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@@ -31,7 +31,7 @@
<a class="navbar-brand me-2" href="https://amr-for-r.org/index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="https://amr-for-r.org/index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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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CLAUDE.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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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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@@ -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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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">

120
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@@ -30,7 +30,7 @@
<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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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">
@@ -91,7 +91,7 @@
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 22 March 2026.</p> generated on 24 March 2026.</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>
@@ -147,21 +147,21 @@ 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">2026-03-22</td> <td align="center">2026-03-24</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">2026-03-22</td> <td align="center">2026-03-24</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">2026-03-22</td> <td align="center">2026-03-24</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>
@@ -266,14 +266,14 @@ user input can be used:</p>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Retrieved values from the `microorganisms.codes` data set for "ESCCOL",</span></span> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Retrieved values from the `microorganisms.codes` data set for "ESCCOL",</span></span>
<span><span class="co">#&gt; "KLEPNE", "STAAUR", and "STRPNE".</span></span> <span><span class="co">#&gt; "KLEPNE", "STAAUR", and "STRPNE".</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Microorganism translation was uncertain for four microorganisms. Run</span></span> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Microorganism translation was uncertain for four microorganisms. Run</span></span>
<span><span class="co">#&gt; `?mo_uncertainties()` to review these uncertainties, or use</span></span> <span><span class="co">#&gt; `mo_uncertainties()` to review these uncertainties, or use</span></span>
<span><span class="co">#&gt; `?add_custom_microorganisms()` to add custom entries.</span></span></code></pre></div> <span><span class="co">#&gt; `add_custom_microorganisms()` to add custom entries.</span></span></code></pre></div>
<p>Apparently, there was some uncertainty about the translation to <p>Apparently, there was some uncertainty about the translation to
taxonomic codes. Let’s check this:</p> taxonomic codes. Let’s check this:</p>
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/as.mo.html">mo_uncertainties</a></span><span class="op">(</span><span class="op">)</span></span> <code class="sourceCode R"><span><span class="fu"><a href="../reference/as.mo.html">mo_uncertainties</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="co">#&gt; Matching scores are based on the resemblance between the input and the full</span></span> <span><span class="co">#&gt; Matching scores are based on the resemblance between the input and the full</span></span>
<span><span class="co">#&gt; taxonomic name, and the pathogenicity in humans. See `?mo_matching_score()`.</span></span> <span><span class="co">#&gt; taxonomic name, and the pathogenicity in humans. See `mo_matching_score()`.</span></span>
<span><span class="co">#&gt; Colour keys: <span style="color: #080808; background-color: #FF5F5F;"> 0.000-0.549 </span><span style="color: #080808; background-color: #FFD787;"> 0.550-0.649 </span><span style="color: #080808; background-color: #FFFF87;"> 0.650-0.749 </span><span style="color: #080808; background-color: #5FD7AF;"> 0.750-1.000 </span></span></span> <span><span class="co">#&gt; Colour keys: <span style="color: #080808; background-color: #FF5F5F;"> 0.000-0.549 </span><span style="color: #080808; background-color: #FFD787;"> 0.550-0.649 </span><span style="color: #080808; background-color: #FFFF87;"> 0.650-0.749 </span><span style="color: #080808; background-color: #5FD7AF;"> 0.750-1.000 </span></span></span>
<span><span class="co">#&gt; <span style="color: #B2B2B2;">-------------------------------------------------------------------------------</span></span></span> <span><span class="co">#&gt; <span style="color: #B2B2B2;">-------------------------------------------------------------------------------</span></span></span>
<span><span class="co">#&gt; <span style="color: #0000BB;">"E. coli"</span> -&gt; <span style="font-weight: bold; font-style: italic;">Escherichia coli</span> (B_ESCHR_COLI, <span style="color: #080808; background-color: #FFFF87;">0.688</span>)</span></span> <span><span class="co">#&gt; <span style="color: #0000BB;">"E. coli"</span> -&gt; <span style="font-weight: bold; font-style: italic;">Escherichia coli</span> (B_ESCHR_COLI, <span style="color: #080808; background-color: #FFFF87;">0.688</span>)</span></span>
@@ -306,8 +306,8 @@ taxonomic codes. Let’s check this:</p>
<span><span class="co">#&gt; <span style="font-style: italic;">Streptococcus gallolyticus pasteurianus</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.526</span>), <span style="font-style: italic;">Salmonella</span> Portanigra<span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.524</span>),</span></span> <span><span class="co">#&gt; <span style="font-style: italic;">Streptococcus gallolyticus pasteurianus</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.526</span>), <span style="font-style: italic;">Salmonella</span> Portanigra<span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.524</span>),</span></span>
<span><span class="co">#&gt; and <span style="font-style: italic;">Streptococcus periodonticum</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.519</span>)</span></span> <span><span class="co">#&gt; and <span style="font-style: italic;">Streptococcus periodonticum</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.519</span>)</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Only the first 10 other matches of each record are shown. Run ``</span></span> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Only the first 10 other matches of each record are shown. Run ``</span></span>
<span><span class="co">#&gt; ?`print(mo_uncertainties(), n = ...)` `` to view more entries, or save</span></span> <span><span class="co">#&gt; `print(mo_uncertainties(), n = ...)` `` to view more entries, or save</span></span>
<span><span class="co">#&gt; `?mo_uncertainties()` to an object.</span></span></code></pre></div> <span><span class="co">#&gt; `mo_uncertainties()` to an object.</span></span></code></pre></div>
<p>That’s all good.</p> <p>That’s all good.</p>
</div> </div>
<div class="section level3"> <div class="section level3">
@@ -337,10 +337,10 @@ dplyr:</p>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 3,000 × 8</span></span></span> <span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 3,000 × 8</span></span></span>
<span><span class="co">#&gt; patient_id hospital date bacteria AMX AMC CIP GEN </span></span> <span><span class="co">#&gt; patient_id hospital date bacteria AMX AMC CIP GEN </span></span>
<span><span class="co">#&gt; <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;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span></span> <span><span class="co">#&gt; <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;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> J3 A 2012-11-21 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FFD787;"> I </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> J3 A 2012-11-21 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #AFFFD7;"> I </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> R7 A 2018-04-03 <span style="color: #949494;">B_</span>KLBSL<span style="color: #949494;">_</span>PNMN <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FFD787;"> I </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> R7 A 2018-04-03 <span style="color: #949494;">B_</span>KLBSL<span style="color: #949494;">_</span>PNMN <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #AFFFD7;"> I </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> P3 A 2014-09-19 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> P3 A 2014-09-19 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> P10 A 2015-12-10 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FFD787;"> I </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> P10 A 2015-12-10 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #AFFFD7;"> I </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> B7 A 2015-03-02 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> B7 A 2015-03-02 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> W3 A 2018-03-31 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> W3 A 2018-03-31 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> J8 A 2016-06-14 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> J8 A 2016-06-14 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
@@ -395,11 +395,11 @@ the methods on the <code><a href="../reference/first_isolate.html">first_isolate
<code class="sourceCode R"><span><span class="va">our_data</span> <span class="op">&lt;-</span> <span class="va">our_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span> <code class="sourceCode R"><span><span class="va">our_data</span> <span class="op">&lt;-</span> <span class="va">our_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>first <span class="op">=</span> <span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span><span class="op">(</span>info <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span> <span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>first <span class="op">=</span> <span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span><span class="op">(</span>info <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Determining first isolates using an episode length of <span style="font-weight: bold;">365 days</span></span></span> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Determining first isolates using an episode length of <span style="font-weight: bold;">365 days</span></span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Using column '<span style="font-weight: bold;">bacteria</span>' as input for `col_mo`.</span></span> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Using column <span style="color: #00BB00; font-weight: bold;">bacteria</span> as input for `col_mo`.</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Column '<span style="font-weight: bold;">first</span>' is SIR eligible (despite only having empty values), since it</span></span> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Column <span style="color: #00BB00; font-weight: bold;">first</span> is SIR eligible (despite only having empty values), since it</span></span>
<span><span class="co">#&gt; seems to be cefozopran (ZOP)</span></span> <span><span class="co">#&gt; seems to be cefozopran (ZOP)</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Using column '<span style="font-weight: bold;">date</span>' as input for `col_date`.</span></span> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Using column <span style="color: #00BB00; font-weight: bold;">date</span> as input for `col_date`.</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Using column '<span style="font-weight: bold;">patient_id</span>' as input for `col_patient_id`.</span></span> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Using column <span style="color: #00BB00; font-weight: bold;">patient_id</span> as input for `col_patient_id`.</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Basing inclusion on all antimicrobial results, using a points threshold of 2</span></span> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Basing inclusion on all antimicrobial results, using a points threshold of 2</span></span>
<span><span class="co">#&gt; =&gt; Found <span style="font-weight: bold;">2,724 'phenotype-based' first isolates</span> (90.8% of total where a</span></span> <span><span class="co">#&gt; =&gt; Found <span style="font-weight: bold;">2,724 'phenotype-based' first isolates</span> (90.8% of total where a</span></span>
<span><span class="co">#&gt; microbial ID was available)</span></span></code></pre></div> <span><span class="co">#&gt; microbial ID was available)</span></span></code></pre></div>
@@ -420,10 +420,10 @@ like:</p>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,724 × 9</span></span></span> <span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,724 × 9</span></span></span>
<span><span class="co">#&gt; patient_id hospital date bacteria AMX AMC CIP GEN first</span></span> <span><span class="co">#&gt; patient_id hospital date bacteria AMX AMC CIP GEN first</span></span>
<span><span class="co">#&gt; <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;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span></span></span> <span><span class="co">#&gt; <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;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> J3 A 2012-11-21 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FFD787;"> I </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> J3 A 2012-11-21 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #AFFFD7;"> I </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> R7 A 2018-04-03 <span style="color: #949494;">B_</span>KLBSL<span style="color: #949494;">_</span>PNMN <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FFD787;"> I </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> R7 A 2018-04-03 <span style="color: #949494;">B_</span>KLBSL<span style="color: #949494;">_</span>PNMN <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #AFFFD7;"> I </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> P3 A 2014-09-19 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> P3 A 2014-09-19 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> P10 A 2015-12-10 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FFD787;"> I </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> P10 A 2015-12-10 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #AFFFD7;"> I </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> B7 A 2015-03-02 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> B7 A 2015-03-02 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> W3 A 2018-03-31 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> W3 A 2018-03-31 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> M3 A 2015-10-25 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> M3 A 2015-10-25 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span>
@@ -519,7 +519,7 @@ in:</p>
<div class="sourceCode" id="cb14"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb14"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span> <code class="sourceCode R"><span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></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">date</span>, <span class="fu"><a href="../reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</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">date</span>, <span class="fu"><a href="../reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `?aminoglycosides()` using column <span style="color: #00BB00; font-weight: bold;">GEN</span></span></span> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using column <span style="color: #00BB00; font-weight: bold;">GEN</span></span></span>
<span><span class="co">#&gt; (gentamicin)</span></span> <span><span class="co">#&gt; (gentamicin)</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,724 × 2</span></span></span> <span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,724 × 2</span></span></span>
<span><span class="co">#&gt; date GEN </span></span> <span><span class="co">#&gt; date GEN </span></span>
@@ -538,15 +538,15 @@ in:</p>
<span></span> <span></span>
<span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span> <span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></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 class="fu"><a href="../reference/antimicrobial_selectors.html">betalactams</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</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 class="fu"><a href="../reference/antimicrobial_selectors.html">betalactams</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `?betalactams()` using columns <span style="color: #00BB00; font-weight: bold;">AMX</span> (amoxicillin) and <span style="color: #00BB00; font-weight: bold;">AMC</span></span></span> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `betalactams()` using columns <span style="color: #00BB00; font-weight: bold;">AMX</span> (amoxicillin) and <span style="color: #00BB00; font-weight: bold;">AMC</span></span></span>
<span><span class="co">#&gt; (amoxicillin/clavulanic acid)</span></span> <span><span class="co">#&gt; (amoxicillin/clavulanic acid)</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,724 × 3</span></span></span> <span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,724 × 3</span></span></span>
