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@ -31,7 +31,7 @@
<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="">2.1.1.9183</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9186</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">
@ -90,7 +90,7 @@
website update since they are based on randomly created values and the
page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
Markdown</a>. However, the methodology remains unchanged. This page was
generated on 03 March 2025.</p>
generated on 07 March 2025.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@ -146,21 +146,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2025-03-03</td>
<td align="center">2025-03-07</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="center">2025-03-03</td>
<td align="center">2025-03-07</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<tr class="odd">
<td align="center">2025-03-03</td>
<td align="center">2025-03-07</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -699,12 +699,12 @@ previously mentioned antibiotic class selectors:</p>
<span><span class="co">#&gt; <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">carbapenems()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem) and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span></span></code></pre></div>
<table class="table">
<colgroup>
<col width="11%">
<col width="15%">
<col width="14%">
<col width="14%">
<col width="14%">
<col width="14%">
<col width="10%">
<col width="14%">
<col width="15%">
<col width="11%">
<col width="15%">
<col width="14%">
</colgroup>
<thead><tr class="header">
@ -719,93 +719,93 @@ previously mentioned antibiotic class selectors:</p>
<tbody>
<tr class="odd">
<td align="left">CoNS</td>
<td align="left">0% (0-8%)</td>
<td align="left">86% (82-90%)</td>
<td align="left">52% (37-67%)</td>
<td align="left">0% (0-8%)</td>
<td align="left">52% (37-67%)</td>
<td align="left">22% (12-35%)</td>
<td align="left">0% (0-8%,N=43)</td>
<td align="left">86% (82-90%,N=309)</td>
<td align="left">52% (37-67%,N=48)</td>
<td align="left">0% (0-8%,N=43)</td>
<td align="left">52% (37-67%,N=48)</td>
<td align="left">22% (12-35%,N=55)</td>
</tr>
<tr class="even">
<td align="left">E. coli</td>
<td align="left">100% (98-100%)</td>
<td align="left">98% (96-99%)</td>
<td align="left">100% (99-100%)</td>
<td align="left">100% (98-100%,N=171)</td>
<td align="left">98% (96-99%,N=460)</td>
<td align="left">100% (99-100%,N=422)</td>
<td align="left"></td>
<td align="left">100% (99-100%)</td>
<td align="left">97% (96-99%)</td>
<td align="left">100% (99-100%,N=418)</td>
<td align="left">97% (96-99%,N=462)</td>
</tr>
<tr class="odd">
<td align="left">E. faecalis</td>
<td align="left">0% (0-9%)</td>
<td align="left">0% (0-9%)</td>
<td align="left">100% (91-100%)</td>
<td align="left">0% (0-9%)</td>
<td align="left">0% (0-9%,N=39)</td>
<td align="left">0% (0-9%,N=39)</td>
<td align="left">100% (91-100%,N=38)</td>
<td align="left">0% (0-9%,N=39)</td>
<td align="left"></td>
<td align="left">0% (0-9%)</td>
<td align="left">0% (0-9%,N=39)</td>
</tr>
<tr class="even">
<td align="left">K. pneumoniae</td>
<td align="left"></td>
<td align="left">90% (79-96%)</td>
<td align="left">100% (93-100%)</td>
<td align="left">90% (79-96%,N=58)</td>
<td align="left">100% (93-100%,N=51)</td>
<td align="left"></td>
<td align="left">100% (93-100%)</td>
<td align="left">90% (79-96%)</td>
<td align="left">100% (93-100%,N=53)</td>
<td align="left">90% (79-96%,N=58)</td>
</tr>
<tr class="odd">
<td align="left">P. aeruginosa</td>
<td align="left"></td>
<td align="left">100% (88-100%)</td>
<td align="left">100% (88-100%,N=30)</td>
<td align="left"></td>
<td align="left">0% (0-12%)</td>
<td align="left">0% (0-12%,N=30)</td>
<td align="left"></td>
<td align="left">100% (88-100%)</td>
<td align="left">100% (88-100%,N=30)</td>
</tr>
<tr class="even">
<td align="left">P. mirabilis</td>
<td align="left"></td>
<td align="left">94% (80-99%)</td>
<td align="left">94% (79-99%)</td>
<td align="left">94% (80-99%,N=34)</td>
<td align="left">94% (79-99%,N=32)</td>
<td align="left"></td>
<td align="left"></td>
<td align="left">94% (80-99%)</td>
<td align="left">94% (80-99%,N=34)</td>
</tr>
<tr class="odd">
