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404.html
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@ -32,7 +32,7 @@
<a class="navbar-brand me-2" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="https://msberends.github.io/AMR/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"> <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
LICENSE-text.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a> <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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

261
articles/AMR.html
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@ -31,7 +31,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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"> <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 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 page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
Markdown</a>. However, the methodology remains unchanged. This page was 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"> <div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a> <h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2> </h2>
@ -146,21 +146,21 @@ make the structure of your data generally look like this:</p>
</tr></thead> </tr></thead>
<tbody> <tbody>
<tr class="odd"> <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">abcd</td>
<td align="center">Escherichia coli</td> <td align="center">Escherichia coli</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
</tr> </tr>
<tr class="even"> <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">abcd</td>
<td align="center">Escherichia coli</td> <td align="center">Escherichia coli</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">R</td> <td align="center">R</td>
</tr> </tr>
<tr class="odd"> <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">efgh</td>
<td align="center">Escherichia coli</td> <td align="center">Escherichia coli</td>
<td align="center">R</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> <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"> <table class="table">
<colgroup> <colgroup>
<col width="11%">
<col width="15%">
<col width="14%"> <col width="14%">
<col width="14%"> <col width="15%">
<col width="14%"> <col width="11%">
<col width="14%"> <col width="15%">
<col width="10%">
<col width="14%">
<col width="14%"> <col width="14%">
</colgroup> </colgroup>
<thead><tr class="header"> <thead><tr class="header">
@ -719,93 +719,93 @@ previously mentioned antibiotic class selectors:</p>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="left">CoNS</td> <td align="left">CoNS</td>
<td align="left">0% (0-8%)</td> <td align="left">0% (0-8%,N=43)</td>
<td align="left">86% (82-90%)</td> <td align="left">86% (82-90%,N=309)</td>
<td align="left">52% (37-67%)</td> <td align="left">52% (37-67%,N=48)</td>
<td align="left">0% (0-8%)</td> <td align="left">0% (0-8%,N=43)</td>
<td align="left">52% (37-67%)</td> <td align="left">52% (37-67%,N=48)</td>
<td align="left">22% (12-35%)</td> <td align="left">22% (12-35%,N=55)</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">E. coli</td> <td align="left">E. coli</td>
<td align="left">100% (98-100%)</td> <td align="left">100% (98-100%,N=171)</td>
<td align="left">98% (96-99%)</td> <td align="left">98% (96-99%,N=460)</td>
<td align="left">100% (99-100%)</td> <td align="left">100% (99-100%,N=422)</td>
<td align="left"></td> <td align="left"></td>
<td align="left">100% (99-100%)</td> <td align="left">100% (99-100%,N=418)</td>
<td align="left">97% (96-99%)</td> <td align="left">97% (96-99%,N=462)</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="left">E. faecalis</td> <td align="left">E. faecalis</td>
<td align="left">0% (0-9%)</td> <td align="left">0% (0-9%,N=39)</td>
<td align="left">0% (0-9%)</td> <td align="left">0% (0-9%,N=39)</td>
<td align="left">100% (91-100%)</td> <td align="left">100% (91-100%,N=38)</td>
<td align="left">0% (0-9%)</td> <td align="left">0% (0-9%,N=39)</td>
<td align="left"></td> <td align="left"></td>
<td align="left">0% (0-9%)</td> <td align="left">0% (0-9%,N=39)</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">K. pneumoniae</td> <td align="left">K. pneumoniae</td>
<td align="left"></td> <td align="left"></td>
<td align="left">90% (79-96%)</td> <td align="left">90% (79-96%,N=58)</td>
<td align="left">100% (93-100%)</td> <td align="left">100% (93-100%,N=51)</td>
<td align="left"></td> <td align="left"></td>
<td align="left">100% (93-100%)</td> <td align="left">100% (93-100%,N=53)</td>
<td align="left">90% (79-96%)</td> <td align="left">90% (79-96%,N=58)</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="left">P. aeruginosa</td> <td align="left">P. aeruginosa</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>
<td align="left"></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"></td>
<td align="left">100% (88-100%)</td> <td align="left">100% (88-100%,N=30)</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">P. mirabilis</td> <td align="left">P. mirabilis</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>
<td align="left">94% (79-99%)</td> <td align="left">94% (79-99%,N=32)</td>
<td align="left"></td> <td align="left"></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>
<tr class="odd"> <tr class="odd">
<td align="left">S. aureus</td> <td align="left">S. aureus</td>
<td align="left"></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"></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>
<tr class="even"> <tr class="even">
<td align="left">S. epidermidis</td> <td align="left">S. epidermidis</td>
<td align="left">0% (0-8%)</td> <td align="left">0% (0-8%,N=44)</td>
<td align="left">79% (71-85%)</td> <td align="left">79% (71-85%,N=163)</td>
<td align="left"></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"></td>
<td align="left">51% (40-61%)</td> <td align="left">51% (40-61%,N=89)</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="left">S. hominis</td> <td align="left">S. hominis</td>
<td align="left"></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"></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>
<tr class="even"> <tr class="even">
<td align="left">S. pneumoniae</td> <td align="left">S. pneumoniae</td>
<td align="left">0% (0-3%)</td> <td align="left">0% (0-3%,N=117)</td>
<td align="left">0% (0-3%)</td> <td align="left">0% (0-3%,N=117)</td>
<td align="left"></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"></td>
<td align="left">0% (0-3%)</td> <td align="left">0% (0-3%,N=117)</td>
</tr> </tr>
</tbody> </tbody>
</table> </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">#&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> <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"> <table class="table">
<colgroup>
<col width="15%">
<col width="21%">
<col width="22%">
<col width="18%">
<col width="21%">
</colgroup>
<thead><tr class="header"> <thead><tr class="header">
<th align="left">Patógeno</th> <th align="left">Patógeno</th>
<th align="left">Amikacina</th> <th align="left">Amikacina</th>
@ -837,17 +844,17 @@ language to be Spanish using the <code>language</code> argument:</p>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="left">Gram negativo</td> <td align="left">Gram negativo</td>
<td align="left">98% (96-99%)</td> <td align="left">98% (96-99%,N=256)</td>
<td align="left">96% (95-98%)</td> <td align="left">96% (95-98%,N=684)</td>
<td align="left">0% (0-10%)</td> <td align="left">0% (0-10%,N=35)</td>
<td align="left">96% (94-97%)</td> <td align="left">96% (94-97%,N=686)</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">Gram positivo</td> <td align="left">Gram positivo</td>
<td align="left">0% (0-1%)</td> <td align="left">0% (0-1%,N=436)</td>
<td align="left">63% (60-66%)</td> <td align="left">63% (60-66%,N=1170)</td>
<td align="left">0% (0-1%)</td> <td align="left">0% (0-1%,N=436)</td>
<td align="left">34% (31-38%)</td> <td align="left">34% (31-38%,N=665)</td>
</tr> </tr>
</tbody> </tbody>
</table> </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> 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> <span><span class="va">combined_ab</span></span></code></pre></div>
<table class="table"> <table class="table">
<colgroup>
<col width="19%">
<col width="26%">
<col width="26%">
<col width="26%">
</colgroup>
<thead><tr class="header"> <thead><tr class="header">
<th align="left">Pathogen</th> <th align="left">Pathogen</th>
<th align="left">TZP</th> <th align="left">TZP</th>
@ -872,57 +885,57 @@ a plus <code>+</code> character like this:</p>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="left">CoNS</td> <td align="left">CoNS</td>
<td align="left">30% (16-49%)</td> <td align="left">30% (16-49%,N=33)</td>
<td align="left">97% (95-99%)</td> <td align="left">97% (95-99%,N=274)</td>
<td align="left"></td> <td align="left"></td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">E. coli</td> <td align="left">E. coli</td>
<td align="left">94% (92-96%)</td> <td align="left">94% (92-96%,N=416)</td>
<td align="left">100% (98-100%)</td> <td align="left">100% (98-100%,N=459)</td>
<td align="left">99% (97-100%)</td> <td align="left">99% (97-100%,N=461)</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="left">K. pneumoniae</td> <td align="left">K. pneumoniae</td>
<td align="left">89% (77-96%)</td> <td align="left">89% (77-96%,N=53)</td>
<td align="left">93% (83-98%)</td> <td align="left">93% (83-98%,N=58)</td>
<td align="left">93% (83-98%)</td> <td align="left">93% (83-98%,N=58)</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">P. aeruginosa</td> <td align="left">P. aeruginosa</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>
<td align="left">100% (88-100%)</td> <td align="left">100% (88-100%,N=30)</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="left">P. mirabilis</td> <td align="left">P. mirabilis</td>
<td align="left"></td> <td align="left"></td>
<td align="left">100% (90-100%)</td> <td align="left">100% (90-100%,N=34)</td>
<td align="left">100% (90-100%)</td> <td align="left">100% (90-100%,N=34)</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">S. aureus</td> <td align="left">S. aureus</td>
<td align="left"></td> <td align="left"></td>
<td align="left">100% (98-100%)</td> <td align="left">100% (98-100%,N=231)</td>
<td align="left">100% (96-100%)</td> <td align="left">100% (96-100%,N=91)</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="left">S. epidermidis</td> <td align="left">S. epidermidis</td>
<td align="left"></td> <td align="left"></td>
<td align="left">100% (97-100%)</td> <td align="left">100% (97-100%,N=128)</td>
<td align="left">100% (92-100%)</td> <td align="left">100% (92-100%,N=46)</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">S. hominis</td> <td align="left">S. hominis</td>
<td align="left"></td> <td align="left"></td>
<td align="left">100% (95-100%)</td> <td align="left">100% (95-100%,N=74)</td>
<td align="left">100% (93-100%)</td> <td align="left">100% (93-100%,N=53)</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="left">S. pneumoniae</td> <td align="left">S. pneumoniae</td>
<td align="left">100% (97-100%)</td> <td align="left">100% (97-100%,N=112)</td>
<td align="left">100% (97-100%)</td> <td align="left">100% (97-100%,N=112)</td>
<td align="left">100% (97-100%)</td> <td align="left">100% (97-100%,N=112)</td>
</tr> </tr>
</tbody> </tbody>
</table> </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">#&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"><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> <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> <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="13%">
<col width="12%">
<col width="12%">
<col width="12%">
<col width="12%">
<col width="9%">
<col width="12%">
<col width="12%">
</colgroup> </colgroup>
<thead><tr class="header"> <thead><tr class="header">
<th align="left">Syndromic Group</th> <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">Clinical</td>
<td align="left">CoNS</td> <td align="left">CoNS</td>
<td align="left"></td> <td align="left"></td>
<td align="left">89% (84-93%)</td> <td align="left">89% (84-93%,N=205)</td>
<td align="left">57% (39-74%)</td> <td align="left">57% (39-74%,N=35)</td>
<td align="left"></td> <td align="left"></td>
<td align="left">57% (39-74%)</td> <td align="left">57% (39-74%,N=35)</td>
<td align="left">26% (12-45%)</td> <td align="left">26% (12-45%,N=31)</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">ICU</td> <td align="left">ICU</td>
<td align="left">CoNS</td> <td align="left">CoNS</td>
<td align="left"></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> <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">Outpatient</td>
<td align="left">CoNS</td> <td align="left">CoNS</td>
<td align="left"></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> <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"> <tr class="even">
<td align="left">Clinical</td> <td align="left">Clinical</td>
<td align="left">E. coli</td> <td align="left">E. coli</td>
<td align="left">100% (97-100%)</td> <td align="left">100% (97-100%,N=104)</td>
<td align="left">98% (96-99%)</td> <td align="left">98% (96-99%,N=297)</td>
<td align="left">100% (99-100%)</td> <td align="left">100% (99-100%,N=266)</td>
<td align="left"></td> <td align="left"></td>
<td align="left">100% (99-100%)</td> <td align="left">100% (99-100%,N=276)</td>
<td align="left">98% (96-99%)</td> <td align="left">98% (96-99%,N=299)</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="left">ICU</td> <td align="left">ICU</td>
<td align="left">E. coli</td> <td align="left">E. coli</td>
<td align="left">100% (93-100%)</td> <td align="left">100% (93-100%,N=52)</td>
<td align="left">99% (95-100%)</td> <td align="left">99% (95-100%,N=137)</td>
<td align="left">100% (97-100%)</td> <td align="left">100% (97-100%,N=133)</td>
<td align="left"></td> <td align="left"></td>
<td align="left">100% (97-100%)</td> <td align="left">100% (97-100%,N=118)</td>
<td align="left">96% (92-99%)</td> <td align="left">96% (92-99%,N=137)</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">Clinical</td> <td align="left">Clinical</td>
<td align="left">K. pneumoniae</td> <td align="left">K. pneumoniae</td>
<td align="left"></td> <td align="left"></td>
<td align="left">92% (81-98%)</td> <td align="left">92% (81-98%,N=51)</td>
<td align="left">100% (92-100%)</td> <td align="left">100% (92-100%,N=44)</td>
<td align="left"></td> <td align="left"></td>
<td align="left">100% (92-100%)</td> <td align="left">100% (92-100%,N=46)</td>
<td align="left">92% (81-98%)</td> <td align="left">92% (81-98%,N=51)</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="left">Clinical</td> <td align="left">Clinical</td>
<td align="left">P. mirabilis</td> <td align="left">P. mirabilis</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>
<td align="left"></td> <td align="left"></td>
<td align="left"></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>
<tr class="even"> <tr class="even">
<td align="left">Clinical</td> <td align="left">Clinical</td>
<td align="left">S. aureus</td> <td align="left">S. aureus</td>
<td align="left"></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"></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>
<tr class="odd"> <tr class="odd">
<td align="left">ICU</td> <td align="left">ICU</td>
<td align="left">S. aureus</td> <td align="left">S. aureus</td>
<td align="left"></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> <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">Clinical</td>
<td align="left">S. epidermidis</td> <td align="left">S. epidermidis</td>
<td align="left"></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"></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>
<tr class="odd"> <tr class="odd">
<td align="left">ICU</td> <td align="left">ICU</td>
<td align="left">S. epidermidis</td> <td align="left">S. epidermidis</td>
<td align="left"></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"></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>
<tr class="even"> <tr class="even">
<td align="left">Clinical</td> <td align="left">Clinical</td>
<td align="left">S. hominis</td> <td align="left">S. hominis</td>
<td align="left"></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"></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>
<tr class="odd"> <tr class="odd">
<td align="left">Clinical</td> <td align="left">Clinical</td>
<td align="left">S. pneumoniae</td> <td align="left">S. pneumoniae</td>
<td align="left">0% (0-5%)</td> <td align="left">0% (0-5%,N=78)</td>
<td align="left">0% (0-5%)</td> <td align="left">0% (0-5%,N=78)</td>
<td align="left"></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"></td>
<td align="left">0% (0-5%)</td> <td align="left">0% (0-5%,N=78)</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">ICU</td> <td align="left">ICU</td>
<td align="left">S. pneumoniae</td> <td align="left">S. pneumoniae</td>
<td align="left">0% (0-12%)</td> <td align="left">0% (0-12%,N=30)</td>
<td align="left">0% (0-12%)</td> <td align="left">0% (0-12%,N=30)</td>
<td align="left"></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"></td>
<td align="left">0% (0-12%)</td> <td align="left">0% (0-12%,N=30)</td>
</tr> </tr>
</tbody> </tbody>
</table> </table>

6
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@ -31,7 +31,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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"> <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> </h3>
<p>As a Python user, you might like that the most important data sets of <p>As a Python user, you might like that the most important data sets of
the <code>AMR</code> R package, <code>microorganisms</code>, 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 <code>example_isolates</code>, are now available as regular Python data
frames:</p> 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> <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> </tr>
</tbody> </tbody>
</table> </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"> <table style="width:100%;" class="table">
<colgroup> <colgroup>
<col width="4%"> <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> <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"> <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> <ul>
<li> <li>
<code><a href="../reference/antimicrobial_selectors.html">aminoglycosides()</a></code> and <code><a href="../reference/antimicrobial_selectors.html">betalactams()</a></code> <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> <li>
<code>drop_na()</code> ensures the model receives complete cases for <code>drop_na()</code> ensures the model receives complete cases for
training.</li> training.</li>

4
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@ -31,7 +31,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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"> <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 <p>A more convenient function is
<code><a href="../reference/mo_property.html">mo_is_intrinsic_resistant()</a></code> that uses the same guideline, <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 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"> <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> <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> <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
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@ -31,7 +31,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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"> <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
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@ -31,7 +31,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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"> <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
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@ -31,7 +31,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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
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@ -31,7 +31,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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"> <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"> <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> <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> <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> <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 interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are
reliable, up-to-date and freely available. We continually export our reliable, up-to-date and freely available. We continually export our
data sets to formats for use in R, MS Excel, Apache Feather, Apache 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> </div>
<div class="section level2"> <div class="section level2">
<h2 id="antibiotics-antibiotic-antifungal-drugs"> <h2 id="antimicrobials-antibiotic-and-antifungal-drugs">
<code>antibiotics</code>: Antibiotic (+Antifungal) Drugs<a class="anchor" aria-label="anchor" href="#antibiotics-antibiotic-antifungal-drugs"></a> <code>antimicrobials</code>: Antibiotic and Antifungal Drugs<a class="anchor" aria-label="anchor" href="#antimicrobials-antibiotic-and-antifungal-drugs"></a>
</h2> </h2>
<p>A data set with 487 rows and 14 columns, containing the following <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>, 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>atc_group1</em>, <em>atc_group2</em>, <em>abbreviations</em>,
<em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</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> <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> you load the <code>AMR</code> package.</p>
<p>It was last updated on 7 February 2025 17:01:22 UTC. Find more info <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/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/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>The tab-separated text, Microsoft Excel, SPSS, and Stata files all <p>The tab-separated text, Microsoft Excel, SPSS, and Stata files all
contain the ATC codes, common abbreviations, trade names and LOINC codes contain the ATC codes, common abbreviations, trade names and LOINC codes
as comma separated values.</p> 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 <p>This data set is in R available as <code>antivirals</code>, after you
load the <code>AMR</code> package.</p> load the <code>AMR</code> package.</p>
<p>It was last updated on 20 October 2023 12:51:48 UTC. Find more info <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> <p><strong>Direct download links:</strong></p>
<ul> <ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.rds" class="external-link">original <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.rds" class="external-link">original

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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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@ -31,7 +31,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

4
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@ -31,7 +31,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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"> <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> translate MIC values and disk diffusion diameters to SIR</li>
<li>Principal component analysis for AMR</li> <li>Principal component analysis for AMR</li>
</ul> </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 interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are
publicly and freely available. We continually export our data sets to 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 formats for use in R, SPSS, Stata and Excel. We also supply flat files