<span><span class="co">#&gt; bacteria AMX AMC </span></span> <span><span class="co">#&gt; bacteria AMX AMC </span></span>
<span><span class="co">#&gt; <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span></span> <span><span class="co">#&gt; <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FFD787;"> I </span></span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #AFFFD7;"> I </span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> <span style="color: #949494;">B_</span>KLBSL<span style="color: #949494;">_</span>PNMN <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FFD787;"> I </span></span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> <span style="color: #949494;">B_</span>KLBSL<span style="color: #949494;">_</span>PNMN <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #AFFFD7;"> I </span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FFD787;"> I </span></span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #AFFFD7;"> I </span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
@@ -560,10 +560,10 @@ in:</p>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,724 × 5</span></span></span> <span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,724 × 5</span></span></span>
<span><span class="co">#&gt; bacteria AMX AMC CIP GEN </span></span> <span><span class="co">#&gt; bacteria AMX AMC CIP GEN </span></span>
<span><span class="co">#&gt; <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span></span> <span><span class="co">#&gt; <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FFD787;"> I </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #AFFFD7;"> I </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> <span style="color: #949494;">B_</span>KLBSL<span style="color: #949494;">_</span>PNMN <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FFD787;"> I </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> <span style="color: #949494;">B_</span>KLBSL<span style="color: #949494;">_</span>PNMN <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #AFFFD7;"> I </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FFD787;"> I </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #AFFFD7;"> I </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
@@ -575,7 +575,7 @@ in:</p>
<span><span class="co"># filtering using AB selectors is also possible:</span></span> <span><span class="co"># filtering using AB selectors is also possible:</span></span>
<span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span> <span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</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="op">==</span> <span class="st">"R"</span><span class="op">)</span><span class="op">)</span></span> <span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</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="op">==</span> <span class="st">"R"</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `?aminoglycosides()` using column <span style="color: #00BB00; font-weight: bold;">GEN</span></span></span> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using column <span style="color: #00BB00; font-weight: bold;">GEN</span></span></span>
<span><span class="co">#&gt; (gentamicin)</span></span> <span><span class="co">#&gt; (gentamicin)</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 981 × 9</span></span></span> <span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 981 × 9</span></span></span>
<span><span class="co">#&gt; patient_id hospital date bacteria AMX AMC CIP GEN first</span></span> <span><span class="co">#&gt; patient_id hospital date bacteria AMX AMC CIP GEN first</span></span>
@@ -594,7 +594,7 @@ in:</p>
<span></span> <span></span>
<span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span> <span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu"><a href="../reference/antimicrobial_selectors.html">betalactams</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span><span class="op">)</span></span> <span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu"><a href="../reference/antimicrobial_selectors.html">betalactams</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `?betalactams()` using columns <span style="color: #00BB00; font-weight: bold;">AMX</span> (amoxicillin) and <span style="color: #00BB00; font-weight: bold;">AMC</span></span></span> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `betalactams()` using columns <span style="color: #00BB00; font-weight: bold;">AMX</span> (amoxicillin) and <span style="color: #00BB00; font-weight: bold;">AMC</span></span></span>
<span><span class="co">#&gt; (amoxicillin/clavulanic acid)</span></span> <span><span class="co">#&gt; (amoxicillin/clavulanic acid)</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 462 × 9</span></span></span> <span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 462 × 9</span></span></span>
<span><span class="co">#&gt; patient_id hospital date bacteria AMX AMC CIP GEN first</span></span> <span><span class="co">#&gt; patient_id hospital date bacteria AMX AMC CIP GEN first</span></span>
@@ -613,7 +613,7 @@ in:</p>
<span></span> <span></span>
<span><span class="co"># even works in base R (since R 3.0):</span></span> <span><span class="co"># even works in base R (since R 3.0):</span></span>
<span><span class="va">our_data_1st</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu"><a href="../reference/antimicrobial_selectors.html">betalactams</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span>, <span class="op">]</span></span> <span><span class="va">our_data_1st</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu"><a href="../reference/antimicrobial_selectors.html">betalactams</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span>, <span class="op">]</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `?betalactams()` using columns <span style="color: #00BB00; font-weight: bold;">AMX</span> (amoxicillin) and <span style="color: #00BB00; font-weight: bold;">AMC</span></span></span> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `betalactams()` using columns <span style="color: #00BB00; font-weight: bold;">AMX</span> (amoxicillin) and <span style="color: #00BB00; font-weight: bold;">AMC</span></span></span>
<span><span class="co">#&gt; (amoxicillin/clavulanic acid)</span></span> <span><span class="co">#&gt; (amoxicillin/clavulanic acid)</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 462 × 9</span></span></span> <span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 462 × 9</span></span></span>
<span><span class="co">#&gt; patient_id hospital date bacteria AMX AMC CIP GEN first</span></span> <span><span class="co">#&gt; patient_id hospital date bacteria AMX AMC CIP GEN first</span></span>
@@ -668,16 +668,16 @@ like:</p>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,000 × 46</span></span></span> <span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,000 × 46</span></span></span>
<span><span class="co">#&gt; date patient age gender ward mo PEN OXA FLC AMX </span></span> <span><span class="co">#&gt; date patient age gender ward mo PEN OXA FLC AMX </span></span>
<span><span class="co">#&gt; <span style="color: #949494; font-style: italic;">&lt;date&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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span></span> <span><span class="co">#&gt; <span style="color: #949494; font-style: italic;">&lt;date&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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> </span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> 2002-01-03 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> </span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> 2002-01-03 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> 2002-01-16 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> 2002-01-16 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> 2002-01-17 858515 79 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #B2B2B2;"> NA</span> </span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> 2002-01-17 858515 79 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #949494;"> NA</span> </span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 1,990 more rows</span></span></span> <span><span class="co">#&gt; <span style="color: #949494;"># ℹ 1,990 more rows</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;,</span></span></span> <span><span class="co">#&gt; <span style="color: #949494;"># ℹ 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;,</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;,</span></span></span> <span><span class="co">#&gt; <span style="color: #949494;"># CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;,</span></span></span>
@@ -695,9 +695,9 @@ previously mentioned antibiotic class selectors:</p>
<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb16"><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> <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>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `?aminoglycosides()` using columns <span style="color: #00BB00; font-weight: bold;">GEN</span> (gentamicin), <span style="color: #00BB00; font-weight: bold;">TOB</span> (tobramycin),</span></span> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns <span style="color: #00BB00; font-weight: bold;">GEN</span> (gentamicin), <span style="color: #00BB00; font-weight: bold;">TOB</span> (tobramycin), <span style="color: #00BB00; font-weight: bold;">AMK</span></span></span>
<span><span class="co">#&gt; <span style="color: #00BB00; font-weight: bold;">AMK</span> (amikacin), and <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin)</span></span> <span><span class="co">#&gt; (amikacin), and <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin)</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `?carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span></span></code></pre></div> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span></span></code></pre></div>
<table class="table"> <table class="table">
<colgroup> <colgroup>
<col width="12%"> <col width="12%">
@@ -826,8 +826,8 @@ language to be Spanish using the <code>language</code> argument:</p>
<span> antibiotics <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> <span> antibiotics <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>
<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> language <span class="op">=</span> <span class="st">"es"</span><span class="op">)</span></span> <span> language <span class="op">=</span> <span class="st">"es"</span><span class="op">)</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `?aminoglycosides()` using columns <span style="color: #00BB00; font-weight: bold;">GEN</span> (gentamicin), <span style="color: #00BB00; font-weight: bold;">TOB</span> (tobramycin),</span></span> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns <span style="color: #00BB00; font-weight: bold;">GEN</span> (gentamicin), <span style="color: #00BB00; font-weight: bold;">TOB</span> (tobramycin), <span style="color: #00BB00; font-weight: bold;">AMK</span></span></span>
<span><span class="co">#&gt; <span style="color: #00BB00; font-weight: bold;">AMK</span> (amikacin), and <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin)</span></span></code></pre></div> <span><span class="co">#&gt; (amikacin), and <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin)</span></span></code></pre></div>
<table class="table"> <table class="table">
<colgroup> <colgroup>
<col width="15%"> <col width="15%">
@@ -952,9 +952,9 @@ argument must be used. This can be any column in the data, or e.g. an
<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> <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> syndromic_group <span class="op">=</span> <span class="st">"ward"</span><span class="op">)</span></span> <span> syndromic_group <span class="op">=</span> <span class="st">"ward"</span><span class="op">)</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `?aminoglycosides()` using columns <span style="color: #00BB00; font-weight: bold;">GEN</span> (gentamicin), <span style="color: #00BB00; font-weight: bold;">TOB</span> (tobramycin),</span></span> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns <span style="color: #00BB00; font-weight: bold;">GEN</span> (gentamicin), <span style="color: #00BB00; font-weight: bold;">TOB</span> (tobramycin), <span style="color: #00BB00; font-weight: bold;">AMK</span></span></span>
<span><span class="co">#&gt; <span style="color: #00BB00; font-weight: bold;">AMK</span> (amikacin), and <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin)</span></span> <span><span class="co">#&gt; (amikacin), and <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin)</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `?carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span></span></code></pre></div> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span></span></code></pre></div>
<table class="table"> <table class="table">
<colgroup> <colgroup>
<col width="10%"> <col width="10%">
@@ -1281,9 +1281,9 @@ I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equa
own:</p> own:</p>
<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb23"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span></span> <code class="sourceCode R"><span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> `?resistance()` assumes the EUCAST guideline and thus considers the 'I'</span></span> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> `resistance()` assumes the EUCAST guideline and thus considers the 'I'</span></span>
<span><span class="co">#&gt; category susceptible. Set the `guideline` argument or the `AMR_guideline`</span></span> <span><span class="co">#&gt; category susceptible. Set the `guideline` argument or the `AMR_guideline`</span></span>
<span><span class="co">#&gt; option to either "CLSI" or "EUCAST", see AMR-options.</span></span> <span><span class="co">#&gt; option to either "CLSI" or "EUCAST", see `?AMR-options`.</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> This message will be shown once per session.</span></span> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> This message will be shown once per session.</span></span>
<span><span class="co">#&gt; [1] 0.4203377</span></span></code></pre></div> <span><span class="co">#&gt; [1] 0.4203377</span></span></code></pre></div>
<p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and <p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and
@@ -1316,15 +1316,15 @@ values for <em>Klebsiella pneumoniae</em> and ciprofloxacin:</p>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 100 × 2</span></span></span> <span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 100 × 2</span></span></span>
<span><span class="co">#&gt; MIC SIR </span></span> <span><span class="co">#&gt; MIC SIR </span></span>
<span><span class="co">#&gt; <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span></span> <span><span class="co">#&gt; <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> <span style="color: #555555;">&lt;=</span>0.0001 <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> <span style="color: #949494;">&lt;=</span>0.0001 <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> 0.016<span style="color: #555555;">0</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> 0.016<span style="color: #949494;">0</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> <span style="color: #555555;">&gt;=</span>8<span style="color: #555555;">.0000</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> <span style="color: #949494;">&gt;=</span>8<span style="color: #949494;">.0000</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> 0.032<span style="color: #555555;">0</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> 0.032<span style="color: #949494;">0</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> 0.008<span style="color: #555555;">0</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> 0.008<span style="color: #949494;">0</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> 64<span style="color: #555555;">.0000</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> 64<span style="color: #949494;">.0000</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> 0.008<span style="color: #555555;">0</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> 0.008<span style="color: #949494;">0</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> 0.125<span style="color: #555555;">0</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> 0.125<span style="color: #949494;">0</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> 0.032<span style="color: #555555;">0</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> 0.032<span style="color: #949494;">0</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> 0.0002 <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> 0.0002 <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 90 more rows</span></span></span></code></pre></div> <span><span class="co">#&gt; <span style="color: #949494;"># ℹ 90 more rows</span></span></span></code></pre></div>
<p>This allows direct interpretation according to EUCAST or CLSI <p>This allows direct interpretation according to EUCAST or CLSI