<td align="left">S. aureus</td>
<td align="left"></td>
<td align="left">99% (97-100%)</td>
<td align="left">99% (97-100%,N=233)</td>
<td align="left"></td>
<td align="left"></td>
<td align="left"></td>
<td align="left">98% (92-100%)</td>
<td align="left">98% (92-100%,N=86)</td>
</tr>
<tr class="even">
<td align="left">S. epidermidis</td>
<td align="left">0% (0-8%)</td>
<td align="left">79% (71-85%)</td>
<td align="left">0% (0-8%,N=44)</td>
<td align="left">79% (71-85%,N=163)</td>
<td align="left"></td>
<td align="left">0% (0-8%)</td>
<td align="left">0% (0-8%,N=44)</td>
<td align="left"></td>
<td align="left">51% (40-61%)</td>
<td align="left">51% (40-61%,N=89)</td>
</tr>
<tr class="odd">
<td align="left">S. hominis</td>
<td align="left"></td>
<td align="left">92% (84-97%)</td>
<td align="left">92% (84-97%,N=80)</td>
<td align="left"></td>
<td align="left"></td>
<td align="left"></td>
<td align="left">85% (74-93%)</td>
<td align="left">85% (74-93%,N=62)</td>
</tr>
<tr class="even">
<td align="left">S. pneumoniae</td>
<td align="left">0% (0-3%)</td>
<td align="left">0% (0-3%)</td>
<td align="left">0% (0-3%,N=117)</td>
<td align="left">0% (0-3%,N=117)</td>
<td align="left"></td>
<td align="left">0% (0-3%)</td>
<td align="left">0% (0-3%,N=117)</td>
<td align="left"></td>
<td align="left">0% (0-3%)</td>
<td align="left">0% (0-3%,N=117)</td>
</tr>
</tbody>
</table>
@ -827,6 +827,13 @@ language to be Spanish using the <code>language</code> argument:</p>
<span><span class="co">#&gt; <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">aminoglycosides()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin), '</span><span style="color: #0000BB; font-weight: bold;">TOB</span><span style="color: #0000BB;">'</span></span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; (tobramycin), '</span><span style="color: #0000BB; font-weight: bold;">AMK</span><span style="color: #0000BB;">' (amikacin), and '</span><span style="color: #0000BB; font-weight: bold;">KAN</span><span style="color: #0000BB;">' (kanamycin)</span></span></span></code></pre></div>
<table class="table">
<colgroup>
<col width="15%">
<col width="21%">
<col width="22%">
<col width="18%">
<col width="21%">
</colgroup>
<thead><tr class="header">
<th align="left">Patógeno</th>
<th align="left">Amikacina</th>
@ -837,17 +844,17 @@ language to be Spanish using the <code>language</code> argument:</p>
<tbody>
<tr class="odd">
<td align="left">Gram negativo</td>
<td align="left">98% (96-99%)</td>
<td align="left">96% (95-98%)</td>
<td align="left">0% (0-10%)</td>
<td align="left">96% (94-97%)</td>
<td align="left">98% (96-99%,N=256)</td>
<td align="left">96% (95-98%,N=684)</td>
<td align="left">0% (0-10%,N=35)</td>
<td align="left">96% (94-97%,N=686)</td>
</tr>
<tr class="even">
<td align="left">Gram positivo</td>
<td align="left">0% (0-1%)</td>
<td align="left">63% (60-66%)</td>
<td align="left">0% (0-1%)</td>
<td align="left">34% (31-38%)</td>
<td align="left">0% (0-1%,N=436)</td>
<td align="left">63% (60-66%,N=1170)</td>
<td align="left">0% (0-1%,N=436)</td>
<td align="left">34% (31-38%,N=665)</td>
</tr>
</tbody>
</table>
@ -863,6 +870,12 @@ a plus <code>+</code> character like this:</p>
<span> ab_transform <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></span>
<span><span class="va">combined_ab</span></span></code></pre></div>
<table class="table">
<colgroup>
<col width="19%">
<col width="26%">
<col width="26%">
<col width="26%">
</colgroup>
<thead><tr class="header">
<th align="left">Pathogen</th>
<th align="left">TZP</th>
@ -872,57 +885,57 @@ a plus <code>+</code> character like this:</p>
<tbody>
<tr class="odd">
<td align="left">CoNS</td>
<td align="left">30% (16-49%)</td>
<td align="left">97% (95-99%)</td>
<td align="left">30% (16-49%,N=33)</td>
<td align="left">97% (95-99%,N=274)</td>
<td align="left"></td>
</tr>
<tr class="even">
<td align="left">E. coli</td>
<td align="left">94% (92-96%)</td>
<td align="left">100% (98-100%)</td>
<td align="left">99% (97-100%)</td>
<td align="left">94% (92-96%,N=416)</td>
<td align="left">100% (98-100%,N=459)</td>
<td align="left">99% (97-100%,N=461)</td>
</tr>
<tr class="odd">
<td align="left">K. pneumoniae</td>
<td align="left">89% (77-96%)</td>