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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a> <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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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@ -34,7 +34,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a> <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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -112,7 +112,7 @@
</h3> </h3>
<p>The <code>AMR</code> package is a <a href="#copyright">free and open-source</a> R package with <a href="https://en.wikipedia.org/wiki/Dependency_hell" class="external-link">zero dependencies</a> to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. <strong>Our aim is to provide a standard</strong> for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. <a href="./authors.html">Many different researchers</a> from around the globe are continually helping us to make this a successful and durable project!</p> <p>The <code>AMR</code> package is a <a href="#copyright">free and open-source</a> R package with <a href="https://en.wikipedia.org/wiki/Dependency_hell" class="external-link">zero dependencies</a> to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. <strong>Our aim is to provide a standard</strong> for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. <a href="./authors.html">Many different researchers</a> from around the globe are continually helping us to make this a successful and durable project!</p>
<p>This work was published in the Journal of Statistical Software (Volume 104(3); <a href="https://doi.org/10.18637/jss.v104.i03" class="external-link">DOI 10.18637/jss.v104.i03</a>) and formed the basis of two PhD theses (<a href="https://doi.org/10.33612/diss.177417131" class="external-link">DOI 10.33612/diss.177417131</a> and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">DOI 10.33612/diss.192486375</a>).</p> <p>This work was published in the Journal of Statistical Software (Volume 104(3); <a href="https://doi.org/10.18637/jss.v104.i03" class="external-link">DOI 10.18637/jss.v104.i03</a>) and formed the basis of two PhD theses (<a href="https://doi.org/10.33612/diss.177417131" class="external-link">DOI 10.33612/diss.177417131</a> and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">DOI 10.33612/diss.192486375</a>).</p>
<p>After installing this package, R knows <a href="./reference/microorganisms.html"><strong>~52,000 distinct microbial species</strong></a> (updated December 2022) and all <a href="./reference/antibiotics.html"><strong>~600 antibiotic, antimycotic and antiviral drugs</strong></a> by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a>, in collaboration with non-profit organisations <a href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p> <p>After installing this package, R knows <a href="./reference/microorganisms.html"><strong>~52,000 distinct microbial species</strong></a> (updated December 2022) and all <a href="./reference/antibiotics.html"><strong>~600 antimicrobial and antiviral drugs</strong></a> by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a>, in collaboration with non-profit organisations <a href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p>
<div class="section level5"> <div class="section level5">
<h5 id="used-in-over-175-countries-available-in-20-languages">Used in over 175 countries, available in 20 languages<a class="anchor" aria-label="anchor" href="#used-in-over-175-countries-available-in-20-languages"></a> <h5 id="used-in-over-175-countries-available-in-20-languages">Used in over 175 countries, available in 20 languages<a class="anchor" aria-label="anchor" href="#used-in-over-175-countries-available-in-20-languages"></a>
</h5> </h5>
@ -142,7 +142,7 @@
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">bacteria</span>,</span> <span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">bacteria</span>,</span>
<span> <span class="fu"><a href="reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>,</span> <span> <span class="fu"><a href="reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> <span class="fu"><a href="reference/antimicrobial_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> <span> <span class="fu"><a href="reference/antimicrobial_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
<p>With only having defined a row filter on Gram-negative bacteria with intrinsic resistance to cefotaxime (<code><a href="reference/mo_property.html">mo_is_gram_negative()</a></code> and <code><a href="reference/mo_property.html">mo_is_intrinsic_resistant()</a></code>) and a column selection on two antibiotic groups (<code><a href="reference/antimicrobial_selectors.html">aminoglycosides()</a></code> and <code><a href="reference/antimicrobial_selectors.html">carbapenems()</a></code>), the reference data about <a href="./reference/microorganisms.html">all microorganisms</a> and <a href="./reference/antibiotics.html">all antibiotics</a> in the <code>AMR</code> package make sure you get what you meant:</p> <p>With only having defined a row filter on Gram-negative bacteria with intrinsic resistance to cefotaxime (<code><a href="reference/mo_property.html">mo_is_gram_negative()</a></code> and <code><a href="reference/mo_property.html">mo_is_intrinsic_resistant()</a></code>) and a column selection on two antibiotic groups (<code><a href="reference/antimicrobial_selectors.html">aminoglycosides()</a></code> and <code><a href="reference/antimicrobial_selectors.html">carbapenems()</a></code>), the reference data about <a href="./reference/microorganisms.html">all microorganisms</a> and <a href="./reference/antimicrobials.html">all antimicrobials</a> in the <code>AMR</code> package make sure you get what you meant:</p>
<table class="table"> <table class="table">
<thead><tr class="header"> <thead><tr class="header">
<th align="left">bacteria</th> <th align="left">bacteria</th>
@ -254,7 +254,8 @@
<p>If used inside <a href="https://rmarkdown.rstudio.com" class="external-link">R Markdown</a> or <a href="https://quarto.org" class="external-link">Quarto</a>, the table will be printed in the right output format automatically (such as markdown, LaTeX, HTML, etc.).</p> <p>If used inside <a href="https://rmarkdown.rstudio.com" class="external-link">R Markdown</a> or <a href="https://quarto.org" class="external-link">Quarto</a>, the table will be printed in the right output format automatically (such as markdown, LaTeX, HTML, etc.).</p>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span> <code class="sourceCode R"><span><span class="fu"><a href="reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
<span> antibiotics <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/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="reference/antimicrobial_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> <span> antibiotics <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/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="reference/antimicrobial_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>,</span>
<span> formatting_type <span class="op">=</span> <span class="fl">14</span><span class="op">)</span></span></code></pre></div>
<table class="table"> <table class="table">
<colgroup> <colgroup>
<col width="16%"> <col width="16%">
@ -371,7 +372,8 @@
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span> <code class="sourceCode R"><span><span class="fu"><a href="reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
<span> antibiotics <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="st">"TZP"</span>, <span class="st">"TZP+TOB"</span>, <span class="st">"TZP+GEN"</span><span class="op">)</span>,</span> <span> antibiotics <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="st">"TZP"</span>, <span class="st">"TZP+TOB"</span>, <span class="st">"TZP+GEN"</span><span class="op">)</span>,</span>
<span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span><span class="op">)</span></span></code></pre></div> <span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span>,</span>
<span> formatting_type <span class="op">=</span> <span class="fl">14</span><span class="op">)</span></span></code></pre></div>
<table style="width:100%;" class="table"> <table style="width:100%;" class="table">
<colgroup> <colgroup>
<col width="12%"> <col width="12%">
@ -406,6 +408,7 @@
<span> antibiotics <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="st">"cipro"</span>, <span class="st">"tobra"</span>, <span class="st">"genta"</span><span class="op">)</span>, <span class="co"># any arbitrary name or code will work</span></span> <span> antibiotics <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="st">"cipro"</span>, <span class="st">"tobra"</span>, <span class="st">"genta"</span><span class="op">)</span>, <span class="co"># any arbitrary name or code will work</span></span>
<span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span>,</span> <span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span>,</span>
<span> ab_transform <span class="op">=</span> <span class="st">"name"</span>,</span> <span> ab_transform <span class="op">=</span> <span class="st">"name"</span>,</span>
<span> formatting_type <span class="op">=</span> <span class="fl">14</span>,</span>
<span> language <span class="op">=</span> <span class="st">"uk"</span><span class="op">)</span> <span class="co"># Ukrainian</span></span></code></pre></div> <span> language <span class="op">=</span> <span class="st">"uk"</span><span class="op">)</span> <span class="co"># Ukrainian</span></span></code></pre></div>
<table class="table"> <table class="table">
<thead><tr class="header"> <thead><tr class="header">

23
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -48,24 +48,25 @@
</div> </div>
<div class="section level2"> <div class="section level2">
<h2 class="pkg-version" data-toc-text="2.1.1.9183" id="amr-2119183">AMR 2.1.1.9183<a class="anchor" aria-label="anchor" href="#amr-2119183"></a></h2> <h2 class="pkg-version" data-toc-text="2.1.1.9186" id="amr-2119186">AMR 2.1.1.9186<a class="anchor" aria-label="anchor" href="#amr-2119186"></a></h2>
<p><em>(this beta version will eventually become v3.0. We’re happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using <a href="https://msberends.github.io/AMR/#latest-development-version">the instructions here</a>.)</em></p> <p><em>(this beta version will eventually become v3.0. We’re happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using <a href="https://msberends.github.io/AMR/#latest-development-version">the instructions here</a>.)</em></p>
<div class="section level5"> <div class="section level5">
<h5 id="a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9183">A New Milestone: AMR v3.0 with One Health Support (= Human + Veterinary + Environmental)<a class="anchor" aria-label="anchor" href="#a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9183"></a></h5> <h5 id="a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9186">A New Milestone: AMR v3.0 with One Health Support (= Human + Veterinary + Environmental)<a class="anchor" aria-label="anchor" href="#a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9186"></a></h5>
<p>This package now supports not only tools for AMR data analysis in clinical settings, but also for veterinary and environmental microbiology. This was made possible through a collaboration with the <a href="https://www.upei.ca/avc" class="external-link">University of Prince Edward Island’s Atlantic Veterinary College</a>, Canada. To celebrate this great improvement of the package, we also updated the package logo to reflect this change.</p> <p>This package now supports not only tools for AMR data analysis in clinical settings, but also for veterinary and environmental microbiology. This was made possible through a collaboration with the <a href="https://www.upei.ca/avc" class="external-link">University of Prince Edward Island’s Atlantic Veterinary College</a>, Canada. To celebrate this great improvement of the package, we also updated the package logo to reflect this change.</p>
</div> </div>
<div class="section level3"> <div class="section level3">
<h3 id="breaking-2-1-1-9183">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9183"></a></h3> <h3 id="breaking-2-1-1-9186">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9186"></a></h3>
<ul><li>Removed all functions and references that used the deprecated <code>rsi</code> class, which were all replaced with their <code>sir</code> equivalents two years ago</li> <ul><li>Dataset <code>antibiotics</code> has been renamed to <code>antimicrobials</code> as the data set contains more than just antibiotics. Calling <code>antibiotics</code> will still work, but now returns a warning.</li>
<li>Removed all functions and references that used the deprecated <code>rsi</code> class, which were all replaced with their <code>sir</code> equivalents two years ago.</li>
</ul></div> </ul></div>
<div class="section level3"> <div class="section level3">
<h3 id="new-2-1-1-9183">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9183"></a></h3> <h3 id="new-2-1-1-9186">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9186"></a></h3>
<ul><li> <ul><li>
<strong>One Health implementation</strong> <strong>One Health implementation</strong>
<ul><li>Function <code><a href="../reference/as.sir.html">as.sir()</a></code> now has extensive support for veterinary breakpoints from CLSI. Use <code>breakpoint_type = "animal"</code> and set the <code>host</code> argument to a variable that contains animal species names.</li> <ul><li>Function <code><a href="../reference/as.sir.html">as.sir()</a></code> now has extensive support for veterinary breakpoints from CLSI. Use <code>breakpoint_type = "animal"</code> and set the <code>host</code> argument to a variable that contains animal species names.</li>
<li>The CLSI VET09 guideline has been implemented to address cases where veterinary breakpoints are missing (only applies when <code>guideline</code> is set to CLSI)</li> <li>The CLSI VET09 guideline has been implemented to address cases where veterinary breakpoints are missing (only applies when <code>guideline</code> is set to CLSI)</li>
<li>The <code>clinical_breakpoints</code> data set contains all these breakpoints, and can be downloaded on our <a href="https://msberends.github.io/AMR/articles/datasets.html">download page</a>.</li> <li>The <code>clinical_breakpoints</code> data set contains all these breakpoints, and can be downloaded on our <a href="https://msberends.github.io/AMR/articles/datasets.html">download page</a>.</li>
<li>The <code>antibiotics</code> data set contains all veterinary antibiotics, such as pradofloxacin and enrofloxacin. All WHOCC codes for veterinary use have been added as well.</li> <li>The (new) <code>antimicrobials</code> data set contains all veterinary antibiotics, such as pradofloxacin and enrofloxacin. All WHOCC codes for veterinary use have been added as well.</li>
<li> <li>
<code><a href="../reference/ab_property.html">ab_atc()</a></code> now supports ATC codes of veterinary antibiotics (that all start with “Q”)</li> <code><a href="../reference/ab_property.html">ab_atc()</a></code> now supports ATC codes of veterinary antibiotics (that all start with “Q”)</li>
<li> <li>
@ -111,7 +112,7 @@
</ul></li> </ul></li>
</ul></div> </ul></div>
<div class="section level3"> <div class="section level3">
<h3 id="changed-2-1-1-9183">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9183"></a></h3> <h3 id="changed-2-1-1-9186">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9186"></a></h3>
<ul><li>SIR interpretation <ul><li>SIR interpretation
<ul><li>It is now possible to use column names for argument <code>ab</code>, <code>mo</code>, and <code>uti</code>: <code>as.sir(..., ab = "column1", mo = "column2", uti = "column3")</code>. This greatly improves the flexibility for users.</li> <ul><li>It is now possible to use column names for argument <code>ab</code>, <code>mo</code>, and <code>uti</code>: <code>as.sir(..., ab = "column1", mo = "column2", uti = "column3")</code>. This greatly improves the flexibility for users.</li>
<li>Users can now set their own criteria (using regular expressions) as to what should be considered S, I, R, SDD, and NI.</li> <li>Users can now set their own criteria (using regular expressions) as to what should be considered S, I, R, SDD, and NI.</li>
@ -135,7 +136,7 @@
<li>The selectors <code><a href="../reference/antimicrobial_selectors.html">lincosamides()</a></code> and <code><a href="../reference/antimicrobial_selectors.html">macrolides()</a></code> do not overlap anymore - each antibiotic is now classified as either of these and not both</li> <li>The selectors <code><a href="../reference/antimicrobial_selectors.html">lincosamides()</a></code> and <code><a href="../reference/antimicrobial_selectors.html">macrolides()</a></code> do not overlap anymore - each antibiotic is now classified as either of these and not both</li>
</ul></li> </ul></li>
<li> <li>
<code>antibiotics</code> data set <code>antimicrobials</code> data set
<ul><li>Added “clindamycin inducible screening” as <code>CLI1</code>. Since clindamycin is a lincosamide, the antimicrobial selector <code><a href="../reference/antimicrobial_selectors.html">lincosamides()</a></code> now contains the argument <code>only_treatable = TRUE</code> (similar to other antibiotic selectors that contain non-treatable drugs)</li> <ul><li>Added “clindamycin inducible screening” as <code>CLI1</code>. Since clindamycin is a lincosamide, the antimicrobial selector <code><a href="../reference/antimicrobial_selectors.html">lincosamides()</a></code> now contains the argument <code>only_treatable = TRUE</code> (similar to other antibiotic selectors that contain non-treatable drugs)</li>
<li>Added Amorolfine (<code>AMO</code>, D01AE16), which is now also part of the <code><a href="../reference/antimicrobial_selectors.html">antifungals()</a></code> selector</li> <li>Added Amorolfine (<code>AMO</code>, D01AE16), which is now also part of the <code><a href="../reference/antimicrobial_selectors.html">antifungals()</a></code> selector</li>
<li>Added Efflux (<code>EFF</code>), to allow mapping to AMRFinderPlus</li> <li>Added Efflux (<code>EFF</code>), to allow mapping to AMRFinderPlus</li>
@ -181,7 +182,7 @@
<li>Added console colours support of <code>sir</code> class for Positron</li> <li>Added console colours support of <code>sir</code> class for Positron</li>
</ul></div> </ul></div>
<div class="section level3"> <div class="section level3">
<h3 id="other-2-1-1-9183">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9183"></a></h3> <h3 id="other-2-1-1-9186">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9186"></a></h3>
<ul><li>Added Dr. Larisse Bolton as contributor for her fantastic implementation of WISCA in a mathematically solid way</li> <ul><li>Added Dr. Larisse Bolton as contributor for her fantastic implementation of WISCA in a mathematically solid way</li>
<li>Added Matthew Saab, Dr. Jordan Stull, and Prof. Javier Sanchez as contributors for their tremendous input on veterinary breakpoints and interpretations</li> <li>Added Matthew Saab, Dr. Jordan Stull, and Prof. Javier Sanchez as contributors for their tremendous input on veterinary breakpoints and interpretations</li>
<li>Greatly improved <code>vctrs</code> integration, a Tidyverse package working in the background for many Tidyverse functions. For users, this means that functions such as <code>dplyr</code>’s <code><a href="https://dplyr.tidyverse.org/reference/bind_rows.html" class="external-link">bind_rows()</a></code>, <code><a href="https://dplyr.tidyverse.org/reference/rowwise.html" class="external-link">rowwise()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/c_across.html" class="external-link">c_across()</a></code> are now supported for e.g. columns of class <code>mic</code>. Despite this, this <code>AMR</code> package is still zero-dependent on any other package, including <code>dplyr</code> and <code>vctrs</code>.</li> <li>Greatly improved <code>vctrs</code> integration, a Tidyverse package working in the background for many Tidyverse functions. For users, this means that functions such as <code>dplyr</code>’s <code><a href="https://dplyr.tidyverse.org/reference/bind_rows.html" class="external-link">bind_rows()</a></code>, <code><a href="https://dplyr.tidyverse.org/reference/rowwise.html" class="external-link">rowwise()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/c_across.html" class="external-link">c_across()</a></code> are now supported for e.g. columns of class <code>mic</code>. Despite this, this <code>AMR</code> package is still zero-dependent on any other package, including <code>dplyr</code> and <code>vctrs</code>.</li>
@ -189,7 +190,7 @@
<li>Stopped support for SAS (<code>.xpt</code>) files, since their file structure and extremely inefficient and requires more disk space than GitHub allows in a single commit.</li> <li>Stopped support for SAS (<code>.xpt</code>) files, since their file structure and extremely inefficient and requires more disk space than GitHub allows in a single commit.</li>
</ul></div> </ul></div>
<div class="section level3"> <div class="section level3">
<h3 id="older-versions-2-1-1-9183">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9183"></a></h3> <h3 id="older-versions-2-1-1-9186">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9186"></a></h3>
<p>This changelog only contains changes from AMR v3.0 (February 2025) and later.</p> <p>This changelog only contains changes from AMR v3.0 (February 2025) and later.</p>
<ul><li>For prior v2 versions, please see <a href="https://github.com/msberends/AMR/blob/v2.1.1/NEWS.md" class="external-link">our v2 archive</a>.</li> <ul><li>For prior v2 versions, please see <a href="https://github.com/msberends/AMR/blob/v2.1.1/NEWS.md" class="external-link">our v2 archive</a>.</li>
<li>For prior v1 versions, please see <a href="https://github.com/msberends/AMR/blob/v1.8.2/NEWS.md" class="external-link">our v1 archive</a>.</li> <li>For prior v1 versions, please see <a href="https://github.com/msberends/AMR/blob/v1.8.2/NEWS.md" class="external-link">our v1 archive</a>.</li>

2
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@ -12,7 +12,7 @@ articles:
resistance_predict: resistance_predict.html resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html welcome_to_AMR: welcome_to_AMR.html
WHONET: WHONET.html WHONET: WHONET.html
last_built: 2025-03-03T18:39Z last_built: 2025-03-07T19:47Z
urls: urls:
reference: https://msberends.github.io/AMR/reference reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles article: https://msberends.github.io/AMR/articles

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@ -1,5 +1,5 @@
<!DOCTYPE html> <!DOCTYPE html>
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Deprecated Functions — AMR-deprecated • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Deprecated Functions — AMR-deprecated"><meta name="description" content="These functions are so-called 'Deprecated'. They will be removed in a future version of this package. Using these functions will give a warning with the name of the function it has been replaced by (if there is one)."><meta property="og:description" content="These functions are so-called 'Deprecated'. They will be removed in a future version of this package. Using these functions will give a warning with the name of the function it has been replaced by (if there is one)."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous"><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script></head><body> <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Deprecated Functions — AMR-deprecated • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Deprecated Functions — AMR-deprecated"><meta name="description" content="These objects are so-called 'Deprecated'. They will be removed in a future version of this package. Using these will give a warning with the name of the alternative object it has been replaced by (if there is one)."><meta property="og:description" content="These objects are so-called 'Deprecated'. They will be removed in a future version of this package. Using these will give a warning with the name of the alternative object it has been replaced by (if there is one)."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous"><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script></head><body>
<a href="#main" class="visually-hidden-focusable">Skip to contents</a> <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -49,18 +49,25 @@
</div> </div>
<div class="ref-description section level2"> <div class="ref-description section level2">
<p>These functions are so-called '<a href="https://rdrr.io/r/base/Deprecated.html" class="external-link">Deprecated</a>'. <strong>They will be removed in a future version of this package.</strong> Using these functions will give a warning with the name of the function it has been replaced by (if there is one).</p> <p>These objects are so-called '<a href="https://rdrr.io/r/base/Deprecated.html" class="external-link">Deprecated</a>'. <strong>They will be removed in a future version of this package.</strong> Using these will give a warning with the name of the alternative object it has been replaced by (if there is one).</p>
</div> </div>
<div class="section level2"> <div class="section level2">
<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <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="fu">ab_class</span><span class="op">(</span><span class="va">...</span><span class="op">)</span></span> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">antibiotics</span></span>
<span></span>
<span><span class="fu">ab_class</span><span class="op">(</span><span class="va">...</span><span class="op">)</span></span>
<span></span> <span></span>
<span><span class="fu">ab_selector</span><span class="op">(</span><span class="va">...</span><span class="op">)</span></span></code></pre></div> <span><span class="fu">ab_selector</span><span class="op">(</span><span class="va">...</span><span class="op">)</span></span></code></pre></div>
</div> </div>
<div class="section level2">
<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
<p>An object of class <code>tbl_df</code> (inherits from <code>tbl</code>, <code>data.frame</code>) with 487 rows and 14 columns.</p>
</div>
</main></div> </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
</nav></aside></div>
<footer><div class="pkgdown-footer-left"> <footer><div class="pkgdown-footer-left">

6
reference/AMR-options.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -57,7 +57,7 @@
<h2 id="options">Options<a class="anchor" aria-label="anchor" href="#options"></a></h2> <h2 id="options">Options<a class="anchor" aria-label="anchor" href="#options"></a></h2>
<ul><li><p><code>AMR_antibiogram_formatting_type</code> <br> A <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> (1-12) to use in <code><a href="antibiogram.html">antibiogram()</a></code>, to indicate which formatting type to use.</p></li> <ul><li><p><code>AMR_antibiogram_formatting_type</code> <br> A <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> (1-22) to use in <code><a href="antibiogram.html">antibiogram()</a></code>, to indicate which formatting type to use.</p></li>
<li><p><code>AMR_breakpoint_type</code> <br> A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> to use in <code><a href="as.sir.html">as.sir()</a></code>, to indicate which breakpoint type to use. This must be either "ECOFF", "animal", or "human".</p></li> <li><p><code>AMR_breakpoint_type</code> <br> A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> to use in <code><a href="as.sir.html">as.sir()</a></code>, to indicate which breakpoint type to use. This must be either "ECOFF", "animal", or "human".</p></li>
<li><p><code>AMR_cleaning_regex</code> <br> A <a href="https://rdrr.io/r/base/regex.html" class="external-link">regular expression</a> (case-insensitive) to use in <code><a href="as.mo.html">as.mo()</a></code> and all <code><a href="mo_property.html">mo_*</a></code> functions, to clean the user input. The default is the outcome of <code><a href="as.mo.html">mo_cleaning_regex()</a></code>, which removes texts between brackets and texts such as "species" and "serovar".</p></li> <li><p><code>AMR_cleaning_regex</code> <br> A <a href="https://rdrr.io/r/base/regex.html" class="external-link">regular expression</a> (case-insensitive) to use in <code><a href="as.mo.html">as.mo()</a></code> and all <code><a href="mo_property.html">mo_*</a></code> functions, to clean the user input. The default is the outcome of <code><a href="as.mo.html">mo_cleaning_regex()</a></code>, which removes texts between brackets and texts such as "species" and "serovar".</p></li>
<li><p><code>AMR_custom_ab</code> <br> A file location to an RDS file, to use custom antimicrobial drugs with this package. This is explained in <code><a href="add_custom_antimicrobials.html">add_custom_antimicrobials()</a></code>.</p></li> <li><p><code>AMR_custom_ab</code> <br> A file location to an RDS file, to use custom antimicrobial drugs with this package. This is explained in <code><a href="add_custom_antimicrobials.html">add_custom_antimicrobials()</a></code>.</p></li>
@ -80,7 +80,7 @@
<p>In this file, you can set options such as...</p> <p>In this file, you can set options such as...</p>
<p></p><div class="sourceCode r"><pre><code><span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">options</a></span><span class="op">(</span>AMR_locale <span class="op">=</span> <span class="st">"pt"</span><span class="op">)</span></span> <p></p><div class="sourceCode r"><pre><code><span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">options</a></span><span class="op">(</span>AMR_locale <span class="op">=</span> <span class="st">"pt"</span><span class="op">)</span></span>
<span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">options</a></span><span class="op">(</span>AMR_include_PKPD <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre><p></p></div> <span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">options</a></span><span class="op">(</span>AMR_include_PKPD <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre><p></p></div>
<p>...to add Portuguese language support of antibiotics, and allow PK/PD rules when interpreting MIC values with <code><a href="as.sir.html">as.sir()</a></code>.</p><div class="section"> <p>...to add Portuguese language support of antimicrobials, and allow PK/PD rules when interpreting MIC values with <code><a href="as.sir.html">as.sir()</a></code>.</p><div class="section">
<h3 id="share-options-within-team">Share Options Within Team<a class="anchor" aria-label="anchor" href="#share-options-within-team"></a></h3> <h3 id="share-options-within-team">Share Options Within Team<a class="anchor" aria-label="anchor" href="#share-options-within-team"></a></h3>