56
articles/AMR.md
View File

@@ -3,7 +3,7 @@
**Note:** values on this page will change with every website update **Note:** values on this page will change with every website update
since they are based on randomly created values and the page was written since they are based on randomly created values and the page was written
in [R Markdown](https://rmarkdown.rstudio.com/). However, the in [R Markdown](https://rmarkdown.rstudio.com/). However, the
methodology remains unchanged. This page was generated on 22 March 2026. methodology remains unchanged. This page was generated on 24 March 2026.
## Introduction ## Introduction
@@ -51,9 +51,9 @@ structure of your data generally look like this:
| date | patient_id | mo | AMX | CIP | | date | patient_id | mo | AMX | CIP |
|:----------:|:----------:|:----------------:|:---:|:---:| |:----------:|:----------:|:----------------:|:---:|:---:|
| 2026-03-22 | abcd | Escherichia coli | S | S | | 2026-03-24 | abcd | Escherichia coli | S | S |
| 2026-03-22 | abcd | Escherichia coli | S | R | | 2026-03-24 | abcd | Escherichia coli | S | R |
| 2026-03-22 | efgh | Escherichia coli | R | S | | 2026-03-24 | efgh | Escherichia coli | R | S |
### Needed R packages ### Needed R packages
@@ -169,8 +169,8 @@ our_data$bacteria <- as.mo(our_data$bacteria, info = TRUE)
#> ℹ Retrieved values from the `microorganisms.codes` data set for "ESCCOL", #> ℹ Retrieved values from the `microorganisms.codes` data set for "ESCCOL",
#> "KLEPNE", "STAAUR", and "STRPNE". #> "KLEPNE", "STAAUR", and "STRPNE".
#> ℹ Microorganism translation was uncertain for four microorganisms. Run #> ℹ Microorganism translation was uncertain for four microorganisms. Run
#> `?mo_uncertainties()` to review these uncertainties, or use #> `mo_uncertainties()` to review these uncertainties, or use
#> `?add_custom_microorganisms()` to add custom entries. #> `add_custom_microorganisms()` to add custom entries.
``` ```
Apparently, there was some uncertainty about the translation to Apparently, there was some uncertainty about the translation to
@@ -179,7 +179,7 @@ taxonomic codes. Let’s check this:
``` r ``` r
mo_uncertainties() mo_uncertainties()
#> Matching scores are based on the resemblance between the input and the full #> Matching scores are based on the resemblance between the input and the full
#> taxonomic name, and the pathogenicity in humans. See `?mo_matching_score()`. #> taxonomic name, and the pathogenicity in humans. See `mo_matching_score()`.
#> Colour keys: 0.000-0.549 0.550-0.649 0.650-0.749 0.750-1.000 #> Colour keys: 0.000-0.549 0.550-0.649 0.650-0.749 0.750-1.000
#> ------------------------------------------------------------------------------- #> -------------------------------------------------------------------------------
#> "E. coli" -> Escherichia coli (B_ESCHR_COLI, 0.688) #> "E. coli" -> Escherichia coli (B_ESCHR_COLI, 0.688)
@@ -212,8 +212,8 @@ mo_uncertainties()
#> Streptococcus gallolyticus pasteurianus (0.526), Salmonella Portanigra (0.524), #> Streptococcus gallolyticus pasteurianus (0.526), Salmonella Portanigra (0.524),
#> and Streptococcus periodonticum (0.519) #> and Streptococcus periodonticum (0.519)
#> ℹ Only the first 10 other matches of each record are shown. Run `` #> ℹ Only the first 10 other matches of each record are shown. Run ``
#> ?`print(mo_uncertainties(), n = ...)` `` to view more entries, or save #> `print(mo_uncertainties(), n = ...)` `` to view more entries, or save
#> `?mo_uncertainties()` to an object. #> `mo_uncertainties()` to an object.
``` ```
That’s all good. That’s all good.
@@ -311,11 +311,11 @@ The outcome of the function can easily be added to our data:
our_data <- our_data %>% our_data <- our_data %>%
mutate(first = first_isolate(info = TRUE)) mutate(first = first_isolate(info = TRUE))
#> ℹ Determining first isolates using an episode length of 365 days #> ℹ Determining first isolates using an episode length of 365 days
#> ℹ Using column 'bacteria' as input for `col_mo`. #> ℹ Using column bacteria as input for `col_mo`.
#> ℹ Column 'first' is SIR eligible (despite only having empty values), since it #> ℹ Column first is SIR eligible (despite only having empty values), since it
#> seems to be cefozopran (ZOP) #> seems to be cefozopran (ZOP)
#> ℹ Using column 'date' as input for `col_date`. #> ℹ Using column date as input for `col_date`.
#> ℹ Using column 'patient_id' as input for `col_patient_id`. #> ℹ Using column patient_id as input for `col_patient_id`.
#> ℹ Basing inclusion on all antimicrobial results, using a points threshold of 2 #> ℹ Basing inclusion on all antimicrobial results, using a points threshold of 2
#> => Found 2,724 'phenotype-based' first isolates (90.8% of total where a #> => Found 2,724 'phenotype-based' first isolates (90.8% of total where a
#> microbial ID was available) #> microbial ID was available)
@@ -447,7 +447,7 @@ in:
``` r ``` r
our_data_1st %>% our_data_1st %>%
select(date, aminoglycosides()) select(date, aminoglycosides())
#> ℹ For `?aminoglycosides()` using column GEN #> ℹ For `aminoglycosides()` using column GEN
#> (gentamicin) #> (gentamicin)
#> # A tibble: 2,724 × 2 #> # A tibble: 2,724 × 2
#> date GEN #> date GEN
@@ -466,7 +466,7 @@ our_data_1st %>%
our_data_1st %>% our_data_1st %>%
select(bacteria, betalactams()) select(bacteria, betalactams())
#> ℹ For `?betalactams()` using columns AMX (amoxicillin) and AMC #> ℹ For `betalactams()` using columns AMX (amoxicillin) and AMC
#> (amoxicillin/clavulanic acid) #> (amoxicillin/clavulanic acid)
#> # A tibble: 2,724 × 3 #> # A tibble: 2,724 × 3
#> bacteria AMX AMC #> bacteria AMX AMC
@@ -503,7 +503,7 @@ our_data_1st %>%
# filtering using AB selectors is also possible: # filtering using AB selectors is also possible:
our_data_1st %>% our_data_1st %>%
filter(any(aminoglycosides() == "R")) filter(any(aminoglycosides() == "R"))
#> ℹ For `?aminoglycosides()` using column GEN #> ℹ For `aminoglycosides()` using column GEN
#> (gentamicin) #> (gentamicin)
#> # A tibble: 981 × 9 #> # A tibble: 981 × 9
#> patient_id hospital date bacteria AMX AMC CIP GEN first #> patient_id hospital date bacteria AMX AMC CIP GEN first
@@ -522,7 +522,7 @@ our_data_1st %>%
our_data_1st %>% our_data_1st %>%
filter(all(betalactams() == "R")) filter(all(betalactams() == "R"))
#> ℹ For `?betalactams()` using columns AMX (amoxicillin) and AMC #> ℹ For `betalactams()` using columns AMX (amoxicillin) and AMC
#> (amoxicillin/clavulanic acid) #> (amoxicillin/clavulanic acid)
#> # A tibble: 462 × 9 #> # A tibble: 462 × 9
#> patient_id hospital date bacteria AMX AMC CIP GEN first #> patient_id hospital date bacteria AMX AMC CIP GEN first
@@ -541,7 +541,7 @@ our_data_1st %>%
# even works in base R (since R 3.0): # even works in base R (since R 3.0):
our_data_1st[all(betalactams() == "R"), ] our_data_1st[all(betalactams() == "R"), ]
#> ℹ For `?betalactams()` using columns AMX (amoxicillin) and AMC #> ℹ For `betalactams()` using columns AMX (amoxicillin) and AMC
#> (amoxicillin/clavulanic acid) #> (amoxicillin/clavulanic acid)
#> # A tibble: 462 × 9 #> # A tibble: 462 × 9
#> patient_id hospital date bacteria AMX AMC CIP GEN first #> patient_id hospital date bacteria AMX AMC CIP GEN first
@@ -624,9 +624,9 @@ antibiotic class selectors:
``` r ``` r
antibiogram(example_isolates, antibiogram(example_isolates,
antibiotics = c(aminoglycosides(), carbapenems())) antibiotics = c(aminoglycosides(), carbapenems()))
#> ℹ For `?aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), #> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK
#> AMK (amikacin), and KAN (kanamycin) #> (amikacin), and KAN (kanamycin)
#> ℹ For `?carbapenems()` using columns IPM (imipenem) and MEM (meropenem) #> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
``` ```
| Pathogen | Amikacin | Gentamicin | Imipenem | Kanamycin | Meropenem | Tobramycin | | Pathogen | Amikacin | Gentamicin | Imipenem | Kanamycin | Meropenem | Tobramycin |
@@ -663,8 +663,8 @@ antibiogram(example_isolates,
antibiotics = aminoglycosides(), antibiotics = aminoglycosides(),
ab_transform = "name", ab_transform = "name",
language = "es") language = "es")
#> ℹ For `?aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), #> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK
#> AMK (amikacin), and KAN (kanamycin) #> (amikacin), and KAN (kanamycin)
``` ```
| Patógeno | Amikacina | Gentamicina | Kanamicina | Tobramicina | | Patógeno | Amikacina | Gentamicina | Kanamicina | Tobramicina |
@@ -707,9 +707,9 @@ on certain columns:
antibiogram(example_isolates, antibiogram(example_isolates,
antibiotics = c(aminoglycosides(), carbapenems()), antibiotics = c(aminoglycosides(), carbapenems()),
syndromic_group = "ward") syndromic_group = "ward")
#> ℹ For `?aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), #> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK
#> AMK (amikacin), and KAN (kanamycin) #> (amikacin), and KAN (kanamycin)
#> ℹ For `?carbapenems()` using columns IPM (imipenem) and MEM (meropenem) #> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
``` ```
| Syndromic Group | Pathogen | Amikacin | Gentamicin | Imipenem | Kanamycin | Meropenem | Tobramycin | | Syndromic Group | Pathogen | Amikacin | Gentamicin | Imipenem | Kanamycin | Meropenem | Tobramycin |
@@ -840,9 +840,9 @@ These functions can be used on their own:
``` r ``` r
our_data_1st %>% resistance(AMX) our_data_1st %>% resistance(AMX)
#> ℹ `?resistance()` assumes the EUCAST guideline and thus considers the 'I' #> ℹ `resistance()` assumes the EUCAST guideline and thus considers the 'I'
#> category susceptible. Set the `guideline` argument or the `AMR_guideline` #> category susceptible. Set the `guideline` argument or the `AMR_guideline`
#> option to either "CLSI" or "EUCAST", see AMR-options. #> option to either "CLSI" or "EUCAST", see `?AMR-options`.
#> ℹ This message will be shown once per session. #> ℹ This message will be shown once per session.
#> [1] 0.4203377 #> [1] 0.4203377
``` ```