<td align="left">93% (83-98%)</td>
<td align="left">93% (83-98%)</td>
<td align="left">89% (77-96%,N=53)</td>
<td align="left">93% (83-98%,N=58)</td>
<td align="left">93% (83-98%,N=58)</td>
</tr>
<tr class="even">
<td align="left">P. aeruginosa</td>
<td align="left"></td>
<td align="left">100% (88-100%)</td>
<td align="left">100% (88-100%)</td>
<td align="left">100% (88-100%,N=30)</td>
<td align="left">100% (88-100%,N=30)</td>
</tr>
<tr class="odd">
<td align="left">P. mirabilis</td>
<td align="left"></td>
<td align="left">100% (90-100%)</td>
<td align="left">100% (90-100%)</td>
<td align="left">100% (90-100%,N=34)</td>
<td align="left">100% (90-100%,N=34)</td>
</tr>
<tr class="even">
<td align="left">S. aureus</td>
<td align="left"></td>
<td align="left">100% (98-100%)</td>
<td align="left">100% (96-100%)</td>
<td align="left">100% (98-100%,N=231)</td>
<td align="left">100% (96-100%,N=91)</td>
</tr>
<tr class="odd">
<td align="left">S. epidermidis</td>
<td align="left"></td>
<td align="left">100% (97-100%)</td>
<td align="left">100% (92-100%)</td>
<td align="left">100% (97-100%,N=128)</td>
<td align="left">100% (92-100%,N=46)</td>
</tr>
<tr class="even">
<td align="left">S. hominis</td>
<td align="left"></td>
<td align="left">100% (95-100%)</td>
<td align="left">100% (93-100%)</td>
<td align="left">100% (95-100%,N=74)</td>
<td align="left">100% (93-100%,N=53)</td>
</tr>
<tr class="odd">
<td align="left">S. pneumoniae</td>
<td align="left">100% (97-100%)</td>
<td align="left">100% (97-100%)</td>
<td align="left">100% (97-100%)</td>
<td align="left">100% (97-100%,N=112)</td>
<td align="left">100% (97-100%,N=112)</td>
<td align="left">100% (97-100%,N=112)</td>
</tr>
</tbody>
</table>
@ -940,16 +953,16 @@ argument must be used. This can be any column in the data, or e.g. an
<span><span class="co">#&gt; <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">aminoglycosides()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin), '</span><span style="color: #0000BB; font-weight: bold;">TOB</span><span style="color: #0000BB;">'</span></span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; (tobramycin), '</span><span style="color: #0000BB; font-weight: bold;">AMK</span><span style="color: #0000BB;">' (amikacin), and '</span><span style="color: #0000BB; font-weight: bold;">KAN</span><span style="color: #0000BB;">' (kanamycin)</span></span></span>
<span><span class="co">#&gt; <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">carbapenems()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem) and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span></span></code></pre></div>
<table style="width:100%;" class="table">
<table class="table">
<colgroup>
<col width="10%">
<col width="10%">
<col width="14%">
<col width="13%">
<col width="14%">
<col width="10%">
<col width="14%">
<col width="13%">
<col width="12%">
<col width="12%">
<col width="12%">
<col width="12%">
<col width="9%">
<col width="12%">
<col width="12%">
</colgroup>
<thead><tr class="header">
<th align="left">Syndromic Group</th>
@ -966,17 +979,17 @@ argument must be used. This can be any column in the data, or e.g. an
<td align="left">Clinical</td>
<td align="left">CoNS</td>
<td align="left"></td>
<td align="left">89% (84-93%)</td>
<td align="left">57% (39-74%)</td>
<td align="left">89% (84-93%,N=205)</td>
<td align="left">57% (39-74%,N=35)</td>
<td align="left"></td>
<td align="left">57% (39-74%)</td>
<td align="left">26% (12-45%)</td>
<td align="left">57% (39-74%,N=35)</td>
<td align="left">26% (12-45%,N=31)</td>
</tr>
<tr class="even">
<td align="left">ICU</td>
<td align="left">CoNS</td>
<td align="left"></td>
<td align="left">79% (68-88%)</td>
<td align="left">79% (68-88%,N=73)</td>
<td align="left"></td>
<td align="left"></td>
<td align="left"></td>
@ -986,7 +999,7 @@ argument must be used. This can be any column in the data, or e.g. an
<td align="left">Outpatient</td>
<td align="left">CoNS</td>
<td align="left"></td>
<td align="left">84% (66-95%)</td>
<td align="left">84% (66-95%,N=31)</td>
<td align="left"></td>
<td align="left"></td>
<td align="left"></td>
@ -995,58 +1008,58 @@ argument must be used. This can be any column in the data, or e.g. an
<tr class="even">