6
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@ -21,7 +21,7 @@ The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish,
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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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@ -69,7 +69,7 @@ The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish,
) and formed the basis of two PhD theses (<a href="https://doi.org/10.33612/diss.177417131" class="external-link">doi:10.33612/diss.177417131</a> ) and formed the basis of two PhD theses (<a href="https://doi.org/10.33612/diss.177417131" class="external-link">doi:10.33612/diss.177417131</a>
and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">doi:10.33612/diss.192486375</a> and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">doi:10.33612/diss.192486375</a>
).</p> ).</p>
<p>After installing this package, R knows <a href="https://msberends.github.io/AMR/reference/microorganisms.html"><strong>~79 000 microorganisms</strong></a> (updated June 2024) and all <a href="https://msberends.github.io/AMR/reference/antibiotics.html"><strong>~610 antibiotic, antimycotic and antiviral drugs</strong></a> by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the public <a href="https://www.rug.nl" class="external-link">University of Groningen</a>, in collaboration with non-profit organisations <a href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p> <p>After installing this package, R knows <a href="https://msberends.github.io/AMR/reference/microorganisms.html"><strong>~79 000 microorganisms</strong></a> (updated June 2024) and all <a href="https://msberends.github.io/AMR/reference/antimicrobials.html"><strong>~610 antibiotic, antimycotic and antiviral drugs</strong></a> by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the public <a href="https://www.rug.nl" class="external-link">University of Groningen</a>, in collaboration with non-profit organisations <a href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p>
<p>The <code>AMR</code> package is available in English, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian, Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swedish, Turkish, and Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.</p> <p>The <code>AMR</code> package is available in English, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian, Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swedish, Turkish, and Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.</p>
</div> </div>
@ -97,7 +97,7 @@ The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish,
<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2> <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 data sets in this <code>AMR</code> package (about microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. 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>All data sets in this <code>AMR</code> package (about microorganisms, antimicrobials, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. 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>
<div class="section level2"> <div class="section level2">
<h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2> <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>

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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -1,5 +1,5 @@
<!DOCTYPE html> <!DOCTYPE html>
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Data Set with 500 Isolates - WHONET Example — WHONET • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Data Set with 500 Isolates - WHONET Example — WHONET"><meta name="description" content="This example data set has the exact same structure as an export file from WHONET. Such files can be used with this package, as this example data set shows. The antibiotic results are from our example_isolates data set. All patient names were created using online surname generators and are only in place for practice purposes."><meta property="og:description" content="This example data set has the exact same structure as an export file from WHONET. Such files can be used with this package, as this example data set shows. The antibiotic results are from our example_isolates data set. All patient names were created using online surname generators and are only in place for practice purposes."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous"><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script></head><body> <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Data Set with 500 Isolates - WHONET Example — WHONET • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Data Set with 500 Isolates - WHONET Example — WHONET"><meta name="description" content="This example data set has the exact same structure as an export file from WHONET. Such files can be used with this package, as this example data set shows. The antimcrobial results are from our example_isolates data set. All patient names were created using online surname generators and are only in place for practice purposes."><meta property="og:description" content="This example data set has the exact same structure as an export file from WHONET. Such files can be used with this package, as this example data set shows. The antimcrobial results are from our example_isolates data set. All patient names were created using online surname generators and are only in place for practice purposes."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous"><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script></head><body>
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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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@ -49,7 +49,7 @@
</div> </div>
<div class="ref-description section level2"> <div class="ref-description section level2">
<p>This example data set has the exact same structure as an export file from WHONET. Such files can be used with this package, as this example data set shows. The antibiotic results are from our <a href="example_isolates.html">example_isolates</a> data set. All patient names were created using online surname generators and are only in place for practice purposes.</p> <p>This example data set has the exact same structure as an export file from WHONET. Such files can be used with this package, as this example data set shows. The antimcrobial results are from our <a href="example_isolates.html">example_isolates</a> data set. All patient names were created using online surname generators and are only in place for practice purposes.</p>
</div> </div>
<div class="section level2"> <div class="section level2">
@ -84,7 +84,7 @@
<li><p><code>Inducible clindamycin resistance</code><br> Clindamycin can be induced?</p></li> <li><p><code>Inducible clindamycin resistance</code><br> Clindamycin can be induced?</p></li>
<li><p><code>Comment</code><br> Other comments</p></li> <li><p><code>Comment</code><br> Other comments</p></li>
<li><p><code>Date of data entry</code><br><a href="https://rdrr.io/r/base/Dates.html" class="external-link">Date</a> this data was entered in WHONET</p></li> <li><p><code>Date of data entry</code><br><a href="https://rdrr.io/r/base/Dates.html" class="external-link">Date</a> this data was entered in WHONET</p></li>
<li><p><code>AMP_ND10:CIP_EE</code><br> 28 different antibiotics. You can lookup the abbreviations in the <a href="antibiotics.html">antibiotics</a> data set, or use e.g. <code><a href="ab_property.html">ab_name("AMP")</a></code> to get the official name immediately. Before analysis, you should transform this to a valid antibiotic class, using <code><a href="as.sir.html">as.sir()</a></code>.</p></li> <li><p><code>AMP_ND10:CIP_EE</code><br> 28 different antimicrobials. You can lookup the abbreviations in the <a href="antimicrobials.html">antimicrobials</a> data set, or use e.g. <code><a href="ab_property.html">ab_name("AMP")</a></code> to get the official name immediately. Before analysis, you should transform this to a valid antimcrobial class, using <code><a href="as.sir.html">as.sir()</a></code>.</p></li>
</ul></div> </ul></div>
<div class="section level2"> <div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>

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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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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@ -76,7 +76,7 @@
<dt id="arg-translate-ab">translate_ab<a class="anchor" aria-label="anchor" href="#arg-translate-ab"></a></dt> <dt id="arg-translate-ab">translate_ab<a class="anchor" aria-label="anchor" href="#arg-translate-ab"></a></dt>
<dd><p>if <code>type = "drug"</code>: a column name of the <a href="antibiotics.html">antibiotics</a> data set to translate the antibiotic abbreviations to, using <code><a href="ab_property.html">ab_property()</a></code>. The default is <code>FALSE</code>. Using <code>TRUE</code> is equal to using "name".</p></dd> <dd><p>if <code>type = "drug"</code>: a column name of the <a href="antimicrobials.html">antimicrobials</a> data set to translate the antibiotic abbreviations to, using <code><a href="ab_property.html">ab_property()</a></code>. The default is <code>FALSE</code>. Using <code>TRUE</code> is equal to using "name".</p></dd>
<dt id="arg-thorough-search">thorough_search<a class="anchor" aria-label="anchor" href="#arg-thorough-search"></a></dt> <dt id="arg-thorough-search">thorough_search<a class="anchor" aria-label="anchor" href="#arg-thorough-search"></a></dt>

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<!DOCTYPE html> <!DOCTYPE html>
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Get Properties of an Antibiotic — ab_property • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Get Properties of an Antibiotic — ab_property"><meta name="description" content="Use these functions to return a specific property of an antibiotic from the antibiotics data set. All input values will be evaluated internally with as.ab()."><meta property="og:description" content="Use these functions to return a specific property of an antibiotic from the antibiotics data set. All input values will be evaluated internally with as.ab()."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous"><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script></head><body> <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Get Properties of an Antibiotic — ab_property • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Get Properties of an Antibiotic — ab_property"><meta name="description" content="Use these functions to return a specific property of an antibiotic from the antimicrobials data set. All input values will be evaluated internally with as.ab()."><meta property="og:description" content="Use these functions to return a specific property of an antibiotic from the antimicrobials data set. All input values will be evaluated internally with as.ab()."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous"><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script></head><body>
<a href="#main" class="visually-hidden-focusable">Skip to contents</a> <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -49,7 +49,7 @@
</div> </div>
<div class="ref-description section level2"> <div class="ref-description section level2">
<p>Use these functions to return a specific property of an antibiotic from the <a href="antibiotics.html">antibiotics</a> data set. All input values will be evaluated internally with <code><a href="as.ab.html">as.ab()</a></code>.</p> <p>Use these functions to return a specific property of an antibiotic from the <a href="antimicrobials.html">antimicrobials</a> data set. All input values will be evaluated internally with <code><a href="as.ab.html">as.ab()</a></code>.</p>
</div> </div>
<div class="section level2"> <div class="section level2">
@ -119,7 +119,7 @@
<dt id="arg-property">property<a class="anchor" aria-label="anchor" href="#arg-property"></a></dt> <dt id="arg-property">property<a class="anchor" aria-label="anchor" href="#arg-property"></a></dt>
<dd><p>one of the column names of one of the <a href="antibiotics.html">antibiotics</a> data set: <code>vector_or(colnames(antibiotics), sort = FALSE)</code>.</p></dd> <dd><p>one of the column names of one of the <a href="antimicrobials.html">antimicrobials</a> data set: <code>vector_or(colnames(antimicrobials), sort = FALSE)</code>.</p></dd>
<dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a></dt> <dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a></dt>
@ -156,11 +156,11 @@
<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2> <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 data sets in this <code>AMR</code> package (about microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. 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>All data sets in this <code>AMR</code> package (about microorganisms, antimicrobials, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. 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>
<div class="section level2"> <div class="section level2">
<h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2> <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
<div class="dont-index"><p><a href="antibiotics.html">antibiotics</a></p></div> <div class="dont-index"><p><a href="antimicrobials.html">antimicrobials</a></p></div>
</div> </div>
<div class="section level2"> <div class="section level2">

12
reference/add_custom_antimicrobials.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -64,14 +64,14 @@
<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt> <dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> resembling the <a href="antibiotics.html">antibiotics</a> data set, at least containing columns "ab" and "name"</p></dd> <dd><p>a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> resembling the <a href="antimicrobials.html">antimicrobials</a> data set, at least containing columns "ab" and "name"</p></dd>
</dl></div> </dl></div>
<div class="section level2"> <div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p><strong>Important:</strong> Due to how <span style="R">R</span> works, the <code>add_custom_antimicrobials()</code> function has to be run in every <span style="R">R</span> session - added antimicrobials are not stored between sessions and are thus lost when <span style="R">R</span> is exited.</p> <p><strong>Important:</strong> Due to how <span style="R">R</span> works, the <code>add_custom_antimicrobials()</code> function has to be run in every <span style="R">R</span> session - added antimicrobials are not stored between sessions and are thus lost when <span style="R">R</span> is exited.</p>
<p>There are two ways to circumvent this and automate the process of adding antimicrobials:</p> <p>There are two ways to circumvent this and automate the process of adding antimicrobials:</p>
<p><strong>Method 1:</strong> Using the package option <code><a href="AMR-options.html">AMR_custom_ab</a></code>, which is the preferred method. To use this method:</p><ol><li><p>Create a data set in the structure of the <a href="antibiotics.html">antibiotics</a> data set (containing at the very least columns "ab" and "name") and save it with <code><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">saveRDS()</a></code> to a location of choice, e.g. <code>"~/my_custom_ab.rds"</code>, or any remote location.</p></li> <p><strong>Method 1:</strong> Using the package option <code><a href="AMR-options.html">AMR_custom_ab</a></code>, which is the preferred method. To use this method:</p><ol><li><p>Create a data set in the structure of the <a href="antimicrobials.html">antimicrobials</a> data set (containing at the very least columns "ab" and "name") and save it with <code><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">saveRDS()</a></code> to a location of choice, e.g. <code>"~/my_custom_ab.rds"</code>, or any remote location.</p></li>
<li><p>Set the file location to the package option <code><a href="AMR-options.html">AMR_custom_ab</a></code>: <code>options(AMR_custom_ab = "~/my_custom_ab.rds")</code>. This can even be a remote file location, such as an https URL. Since options are not saved between <span style="R">R</span> sessions, it is best to save this option to the <code>.Rprofile</code> file so that it will be loaded on start-up of <span style="R">R</span>. To do this, open the <code>.Rprofile</code> file using e.g. <code>utils::file.edit("~/.Rprofile")</code>, add this text and save the file:</p> <li><p>Set the file location to the package option <code><a href="AMR-options.html">AMR_custom_ab</a></code>: <code>options(AMR_custom_ab = "~/my_custom_ab.rds")</code>. This can even be a remote file location, such as an https URL. Since options are not saved between <span style="R">R</span> sessions, it is best to save this option to the <code>.Rprofile</code> file so that it will be loaded on start-up of <span style="R">R</span>. To do this, open the <code>.Rprofile</code> file using e.g. <code>utils::file.edit("~/.Rprofile")</code>, add this text and save the file:</p>
<p></p><div class="sourceCode r"><pre><code><span><span class="co"># Add custom antimicrobial codes:</span></span> <p></p><div class="sourceCode r"><pre><code><span><span class="co"># Add custom antimicrobial codes:</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">options</a></span><span class="op">(</span>AMR_custom_ab <span class="op">=</span> <span class="st">"~/my_custom_ab.rds"</span><span class="op">)</span></span></code></pre><p></p></div> <span><span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">options</a></span><span class="op">(</span>AMR_custom_ab <span class="op">=</span> <span class="st">"~/my_custom_ab.rds"</span><span class="op">)</span></span></code></pre><p></p></div>
@ -106,11 +106,11 @@
<span class="r-in"><span> ab <span class="op">=</span> <span class="st">"TESTAB"</span>,</span></span> <span class="r-in"><span> ab <span class="op">=</span> <span class="st">"TESTAB"</span>,</span></span>
<span class="r-in"><span> name <span class="op">=</span> <span class="st">"Test Antibiotic"</span>,</span></span> <span class="r-in"><span> name <span class="op">=</span> <span class="st">"Test Antibiotic"</span>,</span></span>
<span class="r-in"><span> <span class="co"># you can add any property present in the</span></span></span> <span class="r-in"><span> <span class="co"># you can add any property present in the</span></span></span>
<span class="r-in"><span> <span class="co"># 'antibiotics' data set, such as 'group':</span></span></span> <span class="r-in"><span> <span class="co"># 'antimicrobials' data set, such as 'group':</span></span></span>
<span class="r-in"><span> group <span class="op">=</span> <span class="st">"Test Group"</span></span></span> <span class="r-in"><span> group <span class="op">=</span> <span class="st">"Test Group"</span></span></span>
<span class="r-in"><span> <span class="op">)</span></span></span> <span class="r-in"><span> <span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span> <span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Added one record to the internal </span><span style="color: #0000BB; background-color: #EEEEEE;">antibiotics</span><span style="color: #0000BB;"> data set.</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Added one record to the internal </span><span style="color: #0000BB; background-color: #EEEEEE;">antimicrobials</span><span style="color: #0000BB;"> data set.</span></span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># "testab" is now a new antibiotic:</span></span></span> <span class="r-in"><span><span class="co"># "testab" is now a new antibiotic:</span></span></span>
<span class="r-in"><span><span class="fu"><a href="as.ab.html">as.ab</a></span><span class="op">(</span><span class="st">"testab"</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="as.ab.html">as.ab</a></span><span class="op">(</span><span class="st">"testab"</span><span class="op">)</span></span></span>
@ -179,7 +179,7 @@
<span class="r-in"><span> group <span class="op">=</span> <span class="st">"Beta-lactams/penicillins"</span></span></span> <span class="r-in"><span> group <span class="op">=</span> <span class="st">"Beta-lactams/penicillins"</span></span></span>
<span class="r-in"><span> <span class="op">)</span></span></span> <span class="r-in"><span> <span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span> <span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Added one record to the internal </span><span style="color: #0000BB; background-color: #EEEEEE;">antibiotics</span><span style="color: #0000BB;"> data set.</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Added one record to the internal </span><span style="color: #0000BB; background-color: #EEEEEE;">antimicrobials</span><span style="color: #0000BB;"> data set.</span></span>
<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_atc</a></span><span class="op">(</span><span class="st">"Co-fluampicil"</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_atc</a></span><span class="op">(</span><span class="st">"Co-fluampicil"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "J01CR50"</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "J01CR50"</span>
<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_name</a></span><span class="op">(</span><span class="st">"J01CR50"</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_name</a></span><span class="op">(</span><span class="st">"J01CR50"</span><span class="op">)</span></span></span>

2
reference/add_custom_microorganisms.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

22
reference/age.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -111,16 +111,16 @@
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">df</span></span></span> <span class="r-in"><span><span class="va">df</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> birth_date age age_exact age_at_y2k</span> <span class="r-out co"><span class="r-pr">#&gt;</span> birth_date age age_exact age_at_y2k</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1965-12-05 59 59.24110 34</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 1 1965-12-05 59 59.25205 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1980-03-01 45 45.00548 19</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 2 1980-03-01 45 45.01644 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1949-11-01 75 75.33425 50</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 3 1949-11-01 75 75.34521 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1947-02-14 78 78.04658 52</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 4 1947-02-14 78 78.05753 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1940-02-19 85 85.03288 59</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 5 1940-02-19 85 85.04384 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1988-01-10 37 37.14247 11</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 6 1988-01-10 37 37.15342 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1997-08-27 27 27.51507 2</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 7 1997-08-27 27 27.52603 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1978-01-26 47 47.09863 21</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 8 1978-01-26 47 47.10959 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1972-06-17 52 52.70959 27</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 9 1972-06-17 52 52.72055 27</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1986-08-10 38 38.56164 13</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 10 1986-08-10 38 38.57260 13</span>
</code></pre></div> </code></pre></div>
</div> </div>
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>