2
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@@ -30,7 +30,7 @@
<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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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
articles/AMR_with_tidymodels.html
View File

@@ -30,7 +30,7 @@
<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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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">
@@ -147,16 +147,16 @@ package.</p>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,000 × 46</span></span></span> <span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,000 × 46</span></span></span>
<span><span class="co">#&gt; date patient age gender ward mo PEN OXA FLC AMX </span></span> <span><span class="co">#&gt; date patient age gender ward mo PEN OXA FLC AMX </span></span>
<span><span class="co">#&gt; <span style="color: #949494; font-style: italic;">&lt;date&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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span></span> <span><span class="co">#&gt; <span style="color: #949494; font-style: italic;">&lt;date&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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> </span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> 2002-01-03 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> </span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> 2002-01-03 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> 2002-01-16 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> 2002-01-16 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> 2002-01-17 858515 79 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #B2B2B2;"> NA</span> </span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> 2002-01-17 858515 79 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #949494;"> NA</span> </span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 1,990 more rows</span></span></span> <span><span class="co">#&gt; <span style="color: #949494;"># ℹ 1,990 more rows</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;,</span></span></span> <span><span class="co">#&gt; <span style="color: #949494;"># ℹ 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;,</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;,</span></span></span> <span><span class="co">#&gt; <span style="color: #949494;"># CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;,</span></span></span>
@@ -179,9 +179,9 @@ package.</p>
<span> mo <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">as.factor</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</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> <span> mo <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">as.factor</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</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>
<span> <span class="co"># drop NAs - the ones without a Gramstain (fungi, etc.)</span></span> <span> <span class="co"># drop NAs - the ones without a Gramstain (fungi, etc.)</span></span>
<span> <span class="fu">drop_na</span><span class="op">(</span><span class="op">)</span></span> <span> <span class="fu">drop_na</span><span class="op">(</span><span class="op">)</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `?aminoglycosides()` using columns <span style="color: #00BB00; font-weight: bold;">GEN</span> (gentamicin), <span style="color: #00BB00; font-weight: bold;">TOB</span> (tobramycin),</span></span> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns <span style="color: #00BB00; font-weight: bold;">GEN</span> (gentamicin), <span style="color: #00BB00; font-weight: bold;">TOB</span> (tobramycin), <span style="color: #00BB00; font-weight: bold;">AMK</span></span></span>
<span><span class="co">#&gt; <span style="color: #00BB00; font-weight: bold;">AMK</span> (amikacin), and <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin)</span></span> <span><span class="co">#&gt; (amikacin), and <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin)</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `?betalactams()` using columns <span style="color: #00BB00; font-weight: bold;">PEN</span> (benzylpenicillin), <span style="color: #00BB00; font-weight: bold;">OXA</span> (oxacillin),</span></span> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `betalactams()` using columns <span style="color: #00BB00; font-weight: bold;">PEN</span> (benzylpenicillin), <span style="color: #00BB00; font-weight: bold;">OXA</span> (oxacillin),</span></span>
<span><span class="co">#&gt; <span style="color: #00BB00; font-weight: bold;">FLC</span> (flucloxacillin), <span style="color: #00BB00; font-weight: bold;">AMX</span> (amoxicillin), <span style="color: #00BB00; font-weight: bold;">AMC</span> (amoxicillin/clavulanic acid),</span></span> <span><span class="co">#&gt; <span style="color: #00BB00; font-weight: bold;">FLC</span> (flucloxacillin), <span style="color: #00BB00; font-weight: bold;">AMX</span> (amoxicillin), <span style="color: #00BB00; font-weight: bold;">AMC</span> (amoxicillin/clavulanic acid),</span></span>
<span><span class="co">#&gt; <span style="color: #00BB00; font-weight: bold;">AMP</span> (ampicillin), <span style="color: #00BB00; font-weight: bold;">TZP</span> (piperacillin/tazobactam), <span style="color: #00BB00; font-weight: bold;">CZO</span> (cefazolin), <span style="color: #00BB00; font-weight: bold;">FEP</span></span></span> <span><span class="co">#&gt; <span style="color: #00BB00; font-weight: bold;">AMP</span> (ampicillin), <span style="color: #00BB00; font-weight: bold;">TZP</span> (piperacillin/tazobactam), <span style="color: #00BB00; font-weight: bold;">CZO</span> (cefazolin), <span style="color: #00BB00; font-weight: bold;">FEP</span></span></span>
<span><span class="co">#&gt; (cefepime), <span style="color: #00BB00; font-weight: bold;">CXM</span> (cefuroxime), <span style="color: #00BB00; font-weight: bold;">FOX</span> (cefoxitin), <span style="color: #00BB00; font-weight: bold;">CTX</span> (cefotaxime), <span style="color: #00BB00; font-weight: bold;">CAZ</span></span></span> <span><span class="co">#&gt; (cefepime), <span style="color: #00BB00; font-weight: bold;">CXM</span> (cefuroxime), <span style="color: #00BB00; font-weight: bold;">FOX</span> (cefoxitin), <span style="color: #00BB00; font-weight: bold;">CTX</span> (cefotaxime), <span style="color: #00BB00; font-weight: bold;">CAZ</span></span></span>
@@ -226,9 +226,9 @@ we have with <code>step_corr()</code>, the necessary parameters can be
estimated from a training set using <code>prep()</code>:</p> estimated from a training set using <code>prep()</code>:</p>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu">prep</span><span class="op">(</span><span class="va">resistance_recipe</span><span class="op">)</span></span> <code class="sourceCode R"><span><span class="fu">prep</span><span class="op">(</span><span class="va">resistance_recipe</span><span class="op">)</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `?aminoglycosides()` using columns <span style="color: #00BB00; font-weight: bold;">GEN</span> (gentamicin), <span style="color: #00BB00; font-weight: bold;">TOB</span> (tobramycin),</span></span> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns <span style="color: #00BB00; font-weight: bold;">GEN</span> (gentamicin), <span style="color: #00BB00; font-weight: bold;">TOB</span> (tobramycin), <span style="color: #00BB00; font-weight: bold;">AMK</span></span></span>
<span><span class="co">#&gt; <span style="color: #00BB00; font-weight: bold;">AMK</span> (amikacin), and <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin)</span></span> <span><span class="co">#&gt; (amikacin), and <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin)</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `?betalactams()` using columns <span style="color: #00BB00; font-weight: bold;">PEN</span> (benzylpenicillin), <span style="color: #00BB00; font-weight: bold;">OXA</span> (oxacillin),</span></span> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `betalactams()` using columns <span style="color: #00BB00; font-weight: bold;">PEN</span> (benzylpenicillin), <span style="color: #00BB00; font-weight: bold;">OXA</span> (oxacillin),</span></span>
<span><span class="co">#&gt; <span style="color: #00BB00; font-weight: bold;">FLC</span> (flucloxacillin), <span style="color: #00BB00; font-weight: bold;">AMX</span> (amoxicillin), <span style="color: #00BB00; font-weight: bold;">AMC</span> (amoxicillin/clavulanic acid),</span></span> <span><span class="co">#&gt; <span style="color: #00BB00; font-weight: bold;">FLC</span> (flucloxacillin), <span style="color: #00BB00; font-weight: bold;">AMX</span> (amoxicillin), <span style="color: #00BB00; font-weight: bold;">AMC</span> (amoxicillin/clavulanic acid),</span></span>