<td align="left">Clinical</td>
<td align="left">E. coli</td>
<td align="left">100% (97-100%)</td>
<td align="left">98% (96-99%)</td>
<td align="left">100% (99-100%)</td>
<td align="left">100% (97-100%,N=104)</td>
<td align="left">98% (96-99%,N=297)</td>
<td align="left">100% (99-100%,N=266)</td>
<td align="left"></td>
<td align="left">100% (99-100%)</td>
<td align="left">98% (96-99%)</td>
<td align="left">100% (99-100%,N=276)</td>
<td align="left">98% (96-99%,N=299)</td>
</tr>
<tr class="odd">
<td align="left">ICU</td>
<td align="left">E. coli</td>
<td align="left">100% (93-100%)</td>
<td align="left">99% (95-100%)</td>
<td align="left">100% (97-100%)</td>
<td align="left">100% (93-100%,N=52)</td>
<td align="left">99% (95-100%,N=137)</td>
<td align="left">100% (97-100%,N=133)</td>
<td align="left"></td>
<td align="left">100% (97-100%)</td>
<td align="left">96% (92-99%)</td>
<td align="left">100% (97-100%,N=118)</td>
<td align="left">96% (92-99%,N=137)</td>
</tr>
<tr class="even">
<td align="left">Clinical</td>
<td align="left">K. pneumoniae</td>
<td align="left"></td>
<td align="left">92% (81-98%)</td>
<td align="left">100% (92-100%)</td>
<td align="left">92% (81-98%,N=51)</td>
<td align="left">100% (92-100%,N=44)</td>
<td align="left"></td>
<td align="left">100% (92-100%)</td>
<td align="left">92% (81-98%)</td>
<td align="left">100% (92-100%,N=46)</td>
<td align="left">92% (81-98%,N=51)</td>
</tr>
<tr class="odd">
<td align="left">Clinical</td>
<td align="left">P. mirabilis</td>
<td align="left"></td>
<td align="left">100% (88-100%)</td>
<td align="left">100% (88-100%,N=30)</td>
<td align="left"></td>
<td align="left"></td>
<td align="left"></td>
<td align="left">100% (88-100%)</td>
<td align="left">100% (88-100%,N=30)</td>
</tr>
<tr class="even">
<td align="left">Clinical</td>
<td align="left">S. aureus</td>
<td align="left"></td>
<td align="left">99% (95-100%)</td>
<td align="left">99% (95-100%,N=150)</td>
<td align="left"></td>
<td align="left"></td>
<td align="left"></td>
<td align="left">97% (89-100%)</td>
<td align="left">97% (89-100%,N=63)</td>
</tr>
<tr class="odd">
<td align="left">ICU</td>
<td align="left">S. aureus</td>
<td align="left"></td>
<td align="left">100% (95-100%)</td>
<td align="left">100% (95-100%,N=66)</td>
<td align="left"></td>
<td align="left"></td>
<td align="left"></td>
@ -1056,51 +1069,51 @@ argument must be used. This can be any column in the data, or e.g. an
<td align="left">Clinical</td>
<td align="left">S. epidermidis</td>
<td align="left"></td>
<td align="left">82% (72-90%)</td>
<td align="left">82% (72-90%,N=79)</td>
<td align="left"></td>
<td align="left"></td>
<td align="left"></td>
<td align="left">55% (39-70%)</td>
<td align="left">55% (39-70%,N=44)</td>
</tr>
<tr class="odd">
<td align="left">ICU</td>
<td align="left">S. epidermidis</td>
<td align="left"></td>
<td align="left">72% (60-82%)</td>
<td align="left">72% (60-82%,N=75)</td>
<td align="left"></td>
<td align="left"></td>
<td align="left"></td>
<td align="left">41% (26-58%)</td>
<td align="left">41% (26-58%,N=41)</td>
</tr>
<tr class="even">
<td align="left">Clinical</td>
<td align="left">S. hominis</td>
<td align="left"></td>
<td align="left">96% (85-99%)</td>
<td align="left">96% (85-99%,N=45)</td>
<td align="left"></td>
<td align="left"></td>
<td align="left"></td>
<td align="left">94% (79-99%)</td>
<td align="left">94% (79-99%,N=31)</td>
</tr>
<tr class="odd">
<td align="left">Clinical</td>
<td align="left">S. pneumoniae</td>
<td align="left">0% (0-5%)</td>
<td align="left">0% (0-5%)</td>
<td align="left">0% (0-5%,N=78)</td>
<td align="left">0% (0-5%,N=78)</td>
<td align="left"></td>
<td align="left">0% (0-5%)</td>
<td align="left">0% (0-5%,N=78)</td>
<td align="left"></td>
<td align="left">0% (0-5%)</td>
<td align="left">0% (0-5%,N=78)</td>
</tr>
<tr class="even">
<td align="left">ICU</td>
<td align="left">S. pneumoniae</td>
<td align="left">0% (0-12%)</td>
<td align="left">0% (0-12%)</td>
<td align="left">0% (0-12%,N=30)</td>
<td align="left">0% (0-12%,N=30)</td>
<td align="left"></td>
<td align="left">0% (0-12%)</td>
<td align="left">0% (0-12%,N=30)</td>
<td align="left"></td>
<td align="left">0% (0-12%)</td>
<td align="left">0% (0-12%,N=30)</td>
</tr>