2
reference/age_groups.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

60
reference/antibiogram.html
View File

@ -9,7 +9,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -60,10 +60,10 @@ Adhering to previously described approaches (see Source) and especially the Baye
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">antibiogram</span><span class="op">(</span><span class="va">x</span>, antibiotics <span class="op">=</span> <span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.sir</span><span class="op">)</span>, mo_transform <span class="op">=</span> <span class="st">"shortname"</span>,</span> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">antibiogram</span><span class="op">(</span><span class="va">x</span>, antibiotics <span class="op">=</span> <span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.sir</span><span class="op">)</span>, mo_transform <span class="op">=</span> <span class="st">"shortname"</span>,</span>
<span> ab_transform <span class="op">=</span> <span class="st">"name"</span>, syndromic_group <span class="op">=</span> <span class="cn">NULL</span>, add_total_n <span class="op">=</span> <span class="cn">FALSE</span>,</span> <span> ab_transform <span class="op">=</span> <span class="st">"name"</span>, syndromic_group <span class="op">=</span> <span class="cn">NULL</span>, add_total_n <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span> only_all_tested <span class="op">=</span> <span class="cn">FALSE</span>, digits <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="va">wisca</span>, <span class="fl">1</span>, <span class="fl">0</span><span class="op">)</span>,</span> <span> only_all_tested <span class="op">=</span> <span class="cn">FALSE</span>, digits <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="va">wisca</span>, <span class="fl">1</span>, <span class="fl">0</span><span class="op">)</span>,</span>
<span> formatting_type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_antibiogram_formatting_type"</span>, <span class="fl">14</span><span class="op">)</span>,</span> <span> formatting_type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_antibiogram_formatting_type"</span>,</span>
<span> col_mo <span class="op">=</span> <span class="cn">NULL</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, minimum <span class="op">=</span> <span class="fl">30</span>,</span> <span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="va">wisca</span>, <span class="fl">14</span>, <span class="fl">18</span><span class="op">)</span><span class="op">)</span>, col_mo <span class="op">=</span> <span class="cn">NULL</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> combine_SI <span class="op">=</span> <span class="cn">TRUE</span>, sep <span class="op">=</span> <span class="st">" + "</span>, wisca <span class="op">=</span> <span class="cn">FALSE</span>, simulations <span class="op">=</span> <span class="fl">1000</span>,</span> <span> minimum <span class="op">=</span> <span class="fl">30</span>, combine_SI <span class="op">=</span> <span class="cn">TRUE</span>, sep <span class="op">=</span> <span class="st">" + "</span>, wisca <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span> conf_interval <span class="op">=</span> <span class="fl">0.95</span>, interval_side <span class="op">=</span> <span class="st">"two-tailed"</span>,</span> <span> simulations <span class="op">=</span> <span class="fl">1000</span>, conf_interval <span class="op">=</span> <span class="fl">0.95</span>, interval_side <span class="op">=</span> <span class="st">"two-tailed"</span>,</span>
<span> info <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span> <span> info <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span>
<span></span> <span></span>
<span><span class="fu">wisca</span><span class="op">(</span><span class="va">x</span>, antibiotics <span class="op">=</span> <span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.sir</span><span class="op">)</span>, ab_transform <span class="op">=</span> <span class="st">"name"</span>,</span> <span><span class="fu">wisca</span><span class="op">(</span><span class="va">x</span>, antibiotics <span class="op">=</span> <span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.sir</span><span class="op">)</span>, ab_transform <span class="op">=</span> <span class="st">"name"</span>,</span>
@ -114,7 +114,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
<dt id="arg-ab-transform">ab_transform<a class="anchor" aria-label="anchor" href="#arg-ab-transform"></a></dt> <dt id="arg-ab-transform">ab_transform<a class="anchor" aria-label="anchor" href="#arg-ab-transform"></a></dt>
<dd><p>a character to transform antimicrobial input - must be one of the column names of the <a href="antibiotics.html">antibiotics</a> data set (defaults to <code>"name"</code>): "ab", "cid", "name", "group", "atc", "atc_group1", "atc_group2", "abbreviations", "synonyms", "oral_ddd", "oral_units", "iv_ddd", "iv_units", or "loinc". Can also be <code>NULL</code> to not transform the input.</p></dd> <dd><p>a character to transform antimicrobial input - must be one of the column names of the <a href="antimicrobials.html">antimicrobials</a> data set (defaults to <code>"name"</code>): "ab", "cid", "name", "group", "atc", "atc_group1", "atc_group2", "abbreviations", "synonyms", "oral_ddd", "oral_units", "iv_ddd", "iv_units", or "loinc". Can also be <code>NULL</code> to not transform the input.</p></dd>
<dt id="arg-syndromic-group">syndromic_group<a class="anchor" aria-label="anchor" href="#arg-syndromic-group"></a></dt> <dt id="arg-syndromic-group">syndromic_group<a class="anchor" aria-label="anchor" href="#arg-syndromic-group"></a></dt>
@ -206,7 +206,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
<h3 id="formatting-type">Formatting Type<a class="anchor" aria-label="anchor" href="#formatting-type"></a></h3> <h3 id="formatting-type">Formatting Type<a class="anchor" aria-label="anchor" href="#formatting-type"></a></h3>
<p>The formatting of the 'cells' of the table can be set with the argument <code>formatting_type</code>. In these examples, <code>5</code> is the antimicrobial coverage (<code>4-6</code> indicates the confidence level), <code>15</code> the number of susceptible isolates, and <code>300</code> the number of tested (i.e., available) isolates:</p><ol><li><p>5</p></li> <p>The formatting of the 'cells' of the table can be set with the argument <code>formatting_type</code>. In these examples, <code>5</code> indicates the antimicrobial coverage (<code>4-6</code> the confidence level), <code>15</code> the number of susceptible isolates, and <code>300</code> the number of tested (i.e., available) isolates:</p><ol><li><p>5</p></li>
<li><p>15</p></li> <li><p>15</p></li>
<li><p>300</p></li> <li><p>300</p></li>
<li><p>15/300</p></li> <li><p>15/300</p></li>
@ -219,16 +219,16 @@ Adhering to previously described approaches (see Source) and especially the Baye
<li><p>5 (N=15/300)</p></li> <li><p>5 (N=15/300)</p></li>
<li><p>5% (N=15/300)</p></li> <li><p>5% (N=15/300)</p></li>
<li><p>5 (4-6)</p></li> <li><p>5 (4-6)</p></li>
<li><p>5% (4-6%) - <strong>default</strong></p></li> <li><p>5% (4-6%) - <strong>default for WISCA</strong></p></li>
<li><p>5 (4-6,300)</p></li> <li><p>5 (4-6,300)</p></li>
<li><p>5% (4-6%,300)</p></li> <li><p>5% (4-6%,300)</p></li>
<li><p>5 (4-6,N=300)</p></li> <li><p>5 (4-6,N=300)</p></li>
<li><p>5% (4-6%,N=300)</p></li> <li><p>5% (4-6%,N=300) - <strong>default for non-WISCA</strong></p></li>
<li><p>5 (4-6,15/300)</p></li> <li><p>5 (4-6,15/300)</p></li>
<li><p>5% (4-6%,15/300)</p></li> <li><p>5% (4-6%,15/300)</p></li>
<li><p>5 (4-6,N=15/300)</p></li> <li><p>5 (4-6,N=15/300)</p></li>
<li><p>5% (4-6%,N=15/300)</p></li> <li><p>5% (4-6%,N=15/300)</p></li>
</ol><p>The default is <code>14</code>, which can be set globally with the package option <code><a href="AMR-options.html">AMR_antibiogram_formatting_type</a></code>, e.g. <code>options(AMR_antibiogram_formatting_type = 5)</code>. Do note that for WISCA, the total numbers of tested and susceptible isolates are less useful to report, since these are included in the Bayesian model and apparent from the susceptibility and its confidence level.</p> </ol><p>The default can be set globally with the package option <code><a href="AMR-options.html">AMR_antibiogram_formatting_type</a></code>, e.g. <code>options(AMR_antibiogram_formatting_type = 5)</code>. Do note that for WISCA, the total numbers of tested and susceptible isolates are less useful to report, since these are included in the Bayesian model and apparent from the susceptibility and its confidence level.</p>
<p>Set <code>digits</code> (defaults to <code>0</code>) to alter the rounding of the susceptibility percentages.</p> <p>Set <code>digits</code> (defaults to <code>0</code>) to alter the rounding of the susceptibility percentages.</p>
</div> </div>
@ -414,16 +414,16 @@ $$p_i = \frac{x_i}{\sum_{j=1}^K x_j}$$</p>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram (non-WISCA / 95% CI): 10 × 7</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram (non-WISCA / 95% CI): 10 × 7</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Pathogen Amikacin Gentamicin Imipenem Kanamycin Meropenem Tobramycin</span> <span class="r-out co"><span class="r-pr">#&gt;</span> Pathogen Amikacin Gentamicin Imipenem Kanamycin Meropenem Tobramycin</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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> CoNS 0% (0-8%) 86% (82-9… 52% (37… 0% (0-8%) 52% (37-… 22% (12-3…</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> CoNS 0% (0-8%,N… 86% (82-9… 52% (37… 0% (0-8%… 52% (37-… 22% (12-3…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> E. coli 100% (98-1… 98% (96-9… 100% (9… <span style="color: #BB0000;">NA</span> 100% (99… 97% (96-9…</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> E. coli 100% (98-1… 98% (96-9… 100% (9… <span style="color: #BB0000;">NA</span> 100% (99… 97% (96-9…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> E. faecalis 0% (0-9%) 0% (0-9%) 100% (9… 0% (0-9%) <span style="color: #BB0000;">NA</span> 0% (0-9%) </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> E. faecalis 0% (0-9%,N… 0% (0-9%,… 100% (9… 0% (0-9%… <span style="color: #BB0000;">NA</span> 0% (0-9%,…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> K. pneumoniae <span style="color: #BB0000;">NA</span> 90% (79-9… 100% (9… <span style="color: #BB0000;">NA</span> 100% (93… 90% (79-9…</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> K. pneumoniae <span style="color: #BB0000;">NA</span> 90% (79-9… 100% (9… <span style="color: #BB0000;">NA</span> 100% (93… 90% (79-9…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> P. aeruginosa <span style="color: #BB0000;">NA</span> 100% (88-… <span style="color: #BB0000;">NA</span> 0% (0-12… <span style="color: #BB0000;">NA</span> 100% (88-…</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> P. aeruginosa <span style="color: #BB0000;">NA</span> 100% (88-… <span style="color: #BB0000;">NA</span> 0% (0-12… <span style="color: #BB0000;">NA</span> 100% (88-…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> P. mirabilis <span style="color: #BB0000;">NA</span> 94% (80-9… 94% (79… <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 94% (80-9…</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> P. mirabilis <span style="color: #BB0000;">NA</span> 94% (80-9… 94% (79… <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 94% (80-9…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> S. aureus <span style="color: #BB0000;">NA</span> 99% (97-1… <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 98% (92-1…</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> S. aureus <span style="color: #BB0000;">NA</span> 99% (97-1… <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 98% (92-1…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> S. epidermidis 0% (0-8%) 79% (71-8… <span style="color: #BB0000;">NA</span> 0% (0-8%) <span style="color: #BB0000;">NA</span> 51% (40-6…</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> S. epidermidis 0% (0-8%,N… 79% (71-8… <span style="color: #BB0000;">NA</span> 0% (0-8%… <span style="color: #BB0000;">NA</span> 51% (40-6…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> S. hominis <span style="color: #BB0000;">NA</span> 92% (84-9… <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 85% (74-9…</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> S. hominis <span style="color: #BB0000;">NA</span> 92% (84-9… <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 85% (74-9…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> S. pneumoniae 0% (0-3%) 0% (0-3%) <span style="color: #BB0000;">NA</span> 0% (0-3%) <span style="color: #BB0000;">NA</span> 0% (0-3%) </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> S. pneumoniae 0% (0-3%,N… 0% (0-3%,… <span style="color: #BB0000;">NA</span> 0% (0-3%… <span style="color: #BB0000;">NA</span> 0% (0-3%,…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Use `plot()` or `ggplot2::autoplot()` to create a plot of this antibiogram,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Use `plot()` or `ggplot2::autoplot()` to create a plot of this antibiogram,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># or use it directly in R Markdown or https://quarto.org, see ?antibiogram</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># or use it directly in R Markdown or https://quarto.org, see ?antibiogram</span></span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
@ -437,8 +437,8 @@ $$p_i = \frac{x_i}{\sum_{j=1}^K x_j}$$</p>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram (non-WISCA / 95% CI): 2 × 5</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram (non-WISCA / 95% CI): 2 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Pathogen J01GB01 J01GB03 J01GB04 J01GB06 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> Pathogen J01GB01 J01GB03 J01GB04 J01GB06 </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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Gram-negative 96% (94-97%) 96% (95-98%) 0% (0-10%) 98% (96-99%)</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Gram-negative 96% (94-97%,N=686) 96% (95-98%,N=684) 0% (0-10%,N=35) 98% (96-…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> Gram-positive 34% (31-38%) 63% (60-66%) 0% (0-1%) 0% (0-1%) </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> Gram-positive 34% (31-38%,N=665) 63% (60-66%,N=1170) 0% (0-1%,N=436) 0% (0-1%…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Use `plot()` or `ggplot2::autoplot()` to create a plot of this antibiogram,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Use `plot()` or `ggplot2::autoplot()` to create a plot of this antibiogram,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># or use it directly in R Markdown or https://quarto.org, see ?antibiogram</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># or use it directly in R Markdown or https://quarto.org, see ?antibiogram</span></span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
@ -451,11 +451,11 @@ $$p_i = \frac{x_i}{\sum_{j=1}^K x_j}$$</p>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram (non-WISCA / 95% CI): 5 × 3</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram (non-WISCA / 95% CI): 5 × 3</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Pathogen Imipenem Meropenem </span> <span class="r-out co"><span class="r-pr">#&gt;</span> Pathogen Imipenem Meropenem </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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Coagulase-negative Staphylococcus (CoNS) 52% (37-67%) 52% (37-67%) </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Coagulase-negative Staphylococcus (CoNS) 52% (37-67%,N=48) 52% (37-67%,N=4…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> Enterococcus faecalis 100% (91-100%) <span style="color: #BB0000;">NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> Enterococcus faecalis 100% (91-100%,N=38) <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Escherichia coli 100% (99-100%) 100% (99-100%)</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Escherichia coli 100% (99-100%,N=422) 100% (99-100%,N…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> Klebsiella pneumoniae 100% (93-100%) 100% (93-100%)</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> Klebsiella pneumoniae 100% (93-100%,N=51) 100% (93-100%,N…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">5</span> Proteus mirabilis 94% (79-99%) <span style="color: #BB0000;">NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">5</span> Proteus mirabilis 94% (79-99%,N=32) <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Use `plot()` or `ggplot2::autoplot()` to create a plot of this antibiogram,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Use `plot()` or `ggplot2::autoplot()` to create a plot of this antibiogram,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># or use it directly in R Markdown or https://quarto.org, see ?antibiogram</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># or use it directly in R Markdown or https://quarto.org, see ?antibiogram</span></span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
@ -470,8 +470,8 @@ $$p_i = \frac{x_i}{\sum_{j=1}^K x_j}$$</p>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram (non-WISCA / 95% CI): 2 × 4</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram (non-WISCA / 95% CI): 2 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Pathogen Piperacillin/tazobac…¹ Piperacillin/tazobac…² Piperacillin/tazobac…³</span> <span class="r-out co"><span class="r-pr">#&gt;</span> Pathogen Piperacillin/tazobac…¹ Piperacillin/tazobac…² Piperacillin/tazobac…³</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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Gram-neg… 88% (85-91%) 99% (97-99%) 98% (97-99%) </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Gram-neg… 88% (85-91%,N=641) 99% (97-99%,N=691) 98% (97-99%,N=693) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> Gram-pos… 86% (82-89%) 98% (96-98%) 95% (93-97%) </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> Gram-pos… 86% (82-89%,N=345) 98% (96-98%,N=1044) 95% (93-97%,N=550) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ abbreviated names: ¹​`Piperacillin/tazobactam`,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ abbreviated names: ¹​`Piperacillin/tazobactam`,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ²​`Piperacillin/tazobactam + Gentamicin`,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ²​`Piperacillin/tazobactam + Gentamicin`,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ³​`Piperacillin/tazobactam + Tobramycin`</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ³​`Piperacillin/tazobactam + Tobramycin`</span></span>
@ -488,8 +488,8 @@ $$p_i = \frac{x_i}{\sum_{j=1}^K x_j}$$</p>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram (non-WISCA / 95% CI): 2 × 3</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram (non-WISCA / 95% CI): 2 × 3</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Pathogen Ciprofloxacin `Ciprofloxacin &amp; Gentamicin`</span> <span class="r-out co"><span class="r-pr">#&gt;</span> Pathogen Ciprofloxacin `Ciprofloxacin &amp; Gentamicin`</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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Gram-negative 91% (88-93%) 99% (97-99%) </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Gram-negative 91% (88-93%,N=684) 99% (97-99%,N=694) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> Gram-positive 77% (74-80%) 93% (91-94%) </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> Gram-positive 77% (74-80%,N=724) 93% (91-94%,N=847) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Use `plot()` or `ggplot2::autoplot()` to create a plot of this antibiogram,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Use `plot()` or `ggplot2::autoplot()` to create a plot of this antibiogram,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># or use it directly in R Markdown or https://quarto.org, see ?antibiogram</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># or use it directly in R Markdown or https://quarto.org, see ?antibiogram</span></span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
@ -519,8 +519,8 @@ $$p_i = \frac{x_i}{\sum_{j=1}^K x_j}$$</p>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical S. epider… <span style="color: #BB0000;">NA</span> 82% (72-9… <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical S. epider… <span style="color: #BB0000;">NA</span> 82% (72-9… <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">11</span> ICU S. epider… <span style="color: #BB0000;">NA</span> 72% (60-8… <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">11</span> ICU S. epider… <span style="color: #BB0000;">NA</span> 72% (60-8… <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">12</span> Clinical S. hominis <span style="color: #BB0000;">NA</span> 96% (85-9… <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">12</span> Clinical S. hominis <span style="color: #BB0000;">NA</span> 96% (85-9… <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">13</span> Clinical S. pneumo… 0% (0-5… 0% (0-5%) <span style="color: #BB0000;">NA</span> 0% (0-5%) <span style="color: #BB0000;">NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">13</span> Clinical S. pneumo… 0% (0-5… 0% (0-5%,… <span style="color: #BB0000;">NA</span> 0% (0-5%… <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">14</span> ICU S. pneumo… 0% (0-1… 0% (0-12%) <span style="color: #BB0000;">NA</span> 0% (0-12… <span style="color: #BB0000;">NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">14</span> ICU S. pneumo… 0% (0-1… 0% (0-12%… <span style="color: #BB0000;">NA</span> 0% (0-12… <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 1 more variable: Tobramycin &lt;chr&gt;</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 1 more variable: Tobramycin &lt;chr&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Use `plot()` or `ggplot2::autoplot()` to create a plot of this antibiogram,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Use `plot()` or `ggplot2::autoplot()` to create a plot of this antibiogram,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># or use it directly in R Markdown or https://quarto.org, see ?antibiogram</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># or use it directly in R Markdown or https://quarto.org, see ?antibiogram</span></span>
@ -542,10 +542,10 @@ $$p_i = \frac{x_i}{\sum_{j=1}^K x_j}$$</p>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <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 class="r-msg co"><span class="r-pr">#&gt;</span> <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 class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> (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 class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> (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 class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram (non-WISCA / 95% CI): 2 × 5</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram (non-WISCA / 95% CI): 2 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> `Grupo sindrómico` Patógeno Amikacina Gentamicina Tobramicina </span> <span class="r-out co"><span class="r-pr">#&gt;</span> `Grupo sindrómico` Patógeno Amikacina Gentamicina Tobramicina</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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> No UCI E. coli 100% (97-100%) 98% (96-99%) 98% (96-99%)</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> No UCI E. coli 100% (97-100%,N=119) 98% (96-99%,N=32… 98% (96-99…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> UCI E. coli 100% (93-100%) 99% (95-100%) 96% (92-99%)</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> UCI E. coli 100% (93-100%,N=52) 99% (95-100%,N=1… 96% (92-99…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Use `plot()` or `ggplot2::autoplot()` to create a plot of this antibiogram,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Use `plot()` or `ggplot2::autoplot()` to create a plot of this antibiogram,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># or use it directly in R Markdown or https://quarto.org, see ?antibiogram</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># or use it directly in R Markdown or https://quarto.org, see ?antibiogram</span></span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>