<span><span class="co">#&gt; <span style="color: #00BB00; font-weight: bold;">AMP</span> (ampicillin), <span style="color: #00BB00; font-weight: bold;">TZP</span> (piperacillin/tazobactam), <span style="color: #00BB00; font-weight: bold;">CZO</span> (cefazolin), <span style="color: #00BB00; font-weight: bold;">FEP</span></span></span> <span><span class="co">#&gt; <span style="color: #00BB00; font-weight: bold;">AMP</span> (ampicillin), <span style="color: #00BB00; font-weight: bold;">TZP</span> (piperacillin/tazobactam), <span style="color: #00BB00; font-weight: bold;">CZO</span> (cefazolin), <span style="color: #00BB00; font-weight: bold;">FEP</span></span></span>
<span><span class="co">#&gt; (cefepime), <span style="color: #00BB00; font-weight: bold;">CXM</span> (cefuroxime), <span style="color: #00BB00; font-weight: bold;">FOX</span> (cefoxitin), <span style="color: #00BB00; font-weight: bold;">CTX</span> (cefotaxime), <span style="color: #00BB00; font-weight: bold;">CAZ</span></span></span> <span><span class="co">#&gt; (cefepime), <span style="color: #00BB00; font-weight: bold;">CXM</span> (cefuroxime), <span style="color: #00BB00; font-weight: bold;">FOX</span> (cefoxitin), <span style="color: #00BB00; font-weight: bold;">CTX</span> (cefotaxime), <span style="color: #00BB00; font-weight: bold;">CAZ</span></span></span>
@@ -482,16 +482,16 @@ package.</p>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 500 × 19</span></span></span> <span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 500 × 19</span></span></span>
<span><span class="co">#&gt; esbl genus AMC AMP TZP CXM FOX CTX CAZ GEN TOB TMP SXT</span></span> <span><span class="co">#&gt; esbl genus AMC AMP TZP CXM FOX CTX CAZ GEN TOB TMP SXT</span></span>
<span><span class="co">#&gt; <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span></span></span> <span><span class="co">#&gt; <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> FALSE Esch… 32 32 4 64 64 8<span style="color: #555555;">.00</span> 8<span style="color: #555555;">.00</span> 1 1 16<span style="color: #555555;">.0</span> 20</span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> FALSE Esch… 32 32 4 64 64 8<span style="color: #949494;">.00</span> 8<span style="color: #949494;">.00</span> 1 1 16<span style="color: #949494;">.0</span> 20</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> FALSE Esch… 32 32 4 64 64 4<span style="color: #555555;">.00</span> 8<span style="color: #555555;">.00</span> 1 1 16<span style="color: #555555;">.0</span> 320</span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> FALSE Esch… 32 32 4 64 64 4<span style="color: #949494;">.00</span> 8<span style="color: #949494;">.00</span> 1 1 16<span style="color: #949494;">.0</span> 320</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> FALSE Esch… 4 2 64 8 4 8<span style="color: #555555;">.00</span> 0.12 16 16 0.5 20</span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> FALSE Esch… 4 2 64 8 4 8<span style="color: #949494;">.00</span> 0.12 16 16 0.5 20</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> FALSE Kleb… 32 32 16 64 64 8<span style="color: #555555;">.00</span> 8<span style="color: #555555;">.00</span> 1 1 0.5 20</span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> FALSE Kleb… 32 32 16 64 64 8<span style="color: #949494;">.00</span> 8<span style="color: #949494;">.00</span> 1 1 0.5 20</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> FALSE Esch… 32 32 4 4 4 0.25 2<span style="color: #555555;">.00</span> 1 1 16<span style="color: #555555;">.0</span> 320</span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> FALSE Esch… 32 32 4 4 4 0.25 2<span style="color: #949494;">.00</span> 1 1 16<span style="color: #949494;">.0</span> 320</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> FALSE Citr… 32 32 16 64 64 64<span style="color: #555555;">.00</span> 32<span style="color: #555555;">.00</span> 1 1 0.5 20</span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> FALSE Citr… 32 32 16 64 64 64<span style="color: #949494;">.00</span> 32<span style="color: #949494;">.00</span> 1 1 0.5 20</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> FALSE Morg… 32 32 4 64 64 16<span style="color: #555555;">.00</span> 2<span style="color: #555555;">.00</span> 1 1 0.5 20</span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> FALSE Morg… 32 32 4 64 64 16<span style="color: #949494;">.00</span> 2<span style="color: #949494;">.00</span> 1 1 0.5 20</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> FALSE Prot… 16 32 4 1 4 8<span style="color: #555555;">.00</span> 0.12 1 1 16<span style="color: #555555;">.0</span> 320</span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> FALSE Prot… 16 32 4 1 4 8<span style="color: #949494;">.00</span> 0.12 1 1 16<span style="color: #949494;">.0</span> 320</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> FALSE Ente… 32 32 8 64 64 32<span style="color: #555555;">.00</span> 4<span style="color: #555555;">.00</span> 1 1 0.5 20</span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> FALSE Ente… 32 32 8 64 64 32<span style="color: #949494;">.00</span> 4<span style="color: #949494;">.00</span> 1 1 0.5 20</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> FALSE Citr… 32 32 32 64 64 8<span style="color: #555555;">.00</span> 64<span style="color: #555555;">.00</span> 1 1 16<span style="color: #555555;">.0</span> 320</span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> FALSE Citr… 32 32 32 64 64 8<span style="color: #949494;">.00</span> 64<span style="color: #949494;">.00</span> 1 1 16<span style="color: #949494;">.0</span> 320</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 490 more rows</span></span></span> <span><span class="co">#&gt; <span style="color: #949494;"># ℹ 490 more rows</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 6 more variables: NIT &lt;mic&gt;, FOS &lt;mic&gt;, CIP &lt;mic&gt;, IPM &lt;mic&gt;, MEM &lt;mic&gt;,</span></span></span> <span><span class="co">#&gt; <span style="color: #949494;"># ℹ 6 more variables: NIT &lt;mic&gt;, FOS &lt;mic&gt;, CIP &lt;mic&gt;, IPM &lt;mic&gt;, MEM &lt;mic&gt;,</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># COL &lt;mic&gt;</span></span></span> <span><span class="co">#&gt; <span style="color: #949494;"># COL &lt;mic&gt;</span></span></span>
@@ -746,10 +746,10 @@ into a structured time-series format.</p>
<span> .names <span class="op">=</span> <span class="st">"res_{.col}"</span><span class="op">)</span>, </span> <span> .names <span class="op">=</span> <span class="st">"res_{.col}"</span><span class="op">)</span>, </span>
<span> .groups <span class="op">=</span> <span class="st">"drop"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span> <span> .groups <span class="op">=</span> <span class="st">"drop"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na</a></span><span class="op">(</span><span class="va">res_AMX</span><span class="op">)</span> <span class="op">&amp;</span> <span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na</a></span><span class="op">(</span><span class="va">res_AMC</span><span class="op">)</span> <span class="op">&amp;</span> <span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na</a></span><span class="op">(</span><span class="va">res_CIP</span><span class="op">)</span><span class="op">)</span> <span class="co"># Drop missing values</span></span> <span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na</a></span><span class="op">(</span><span class="va">res_AMX</span><span class="op">)</span> <span class="op">&amp;</span> <span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na</a></span><span class="op">(</span><span class="va">res_AMC</span><span class="op">)</span> <span class="op">&amp;</span> <span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na</a></span><span class="op">(</span><span class="va">res_CIP</span><span class="op">)</span><span class="op">)</span> <span class="co"># Drop missing values</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Using column '<span style="font-weight: bold;">mo</span>' as input for `col_mo`.</span></span> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Using column <span style="color: #00BB00; font-weight: bold;">mo</span> as input for `col_mo`.</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> `?resistance()` assumes the EUCAST guideline and thus considers the 'I'</span></span> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> `resistance()` assumes the EUCAST guideline and thus considers the 'I'</span></span>
<span><span class="co">#&gt; category susceptible. Set the `guideline` argument or the `AMR_guideline`</span></span> <span><span class="co">#&gt; category susceptible. Set the `guideline` argument or the `AMR_guideline`</span></span>
<span><span class="co">#&gt; option to either "CLSI" or "EUCAST", see AMR-options.</span></span> <span><span class="co">#&gt; option to either "CLSI" or "EUCAST", see `?AMR-options`.</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> This message will be shown once per session.</span></span> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> This message will be shown once per session.</span></span>
<span></span> <span></span>
<span><span class="va">data_time</span></span> <span><span class="va">data_time</span></span>

