td>
<td align="right">0.368</td>
<td align="right">0.605</td>
<td align="right">NA</td>
<td align="right">0.889</td>
</tr>
</tbody>
</table>
@ -373,45 +365,37 @@
<span><span class="va">out</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="reference/ab_property.html">set_ab_names</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<table class="table">
<thead><tr class="header">
<th align="left">hospital_id</th>
<th align="center">gentamicin</th>
<th align="center">tobramycin</th>
<th align="left">amikacin</th>
<th align="center">kanamycin</th>
<th align="center">colistin</th>
<th align="left">ward</th>
<th align="right">gentamicin</th>
<th align="right">tobramycin</th>
<th>amikacin</th>
<th align="right">kanamycin</th>
<th align="right">colistin</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">A</td>
<td align="center">0.203</td>
<td align="center">0.328</td>
<td align="left">0.657</td>
<td align="center">1</td>
<td align="center">0.853</td>
<td align="left">Clinical</td>
<td align="right">0.229</td>
<td align="right">0.315</td>
<td>0.626</td>
<td align="right">1</td>
<td align="right">0.780</td>
</tr>
<tr class="even">
<td align="left">B</td>
<td align="center">0.274</td>
<td align="center">0.367</td>
<td align="left">0.645</td>
<td align="center">1</td>
<td align="center">0.845</td>
<td align="left">ICU</td>
<td align="right">0.290</td>
<td align="right">0.400</td>
<td>0.662</td>
<td align="right">1</td>
<td align="right">0.857</td>
</tr>
<tr class="odd">
<td align="left">C</td>
<td align="center">0.212</td>
<td align="center">0.342</td>
<td align="left">0.582</td>
<td align="center">1</td>
<td align="center">0.865</td>
</tr>
<tr class="even">
<td align="left">D</td>
<td align="center">0.251</td>
<td align="center">0.332</td>
<td align="left">0.642</td>
<td align="center">1</td>
<td align="center">0.745</td>
<td align="left">Outpatient</td>
<td align="right">0.200</td>
<td align="right">0.368</td>
<td>0.605</td>
<td align="right">NA</td>
<td align="right">0.889</td>
</tr>
</tbody>
</table>
@ -420,45 +404,37 @@
<span><span class="va">out</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="reference/ab_property.html">set_ab_names</a></span><span class="op">(</span>property <span class="op">=</span> <span class="st">"atc"</span><span class="op">)</span></span></code></pre></div>
<table class="table">
<thead><tr class="header">
<th align="left">hospital_id</th>
<th align="center">J01GB03</th>
<th align="center">J01GB01</th>
<th align="left">J01GB06</th>
<th align="center">J01GB04</th>
<th align="center">J01XB01</th>
<th align="left">ward</th>
<th align="right">J01GB03</th>
<th align="right">J01GB01</th>
<th>J01GB06</th>
<th align="right">J01GB04</th>
<th align="right">J01XB01</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">A</td>
<td align="center">0.203</td>
<td align="center">0.328</td>
<td align="left">0.657</td>
<td align="center">1</td>
<td align="center">0.853</td>
<td align="left">Clinical</td>
<td align="right">0.229</td>
<td align="right">0.315</td>
<td>0.626</td>
<td align="right">1</td>
<td align="right">0.780</td>
</tr>
<tr class="even">
<td align="left">B</td>
<td align="center">0.274</td>
<td align="center">0.367</td>
<td align="left">0.645</td>
<td align="center">1</td>
<td align="center">0.845</td>
<td align="left">ICU</td>
<td align="right">0.290</td>
<td align="right">0.400</td>
<td>0.662</td>
<td align="right">1</td>
<td align="right">0.857</td>
</tr>
<tr class="odd">
<td align="left">C</td>
<td align="center">0.212</td>
<td align="center">0.342</td>
<td align="left">0.582</td>
<td align="center">1</td>
<td align="center">0.865</td>
</tr>
<tr class="even">
<td align="left">D</td>
<td align="center">0.251</td>
<td align="center">0.332</td>
<td align="left">0.642</td>
<td align="center">1</td>
<td align="center">0.745</td>
<td align="left">Outpatient</td>
<td align="right">0.200</td>
<td align="right">0.368</td>
<td>0.605</td>
<td align="right">NA</td>
<td align="right">0.889</td>
</tr>
</tbody>
</table>