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@ -1,190 +1,8 @@
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<img src="../logo.svg" class="logo" alt=""><h1>Data Sets with 607 Antimicrobial Drugs</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>antibiotics.Rd</code></div>
</div>
<div class="ref-description section level2">
<p>Two data sets containing all antibiotics/antimycotics and antivirals. Use <code><a href="as.ab.html">as.ab()</a></code> or one of the <code><a href="ab_property.html">ab_*</a></code> functions to retrieve values from the antibiotics data set. Three identifiers are included in this data set: an antibiotic ID (<code>ab</code>, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (<code>atc</code>) as defined by the WHO, and a Compound ID (<code>cid</code>) as found in PubChem. Other properties in this data set are derived from one or more of these codes. Note that some drugs have multiple ATC codes.</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">antibiotics</span></span>
<span></span>
<span><span class="va">antivirals</span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
<div class="section">
<h3 id="for-the-antibiotics-data-set-a-tibble-with-observations-and-variables-">For the antibiotics data set: a <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 487 observations and 14 variables:<a class="anchor" aria-label="anchor" href="#for-the-antibiotics-data-set-a-tibble-with-observations-and-variables-"></a></h3>
<ul><li><p><code>ab</code><br> Antibiotic ID as used in this package (such as <code>AMC</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available. <em><strong>This is a unique identifier.</strong></em></p></li>
<li><p><code>cid</code><br> Compound ID as found in PubChem. <em><strong>This is a unique identifier.</strong></em></p></li>
<li><p><code>name</code><br> Official name as used by WHONET/EARS-Net or the WHO. <em><strong>This is a unique identifier.</strong></em></p></li>
<li><p><code>group</code><br> A short and concise group name, based on WHONET and WHOCC definitions</p></li>
<li><p><code>atc</code><br> ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC, like <code>J01CR02</code></p></li>
<li><p><code>atc_group1</code><br> Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC, like <code>"Macrolides, lincosamides and streptogramins"</code></p></li>
<li><p><code>atc_group2</code><br> Official chemical subgroup (4th level ATC code) as defined by the WHOCC, like <code>"Macrolides"</code></p></li>
<li><p><code>abbr</code><br> List of abbreviations as used in many countries, also for antibiotic susceptibility testing (AST)</p></li>
<li><p><code>synonyms</code><br> Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID</p></li>
<li><p><code>oral_ddd</code><br> Defined Daily Dose (DDD), oral treatment, currently available for 179 drugs</p></li>
<li><p><code>oral_units</code><br> Units of <code>oral_ddd</code></p></li>
<li><p><code>iv_ddd</code><br> Defined Daily Dose (DDD), parenteral (intravenous) treatment, currently available for 153 drugs</p></li>
<li><p><code>iv_units</code><br> Units of <code>iv_ddd</code></p></li>
<li><p><code>loinc</code><br> All codes associated with the name of the antimicrobial drug from Logical Observation Identifiers Names and Codes (LOINC), Version 2.76 (18 September, 2023). Use <code><a href="ab_property.html">ab_loinc()</a></code> to retrieve them quickly, see <code><a href="ab_property.html">ab_property()</a></code>.</p></li>
</ul></div>
<div class="section">
<h3 id="for-the-antivirals-data-set-a-tibble-with-observations-and-variables-">For the antivirals data set: a <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 120 observations and 11 variables:<a class="anchor" aria-label="anchor" href="#for-the-antivirals-data-set-a-tibble-with-observations-and-variables-"></a></h3>
<ul><li><p><code>av</code><br> Antiviral ID as used in this package (such as <code>ACI</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available. <em><strong>This is a unique identifier.</strong></em> Combinations are codes that contain a <code>+</code> to indicate this, such as <code>ATA+COBI</code> for atazanavir/cobicistat.</p></li>
<li><p><code>name</code><br> Official name as used by WHONET/EARS-Net or the WHO. <em><strong>This is a unique identifier.</strong></em></p></li>
<li><p><code>atc</code><br> ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC</p></li>
<li><p><code>cid</code><br> Compound ID as found in PubChem. <em><strong>This is a unique identifier.</strong></em></p></li>
<li><p><code>atc_group</code><br> Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC</p></li>
<li><p><code>synonyms</code><br> Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID</p></li>
<li><p><code>oral_ddd</code><br> Defined Daily Dose (DDD), oral treatment</p></li>
<li><p><code>oral_units</code><br> Units of <code>oral_ddd</code></p></li>
<li><p><code>iv_ddd</code><br> Defined Daily Dose (DDD), parenteral treatment</p></li>
<li><p><code>iv_units</code><br> Units of <code>iv_ddd</code></p></li>
<li><p><code>loinc</code><br> All codes associated with the name of the antiviral drug from Logical Observation Identifiers Names and Codes (LOINC), Version 2.76 (18 September, 2023). Use <code><a href="av_property.html">av_loinc()</a></code> to retrieve them quickly, see <code><a href="av_property.html">av_property()</a></code>.</p></li>
</ul></div>
<p>An object of class <code>tbl_df</code> (inherits from <code>tbl</code>, <code>data.frame</code>) with 120 rows and 11 columns.</p>
</div>
<div class="section level2">
<h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
<ul><li><p>World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology (WHOCC): <a href="https://atcddd.fhi.no/atc_ddd_index/" class="external-link">https://atcddd.fhi.no/atc_ddd_index/</a></p></li>
<li><p>Logical Observation Identifiers Names and Codes (LOINC), Version 2.76 (18 September, 2023). Accessed from <a href="https://loinc.org" class="external-link">https://loinc.org</a> on October 19th, 2023.</p></li>
<li><p>European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: <a href="https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm" class="external-link">https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm</a></p></li>
</ul></div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p>Properties that are based on an ATC code are only available when an ATC is available. These properties are: <code>atc_group1</code>, <code>atc_group2</code>, <code>oral_ddd</code>, <code>oral_units</code>, <code>iv_ddd</code> and <code>iv_units</code>.</p>
<p>Synonyms (i.e. trade names) were derived from the PubChem Compound ID (column <code>cid</code>) and consequently only available where a CID is available.</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, these data sets are 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>
</div>
</div>
<div class="section level2">
<h2 id="whocc">WHOCC<a class="anchor" aria-label="anchor" href="#whocc"></a></h2>
<p>This package contains <strong>all ~550 antibiotic, antimycotic and antiviral drugs</strong> and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href="https://atcddd.fhi.no" class="external-link">https://atcddd.fhi.no</a>) and the Pharmaceuticals Community Register of the European Commission (<a href="https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm" class="external-link">https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm</a>).</p>
<p>These have become the gold standard for international drug utilisation monitoring and research.</p>
<p>The WHOCC is located in Oslo at the Norwegian Institute of Public Health and funded by the Norwegian government. The European Commission is the executive of the European Union and promotes its general interest.</p>
<p><strong>NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package.</strong> See <a href="https://atcddd.fhi.no/copyright_disclaimer/." class="external-link">https://atcddd.fhi.no/copyright_disclaimer/.</a></p>
</div>
<div class="section level2">
<h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
<div class="dont-index"><p><a href="microorganisms.html">microorganisms</a>, <a href="intrinsic_resistant.html">intrinsic_resistant</a></p></div>
</div>
<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">antibiotics</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 487 × 14</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ab cid name group atc atc_group1 atc_group2 abbreviations synonyms</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lis&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;list&gt;</span> <span style="color: #949494; font-style: italic;">&lt;named &gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> AMA <span style="text-decoration: underline;">4</span>649 4-ami… Anti… <span style="color: #949494;">&lt;chr&gt;</span> Drugs for… Aminosali… <span style="color: #949494;">&lt;chr [1]&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> ACM 6<span style="text-decoration: underline;">450</span>012 Acety… Macr… <span style="color: #949494;">&lt;chr&gt;</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #949494;">&lt;chr [1]&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> ASP 49<span style="text-decoration: underline;">787</span>020 Acety… Macr… <span style="color: #949494;">&lt;chr&gt;</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #949494;">&lt;chr [1]&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> ALS <span style="text-decoration: underline;">8</span>954 Aldes… Othe… <span style="color: #949494;">&lt;chr&gt;</span> Drugs for… Drugs for… <span style="color: #949494;">&lt;chr [1]&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> AMK <span style="text-decoration: underline;">37</span>768 Amika… Amin… <span style="color: #949494;">&lt;chr&gt;</span> Aminoglyc… Other ami… <span style="color: #949494;">&lt;chr [5]&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> AKF <span style="color: #BB0000;">NA</span> Amika… Amin… <span style="color: #949494;">&lt;chr&gt;</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #949494;">&lt;chr [1]&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> AMO <span style="text-decoration: underline;">54</span>260 Amoro… Anti… <span style="color: #949494;">&lt;chr&gt;</span> Antifunga… Other ant… <span style="color: #949494;">&lt;chr [1]&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> AMX <span style="text-decoration: underline;">33</span>613 Amoxi… Beta… <span style="color: #949494;">&lt;chr&gt;</span> Beta-lact… Penicilli… <span style="color: #949494;">&lt;chr [3]&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> AMC 23<span style="text-decoration: underline;">665</span>637 Amoxi… Beta… <span style="color: #949494;">&lt;chr&gt;</span> Beta-lact… Combinati… <span style="color: #949494;">&lt;chr [5]&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> AXS <span style="text-decoration: underline;">465</span>441 Amoxi… Beta… <span style="color: #949494;">&lt;chr&gt;</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #949494;">&lt;chr [1]&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 477 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 5 more variables: oral_ddd &lt;dbl&gt;, oral_units &lt;chr&gt;, iv_ddd &lt;dbl&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># iv_units &lt;chr&gt;, loinc &lt;list&gt;</span></span>
<span class="r-in"><span><span class="va">antivirals</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 120 × 11</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> av name atc cid atc_group synonyms oral_ddd oral_units iv_ddd</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;av&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;list&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> ABA Abacavir J05A… 4.41<span style="color: #949494;">e</span>5 Nucleosi… <span style="color: #949494;">&lt;chr&gt;</span> 0.6 g <span style="color: #BB0000;">NA</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> ACI Aciclovir J05A… 1.35<span style="color: #949494;">e</span>8 Nucleosi… <span style="color: #949494;">&lt;chr&gt;</span> 4 g 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> ADD Adefovir… J05A… 6.09<span style="color: #949494;">e</span>4 Nucleosi… <span style="color: #949494;">&lt;chr&gt;</span> 10 mg <span style="color: #BB0000;">NA</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> AME Amenamev… J05A… 1.14<span style="color: #949494;">e</span>7 Other an… <span style="color: #949494;">&lt;chr&gt;</span> 0.4 g <span style="color: #BB0000;">NA</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> AMP Amprenav… J05A… 6.50<span style="color: #949494;">e</span>4 Protease… <span style="color: #949494;">&lt;chr&gt;</span> 1.2 g <span style="color: #BB0000;">NA</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> ASU Asunapre… J05A… 1.61<span style="color: #949494;">e</span>7 Antivira… <span style="color: #949494;">&lt;chr&gt;</span> 0.2 g <span style="color: #BB0000;">NA</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> ATA Atazanav… J05A… 1.48<span style="color: #949494;">e</span>5 Protease… <span style="color: #949494;">&lt;chr&gt;</span> 0.3 g <span style="color: #BB0000;">NA</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> ATA<span style="color: #949494;">+</span>COBI Atazanav… J05A… 8.66<span style="color: #949494;">e</span>7 Antivira… <span style="color: #949494;">&lt;chr&gt;</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> ATA<span style="color: #949494;">+</span>RIT Atazanav… J05A… 2.51<span style="color: #949494;">e</span>7 Antivira… <span style="color: #949494;">&lt;chr&gt;</span> 0.3 g <span style="color: #BB0000;">NA</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> BAM Baloxavi… J05A… 1.24<span style="color: #949494;">e</span>8 Other an… <span style="color: #949494;">&lt;chr&gt;</span> 40 mg <span style="color: #BB0000;">NA</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 110 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 2 more variables: iv_units &lt;chr&gt;, loinc &lt;list&gt;</span></span>
</code></pre></div>
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18
reference/antimicrobial_selectors.html
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@ -17,7 +17,7 @@ my_data_with_all_these_columns %&amp;gt;%
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -171,11 +171,11 @@ my_data_with_all_these_columns %&amp;gt;%
<dt id="arg-amr-class">amr_class<a class="anchor" aria-label="anchor" href="#arg-amr-class"></a></dt> <dt id="arg-amr-class">amr_class<a class="anchor" aria-label="anchor" href="#arg-amr-class"></a></dt>
<dd><p>an antimicrobial class or a part of it, such as <code>"carba"</code> and <code>"carbapenems"</code>. The columns <code>group</code>, <code>atc_group1</code> and <code>atc_group2</code> of the <a href="antibiotics.html">antibiotics</a> data set will be searched (case-insensitive) for this value.</p></dd> <dd><p>an antimicrobial class or a part of it, such as <code>"carba"</code> and <code>"carbapenems"</code>. The columns <code>group</code>, <code>atc_group1</code> and <code>atc_group2</code> of the <a href="antimicrobials.html">antimicrobials</a> data set will be searched (case-insensitive) for this value.</p></dd>
<dt id="arg-filter">filter<a class="anchor" aria-label="anchor" href="#arg-filter"></a></dt> <dt id="arg-filter">filter<a class="anchor" aria-label="anchor" href="#arg-filter"></a></dt>
<dd><p>an <a href="https://rdrr.io/r/base/expression.html" class="external-link">expression</a> to be evaluated in the <a href="antibiotics.html">antibiotics</a> data set, such as <code>name %like% "trim"</code></p></dd> <dd><p>an <a href="https://rdrr.io/r/base/expression.html" class="external-link">expression</a> to be evaluated in the <a href="antimicrobials.html">antimicrobials</a> data set, such as <code>name %like% "trim"</code></p></dd>
<dt id="arg-col-mo">col_mo<a class="anchor" aria-label="anchor" href="#arg-col-mo"></a></dt> <dt id="arg-col-mo">col_mo<a class="anchor" aria-label="anchor" href="#arg-col-mo"></a></dt>
@ -194,10 +194,10 @@ my_data_with_all_these_columns %&amp;gt;%
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p>These functions can be used in data set calls for selecting columns and filtering rows. They work with base <span style="R">R</span>, the Tidyverse, and <code>data.table</code>. They are heavily inspired by the <a href="https://tidyselect.r-lib.org/reference/language.html" class="external-link">Tidyverse selection helpers</a> such as <code><a href="https://tidyselect.r-lib.org/reference/everything.html" class="external-link">everything()</a></code>, but are not limited to <code>dplyr</code> verbs. Nonetheless, they are very convenient to use with <code>dplyr</code> functions such as <code><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select()</a></code>, <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, see <em>Examples</em>.</p> <p>These functions can be used in data set calls for selecting columns and filtering rows. They work with base <span style="R">R</span>, the Tidyverse, and <code>data.table</code>. They are heavily inspired by the <a href="https://tidyselect.r-lib.org/reference/language.html" class="external-link">Tidyverse selection helpers</a> such as <code><a href="https://tidyselect.r-lib.org/reference/everything.html" class="external-link">everything()</a></code>, but are not limited to <code>dplyr</code> verbs. Nonetheless, they are very convenient to use with <code>dplyr</code> functions such as <code><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select()</a></code>, <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, see <em>Examples</em>.</p>
<p>All selectors can also be used in <code>tidymodels</code> packages such as <code>recipe</code> and <code>parsnip</code>. See for more info <a href="https://msberends.github.io/AMR/articles/AMR_with_tidymodels.html">our tutorial</a> on using antimicrobial selectors for predictive modelling.</p> <p>All selectors can also be used in <code>tidymodels</code> packages such as <code>recipe</code> and <code>parsnip</code>. See for more info <a href="https://msberends.github.io/AMR/articles/AMR_with_tidymodels.html">our tutorial</a> on using antimicrobial selectors for predictive modelling.</p>
<p>All columns in the data in which these functions are called will be searched for known antimicrobial names, abbreviations, brand names, and codes (ATC, EARS-Net, WHO, etc.) according to the <a href="antibiotics.html">antibiotics</a> data set. This means that a selector such as <code>aminoglycosides()</code> will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.</p> <p>All columns in the data in which these functions are called will be searched for known antimicrobial names, abbreviations, brand names, and codes (ATC, EARS-Net, WHO, etc.) according to the <a href="antimicrobials.html">antimicrobials</a> data set. This means that a selector such as <code>aminoglycosides()</code> will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.</p>
<p>The <code>amr_class()</code> function can be used to filter/select on a manually defined antimicrobial class. It searches for results in the <a href="antibiotics.html">antibiotics</a> data set within the columns <code>group</code>, <code>atc_group1</code> and <code>atc_group2</code>.</p> <p>The <code>amr_class()</code> function can be used to filter/select on a manually defined antimicrobial class. It searches for results in the <a href="antimicrobials.html">antimicrobials</a> data set within the columns <code>group</code>, <code>atc_group1</code> and <code>atc_group2</code>.</p>
<p>The <code>administrable_per_os()</code> and <code>administrable_iv()</code> functions also rely on the <a href="antibiotics.html">antibiotics</a> data set - antimicrobials will be matched where a DDD (defined daily dose) for resp. oral and IV treatment is available in the <a href="antibiotics.html">antibiotics</a> data set.</p> <p>The <code>administrable_per_os()</code> and <code>administrable_iv()</code> functions also rely on the <a href="antimicrobials.html">antimicrobials</a> data set - antimicrobials will be matched where a DDD (defined daily dose) for resp. oral and IV treatment is available in the <a href="antimicrobials.html">antimicrobials</a> data set.</p>
<p>The <code>amr_selector()</code> function can be used to internally filter the <a href="antibiotics.html">antibiotics</a> data set on any results, see <em>Examples</em>. It allows for filtering on a (part of) a certain name, and/or a group name or even a minimum of DDDs for oral treatment. This function yields the highest flexibility, but is also the least user-friendly, since it requires a hard-coded filter to set.</p> <p>The <code>amr_selector()</code> function can be used to internally filter the <a href="antimicrobials.html">antimicrobials</a> data set on any results, see <em>Examples</em>. It allows for filtering on a (part of) a certain name, and/or a group name or even a minimum of DDDs for oral treatment. This function yields the highest flexibility, but is also the least user-friendly, since it requires a hard-coded filter to set.</p>
<p>The <code>not_intrinsic_resistant()</code> function can be used to only select antimicrobials that pose no intrinsic resistance for the microorganisms in the data set. For example, if a data set contains only microorganism codes or names of <em>E. coli</em> and <em>K. pneumoniae</em> and contains a column "vancomycin", this column will be removed (or rather, unselected) using this function. It currently applies <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) to determine intrinsic resistance, using the <code><a href="eucast_rules.html">eucast_rules()</a></code> function internally. Because of this determination, this function is quite slow in terms of performance.</p> <p>The <code>not_intrinsic_resistant()</code> function can be used to only select antimicrobials that pose no intrinsic resistance for the microorganisms in the data set. For example, if a data set contains only microorganism codes or names of <em>E. coli</em> and <em>K. pneumoniae</em> and contains a column "vancomycin", this column will be removed (or rather, unselected) using this function. It currently applies <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) to determine intrinsic resistance, using the <code><a href="eucast_rules.html">eucast_rules()</a></code> function internally. Because of this determination, this function is quite slow in terms of performance.</p>
</div> </div>
<div class="section level2"> <div class="section level2">
@ -240,7 +240,7 @@ my_data_with_all_these_columns %&amp;gt;%
<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2> <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 data sets in this <code>AMR</code> package (about microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. 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>All data sets in this <code>AMR</code> package (about microorganisms, antimicrobials, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. 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>
<div class="section level2"> <div class="section level2">
@ -617,7 +617,7 @@ my_data_with_all_these_columns %&amp;gt;%
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 1,990 more rows</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 1,990 more rows</span></span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># amr_selector() applies a filter in the `antibiotics` data set and is thus</span></span></span> <span class="r-in"><span><span class="co"># amr_selector() applies a filter in the `antimicrobials` data set and is thus</span></span></span>
<span class="r-in"><span><span class="co"># very flexible. For instance, to select antimicrobials with an oral DDD</span></span></span> <span class="r-in"><span><span class="co"># very flexible. For instance, to select antimicrobials with an oral DDD</span></span></span>
<span class="r-in"><span><span class="co"># of at least 1 gram:</span></span></span> <span class="r-in"><span><span class="co"># of at least 1 gram:</span></span></span>
<span class="r-in"><span><span class="va">example_isolates</span><span class="op">[</span>, <span class="fu">amr_selector</span><span class="op">(</span><span class="va">oral_ddd</span> <span class="op">&gt;</span> <span class="fl">1</span> <span class="op">&amp;</span> <span class="va">oral_units</span> <span class="op">==</span> <span class="st">"g"</span><span class="op">)</span><span class="op">]</span></span></span> <span class="r-in"><span><span class="va">example_isolates</span><span class="op">[</span>, <span class="fu">amr_selector</span><span class="op">(</span><span class="va">oral_ddd</span> <span class="op">&gt;</span> <span class="fl">1</span> <span class="op">&amp;</span> <span class="va">oral_units</span> <span class="op">==</span> <span class="st">"g"</span><span class="op">)</span><span class="op">]</span></span></span>