18
articles/AMR_with_tidymodels.md
View File

@@ -94,9 +94,9 @@ data <- example_isolates %>%
mo = as.factor(mo_gramstain(mo))) %>% mo = as.factor(mo_gramstain(mo))) %>%
# drop NAs - the ones without a Gramstain (fungi, etc.) # drop NAs - the ones without a Gramstain (fungi, etc.)
drop_na() drop_na()
#> ℹ For `?aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), #> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK
#> AMK (amikacin), and KAN (kanamycin) #> (amikacin), and KAN (kanamycin)
#> ℹ For `?betalactams()` using columns PEN (benzylpenicillin), OXA (oxacillin), #> ℹ For `betalactams()` using columns PEN (benzylpenicillin), OXA (oxacillin),
#> FLC (flucloxacillin), AMX (amoxicillin), AMC (amoxicillin/clavulanic acid), #> FLC (flucloxacillin), AMX (amoxicillin), AMC (amoxicillin/clavulanic acid),
#> AMP (ampicillin), TZP (piperacillin/tazobactam), CZO (cefazolin), FEP #> AMP (ampicillin), TZP (piperacillin/tazobactam), CZO (cefazolin), FEP
#> (cefepime), CXM (cefuroxime), FOX (cefoxitin), CTX (cefotaxime), CAZ #> (cefepime), CXM (cefuroxime), FOX (cefoxitin), CTX (cefotaxime), CAZ
@@ -143,9 +143,9 @@ a training set using `prep()`:
``` r ``` r
prep(resistance_recipe) prep(resistance_recipe)
#> ℹ For `?aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), #> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK
#> AMK (amikacin), and KAN (kanamycin) #> (amikacin), and KAN (kanamycin)
#> ℹ For `?betalactams()` using columns PEN (benzylpenicillin), OXA (oxacillin), #> ℹ For `betalactams()` using columns PEN (benzylpenicillin), OXA (oxacillin),
#> FLC (flucloxacillin), AMX (amoxicillin), AMC (amoxicillin/clavulanic acid), #> FLC (flucloxacillin), AMX (amoxicillin), AMC (amoxicillin/clavulanic acid),
#> AMP (ampicillin), TZP (piperacillin/tazobactam), CZO (cefazolin), FEP #> AMP (ampicillin), TZP (piperacillin/tazobactam), CZO (cefazolin), FEP
#> (cefepime), CXM (cefuroxime), FOX (cefoxitin), CTX (cefotaxime), CAZ #> (cefepime), CXM (cefuroxime), FOX (cefoxitin), CTX (cefotaxime), CAZ
@@ -644,10 +644,10 @@ data_time <- example_isolates %>%
.names = "res_{.col}"), .names = "res_{.col}"),
.groups = "drop") %>% .groups = "drop") %>%
filter(!is.na(res_AMX) & !is.na(res_AMC) & !is.na(res_CIP)) # Drop missing values filter(!is.na(res_AMX) & !is.na(res_AMC) & !is.na(res_CIP)) # Drop missing values
#> ℹ Using column 'mo' as input for `col_mo`. #> ℹ Using column mo as input for `col_mo`.
#> ℹ `?resistance()` assumes the EUCAST guideline and thus considers the 'I' #> ℹ `resistance()` assumes the EUCAST guideline and thus considers the 'I'
#> category susceptible. Set the `guideline` argument or the `AMR_guideline` #> category susceptible. Set the `guideline` argument or the `AMR_guideline`
#> option to either "CLSI" or "EUCAST", see AMR-options. #> option to either "CLSI" or "EUCAST", see `?AMR-options`.
#> ℹ This message will be shown once per session. #> ℹ This message will be shown once per session.
data_time data_time

2
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@@ -30,7 +30,7 @@
<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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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
articles/PCA.html
View File

@@ -30,7 +30,7 @@
<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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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">
@@ -163,9 +163,9 @@ per taxonomic order and genus:</p>
<span> <span class="va">order</span>, <span class="va">genus</span>, <span class="va">AMC</span>, <span class="va">CXM</span>, <span class="va">CTX</span>,</span> <span> <span class="va">order</span>, <span class="va">genus</span>, <span class="va">AMC</span>, <span class="va">CXM</span>, <span class="va">CTX</span>,</span>
<span> <span class="va">CAZ</span>, <span class="va">GEN</span>, <span class="va">TOB</span>, <span class="va">TMP</span>, <span class="va">SXT</span></span> <span> <span class="va">CAZ</span>, <span class="va">GEN</span>, <span class="va">TOB</span>, <span class="va">TMP</span>, <span class="va">SXT</span></span>
<span> <span class="op">)</span> <span class="co"># and select only relevant columns</span></span> <span> <span class="op">)</span> <span class="co"># and select only relevant columns</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> `?resistance()` assumes the EUCAST guideline and thus considers the 'I'</span></span> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> `resistance()` assumes the EUCAST guideline and thus considers the 'I'</span></span>
<span><span class="co">#&gt; category susceptible. Set the `guideline` argument or the `AMR_guideline`</span></span> <span><span class="co">#&gt; category susceptible. Set the `guideline` argument or the `AMR_guideline`</span></span>
<span><span class="co">#&gt; option to either "CLSI" or "EUCAST", see AMR-options.</span></span> <span><span class="co">#&gt; option to either "CLSI" or "EUCAST", see `?AMR-options`.</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> This message will be shown once per session.</span></span> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> This message will be shown once per session.</span></span>
<span></span> <span></span>
<span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">resistance_data</span><span class="op">)</span></span> <span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">resistance_data</span><span class="op">)</span></span>

4
articles/PCA.md
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@@ -78,9 +78,9 @@ resistance_data <- example_isolates %>%
order, genus, AMC, CXM, CTX, order, genus, AMC, CXM, CTX,
CAZ, GEN, TOB, TMP, SXT CAZ, GEN, TOB, TMP, SXT
) # and select only relevant columns ) # and select only relevant columns
#> ℹ `?resistance()` assumes the EUCAST guideline and thus considers the 'I' #> ℹ `resistance()` assumes the EUCAST guideline and thus considers the 'I'
#> category susceptible. Set the `guideline` argument or the `AMR_guideline` #> category susceptible. Set the `guideline` argument or the `AMR_guideline`
#> option to either "CLSI" or "EUCAST", see AMR-options. #> option to either "CLSI" or "EUCAST", see `?AMR-options`.
#> ℹ This message will be shown once per session. #> ℹ This message will be shown once per session.
head(resistance_data) head(resistance_data)

6
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@@ -30,7 +30,7 @@
<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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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">
@@ -255,9 +255,9 @@ Longest: 40</p>
<code class="sourceCode R"><span><span class="co"># our transformed antibiotic columns</span></span> <code class="sourceCode R"><span><span class="co"># our transformed antibiotic columns</span></span>
<span><span class="co"># amoxicillin/clavulanic acid (J01CR02) as an example</span></span> <span><span class="co"># amoxicillin/clavulanic acid (J01CR02) as an example</span></span>
<span><span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://msberends.github.io/cleaner/reference/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">AMC_ND2</span><span class="op">)</span></span> <span><span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://msberends.github.io/cleaner/reference/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">AMC_ND2</span><span class="op">)</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> `?susceptibility()` assumes the EUCAST guideline and thus considers the 'I'</span></span> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> `susceptibility()` assumes the EUCAST guideline and thus considers the 'I'</span></span>
<span><span class="co">#&gt; category susceptible. Set the `guideline` argument or the `AMR_guideline`</span></span> <span><span class="co">#&gt; category susceptible. Set the `guideline` argument or the `AMR_guideline`</span></span>
<span><span class="co">#&gt; option to either "CLSI" or "EUCAST", see AMR-options.</span></span> <span><span class="co">#&gt; option to either "CLSI" or "EUCAST", see `?AMR-options`.</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> This message will be shown once per session.</span></span></code></pre></div> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> This message will be shown once per session.</span></span></code></pre></div>
<p><strong>Frequency table</strong></p> <p><strong>Frequency table</strong></p>
<p>Class: factor &gt; ordered &gt; sir (numeric)<br> <p>Class: factor &gt; ordered &gt; sir (numeric)<br>

4
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@@ -101,9 +101,9 @@ Longest: 40
# our transformed antibiotic columns # our transformed antibiotic columns
# amoxicillin/clavulanic acid (J01CR02) as an example # amoxicillin/clavulanic acid (J01CR02) as an example
data %>% freq(AMC_ND2) data %>% freq(AMC_ND2)
#> ℹ `?susceptibility()` assumes the EUCAST guideline and thus considers the 'I' #> ℹ `susceptibility()` assumes the EUCAST guideline and thus considers the 'I'
#> category susceptible. Set the `guideline` argument or the `AMR_guideline` #> category susceptible. Set the `guideline` argument or the `AMR_guideline`
#> option to either "CLSI" or "EUCAST", see AMR-options. #> option to either "CLSI" or "EUCAST", see `?AMR-options`.
#> ℹ This message will be shown once per session. #> ℹ This message will be shown once per session.
``` ```

22
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@@ -30,7 +30,7 @@
<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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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">
@@ -253,16 +253,16 @@ I (intermediate [CLSI], or susceptible, increased exposure
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,000 × 46</span></span></span> <span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,000 × 46</span></span></span>
<span><span class="co">#&gt; date patient age gender ward mo PEN OXA FLC AMX </span></span> <span><span class="co">#&gt; date patient age gender ward mo PEN OXA FLC AMX </span></span>
<span><span class="co">#&gt; <span style="color: #949494; font-style: italic;">&lt;date&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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span></span> <span><span class="co">#&gt; <span style="color: #949494; font-style: italic;">&lt;date&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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> </span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> 2002-01-03 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> </span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> 2002-01-03 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> 2002-01-16 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> 2002-01-16 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> 2002-01-17 858515 79 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #B2B2B2;"> NA</span> </span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> 2002-01-17 858515 79 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #949494;"> NA</span> </span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 1,990 more rows</span></span></span> <span><span class="co">#&gt; <span style="color: #949494;"># ℹ 1,990 more rows</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;,</span></span></span> <span><span class="co">#&gt; <span style="color: #949494;"># ℹ 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;,</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;,</span></span></span> <span><span class="co">#&gt; <span style="color: #949494;"># CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;,</span></span></span>

6
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@@ -30,7 +30,7 @@
<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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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">
@@ -80,7 +80,7 @@
<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>Download data sets for download / own use</h1> <img src="../logo.svg" class="logo" alt=""><h1>Download data sets for download / own use</h1>
<h4 data-toc-skip class="date">22 March 2026</h4> <h4 data-toc-skip class="date">24 March 2026</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>
@@ -424,7 +424,7 @@ column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>a
<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>antimicrobials</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 22 March 2026 21:16:59 UTC. Find more info <p>It was last updated on 23 March 2026 09:38:28 UTC. Find more info
about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/antimicrobials.html">data set about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/antimicrobials.html">data set
here</a>.</p> here</a>.</p>
<p><strong>Direct download links:</strong></p> <p><strong>Direct download links:</strong></p>

2
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@@ -100,7 +100,7 @@ names:
This data set is in R available as `antimicrobials`, after you load the This data set is in R available as `antimicrobials`, after you load the
`AMR` package. `AMR` package.
It was last updated on 22 March 2026 21:16:59 UTC. Find more info about It was last updated on 23 March 2026 09:38:28 UTC. Find more info about
the contents, (scientific) source, and structure of this [data set the contents, (scientific) source, and structure of this [data set
here](https://amr-for-r.org/reference/antimicrobials.html). here](https://amr-for-r.org/reference/antimicrobials.html).