</tbody>
</table>

6
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@ -31,7 +31,7 @@
<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="">2.1.1.9183</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9186</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">
@ -329,7 +329,7 @@ antibiotics.</p>
</h3>
<p>As a Python user, you might like that the most important data sets of
the <code>AMR</code> R package, <code>microorganisms</code>,
<code>antibiotics</code>, <code>clinical_breakpoints</code>, and
<code>antimicrobials</code>, <code>clinical_breakpoints</code>, and
<code>example_isolates</code>, are now available as regular Python data
frames:</p>
<div class="sourceCode" id="cb9"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb9-1"><a href="#cb9-1" tabindex="-1"></a>AMR.microorganisms</span></code></pre></div>
@ -467,7 +467,7 @@ frames:</p>
</tr>
</tbody>
</table>
<div class="sourceCode" id="cb10"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb10-1"><a href="#cb10-1" tabindex="-1"></a>AMR.antibiotics</span></code></pre></div>
<div class="sourceCode" id="cb10"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb10-1"><a href="#cb10-1" tabindex="-1"></a>AMR.antimicrobials</span></code></pre></div>
<table style="width:100%;" class="table">
<colgroup>
<col width="4%">

4
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@ -31,7 +31,7 @@
<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="">2.1.1.9183</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9186</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">
@ -170,7 +170,7 @@ package.</p>
<ul>
<li>
<code><a href="../reference/antimicrobial_selectors.html">aminoglycosides()</a></code> and <code><a href="../reference/antimicrobial_selectors.html">betalactams()</a></code>
dynamically select columns for antibiotics in these classes.</li>
dynamically select columns for antimicrobials in these classes.</li>
<li>
<code>drop_na()</code> ensures the model receives complete cases for
training.</li>

4
articles/EUCAST.html
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@ -31,7 +31,7 @@
<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="">2.1.1.9183</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9186</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">
@ -142,7 +142,7 @@ be applied using <code><a href="../reference/eucast_rules.html">eucast_rules()</
<p>A more convenient function is
<code><a href="../reference/mo_property.html">mo_is_intrinsic_resistant()</a></code> that uses the same guideline,
but allows to check for one or more specific microorganisms or
antibiotics:</p>
antimicrobials:</p>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span></span>
<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="st">"Klebsiella"</span>, <span class="st">"Escherichia"</span><span class="op">)</span>,</span>

2
articles/MDR.html
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@ -31,7 +31,7 @@
<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="">2.1.1.9183</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9186</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">

2
articles/PCA.html
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@ -31,7 +31,7 @@
<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="">2.1.1.9183</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9186</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">

2
articles/WHONET.html
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@ -31,7 +31,7 @@
<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="">2.1.1.9183</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9186</small>
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41
articles/datasets.html
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@ -31,7 +31,7 @@
<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="">2.1.1.9183</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9186</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">
@ -79,7 +79,7 @@
<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">03 March 2025</h4>
<h4 data-toc-skip class="date">07 March 2025</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<div class="d-none name"><code>datasets.Rmd</code></div>
@ -87,7 +87,7 @@