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@ -0,0 +1,190 @@
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<img src="../logo.svg" class="logo" alt=""><h1>Data Sets with 607 Antimicrobial Drugs</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>antimicrobials.Rd</code></div>
</div>
<div class="ref-description section level2">
<p>Two data sets containing all antimicrobials and antivirals. Use <code><a href="as.ab.html">as.ab()</a></code> or one of the <code><a href="ab_property.html">ab_*</a></code> functions to retrieve values from the antimicrobials data set. Three identifiers are included in this data set: an antimcrobial ID (<code>ab</code>, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (<code>atc</code>) as defined by the WHO, and a Compound ID (<code>cid</code>) as found in PubChem. Other properties in this data set are derived from one or more of these codes. Note that some drugs have multiple ATC codes.</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">antimicrobials</span></span>
<span></span>
<span><span class="va">antivirals</span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
<div class="section">
<h3 id="for-the-antimicrobials-data-set-a-tibble-with-observations-and-variables-">For the antimicrobials data set: a <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 487 observations and 14 variables:<a class="anchor" aria-label="anchor" href="#for-the-antimicrobials-data-set-a-tibble-with-observations-and-variables-"></a></h3>
<ul><li><p><code>ab</code><br> antimcrobial ID as used in this package (such as <code>AMC</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available. <em><strong>This is a unique identifier.</strong></em></p></li>
<li><p><code>cid</code><br> Compound ID as found in PubChem. <em><strong>This is a unique identifier.</strong></em></p></li>
<li><p><code>name</code><br> Official name as used by WHONET/EARS-Net or the WHO. <em><strong>This is a unique identifier.</strong></em></p></li>
<li><p><code>group</code><br> A short and concise group name, based on WHONET and WHOCC definitions</p></li>
<li><p><code>atc</code><br> ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC, like <code>J01CR02</code></p></li>
<li><p><code>atc_group1</code><br> Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC, like <code>"Macrolides, lincosamides and streptogramins"</code></p></li>
<li><p><code>atc_group2</code><br> Official chemical subgroup (4th level ATC code) as defined by the WHOCC, like <code>"Macrolides"</code></p></li>
<li><p><code>abbr</code><br> List of abbreviations as used in many countries, also for antimcrobial susceptibility testing (AST)</p></li>
<li><p><code>synonyms</code><br> Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID</p></li>
<li><p><code>oral_ddd</code><br> Defined Daily Dose (DDD), oral treatment, currently available for 179 drugs</p></li>
<li><p><code>oral_units</code><br> Units of <code>oral_ddd</code></p></li>
<li><p><code>iv_ddd</code><br> Defined Daily Dose (DDD), parenteral (intravenous) treatment, currently available for 153 drugs</p></li>
<li><p><code>iv_units</code><br> Units of <code>iv_ddd</code></p></li>
<li><p><code>loinc</code><br> All codes associated with the name of the antimicrobial drug from Logical Observation Identifiers Names and Codes (LOINC), Version 2.76 (18 September, 2023). Use <code><a href="ab_property.html">ab_loinc()</a></code> to retrieve them quickly, see <code><a href="ab_property.html">ab_property()</a></code>.</p></li>
</ul></div>
<div class="section">
<h3 id="for-the-antivirals-data-set-a-tibble-with-observations-and-variables-">For the antivirals data set: a <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 120 observations and 11 variables:<a class="anchor" aria-label="anchor" href="#for-the-antivirals-data-set-a-tibble-with-observations-and-variables-"></a></h3>
<ul><li><p><code>av</code><br> Antiviral ID as used in this package (such as <code>ACI</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available. <em><strong>This is a unique identifier.</strong></em> Combinations are codes that contain a <code>+</code> to indicate this, such as <code>ATA+COBI</code> for atazanavir/cobicistat.</p></li>
<li><p><code>name</code><br> Official name as used by WHONET/EARS-Net or the WHO. <em><strong>This is a unique identifier.</strong></em></p></li>
<li><p><code>atc</code><br> ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC</p></li>
<li><p><code>cid</code><br> Compound ID as found in PubChem. <em><strong>This is a unique identifier.</strong></em></p></li>
<li><p><code>atc_group</code><br> Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC</p></li>
<li><p><code>synonyms</code><br> Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID</p></li>
<li><p><code>oral_ddd</code><br> Defined Daily Dose (DDD), oral treatment</p></li>
<li><p><code>oral_units</code><br> Units of <code>oral_ddd</code></p></li>
<li><p><code>iv_ddd</code><br> Defined Daily Dose (DDD), parenteral treatment</p></li>
<li><p><code>iv_units</code><br> Units of <code>iv_ddd</code></p></li>
<li><p><code>loinc</code><br> All codes associated with the name of the antiviral drug from Logical Observation Identifiers Names and Codes (LOINC), Version 2.76 (18 September, 2023). Use <code><a href="av_property.html">av_loinc()</a></code> to retrieve them quickly, see <code><a href="av_property.html">av_property()</a></code>.</p></li>
</ul></div>
<p>An object of class <code>tbl_df</code> (inherits from <code>tbl</code>, <code>data.frame</code>) with 120 rows and 11 columns.</p>
</div>
<div class="section level2">
<h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
<ul><li><p>World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology (WHOCC): <a href="https://atcddd.fhi.no/atc_ddd_index/" class="external-link">https://atcddd.fhi.no/atc_ddd_index/</a></p></li>
<li><p>Logical Observation Identifiers Names and Codes (LOINC), Version 2.76 (18 September, 2023). Accessed from <a href="https://loinc.org" class="external-link">https://loinc.org</a> on October 19th, 2023.</p></li>
<li><p>European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: <a href="https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm" class="external-link">https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm</a></p></li>
</ul></div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p>Properties that are based on an ATC code are only available when an ATC is available. These properties are: <code>atc_group1</code>, <code>atc_group2</code>, <code>oral_ddd</code>, <code>oral_units</code>, <code>iv_ddd</code> and <code>iv_units</code>.</p>
<p>Synonyms (i.e. trade names) were derived from the PubChem Compound ID (column <code>cid</code>) and consequently only available where a CID is available.</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, these data sets are 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>
</div>
</div>
<div class="section level2">
<h2 id="whocc">WHOCC<a class="anchor" aria-label="anchor" href="#whocc"></a></h2>
<p>This package contains <strong>all ~550 antibiotic, antimycotic and antiviral drugs</strong> and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href="https://atcddd.fhi.no" class="external-link">https://atcddd.fhi.no</a>) and the Pharmaceuticals Community Register of the European Commission (<a href="https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm" class="external-link">https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm</a>).</p>
<p>These have become the gold standard for international drug utilisation monitoring and research.</p>
<p>The WHOCC is located in Oslo at the Norwegian Institute of Public Health and funded by the Norwegian government. The European Commission is the executive of the European Union and promotes its general interest.</p>
<p><strong>NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package.</strong> See <a href="https://atcddd.fhi.no/copyright_disclaimer/." class="external-link">https://atcddd.fhi.no/copyright_disclaimer/.</a></p>
</div>
<div class="section level2">
<h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
<div class="dont-index"><p><a href="microorganisms.html">microorganisms</a>, <a href="intrinsic_resistant.html">intrinsic_resistant</a></p></div>
</div>
<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">antimicrobials</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 487 × 14</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ab cid name group atc atc_group1 atc_group2 abbreviations synonyms</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lis&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;list&gt;</span> <span style="color: #949494; font-style: italic;">&lt;named &gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> AMA <span style="text-decoration: underline;">4</span>649 4-ami… Anti… <span style="color: #949494;">&lt;chr&gt;</span> Drugs for… Aminosali… <span style="color: #949494;">&lt;chr [1]&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> ACM 6<span style="text-decoration: underline;">450</span>012 Acety… Macr… <span style="color: #949494;">&lt;chr&gt;</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #949494;">&lt;chr [1]&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> ASP 49<span style="text-decoration: underline;">787</span>020 Acety… Macr… <span style="color: #949494;">&lt;chr&gt;</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #949494;">&lt;chr [1]&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> ALS <span style="text-decoration: underline;">8</span>954 Aldes… Othe… <span style="color: #949494;">&lt;chr&gt;</span> Drugs for… Drugs for… <span style="color: #949494;">&lt;chr [1]&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> AMK <span style="text-decoration: underline;">37</span>768 Amika… Amin… <span style="color: #949494;">&lt;chr&gt;</span> Aminoglyc… Other ami… <span style="color: #949494;">&lt;chr [5]&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> AKF <span style="color: #BB0000;">NA</span> Amika… Amin… <span style="color: #949494;">&lt;chr&gt;</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #949494;">&lt;chr [1]&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> AMO <span style="text-decoration: underline;">54</span>260 Amoro… Anti… <span style="color: #949494;">&lt;chr&gt;</span> Antifunga… Other ant… <span style="color: #949494;">&lt;chr [1]&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> AMX <span style="text-decoration: underline;">33</span>613 Amoxi… Beta… <span style="color: #949494;">&lt;chr&gt;</span> Beta-lact… Penicilli… <span style="color: #949494;">&lt;chr [3]&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> AMC 23<span style="text-decoration: underline;">665</span>637 Amoxi… Beta… <span style="color: #949494;">&lt;chr&gt;</span> Beta-lact… Combinati… <span style="color: #949494;">&lt;chr [5]&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> AXS <span style="text-decoration: underline;">465</span>441 Amoxi… Beta… <span style="color: #949494;">&lt;chr&gt;</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #949494;">&lt;chr [1]&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 477 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 5 more variables: oral_ddd &lt;dbl&gt;, oral_units &lt;chr&gt;, iv_ddd &lt;dbl&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># iv_units &lt;chr&gt;, loinc &lt;list&gt;</span></span>
<span class="r-in"><span><span class="va">antivirals</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 120 × 11</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> av name atc cid atc_group synonyms oral_ddd oral_units iv_ddd</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;av&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;list&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> ABA Abacavir J05A… 4.41<span style="color: #949494;">e</span>5 Nucleosi… <span style="color: #949494;">&lt;chr&gt;</span> 0.6 g <span style="color: #BB0000;">NA</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> ACI Aciclovir J05A… 1.35<span style="color: #949494;">e</span>8 Nucleosi… <span style="color: #949494;">&lt;chr&gt;</span> 4 g 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> ADD Adefovir… J05A… 6.09<span style="color: #949494;">e</span>4 Nucleosi… <span style="color: #949494;">&lt;chr&gt;</span> 10 mg <span style="color: #BB0000;">NA</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> AME Amenamev… J05A… 1.14<span style="color: #949494;">e</span>7 Other an… <span style="color: #949494;">&lt;chr&gt;</span> 0.4 g <span style="color: #BB0000;">NA</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> AMP Amprenav… J05A… 6.50<span style="color: #949494;">e</span>4 Protease… <span style="color: #949494;">&lt;chr&gt;</span> 1.2 g <span style="color: #BB0000;">NA</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> ASU Asunapre… J05A… 1.61<span style="color: #949494;">e</span>7 Antivira… <span style="color: #949494;">&lt;chr&gt;</span> 0.2 g <span style="color: #BB0000;">NA</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> ATA Atazanav… J05A… 1.48<span style="color: #949494;">e</span>5 Protease… <span style="color: #949494;">&lt;chr&gt;</span> 0.3 g <span style="color: #BB0000;">NA</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> ATA<span style="color: #949494;">+</span>COBI Atazanav… J05A… 8.66<span style="color: #949494;">e</span>7 Antivira… <span style="color: #949494;">&lt;chr&gt;</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> ATA<span style="color: #949494;">+</span>RIT Atazanav… J05A… 2.51<span style="color: #949494;">e</span>7 Antivira… <span style="color: #949494;">&lt;chr&gt;</span> 0.3 g <span style="color: #BB0000;">NA</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> BAM Baloxavi… J05A… 1.24<span style="color: #949494;">e</span>8 Other an… <span style="color: #949494;">&lt;chr&gt;</span> 40 mg <span style="color: #BB0000;">NA</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 110 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 2 more variables: iv_units &lt;chr&gt;, loinc &lt;list&gt;</span></span>
</code></pre></div>
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<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Transform Input to an Antibiotic ID — as.ab • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Transform Input to an Antibiotic ID — as.ab"><meta name="description" content="Use this function to determine the antibiotic drug code of one or more antibiotics. The data set antibiotics will be searched for abbreviations, official names and synonyms (brand names)."><meta property="og:description" content="Use this function to determine the antibiotic drug code of one or more antibiotics. The data set antibiotics will be searched for abbreviations, official names and synonyms (brand names)."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous"><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script></head><body> <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Transform Input to an Antibiotic ID — as.ab • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Transform Input to an Antibiotic ID — as.ab"><meta name="description" content="Use this function to determine the antimicrobial drug code of one or more antimicrobials. The data set antimicrobials will be searched for abbreviations, official names and synonyms (brand names)."><meta property="og:description" content="Use this function to determine the antimicrobial drug code of one or more antimicrobials. The data set antimicrobials will be searched for abbreviations, official names and synonyms (brand names)."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous"><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script></head><body>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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</div> </div>
<div class="ref-description section level2"> <div class="ref-description section level2">
<p>Use this function to determine the antibiotic drug code of one or more antibiotics. The data set <a href="antibiotics.html">antibiotics</a> will be searched for abbreviations, official names and synonyms (brand names).</p> <p>Use this function to determine the antimicrobial drug code of one or more antimicrobials. The data set <a href="antimicrobials.html">antimicrobials</a> will be searched for abbreviations, official names and synonyms (brand names).</p>
</div> </div>
<div class="section level2"> <div class="section level2">
@ -92,7 +92,7 @@
</div> </div>
<div class="section level2"> <div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p>All entries in the <a href="antibiotics.html">antibiotics</a> data set have three different identifiers: a human readable EARS-Net code (column <code>ab</code>, used by ECDC and WHONET), an ATC code (column <code>atc</code>, used by WHO), and a CID code (column <code>cid</code>, Compound ID, used by PubChem). The data set contains more than 5,000 official brand names from many different countries, as found in PubChem. Not that some drugs contain multiple ATC codes.</p> <p>All entries in the <a href="antimicrobials.html">antimicrobials</a> data set have three different identifiers: a human readable EARS-Net code (column <code>ab</code>, used by ECDC and WHONET), an ATC code (column <code>atc</code>, used by WHO), and a CID code (column <code>cid</code>, Compound ID, used by PubChem). The data set contains more than 5,000 official brand names from many different countries, as found in PubChem. Not that some drugs contain multiple ATC codes.</p>
<p>All these properties will be searched for the user input. The <code>as.ab()</code> can correct for different forms of misspelling:</p><ul><li><p>Wrong spelling of drug names (such as "tobramicin" or "gentamycin"), which corrects for most audible similarities such as f/ph, x/ks, c/z/s, t/th, etc.</p></li> <p>All these properties will be searched for the user input. The <code>as.ab()</code> can correct for different forms of misspelling:</p><ul><li><p>Wrong spelling of drug names (such as "tobramicin" or "gentamycin"), which corrects for most audible similarities such as f/ph, x/ks, c/z/s, t/th, etc.</p></li>
<li><p>Too few or too many vowels or consonants</p></li> <li><p>Too few or too many vowels or consonants</p></li>
<li><p>Switching two characters (such as "mreopenem", often the case in clinical data, when doctors typed too fast)</p></li> <li><p>Switching two characters (such as "mreopenem", often the case in clinical data, when doctors typed too fast)</p></li>
@ -121,12 +121,12 @@
<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2> <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 data sets in this <code>AMR</code> package (about microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. 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>All data sets in this <code>AMR</code> package (about microorganisms, antimicrobials, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. 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>
<div class="section level2"> <div class="section level2">
<h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2> <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
<div class="dont-index"> <div class="dont-index">
<ul><li><p><a href="antibiotics.html">antibiotics</a> for the <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> that is being used to determine ATCs</p></li> <ul><li><p><a href="antimicrobials.html">antimicrobials</a> for the <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> that is being used to determine ATCs</p></li>
<li><p><code><a href="ab_from_text.html">ab_from_text()</a></code> for a function to retrieve antimicrobial drugs from clinical text (from health care records)</p></li> <li><p><code><a href="ab_from_text.html">ab_from_text()</a></code> for a function to retrieve antimicrobial drugs from clinical text (from health care records)</p></li>
</ul></div> </ul></div>
</div> </div>

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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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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@ -49,7 +49,7 @@
</div> </div>
<div class="ref-description section level2"> <div class="ref-description section level2">
<p>Use this function to determine the antiviral drug code of one or more antiviral drugs. The data set <a href="antibiotics.html">antivirals</a> will be searched for abbreviations, official names and synonyms (brand names).</p> <p>Use this function to determine the antiviral drug code of one or more antiviral drugs. The data set <a href="antimicrobials.html">antivirals</a> will be searched for abbreviations, official names and synonyms (brand names).</p>
</div> </div>
<div class="section level2"> <div class="section level2">
@ -85,7 +85,7 @@
</div> </div>
<div class="section level2"> <div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p>All entries in the <a href="antibiotics.html">antivirals</a> data set have three different identifiers: a human readable EARS-Net code (column <code>ab</code>, used by ECDC and WHONET), an ATC code (column <code>atc</code>, used by WHO), and a CID code (column <code>cid</code>, Compound ID, used by PubChem). The data set contains more than 5,000 official brand names from many different countries, as found in PubChem. Not that some drugs contain multiple ATC codes.</p> <p>All entries in the <a href="antimicrobials.html">antivirals</a> data set have three different identifiers: a human readable EARS-Net code (column <code>ab</code>, used by ECDC and WHONET), an ATC code (column <code>atc</code>, used by WHO), and a CID code (column <code>cid</code>, Compound ID, used by PubChem). The data set contains more than 5,000 official brand names from many different countries, as found in PubChem. Not that some drugs contain multiple ATC codes.</p>
<p>All these properties will be searched for the user input. The <code>as.av()</code> can correct for different forms of misspelling:</p><ul><li><p>Wrong spelling of drug names (such as "acyclovir"), which corrects for most audible similarities such as f/ph, x/ks, c/z/s, t/th, etc.</p></li> <p>All these properties will be searched for the user input. The <code>as.av()</code> can correct for different forms of misspelling:</p><ul><li><p>Wrong spelling of drug names (such as "acyclovir"), which corrects for most audible similarities such as f/ph, x/ks, c/z/s, t/th, etc.</p></li>
<li><p>Too few or too many vowels or consonants</p></li> <li><p>Too few or too many vowels or consonants</p></li>
<li><p>Switching two characters (such as "aycclovir", often the case in clinical data, when doctors typed too fast)</p></li> <li><p>Switching two characters (such as "aycclovir", often the case in clinical data, when doctors typed too fast)</p></li>
@ -113,12 +113,12 @@
<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2> <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 data sets in this <code>AMR</code> package (about microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. 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>All data sets in this <code>AMR</code> package (about microorganisms, antimicrobials, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. 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>
<div class="section level2"> <div class="section level2">
<h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2> <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
<div class="dont-index"> <div class="dont-index">
<ul><li><p><a href="antibiotics.html">antivirals</a> for the <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> that is being used to determine ATCs</p></li> <ul><li><p><a href="antimicrobials.html">antivirals</a> for the <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> that is being used to determine ATCs</p></li>
<li><p><code><a href="av_from_text.html">av_from_text()</a></code> for a function to retrieve antimicrobial drugs from clinical text (from health care records)</p></li> <li><p><code><a href="av_from_text.html">av_from_text()</a></code> for a function to retrieve antimicrobial drugs from clinical text (from health care records)</p></li>
</ul></div> </ul></div>
</div> </div>

2
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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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@ -245,7 +245,7 @@
<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2> <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 data sets in this <code>AMR</code> package (about microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. 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>All data sets in this <code>AMR</code> package (about microorganisms, antimicrobials, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. 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>
<div class="section level2"> <div class="section level2">
<h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2> <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>

24
reference/as.sir.html
View File

@ -21,7 +21,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -297,7 +297,7 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2> <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 data sets in this <code>AMR</code> package (about microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. 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>All data sets in this <code>AMR</code> package (about microorganisms, antimicrobials, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. 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>
<div class="section level2"> <div class="section level2">
<h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2> <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
@ -810,16 +810,16 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 57 × 16</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 57 × 16</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index ab_given mo_given host_given ab mo </span> <span class="r-out co"><span class="r-pr">#&gt;</span> datetime index ab_given mo_given host_given ab mo </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&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: #949494; font-style: italic;">&lt;dttm&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&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> 2025-03-03 <span style="color: #949494;">18:39:40</span> 4 AMX B_STRPT… human AMX <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2025-03-07 <span style="color: #949494;">19:48:01</span> 4 AMX B_STRPT… human AMX <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2025-03-03 <span style="color: #949494;">18:39:47</span> 4 genta Escheri… human GEN <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBCTR</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2025-03-07 <span style="color: #949494;">19:48:08</span> 4 genta Escheri… human GEN <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2025-03-03 <span style="color: #949494;">18:39:47</span> 4 genta Escheri… human GEN <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBCTR</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2025-03-07 <span style="color: #949494;">19:48:08</span> 4 genta Escheri… human GEN <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2025-03-03 <span style="color: #949494;">18:39:48</span> 4 genta Escheri… cattle GEN <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2025-03-07 <span style="color: #949494;">19:48:09</span> 4 genta Escheri… cattle GEN <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2025-03-03 <span style="color: #949494;">18:39:48</span> 4 genta Escheri… cattle GEN <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2025-03-07 <span style="color: #949494;">19:48:09</span> 4 genta Escheri… cattle GEN <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2025-03-03 <span style="color: #949494;">18:39:40</span> 3 AMX B_STRPT… human AMX <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2025-03-07 <span style="color: #949494;">19:48:01</span> 3 AMX B_STRPT… human AMX <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2025-03-03 <span style="color: #949494;">18:39:47</span> 3 tobra Escheri… human TOB <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBCTR</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2025-03-07 <span style="color: #949494;">19:48:08</span> 3 tobra Escheri… human TOB <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2025-03-03 <span style="color: #949494;">18:39:47</span> 3 tobra Escheri… human TOB <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBCTR</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2025-03-07 <span style="color: #949494;">19:48:08</span> 3 tobra Escheri… human TOB <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2025-03-03 <span style="color: #949494;">18:39:48</span> 3 tobra Escheri… horses TOB <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2025-03-07 <span style="color: #949494;">19:48:09</span> 3 tobra Escheri… horses TOB <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2025-03-03 <span style="color: #949494;">18:39:48</span> 3 tobra Escheri… horses TOB <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2025-03-07 <span style="color: #949494;">19:48:09</span> 3 tobra Escheri… horses TOB <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 47 more rows</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 47 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 9 more variables: host &lt;chr&gt;, method &lt;chr&gt;, input &lt;chr&gt;, outcome &lt;sir&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 9 more variables: host &lt;chr&gt;, method &lt;chr&gt;, input &lt;chr&gt;, outcome &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># notes &lt;chr&gt;, guideline &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># notes &lt;chr&gt;, guideline &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;,</span></span>

8
reference/atc_online.html
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@ -1,5 +1,5 @@
<!DOCTYPE html> <!DOCTYPE html>
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Get ATC Properties from WHOCC Website — atc_online_property • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Get ATC Properties from WHOCC Website — atc_online_property"><meta name="description" content="Gets data from the WHOCC website to determine properties of an Anatomical Therapeutic Chemical (ATC) (e.g. an antibiotic), such as the name, defined daily dose (DDD) or standard unit."><meta property="og:description" content="Gets data from the WHOCC website to determine properties of an Anatomical Therapeutic Chemical (ATC) (e.g. an antibiotic), such as the name, defined daily dose (DDD) or standard unit."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous"><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script></head><body> <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Get ATC Properties from WHOCC Website — atc_online_property • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Get ATC Properties from WHOCC Website — atc_online_property"><meta name="description" content="Gets data from the WHOCC website to determine properties of an Anatomical Therapeutic Chemical (ATC) (e.g. an antimicrobial), such as the name, defined daily dose (DDD) or standard unit."><meta property="og:description" content="Gets data from the WHOCC website to determine properties of an Anatomical Therapeutic Chemical (ATC) (e.g. an antimicrobial), such as the name, defined daily dose (DDD) or standard unit."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous"><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script></head><body>
<a href="#main" class="visually-hidden-focusable">Skip to contents</a> <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -49,7 +49,7 @@
</div> </div>
<div class="ref-description section level2"> <div class="ref-description section level2">
<p>Gets data from the WHOCC website to determine properties of an Anatomical Therapeutic Chemical (ATC) (e.g. an antibiotic), such as the name, defined daily dose (DDD) or standard unit.</p> <p>Gets data from the WHOCC website to determine properties of an Anatomical Therapeutic Chemical (ATC) (e.g. an antimicrobial), such as the name, defined daily dose (DDD) or standard unit.</p>
</div> </div>
<div class="section level2"> <div class="section level2">
@ -74,7 +74,7 @@
<dl><dt id="arg-atc-code">atc_code<a class="anchor" aria-label="anchor" href="#arg-atc-code"></a></dt> <dl><dt id="arg-atc-code">atc_code<a class="anchor" aria-label="anchor" href="#arg-atc-code"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> (vector) with ATC code(s) of antibiotics, will be coerced with <code><a href="as.ab.html">as.ab()</a></code> and <code><a href="ab_property.html">ab_atc()</a></code> internally if not a valid ATC code</p></dd> <dd><p>a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> (vector) with ATC code(s) of antimicrobials, will be coerced with <code><a href="as.ab.html">as.ab()</a></code> and <code><a href="ab_property.html">ab_atc()</a></code> internally if not a valid ATC code</p></dd>
<dt id="arg-property">property<a class="anchor" aria-label="anchor" href="#arg-property"></a></dt> <dt id="arg-property">property<a class="anchor" aria-label="anchor" href="#arg-property"></a></dt>