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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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
authors.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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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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@@ -33,7 +33,7 @@
<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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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">

12
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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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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">
@@ -49,9 +49,9 @@
</div> </div>
<div class="section level2"> <div class="section level2">
<h2 class="pkg-version" data-toc-text="3.0.1.9038" id="amr-3019038">AMR 3.0.1.9038<a class="anchor" aria-label="anchor" href="#amr-3019038"></a></h2> <h2 class="pkg-version" data-toc-text="3.0.1.9040" id="amr-3019040">AMR 3.0.1.9040<a class="anchor" aria-label="anchor" href="#amr-3019040"></a></h2>
<div class="section level4"> <div class="section level4">
<h4 id="new-3-0-1-9038">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9038"></a></h4> <h4 id="new-3-0-1-9040">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9040"></a></h4>
<ul><li>Integration with the <strong>tidymodels</strong> framework to allow seamless use of SIR, MIC and disk data in modelling pipelines via <code>recipes</code> <ul><li>Integration with the <strong>tidymodels</strong> framework to allow seamless use of SIR, MIC and disk data in modelling pipelines via <code>recipes</code>
<ul><li> <ul><li>
<code><a href="../reference/amr-tidymodels.html">step_mic_log2()</a></code> to transform <code>&lt;mic&gt;</code> columns with log2, and <code><a href="../reference/amr-tidymodels.html">step_sir_numeric()</a></code> to convert <code>&lt;sir&gt;</code> columns to numeric</li> <code><a href="../reference/amr-tidymodels.html">step_mic_log2()</a></code> to transform <code>&lt;mic&gt;</code> columns with log2, and <code><a href="../reference/amr-tidymodels.html">step_sir_numeric()</a></code> to convert <code>&lt;sir&gt;</code> columns to numeric</li>
@@ -83,12 +83,14 @@
<li>Function <code><a href="../reference/amr_course.html">amr_course()</a></code>, which allows for automated download and unpacking of a GitHub repository for e.g. webinar use</li> <li>Function <code><a href="../reference/amr_course.html">amr_course()</a></code>, which allows for automated download and unpacking of a GitHub repository for e.g. webinar use</li>
</ul></div> </ul></div>
<div class="section level4"> <div class="section level4">
<h4 id="fixes-3-0-1-9038">Fixes<a class="anchor" aria-label="anchor" href="#fixes-3-0-1-9038"></a></h4> <h4 id="fixes-3-0-1-9040">Fixes<a class="anchor" aria-label="anchor" href="#fixes-3-0-1-9040"></a></h4>
<ul><li>Fixed a bug in <code><a href="../reference/as.sir.html">as.sir()</a></code> where values that were purely numeric (e.g., <code>"1"</code>) and matched the broad SIR-matching regex would be incorrectly stripped of all content by the Unicode letter filter</li> <ul><li>Fixed a bug in <code><a href="../reference/as.sir.html">as.sir()</a></code> where values that were purely numeric (e.g., <code>"1"</code>) and matched the broad SIR-matching regex would be incorrectly stripped of all content by the Unicode letter filter</li>
<li>Fixed a bug in <code><a href="../reference/as.mic.html">as.mic()</a></code> where MIC values in scientific notation (e.g., <code>"1e-3"</code>) were incorrectly handled because the letter <code>e</code> was removed along with other Unicode letters; scientific notation <code>e</code> is now preserved</li> <li>Fixed a bug in <code><a href="../reference/as.mic.html">as.mic()</a></code> where MIC values in scientific notation (e.g., <code>"1e-3"</code>) were incorrectly handled because the letter <code>e</code> was removed along with other Unicode letters; scientific notation <code>e</code> is now preserved</li>
<li>Fixed a bug in <code><a href="../reference/as.ab.html">as.ab()</a></code> where certain AB codes containing “PH” or “TH” (such as <code>ETH</code>, <code>MTH</code>, <code>PHE</code>, <code>PHN</code>, <code>STH</code>, <code>THA</code>, <code>THI1</code>) would incorrectly return <code>NA</code> when combined in a vector with any untranslatable value (<a href="https://github.com/msberends/AMR/issues/245" class="external-link">#245</a>)</li> <li>Fixed a bug in <code><a href="../reference/as.ab.html">as.ab()</a></code> where certain AB codes containing “PH” or “TH” (such as <code>ETH</code>, <code>MTH</code>, <code>PHE</code>, <code>PHN</code>, <code>STH</code>, <code>THA</code>, <code>THI1</code>) would incorrectly return <code>NA</code> when combined in a vector with any untranslatable value (<a href="https://github.com/msberends/AMR/issues/245" class="external-link">#245</a>)</li>
<li>Fixed a bug in <code><a href="../reference/antibiogram.html">antibiogram()</a></code> for when no antimicrobials are set</li> <li>Fixed a bug in <code><a href="../reference/antibiogram.html">antibiogram()</a></code> for when no antimicrobials are set</li>
<li>Fixed a bug in <code><a href="../reference/as.sir.html">as.sir()</a></code> where for numeric input the arguments <code>S</code>, <code>I</code>, and <code>R</code> would not be considered (<a href="https://github.com/msberends/AMR/issues/244" class="external-link">#244</a>)</li> <li>Fixed a bug in <code><a href="../reference/as.sir.html">as.sir()</a></code> where for numeric input the arguments <code>S</code>, <code>I</code>, and <code>R</code> would not be considered (<a href="https://github.com/msberends/AMR/issues/244" class="external-link">#244</a>)</li>
<li>Fixed a bug in plotting MIC values when <code>keep_operators = "all"</code>
</li>
<li>Fixed some foreign translations of antimicrobial drugs</li> <li>Fixed some foreign translations of antimicrobial drugs</li>
<li>Fixed a bug for printing column names to the console when using <code>mutate_at(vars(...), as.mic)</code> (<a href="https://github.com/msberends/AMR/issues/249" class="external-link">#249</a>)</li> <li>Fixed a bug for printing column names to the console when using <code>mutate_at(vars(...), as.mic)</code> (<a href="https://github.com/msberends/AMR/issues/249" class="external-link">#249</a>)</li>
<li>Fixed a bug to disregard <code>NI</code> for susceptibility proportion functions</li> <li>Fixed a bug to disregard <code>NI</code> for susceptibility proportion functions</li>
@@ -96,7 +98,7 @@
<li>Fixed SIR and MIC coercion of combined values, e.g. <code>as.sir("&lt;= 0.002; S")</code> or <code>as.mic("S; 0.002")</code> (<a href="https://github.com/msberends/AMR/issues/252" class="external-link">#252</a>)</li> <li>Fixed SIR and MIC coercion of combined values, e.g. <code>as.sir("&lt;= 0.002; S")</code> or <code>as.mic("S; 0.002")</code> (<a href="https://github.com/msberends/AMR/issues/252" class="external-link">#252</a>)</li>
</ul></div> </ul></div>
<div class="section level4"> <div class="section level4">
<h4 id="updates-3-0-1-9038">Updates<a class="anchor" aria-label="anchor" href="#updates-3-0-1-9038"></a></h4> <h4 id="updates-3-0-1-9040">Updates<a class="anchor" aria-label="anchor" href="#updates-3-0-1-9040"></a></h4>
<ul><li>Extensive <code>cli</code> integration for better message handling and clickable links in messages and warnings (<a href="https://github.com/msberends/AMR/issues/191" class="external-link">#191</a>, <a href="https://github.com/msberends/AMR/issues/265" class="external-link">#265</a>)</li> <ul><li>Extensive <code>cli</code> integration for better message handling and clickable links in messages and warnings (<a href="https://github.com/msberends/AMR/issues/191" class="external-link">#191</a>, <a href="https://github.com/msberends/AMR/issues/265" class="external-link">#265</a>)</li>
<li> <li>
<code><a href="../reference/mdro.html">mdro()</a></code> now infers resistance for a <em>missing</em> base drug column from an <em>available</em> corresponding drug+inhibitor combination showing resistance (e.g., piperacillin is absent but required, while piperacillin/tazobactam available and resistant). Can be set with the new argument <code>infer_from_combinations</code>, which defaults to <code>TRUE</code> (<a href="https://github.com/msberends/AMR/issues/209" class="external-link">#209</a>). Note that this can yield a higher MDRO detection (which is a good thing as it has become more reliable).</li> <code><a href="../reference/mdro.html">mdro()</a></code> now infers resistance for a <em>missing</em> base drug column from an <em>available</em> corresponding drug+inhibitor combination showing resistance (e.g., piperacillin is absent but required, while piperacillin/tazobactam available and resistant). Can be set with the new argument <code>infer_from_combinations</code>, which defaults to <code>TRUE</code> (<a href="https://github.com/msberends/AMR/issues/209" class="external-link">#209</a>). Note that this can yield a higher MDRO detection (which is a good thing as it has become more reliable).</li>