<p>All reference data (about microorganisms, antibiotics, SIR
<p>All reference data (about microorganisms, antimicrobials, SIR
interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are
reliable, up-to-date and freely available. We continually export our
data sets to formats for use in R, MS Excel, Apache Feather, Apache
@ -437,41 +437,18 @@ Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a hre
</div>
</div>
<div class="section level2">
<h2 id="antibiotics-antibiotic-antifungal-drugs">
<code>antibiotics</code>: Antibiotic (+Antifungal) Drugs<a class="anchor" aria-label="anchor" href="#antibiotics-antibiotic-antifungal-drugs"></a>
<h2 id="antimicrobials-antibiotic-and-antifungal-drugs">
<code>antimicrobials</code>: Antibiotic and Antifungal Drugs<a class="anchor" aria-label="anchor" href="#antimicrobials-antibiotic-and-antifungal-drugs"></a>
</h2>
<p>A data set with 487 rows and 14 columns, containing the following
column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>atc</em>,
<em>atc_group1</em>, <em>atc_group2</em>, <em>abbreviations</em>,
<em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>,
<em>iv_ddd</em>, <em>iv_units</em>, and <em>loinc</em>.</p>
<p>This data set is in R available as <code>antibiotics</code>, after
<p>This data set is in R available as <code>antimicrobials</code>, after
you load the <code>AMR</code> package.</p>
<p>It was last updated on 7 February 2025 17:01:22 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.rds" class="external-link">original
R Data Structure (RDS) file</a> (42 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.txt" class="external-link">tab-separated
text file</a> (0.1 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.xlsx" class="external-link">Microsoft
Excel workbook</a> (74 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.feather" class="external-link">Apache
Feather file</a> (0.1 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.parquet" class="external-link">Apache
Parquet file</a> (0.1 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.sav" class="external-link">IBM
SPSS Statistics data file</a> (0.4 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.dta" class="external-link">Stata
DTA file</a> (0.4 MB)</li>
</ul>
<p>It was last updated on 7 March 2025 19:43:26 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antimicrobials.html">here</a>.</p>
<p>The tab-separated text, Microsoft Excel, SPSS, and Stata files all
contain the ATC codes, common abbreviations, trade names and LOINC codes
as comma separated values.</p>
@ -645,7 +622,7 @@ column names:<br><em>av</em>, <em>name</em>, <em>atc</em>, <em>cid</em>,
<p>This data set is in R available as <code>antivirals</code>, after you
load the <code>AMR</code> package.</p>
<p>It was last updated on 20 October 2023 12:51:48 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antimicrobials.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.rds" class="external-link">original

2
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@ -7,7 +7,7 @@
<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="">2.1.1.9183</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9186</small>
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2
articles/resistance_predict.html
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@ -31,7 +31,7 @@
<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="">2.1.1.9183</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9186</small>
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4
articles/welcome_to_AMR.html
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@ -31,7 +31,7 @@
<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="">2.1.1.9183</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9186</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">
@ -158,7 +158,7 @@ antibiotic based on a LOINC code</li>
translate MIC values and disk diffusion diameters to SIR</li>
<li>Principal component analysis for AMR</li>
</ul>
<p>All reference data sets (about microorganisms, antibiotics, SIR
<p>All reference data sets (about microorganisms, antimicrobials, SIR
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, Stata and Excel. We also supply flat files