4
reference/av_from_text.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -76,7 +76,7 @@
<dt id="arg-translate-av">translate_av<a class="anchor" aria-label="anchor" href="#arg-translate-av"></a></dt> <dt id="arg-translate-av">translate_av<a class="anchor" aria-label="anchor" href="#arg-translate-av"></a></dt>
<dd><p>if <code>type = "drug"</code>: a column name of the <a href="antibiotics.html">antivirals</a> data set to translate the antibiotic abbreviations to, using <code><a href="av_property.html">av_property()</a></code>. The default is <code>FALSE</code>. Using <code>TRUE</code> is equal to using "name".</p></dd> <dd><p>if <code>type = "drug"</code>: a column name of the <a href="antimicrobials.html">antivirals</a> data set to translate the antibiotic abbreviations to, using <code><a href="av_property.html">av_property()</a></code>. The default is <code>FALSE</code>. Using <code>TRUE</code> is equal to using "name".</p></dd>
<dt id="arg-thorough-search">thorough_search<a class="anchor" aria-label="anchor" href="#arg-thorough-search"></a></dt> <dt id="arg-thorough-search">thorough_search<a class="anchor" aria-label="anchor" href="#arg-thorough-search"></a></dt>

10
reference/av_property.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -49,7 +49,7 @@
</div> </div>
<div class="ref-description section level2"> <div class="ref-description section level2">
<p>Use these functions to return a specific property of an antiviral drug from the <a href="antibiotics.html">antivirals</a> data set. All input values will be evaluated internally with <code><a href="as.av.html">as.av()</a></code>.</p> <p>Use these functions to return a specific property of an antiviral drug from the <a href="antimicrobials.html">antivirals</a> data set. All input values will be evaluated internally with <code><a href="as.av.html">as.av()</a></code>.</p>
</div> </div>
<div class="section level2"> <div class="section level2">
@ -108,7 +108,7 @@
<dt id="arg-property">property<a class="anchor" aria-label="anchor" href="#arg-property"></a></dt> <dt id="arg-property">property<a class="anchor" aria-label="anchor" href="#arg-property"></a></dt>
<dd><p>one of the column names of one of the <a href="antibiotics.html">antivirals</a> data set: <code>vector_or(colnames(antivirals), sort = FALSE)</code>.</p></dd> <dd><p>one of the column names of one of the <a href="antimicrobials.html">antivirals</a> data set: <code>vector_or(colnames(antivirals), sort = FALSE)</code>.</p></dd>
</dl></div> </dl></div>
<div class="section level2"> <div class="section level2">
@ -135,11 +135,11 @@
<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2> <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 data sets in this <code>AMR</code> package (about microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. 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>All data sets in this <code>AMR</code> package (about microorganisms, antimicrobials, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. 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>
<div class="section level2"> <div class="section level2">
<h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2> <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
<div class="dont-index"><p><a href="antibiotics.html">antivirals</a></p></div> <div class="dont-index"><p><a href="antimicrobials.html">antivirals</a></p></div>
</div> </div>
<div class="section level2"> <div class="section level2">

2
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

6
reference/bug_drug_combinations.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -70,7 +70,7 @@
<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt> <dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
<dd><p>a data set with antibiotic columns, such as <code>amox</code>, <code>AMX</code> and <code>AMC</code></p></dd> <dd><p>a data set with antimicrobials columns, such as <code>amox</code>, <code>AMX</code> and <code>AMC</code></p></dd>
<dt id="arg-col-mo">col_mo<a class="anchor" aria-label="anchor" href="#arg-col-mo"></a></dt> <dt id="arg-col-mo">col_mo<a class="anchor" aria-label="anchor" href="#arg-col-mo"></a></dt>
@ -90,7 +90,7 @@
<dt id="arg-translate-ab">translate_ab<a class="anchor" aria-label="anchor" href="#arg-translate-ab"></a></dt> <dt id="arg-translate-ab">translate_ab<a class="anchor" aria-label="anchor" href="#arg-translate-ab"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> of length 1 containing column names of the <a href="antibiotics.html">antibiotics</a> data set</p></dd> <dd><p>a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> of length 1 containing column names of the <a href="antimicrobials.html">antimicrobials</a> data set</p></dd>
<dt id="arg-language">language<a class="anchor" aria-label="anchor" href="#arg-language"></a></dt> <dt id="arg-language">language<a class="anchor" aria-label="anchor" href="#arg-language"></a></dt>

4
reference/clinical_breakpoints.html
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@ -21,7 +21,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -84,7 +84,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
<li><p><code>site</code><br> Body site for which the breakpoint must be applied, e.g. "Oral" or "Respiratory"</p></li> <li><p><code>site</code><br> Body site for which the breakpoint must be applied, e.g. "Oral" or "Respiratory"</p></li>
<li><p><code>mo</code><br> Microbial ID, see <code><a href="as.mo.html">as.mo()</a></code></p></li> <li><p><code>mo</code><br> Microbial ID, see <code><a href="as.mo.html">as.mo()</a></code></p></li>
<li><p><code>rank_index</code><br> Taxonomic rank index of <code>mo</code> from 1 (subspecies/infraspecies) to 5 (unknown microorganism)</p></li> <li><p><code>rank_index</code><br> Taxonomic rank index of <code>mo</code> from 1 (subspecies/infraspecies) to 5 (unknown microorganism)</p></li>
<li><p><code>ab</code><br> Antibiotic code as used by this package, EARS-Net and WHONET, see <code><a href="as.ab.html">as.ab()</a></code></p></li> <li><p><code>ab</code><br> Antimcrobial code as used by this package, EARS-Net and WHONET, see <code><a href="as.ab.html">as.ab()</a></code></p></li>
<li><p><code>ref_tbl</code><br> Info about where the guideline rule can be found</p></li> <li><p><code>ref_tbl</code><br> Info about where the guideline rule can be found</p></li>
<li><p><code>disk_dose</code><br> Dose of the used disk diffusion method</p></li> <li><p><code>disk_dose</code><br> Dose of the used disk diffusion method</p></li>
<li><p><code>breakpoint_S</code><br> Lowest MIC value or highest number of millimetres that leads to "S"</p></li> <li><p><code>breakpoint_S</code><br> Lowest MIC value or highest number of millimetres that leads to "S"</p></li>

10
reference/count.html
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@ -9,7 +9,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -88,7 +88,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<dt id="arg-only-all-tested">only_all_tested<a class="anchor" aria-label="anchor" href="#arg-only-all-tested"></a></dt> <dt id="arg-only-all-tested">only_all_tested<a class="anchor" aria-label="anchor" href="#arg-only-all-tested"></a></dt>
<dd><p>(for combination therapies, i.e. using more than one variable for <code>...</code>): a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that isolates must be tested for all antibiotics, see section <em>Combination Therapy</em> below</p></dd> <dd><p>(for combination therapies, i.e. using more than one variable for <code>...</code>): a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that isolates must be tested for all antimicrobials, see section <em>Combination Therapy</em> below</p></dd>
<dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a></dt> <dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a></dt>
@ -96,7 +96,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<dt id="arg-translate-ab">translate_ab<a class="anchor" aria-label="anchor" href="#arg-translate-ab"></a></dt> <dt id="arg-translate-ab">translate_ab<a class="anchor" aria-label="anchor" href="#arg-translate-ab"></a></dt>
<dd><p>a column name of the <a href="antibiotics.html">antibiotics</a> data set to translate the antibiotic abbreviations to, using <code><a href="ab_property.html">ab_property()</a></code></p></dd> <dd><p>a column name of the <a href="antimicrobials.html">antimicrobials</a> data set to translate the antibiotic abbreviations to, using <code><a href="ab_property.html">ab_property()</a></code></p></dd>
<dt id="arg-language">language<a class="anchor" aria-label="anchor" href="#arg-language"></a></dt> <dt id="arg-language">language<a class="anchor" aria-label="anchor" href="#arg-language"></a></dt>
@ -115,7 +115,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p>These functions are meant to count isolates. Use the <code><a href="proportion.html">resistance()</a></code>/<code><a href="proportion.html">susceptibility()</a></code> functions to calculate microbial resistance/susceptibility.</p> <p>These functions are meant to count isolates. Use the <code><a href="proportion.html">resistance()</a></code>/<code><a href="proportion.html">susceptibility()</a></code> functions to calculate microbial resistance/susceptibility.</p>
<p>The function <code>count_resistant()</code> is equal to the function <code>count_R()</code>. The function <code>count_susceptible()</code> is equal to the function <code>count_SI()</code>.</p> <p>The function <code>count_resistant()</code> is equal to the function <code>count_R()</code>. The function <code>count_susceptible()</code> is equal to the function <code>count_SI()</code>.</p>
<p>The function <code>n_sir()</code> is an alias of <code>count_all()</code>. They can be used to count all available isolates, i.e. where all input antibiotics have an available result (S, I or R). Their use is equal to <code><a href="https://dplyr.tidyverse.org/reference/n_distinct.html" class="external-link">n_distinct()</a></code>. Their function is equal to <code>count_susceptible(...) + count_resistant(...)</code>.</p> <p>The function <code>n_sir()</code> is an alias of <code>count_all()</code>. They can be used to count all available isolates, i.e. where all input antimicrobials have an available result (S, I or R). Their use is equal to <code><a href="https://dplyr.tidyverse.org/reference/n_distinct.html" class="external-link">n_distinct()</a></code>. Their function is equal to <code>count_susceptible(...) + count_resistant(...)</code>.</p>
<p>The function <code>count_df()</code> takes any variable from <code>data</code> that has an <code><a href="as.sir.html">sir</a></code> class (created with <code><a href="as.sir.html">as.sir()</a></code>) and counts the number of S's, I's and R's. It also supports grouped variables. The function <code><a href="proportion.html">sir_df()</a></code> works exactly like <code>count_df()</code>, but adds the percentage of S, I and R.</p> <p>The function <code>count_df()</code> takes any variable from <code>data</code> that has an <code><a href="as.sir.html">sir</a></code> class (created with <code><a href="as.sir.html">as.sir()</a></code>) and counts the number of S's, I's and R's. It also supports grouped variables. The function <code><a href="proportion.html">sir_df()</a></code> works exactly like <code>count_df()</code>, but adds the percentage of S, I and R.</p>
</div> </div>
<div class="section level2"> <div class="section level2">
@ -135,7 +135,7 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<h2 id="combination-therapy">Combination Therapy<a class="anchor" aria-label="anchor" href="#combination-therapy"></a></h2> <h2 id="combination-therapy">Combination Therapy<a class="anchor" aria-label="anchor" href="#combination-therapy"></a></h2>
<p>When using more than one variable for <code>...</code> (= combination therapy), use <code>only_all_tested</code> to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antibiotics, Drug A and Drug B, about how <code><a href="proportion.html">susceptibility()</a></code> works to calculate the %SI:</p> <p>When using more than one variable for <code>...</code> (= combination therapy), use <code>only_all_tested</code> to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antimicrobials, Drug A and Drug B, about how <code><a href="proportion.html">susceptibility()</a></code> works to calculate the %SI:</p>
<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="sc">--------------------------------------------------------------------</span></span> <p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="sc">--------------------------------------------------------------------</span></span>
<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a> only_all_tested <span class="ot">=</span> <span class="cn">FALSE</span> only_all_tested <span class="ot">=</span> <span class="cn">TRUE</span></span> <span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a> only_all_tested <span class="ot">=</span> <span class="cn">FALSE</span> only_all_tested <span class="ot">=</span> <span class="cn">TRUE</span></span>
<span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a> <span class="sc">-----------------------</span> <span class="sc">-----------------------</span></span> <span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a> <span class="sc">-----------------------</span> <span class="sc">-----------------------</span></span>

10
reference/custom_eucast_rules.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -124,18 +124,18 @@
</div> </div>
<div class="section"> <div class="section">
<h3 id="usage-of-multiple-antibiotics-and-antibiotic-group-names">Usage of multiple antibiotics and antibiotic group names<a class="anchor" aria-label="anchor" href="#usage-of-multiple-antibiotics-and-antibiotic-group-names"></a></h3> <h3 id="usage-of-multiple-antimicrobials-and-antimicrobial-group-names">Usage of multiple antimicrobials and antimicrobial group names<a class="anchor" aria-label="anchor" href="#usage-of-multiple-antimicrobials-and-antimicrobial-group-names"></a></h3>
<p>You can define antibiotic groups instead of single antibiotics for the rule consequence, which is the part <em>after</em> the tilde (~). In the examples above, the antibiotic group <code>aminopenicillins</code> includes both ampicillin and amoxicillin.</p> <p>You can define antimicrobial groups instead of single antimicrobials for the rule consequence, which is the part <em>after</em> the tilde (~). In the examples above, the antimicrobial group <code>aminopenicillins</code> includes both ampicillin and amoxicillin.</p>
<p>Rules can also be applied to multiple antibiotics and antibiotic groups simultaneously. Use the <code><a href="https://rdrr.io/r/base/c.html" class="external-link">c()</a></code> function to combine multiple antibiotics. For instance, the following example sets all aminopenicillins and ureidopenicillins to "R" if column TZP (piperacillin/tazobactam) is "R":</p> <p>Rules can also be applied to multiple antimicrobials and antimicrobial groups simultaneously. Use the <code><a href="https://rdrr.io/r/base/c.html" class="external-link">c()</a></code> function to combine multiple antimicrobials. For instance, the following example sets all aminopenicillins and ureidopenicillins to "R" if column TZP (piperacillin/tazobactam) is "R":</p>
<p></p><div class="sourceCode r"><pre><code><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/custom_eucast_rules.html">custom_eucast_rules</a></span><span class="op">(</span><span class="va">TZP</span> <span class="op">==</span> <span class="st">"R"</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="va">aminopenicillins</span>, <span class="va">ureidopenicillins</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span></span> <p></p><div class="sourceCode r"><pre><code><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/custom_eucast_rules.html">custom_eucast_rules</a></span><span class="op">(</span><span class="va">TZP</span> <span class="op">==</span> <span class="st">"R"</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="va">aminopenicillins</span>, <span class="va">ureidopenicillins</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span></span>
<span><span class="va">x</span></span> <span><span class="va">x</span></span>
<span><span class="co">#&gt; A set of custom EUCAST rules:</span></span> <span><span class="co">#&gt; A set of custom EUCAST rules:</span></span>
<span><span class="co">#&gt;</span></span> <span><span class="co">#&gt;</span></span>
<span><span class="co">#&gt; 1. If TZP is "R" then set to "R":</span></span> <span><span class="co">#&gt; 1. If TZP is "R" then set to "R":</span></span>
<span><span class="co">#&gt; amoxicillin (AMX), ampicillin (AMP), azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP), piperacillin/tazobactam (TZP)</span></span></code></pre><p></p></div> <span><span class="co">#&gt; amoxicillin (AMX), ampicillin (AMP), azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP), piperacillin/tazobactam (TZP)</span></span></code></pre><p></p></div>
<p>These 34 antibiotic groups are allowed in the rules (case-insensitive) and can be used in any combination:</p><ul><li><p>aminoglycosides<br>(amikacin, amikacin/fosfomycin, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin, and tobramycin-high)</p></li> <p>These 34 antimicrobial groups are allowed in the rules (case-insensitive) and can be used in any combination:</p><ul><li><p>aminoglycosides<br>(amikacin, amikacin/fosfomycin, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin, and tobramycin-high)</p></li>
<li><p>aminopenicillins<br>(amoxicillin and ampicillin)</p></li> <li><p>aminopenicillins<br>(amoxicillin and ampicillin)</p></li>
<li><p>antifungals<br>(amorolfine, amphotericin B, amphotericin B-high, anidulafungin, butoconazole, caspofungin, ciclopirox, clotrimazole, econazole, fluconazole, flucytosine, fosfluconazole, griseofulvin, hachimycin, ibrexafungerp, isavuconazole, isoconazole, itraconazole, ketoconazole, manogepix, micafungin, miconazole, nystatin, oteseconazole, pimaricin, posaconazole, rezafungin, ribociclib, sulconazole, terbinafine, terconazole, and voriconazole)</p></li> <li><p>antifungals<br>(amorolfine, amphotericin B, amphotericin B-high, anidulafungin, butoconazole, caspofungin, ciclopirox, clotrimazole, econazole, fluconazole, flucytosine, fosfluconazole, griseofulvin, hachimycin, ibrexafungerp, isavuconazole, isoconazole, itraconazole, ketoconazole, manogepix, micafungin, miconazole, nystatin, oteseconazole, pimaricin, posaconazole, rezafungin, ribociclib, sulconazole, terbinafine, terconazole, and voriconazole)</p></li>
<li><p>antimycobacterials<br>(4-aminosalicylic acid, calcium aminosalicylate, capreomycin, clofazimine, delamanid, enviomycin, ethambutol, ethambutol/isoniazid, ethionamide, isoniazid, isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, morinamide, p-aminosalicylic acid, pretomanid, protionamide, pyrazinamide, rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, rifapentine, simvastatin/fenofibrate, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone, thioacetazone/isoniazid, tiocarlide, and viomycin)</p></li> <li><p>antimycobacterials<br>(4-aminosalicylic acid, calcium aminosalicylate, capreomycin, clofazimine, delamanid, enviomycin, ethambutol, ethambutol/isoniazid, ethionamide, isoniazid, isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, morinamide, p-aminosalicylic acid, pretomanid, protionamide, pyrazinamide, rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, rifapentine, simvastatin/fenofibrate, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone, thioacetazone/isoniazid, tiocarlide, and viomycin)</p></li>

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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -59,7 +59,7 @@
<div class="section level2"> <div class="section level2">
<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2> <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 503 observations and 9 variables:</p><ul><li><p><code>ab</code><br> Antibiotic ID as used in this package (such as <code>AMC</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available</p></li> <p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 503 observations and 9 variables:</p><ul><li><p><code>ab</code><br> Antimcrobial ID as used in this package (such as <code>AMC</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available</p></li>
<li><p><code>name</code><br> Official name of the antimicrobial drug as used by WHONET/EARS-Net or the WHO</p></li> <li><p><code>name</code><br> Official name of the antimicrobial drug as used by WHONET/EARS-Net or the WHO</p></li>
<li><p><code>type</code><br> Type of the dosage, either "high_dosage", "standard_dosage", or "uncomplicated_uti"</p></li> <li><p><code>type</code><br> Type of the dosage, either "high_dosage", "standard_dosage", or "uncomplicated_uti"</p></li>
<li><p><code>dose</code><br> Dose, such as "2 g" or "25 mg/kg"</p></li> <li><p><code>dose</code><br> Dose, such as "2 g" or "25 mg/kg"</p></li>

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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -65,7 +65,7 @@
<li><p><code>gender</code><br> Gender of the patient, either "F" or "M"</p></li> <li><p><code>gender</code><br> Gender of the patient, either "F" or "M"</p></li>
<li><p><code>ward</code><br> Ward type where the patient was admitted, either "Clinical", "ICU", or "Outpatient"</p></li> <li><p><code>ward</code><br> Ward type where the patient was admitted, either "Clinical", "ICU", or "Outpatient"</p></li>
<li><p><code>mo</code><br> ID of microorganism created with <code><a href="as.mo.html">as.mo()</a></code>, see also the <a href="microorganisms.html">microorganisms</a> data set</p></li> <li><p><code>mo</code><br> ID of microorganism created with <code><a href="as.mo.html">as.mo()</a></code>, see also the <a href="microorganisms.html">microorganisms</a> data set</p></li>
<li><p><code>PEN:RIF</code><br> 40 different antibiotics with class <code><a href="as.sir.html">sir</a></code> (see <code><a href="as.sir.html">as.sir()</a></code>); these column names occur in the <a href="antibiotics.html">antibiotics</a> data set and can be translated with <code><a href="ab_property.html">set_ab_names()</a></code> or <code><a href="ab_property.html">ab_name()</a></code></p></li> <li><p><code>PEN:RIF</code><br> 40 different antimicrobials with class <code><a href="as.sir.html">sir</a></code> (see <code><a href="as.sir.html">as.sir()</a></code>); these column names occur in the <a href="antimicrobials.html">antimicrobials</a> data set and can be translated with <code><a href="ab_property.html">set_ab_names()</a></code> or <code><a href="ab_property.html">ab_name()</a></code></p></li>
</ul></div> </ul></div>
<div class="section level2"> <div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>

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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -63,7 +63,7 @@
<li><p><code>date</code><br> date of receipt at the laboratory</p></li> <li><p><code>date</code><br> date of receipt at the laboratory</p></li>
<li><p><code>hospital</code><br> ID of the hospital, from A to C</p></li> <li><p><code>hospital</code><br> ID of the hospital, from A to C</p></li>
<li><p><code>bacteria</code><br> info about microorganism that can be transformed with <code><a href="as.mo.html">as.mo()</a></code>, see also <a href="microorganisms.html">microorganisms</a></p></li> <li><p><code>bacteria</code><br> info about microorganism that can be transformed with <code><a href="as.mo.html">as.mo()</a></code>, see also <a href="microorganisms.html">microorganisms</a></p></li>
<li><p><code>AMX:GEN</code><br> 4 different antibiotics that have to be transformed with <code><a href="as.sir.html">as.sir()</a></code></p></li> <li><p><code>AMX:GEN</code><br> 4 different antimicrobials that have to be transformed with <code><a href="as.sir.html">as.sir()</a></code></p></li>
</ul></div> </ul></div>
<div class="section level2"> <div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>

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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -101,7 +101,7 @@
<dt id="arg-translate-ab">translate_ab<a class="anchor" aria-label="anchor" href="#arg-translate-ab"></a></dt> <dt id="arg-translate-ab">translate_ab<a class="anchor" aria-label="anchor" href="#arg-translate-ab"></a></dt>
<dd><p>a column name of the <a href="antibiotics.html">antibiotics</a> data set to translate the antibiotic abbreviations to, using <code><a href="ab_property.html">ab_property()</a></code></p></dd> <dd><p>a column name of the <a href="antimicrobials.html">antimicrobials</a> data set to translate the antibiotic abbreviations to, using <code><a href="ab_property.html">ab_property()</a></code></p></dd>
<dt id="arg-combine-si">combine_SI<a class="anchor" aria-label="anchor" href="#arg-combine-si"></a></dt> <dt id="arg-combine-si">combine_SI<a class="anchor" aria-label="anchor" href="#arg-combine-si"></a></dt>
@ -162,8 +162,8 @@
</dl></div> </dl></div>
<div class="section level2"> <div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p>At default, the names of antibiotics will be shown on the plots using <code><a href="ab_property.html">ab_name()</a></code>. This can be set with the <code>translate_ab</code> argument. See <code><a href="count.html">count_df()</a></code>.</p> <p>At default, the names of antimicrobials will be shown on the plots using <code><a href="ab_property.html">ab_name()</a></code>. This can be set with the <code>translate_ab</code> argument. See <code><a href="count.html">count_df()</a></code>.</p>
<p><code>geom_sir()</code> will take any variable from the data that has an <code><a href="as.sir.html">sir</a></code> class (created with <code><a href="as.sir.html">as.sir()</a></code>) using <code><a href="proportion.html">sir_df()</a></code> and will plot bars with the percentage S, I, and R. The default behaviour is to have the bars stacked and to have the different antibiotics on the x axis.</p> <p><code>geom_sir()</code> will take any variable from the data that has an <code><a href="as.sir.html">sir</a></code> class (created with <code><a href="as.sir.html">as.sir()</a></code>) using <code><a href="proportion.html">sir_df()</a></code> and will plot bars with the percentage S, I, and R. The default behaviour is to have the bars stacked and to have the different antimicrobials on the x axis.</p>
<p>Additional functions include:</p><ul><li><p><code><a href="plot.html">facet_sir()</a></code> creates 2d plots (at default based on S/I/R) using <code><a href="https://ggplot2.tidyverse.org/reference/facet_wrap.html" class="external-link">ggplot2::facet_wrap()</a></code>.</p></li> <p>Additional functions include:</p><ul><li><p><code><a href="plot.html">facet_sir()</a></code> creates 2d plots (at default based on S/I/R) using <code><a href="https://ggplot2.tidyverse.org/reference/facet_wrap.html" class="external-link">ggplot2::facet_wrap()</a></code>.</p></li>
<li><p><code><a href="plot.html">scale_y_percent()</a></code> transforms the y axis to a 0 to 100% range using <code><a href="https://ggplot2.tidyverse.org/reference/scale_continuous.html" class="external-link">ggplot2::scale_y_continuous()</a></code>.</p></li> <li><p><code><a href="plot.html">scale_y_percent()</a></code> transforms the y axis to a 0 to 100% range using <code><a href="https://ggplot2.tidyverse.org/reference/scale_continuous.html" class="external-link">ggplot2::scale_y_continuous()</a></code>.</p></li>
<li><p><code><a href="plot.html">scale_sir_colours()</a></code> sets colours to the bars (green for S, yellow for I, and red for R). with multilingual support. The default colours are colour-blind friendly, while maintaining the convention that e.g. 'susceptible' should be green and 'resistant' should be red.</p></li> <li><p><code><a href="plot.html">scale_sir_colours()</a></code> sets colours to the bars (green for S, yellow for I, and red for R). with multilingual support. The default colours are colour-blind friendly, while maintaining the convention that e.g. 'susceptible' should be green and 'resistant' should be red.</p></li>

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<!DOCTYPE html> <!DOCTYPE html>
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Guess Antibiotic Column — guess_ab_col • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Guess Antibiotic Column — guess_ab_col"><meta name="description" content="This tries to find a column name in a data set based on information from the antibiotics data set. Also supports WHONET abbreviations."><meta property="og:description" content="This tries to find a column name in a data set based on information from the antibiotics data set. Also supports WHONET abbreviations."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous"><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script></head><body> <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Guess Antibiotic Column — guess_ab_col • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Guess Antibiotic Column — guess_ab_col"><meta name="description" content="This tries to find a column name in a data set based on information from the antimicrobials data set. Also supports WHONET abbreviations."><meta property="og:description" content="This tries to find a column name in a data set based on information from the antimicrobials data set. Also supports WHONET abbreviations."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous"><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script></head><body>
<a href="#main" class="visually-hidden-focusable">Skip to contents</a> <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -49,7 +49,7 @@
</div> </div>
<div class="ref-description section level2"> <div class="ref-description section level2">
<p>This tries to find a column name in a data set based on information from the <a href="antibiotics.html">antibiotics</a> data set. Also supports WHONET abbreviations.</p> <p>This tries to find a column name in a data set based on information from the <a href="antimicrobials.html">antimicrobials</a> data set. Also supports WHONET abbreviations.</p>
</div> </div>
<div class="section level2"> <div class="section level2">
@ -84,7 +84,7 @@
</div> </div>
<div class="section level2"> <div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p>You can look for an antibiotic (trade) name or abbreviation and it will search <code>x</code> and the <a href="antibiotics.html">antibiotics</a> data set for any column containing a name or code of that antibiotic.</p> <p>You can look for an antibiotic (trade) name or abbreviation and it will search <code>x</code> and the <a href="antimicrobials.html">antimicrobials</a> data set for any column containing a name or code of that antibiotic.</p>
</div> </div>
<div class="section level2"> <div class="section level2">

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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -99,9 +99,9 @@
</dt> </dt>
<dd>User-Defined Reference Data Set for Microorganisms</dd> <dd>User-Defined Reference Data Set for Microorganisms</dd>
</dl></div><div class="section level2"> </dl></div><div class="section level2">
<h2 id="preparing-data-antibiotics">Preparing data: antibiotics<a class="anchor" aria-label="anchor" href="#preparing-data-antibiotics"></a></h2> <h2 id="preparing-data-antimicrobials">Preparing data: antimicrobials<a class="anchor" aria-label="anchor" href="#preparing-data-antimicrobials"></a></h2>
<div class="section-desc"><p>Use these functions to get valid properties of antibiotics from any input or to clean your input. You can even retrieve drug names and doses from clinical text records, using <code><a href="../reference/ab_from_text.html">ab_from_text()</a></code>.</p></div> <div class="section-desc"><p>Use these functions to get valid properties of antimicrobials from any input or to clean your input. You can even retrieve drug names and doses from clinical text records, using <code><a href="../reference/ab_from_text.html">ab_from_text()</a></code>.</p></div>
</div><div class="section level2"> </div><div class="section level2">
@ -363,7 +363,7 @@
<dd>Data Set with 78 678 Taxonomic Records of Microorganisms</dd> <dd>Data Set with 78 678 Taxonomic Records of Microorganisms</dd>
</dl><dl><dt> </dl><dl><dt>
<code><a href="antibiotics.html">antibiotics</a></code> <code><a href="antibiotics.html">antivirals</a></code> <code><a href="antimicrobials.html">antimicrobials</a></code> <code><a href="antimicrobials.html">antivirals</a></code>
</dt> </dt>
<dd>Data Sets with 607 Antimicrobial Drugs</dd> <dd>Data Sets with 607 Antimicrobial Drugs</dd>
@ -540,7 +540,7 @@
<dl><dt> <dl><dt>
<code><a href="AMR-deprecated.html">ab_class()</a></code> <code><a href="AMR-deprecated.html">ab_selector()</a></code> <code><a href="AMR-deprecated.html">antibiotics</a></code> <code><a href="AMR-deprecated.html">ab_class()</a></code> <code><a href="AMR-deprecated.html">ab_selector()</a></code>
</dt> </dt>
<dd>Deprecated Functions</dd> <dd>Deprecated Functions</dd>

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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -60,7 +60,7 @@
<div class="section level2"> <div class="section level2">
<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2> <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> <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> <li><p><code>ab</code><br> Antimcrobial ID</p></li>
</ul></div> </ul></div>
<div class="section level2"> <div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>

2
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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"> <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
reference/join.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

6
reference/key_antimicrobials.html
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -74,7 +74,7 @@
<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt> <dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with antibiotics columns, like <code>AMX</code> or <code>amox</code>. Can be left blank to determine automatically</p></dd> <dd><p>a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with antimicrobials columns, like <code>AMX</code> or <code>amox</code>. Can be left blank to determine automatically.</p></dd>
<dt id="arg-col-mo">col_mo<a class="anchor" aria-label="anchor" href="#arg-col-mo"></a></dt> <dt id="arg-col-mo">col_mo<a class="anchor" aria-label="anchor" href="#arg-col-mo"></a></dt>
@ -176,7 +176,7 @@
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># \donttest{</span></span></span> <span class="r-in"><span><span class="co"># \donttest{</span></span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span> <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="co"># set key antibiotics to a new variable</span></span></span> <span class="r-in"><span> <span class="co"># set key antimicrobials to a new variable</span></span></span>
<span class="r-in"><span> <span class="va">my_patients</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="r-in"><span> <span class="va">my_patients</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="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>keyab <span class="op">=</span> <span class="fu">key_antimicrobials</span><span class="op">(</span>antifungal <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="co"># no need to define `x`</span></span></span> <span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>keyab <span class="op">=</span> <span class="fu">key_antimicrobials</span><span class="op">(</span>antifungal <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="co"># no need to define `x`</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span></span></span> <span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span></span></span>

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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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"> <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
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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reference/microorganisms.codes.html
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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reference/microorganisms.groups.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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2
reference/microorganisms.html
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@ -9,7 +9,7 @@ This data set is carefully crafted, yet made 100% reproducible from public and a
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4
reference/mo_matching_score.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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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@ -104,7 +104,7 @@
<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2> <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 data sets in this <code>AMR</code> package (about microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. 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>All data sets in this <code>AMR</code> package (about microorganisms, antimicrobials, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. 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>
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<div class="section level2"> <div class="section level2">

6
reference/mo_property.html
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@ -7,7 +7,7 @@
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<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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@ -219,7 +219,7 @@
). This function returns a <a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a> with the levels <em>Pathogenic</em>, <em>Potentially pathogenic</em>, <em>Non-pathogenic</em>, and <em>Unknown</em>.</p> ). This function returns a <a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a> with the levels <em>Pathogenic</em>, <em>Potentially pathogenic</em>, <em>Non-pathogenic</em>, and <em>Unknown</em>.</p>
<p>Determination of the Gram stain (<code>mo_gramstain()</code>) will be based on the taxonomic kingdom and phylum. Originally, Cavalier-Smith defined the so-called subkingdoms Negibacteria and Posibacteria (2002, <a href="https://pubmed.ncbi.nlm.nih.gov/11837318/" class="external-link">PMID 11837318</a>), and only considered these phyla as Posibacteria: Actinobacteria, Chloroflexi, Firmicutes, and Tenericutes. These phyla were later renamed to Actinomycetota, Chloroflexota, Bacillota, and Mycoplasmatota (2021, <a href="https://pubmed.ncbi.nlm.nih.gov/34694987/" class="external-link">PMID 34694987</a>). Bacteria in these phyla are considered Gram-positive in this <code>AMR</code> package, except for members of the class Negativicutes (within phylum Bacillota) which are Gram-negative. All other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value <code>NA</code>. Functions <code>mo_is_gram_negative()</code> and <code>mo_is_gram_positive()</code> always return <code>TRUE</code> or <code>FALSE</code> (or <code>NA</code> when the input is <code>NA</code> or the MO code is <code>UNKNOWN</code>), thus always return <code>FALSE</code> for species outside the taxonomic kingdom of Bacteria.</p> <p>Determination of the Gram stain (<code>mo_gramstain()</code>) will be based on the taxonomic kingdom and phylum. Originally, Cavalier-Smith defined the so-called subkingdoms Negibacteria and Posibacteria (2002, <a href="https://pubmed.ncbi.nlm.nih.gov/11837318/" class="external-link">PMID 11837318</a>), and only considered these phyla as Posibacteria: Actinobacteria, Chloroflexi, Firmicutes, and Tenericutes. These phyla were later renamed to Actinomycetota, Chloroflexota, Bacillota, and Mycoplasmatota (2021, <a href="https://pubmed.ncbi.nlm.nih.gov/34694987/" class="external-link">PMID 34694987</a>). Bacteria in these phyla are considered Gram-positive in this <code>AMR</code> package, except for members of the class Negativicutes (within phylum Bacillota) which are Gram-negative. All other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value <code>NA</code>. Functions <code>mo_is_gram_negative()</code> and <code>mo_is_gram_positive()</code> always return <code>TRUE</code> or <code>FALSE</code> (or <code>NA</code> when the input is <code>NA</code> or the MO code is <code>UNKNOWN</code>), thus always return <code>FALSE</code> for species outside the taxonomic kingdom of Bacteria.</p>
<p>Determination of yeasts (<code>mo_is_yeast()</code>) will be based on the taxonomic kingdom and class. <em>Budding yeasts</em> are yeasts that reproduce asexually through a process called budding, where a new cell develops from a small protrusion on the parent cell. Taxonomically, these are members of the phylum Ascomycota, class Saccharomycetes (also called Hemiascomycetes) or Pichiomycetes. <em>True yeasts</em> quite specifically refers to yeasts in the underlying order Saccharomycetales (such as <em>Saccharomyces cerevisiae</em>). Thus, for all microorganisms that are member of the taxonomic class Saccharomycetes or Pichiomycetes, the function will return <code>TRUE</code>. It returns <code>FALSE</code> otherwise (or <code>NA</code> when the input is <code>NA</code> or the MO code is <code>UNKNOWN</code>).</p> <p>Determination of yeasts (<code>mo_is_yeast()</code>) will be based on the taxonomic kingdom and class. <em>Budding yeasts</em> are yeasts that reproduce asexually through a process called budding, where a new cell develops from a small protrusion on the parent cell. Taxonomically, these are members of the phylum Ascomycota, class Saccharomycetes (also called Hemiascomycetes) or Pichiomycetes. <em>True yeasts</em> quite specifically refers to yeasts in the underlying order Saccharomycetales (such as <em>Saccharomyces cerevisiae</em>). Thus, for all microorganisms that are member of the taxonomic class Saccharomycetes or Pichiomycetes, the function will return <code>TRUE</code>. It returns <code>FALSE</code> otherwise (or <code>NA</code> when the input is <code>NA</code> or the MO code is <code>UNKNOWN</code>).</p>
<p>Determination of intrinsic resistance (<code>mo_is_intrinsic_resistant()</code>) will be based on the <a href="intrinsic_resistant.html">intrinsic_resistant</a> data set, which 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). The <code>mo_is_intrinsic_resistant()</code> function can be vectorised over both argument <code>x</code> (input for microorganisms) and <code>ab</code> (input for antibiotics).</p> <p>Determination of intrinsic resistance (<code>mo_is_intrinsic_resistant()</code>) will be based on the <a href="intrinsic_resistant.html">intrinsic_resistant</a> data set, which 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). The <code>mo_is_intrinsic_resistant()</code> function can be vectorised over both argument <code>x</code> (input for microorganisms) and <code>ab</code> (input for antimicrobials).</p>
<p>Determination of bacterial oxygen tolerance (<code>mo_oxygen_tolerance()</code>) will be based on BacDive, see <em>Source</em>. The function <code>mo_is_anaerobic()</code> only returns <code>TRUE</code> if the oxygen tolerance is <code>"anaerobe"</code>, indicting an obligate anaerobic species or genus. It always returns <code>FALSE</code> for species outside the taxonomic kingdom of Bacteria.</p> <p>Determination of bacterial oxygen tolerance (<code>mo_oxygen_tolerance()</code>) will be based on BacDive, see <em>Source</em>. The function <code>mo_is_anaerobic()</code> only returns <code>TRUE</code> if the oxygen tolerance is <code>"anaerobe"</code>, indicting an obligate anaerobic species or genus. It always returns <code>FALSE</code> for species outside the taxonomic kingdom of Bacteria.</p>
<p>The function <code>mo_url()</code> will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species. <a href="https://www.mycobank.org" class="external-link">This MycoBank URL</a> will be used for fungi wherever available , <a href="https://www.mycobank.org" class="external-link">this LPSN URL</a> for bacteria wherever available, and <a href="https://www.gbif.org" class="external-link">this GBIF link</a> otherwise.</p> <p>The function <code>mo_url()</code> will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species. <a href="https://www.mycobank.org" class="external-link">This MycoBank URL</a> will be used for fungi wherever available , <a href="https://www.mycobank.org" class="external-link">this LPSN URL</a> for bacteria wherever available, and <a href="https://www.gbif.org" class="external-link">this GBIF link</a> otherwise.</p>
<p>SNOMED codes (<code>mo_snomed()</code>) was last updated on July 16th, 2024. See <em>Source</em> and the <a href="microorganisms.html">microorganisms</a> data set for more info.</p> <p>SNOMED codes (<code>mo_snomed()</code>) was last updated on July 16th, 2024. See <em>Source</em> and the <a href="microorganisms.html">microorganisms</a> data set for more info.</p>
@ -252,7 +252,7 @@
<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2> <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 data sets in this <code>AMR</code> package (about microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. 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>All data sets in this <code>AMR</code> package (about microorganisms, antimicrobials, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. 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>
<div class="section level2"> <div class="section level2">
<h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2> <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>

2
reference/mo_source.html
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@ -9,7 +9,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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reference/pca.html
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@ -7,7 +7,7 @@
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4
reference/plot.html
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@ -9,7 +9,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
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@ -236,7 +236,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<dt id="arg-translate-ab">translate_ab<a class="anchor" aria-label="anchor" href="#arg-translate-ab"></a></dt> <dt id="arg-translate-ab">translate_ab<a class="anchor" aria-label="anchor" href="#arg-translate-ab"></a></dt>
<dd><p>a column name of the <a href="antibiotics.html">antibiotics</a> data set to translate the antibiotic abbreviations to, using <code><a href="ab_property.html">ab_property()</a></code></p></dd> <dd><p>a column name of the <a href="antimicrobials.html">antimicrobials</a> data set to translate the antibiotic abbreviations to, using <code><a href="ab_property.html">ab_property()</a></code></p></dd>
<dt id="arg-minimum">minimum<a class="anchor" aria-label="anchor" href="#arg-minimum"></a></dt> <dt id="arg-minimum">minimum<a class="anchor" aria-label="anchor" href="#arg-minimum"></a></dt>

8
reference/proportion.html
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@ -9,7 +9,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
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@ -112,7 +112,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<dt id="arg-only-all-tested">only_all_tested<a class="anchor" aria-label="anchor" href="#arg-only-all-tested"></a></dt> <dt id="arg-only-all-tested">only_all_tested<a class="anchor" aria-label="anchor" href="#arg-only-all-tested"></a></dt>
<dd><p>(for combination therapies, i.e. using more than one variable for <code>...</code>): a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that isolates must be tested for all antibiotics, see section <em>Combination Therapy</em> below</p></dd> <dd><p>(for combination therapies, i.e. using more than one variable for <code>...</code>): a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that isolates must be tested for all antimicrobials, see section <em>Combination Therapy</em> below</p></dd>
<dt id="arg-ab-result">ab_result<a class="anchor" aria-label="anchor" href="#arg-ab-result"></a></dt> <dt id="arg-ab-result">ab_result<a class="anchor" aria-label="anchor" href="#arg-ab-result"></a></dt>
@ -136,7 +136,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<dt id="arg-translate-ab">translate_ab<a class="anchor" aria-label="anchor" href="#arg-translate-ab"></a></dt> <dt id="arg-translate-ab">translate_ab<a class="anchor" aria-label="anchor" href="#arg-translate-ab"></a></dt>
<dd><p>a column name of the <a href="antibiotics.html">antibiotics</a> data set to translate the antibiotic abbreviations to, using <code><a href="ab_property.html">ab_property()</a></code></p></dd> <dd><p>a column name of the <a href="antimicrobials.html">antimicrobials</a> data set to translate the antibiotic abbreviations to, using <code><a href="ab_property.html">ab_property()</a></code></p></dd>
<dt id="arg-language">language<a class="anchor" aria-label="anchor" href="#arg-language"></a></dt> <dt id="arg-language">language<a class="anchor" aria-label="anchor" href="#arg-language"></a></dt>
@ -164,7 +164,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<h2 id="combination-therapy">Combination Therapy<a class="anchor" aria-label="anchor" href="#combination-therapy"></a></h2> <h2 id="combination-therapy">Combination Therapy<a class="anchor" aria-label="anchor" href="#combination-therapy"></a></h2>
<p>When using more than one variable for <code>...</code> (= combination therapy), use <code>only_all_tested</code> to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antibiotics, Drug A and Drug B, about how <code>susceptibility()</code> works to calculate the %SI:</p> <p>When using more than one variable for <code>...</code> (= combination therapy), use <code>only_all_tested</code> to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antimicrobials, Drug A and Drug B, about how <code>susceptibility()</code> works to calculate the %SI:</p>
<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="sc">--------------------------------------------------------------------</span></span> <p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="sc">--------------------------------------------------------------------</span></span>
<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a> only_all_tested <span class="ot">=</span> <span class="cn">FALSE</span> only_all_tested <span class="ot">=</span> <span class="cn">TRUE</span></span> <span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a> only_all_tested <span class="ot">=</span> <span class="cn">FALSE</span> only_all_tested <span class="ot">=</span> <span class="cn">TRUE</span></span>
<span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a> <span class="sc">-----------------------</span> <span class="sc">-----------------------</span></span> <span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a> <span class="sc">-----------------------</span> <span class="sc">-----------------------</span></span>

2
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@ -7,7 +7,7 @@
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2
reference/resistance_predict.html
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@ -7,7 +7,7 @@
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reference/skewness.html
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@ -9,7 +9,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
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reference/top_n_microorganisms.html
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@ -7,7 +7,7 @@
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