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@@ -1,6 +1,6 @@
# Changelog # Changelog
## AMR 3.0.1.9038 ## AMR 3.0.1.9040
#### New #### New
@@ -67,6 +67,7 @@
- Fixed a bug in [`as.sir()`](https://amr-for-r.org/reference/as.sir.md) - Fixed a bug in [`as.sir()`](https://amr-for-r.org/reference/as.sir.md)
where for numeric input the arguments `S`, `I`, and `R` would not be where for numeric input the arguments `S`, `I`, and `R` would not be
considered ([\#244](https://github.com/msberends/AMR/issues/244)) considered ([\#244](https://github.com/msberends/AMR/issues/244))
- Fixed a bug in plotting MIC values when `keep_operators = "all"`
- Fixed some foreign translations of antimicrobial drugs - Fixed some foreign translations of antimicrobial drugs
- Fixed a bug for printing column names to the console when using - Fixed a bug for printing column names to the console when using
`mutate_at(vars(...), as.mic)` `mutate_at(vars(...), as.mic)`

2
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@@ -10,7 +10,7 @@ articles:
PCA: PCA.html PCA: PCA.html
WHONET: WHONET.html WHONET: WHONET.html
WISCA: WISCA.html WISCA: WISCA.html
last_built: 2026-03-22T21:26Z last_built: 2026-03-24T12:29Z
urls: urls:
reference: https://amr-for-r.org/reference reference: https://amr-for-r.org/reference
article: https://amr-for-r.org/articles article: https://amr-for-r.org/articles

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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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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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@@ -9,7 +9,7 @@ options(AMR_guideline = "CLSI")'><meta property="og:image" content="https://amr-
<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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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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@@ -21,7 +21,7 @@ The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish
<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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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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@@ -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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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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@@ -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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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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@@ -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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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/ab_property.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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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
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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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">
@@ -197,7 +197,7 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> random_column coflu ampicillin</span> <span class="r-out co"><span class="r-pr">#&gt;</span> random_column coflu ampicillin</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 some value S R</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 1 some value S R</span>
<span class="r-in"><span><span class="va">x</span><span class="op">[</span>, <span class="fu"><a href="antimicrobial_selectors.html">betalactams</a></span><span class="op">(</span><span class="op">)</span><span class="op">]</span></span></span> <span class="r-in"><span><span class="va">x</span><span class="op">[</span>, <span class="fu"><a href="antimicrobial_selectors.html">betalactams</a></span><span class="op">(</span><span class="op">)</span><span class="op">]</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?betalactams()` using columns <span style="color: #00BB00; font-weight: bold;">coflu</span> (co-fluampicil) and <span style="color: #00BB00; font-weight: bold;">ampicillin</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `betalactams()` using columns <span style="color: #00BB00; font-weight: bold;">coflu</span> (co-fluampicil) and <span style="color: #00BB00; font-weight: bold;">ampicillin</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> coflu ampicillin</span> <span class="r-out co"><span class="r-pr">#&gt;</span> coflu ampicillin</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 S R</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 1 S R</span>
<span class="r-in"><span><span class="co"># }</span></span></span> <span class="r-in"><span><span class="co"># }</span></span></span>

2
reference/add_custom_antimicrobials.md
View File

@@ -185,7 +185,7 @@ x
#> random_column coflu ampicillin #> random_column coflu ampicillin
#> 1 some value S R #> 1 some value S R
x[, betalactams()] x[, betalactams()]
#> ℹ For `?betalactams()` using columns coflu (co-fluampicil) and ampicillin #> ℹ For `betalactams()` using columns coflu (co-fluampicil) and ampicillin
#> coflu ampicillin #> coflu ampicillin
#> 1 S R #> 1 S R
# } # }

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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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
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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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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">
@@ -112,16 +112,16 @@
<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 1999-06-30 26 26.72603 0</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 1 1999-06-30 26 26.73151 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1968-01-29 58 58.14247 31</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 2 1968-01-29 58 58.14795 31</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1965-12-05 60 60.29315 34</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 3 1965-12-05 60 60.29863 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1980-03-01 46 46.05753 19</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 4 1980-03-01 46 46.06301 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1949-11-01 76 76.38630 50</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 5 1949-11-01 76 76.39178 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1947-02-14 79 79.09863 52</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 6 1947-02-14 79 79.10411 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1940-02-19 86 86.08493 59</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 7 1940-02-19 86 86.09041 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1988-01-10 38 38.19452 11</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 8 1988-01-10 38 38.20000 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1997-08-27 28 28.56712 2</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 9 1997-08-27 28 28.57260 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1978-01-26 48 48.15068 21</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 10 1978-01-26 48 48.15616 21</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>

20
reference/age.md
View File

@@ -81,14 +81,14 @@ df$age_at_y2k <- age(df$birth_date, "2000-01-01")
df df
#> birth_date age age_exact age_at_y2k #> birth_date age age_exact age_at_y2k
#> 1 1999-06-30 26 26.72603 0 #> 1 1999-06-30 26 26.73151 0
#> 2 1968-01-29 58 58.14247 31 #> 2 1968-01-29 58 58.14795 31
#> 3 1965-12-05 60 60.29315 34 #> 3 1965-12-05 60 60.29863 34
#> 4 1980-03-01 46 46.05753 19 #> 4 1980-03-01 46 46.06301 19
#> 5 1949-11-01 76 76.38630 50 #> 5 1949-11-01 76 76.39178 50
#> 6 1947-02-14 79 79.09863 52 #> 6 1947-02-14 79 79.10411 52
#> 7 1940-02-19 86 86.08493 59 #> 7 1940-02-19 86 86.09041 59
#> 8 1988-01-10 38 38.19452 11 #> 8 1988-01-10 38 38.20000 11
#> 9 1997-08-27 28 28.56712 2 #> 9 1997-08-27 28 28.57260 2
#> 10 1978-01-26 48 48.15068 21 #> 10 1978-01-26 48 48.15616 21
``` ```

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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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/amr-tidymodels.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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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/amr_course.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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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">

50
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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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">
@@ -384,16 +384,16 @@ Adhering to previously described approaches (see Source) and especially the Baye
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2,000 × 46</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2,000 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span> <span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </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;"> 1</span> 2002-01-02 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2002-01-03 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </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;"> 2</span> 2002-01-03 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2002-01-16 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2002-01-16 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2002-01-17 858515 79 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </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> 2002-01-17 858515 79 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #949494;"> 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-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;,</span></span>
@@ -408,9 +408,9 @@ Adhering to previously described approaches (see Source) and especially the Baye
<span class="r-in"><span><span class="fu">antibiogram</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span> <span class="r-in"><span><span class="fu">antibiogram</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
<span class="r-in"><span> antimicrobials <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="antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="antimicrobial_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-in"><span> antimicrobials <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="antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="antimicrobial_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</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: #00BBBB;">ℹ</span> For `?aminoglycosides()` using columns <span style="color: #00BB00; font-weight: bold;">GEN</span> (gentamicin), <span style="color: #00BB00; font-weight: bold;">TOB</span> (tobramycin),</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns <span style="color: #00BB00; font-weight: bold;">GEN</span> (gentamicin), <span style="color: #00BB00; font-weight: bold;">TOB</span> (tobramycin), <span style="color: #00BB00; font-weight: bold;">AMK</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00; font-weight: bold;">AMK</span> (amikacin), and <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin)</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> (amikacin), and <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram: 10 × 7</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram: 10 × 7</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Type: Non-WISCA with 95% CI</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Type: Non-WISCA with 95% CI</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>
@@ -433,8 +433,8 @@ Adhering to previously described approaches (see Source) and especially the Baye
<span class="r-in"><span> ab_transform <span class="op">=</span> <span class="st">"atc"</span>,</span></span> <span class="r-in"><span> ab_transform <span class="op">=</span> <span class="st">"atc"</span>,</span></span>
<span class="r-in"><span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span></span></span> <span class="r-in"><span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</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: #00BBBB;">ℹ</span> For `?aminoglycosides()` using columns <span style="color: #00BB00; font-weight: bold;">GEN</span> (gentamicin), <span style="color: #00BB00; font-weight: bold;">TOB</span> (tobramycin),</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns <span style="color: #00BB00; font-weight: bold;">GEN</span> (gentamicin), <span style="color: #00BB00; font-weight: bold;">TOB</span> (tobramycin), <span style="color: #00BB00; font-weight: bold;">AMK</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00; font-weight: bold;">AMK</span> (amikacin), and <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin)</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> (amikacin), and <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram: 2 × 5</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram: 2 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Type: Non-WISCA with 95% CI</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Type: Non-WISCA with 95% CI</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>
@@ -449,7 +449,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
<span class="r-in"><span> ab_transform <span class="op">=</span> <span class="st">"name"</span>,</span></span> <span class="r-in"><span> ab_transform <span class="op">=</span> <span class="st">"name"</span>,</span></span>
<span class="r-in"><span> mo_transform <span class="op">=</span> <span class="st">"name"</span></span></span> <span class="r-in"><span> mo_transform <span class="op">=</span> <span class="st">"name"</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: #00BBBB;">ℹ</span> For `?carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram: 5 × 3</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram: 5 × 3</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Type: Non-WISCA with 95% CI</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Type: Non-WISCA with 95% CI</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>
@@ -487,7 +487,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
<span class="r-in"><span> antimicrobials <span class="op">=</span> <span class="fu"><a href="antimicrobial_selectors.html">ureidopenicillins</a></span><span class="op">(</span><span class="op">)</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="st">""</span>, <span class="st">"GEN"</span>, <span class="st">"tobra"</span><span class="op">)</span>,</span></span> <span class="r-in"><span> antimicrobials <span class="op">=</span> <span class="fu"><a href="antimicrobial_selectors.html">ureidopenicillins</a></span><span class="op">(</span><span class="op">)</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="st">""</span>, <span class="st">"GEN"</span>, <span class="st">"tobra"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span></span></span> <span class="r-in"><span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</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: #00BBBB;">ℹ</span> For `?ureidopenicillins()` using column <span style="color: #00BB00; font-weight: bold;">TZP</span> (piperacillin/tazobactam)</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `ureidopenicillins()` using column <span style="color: #00BB00; font-weight: bold;">TZP</span> (piperacillin/tazobactam)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram: 2 × 4</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram: 2 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Type: Non-WISCA with 95% CI</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Type: Non-WISCA with 95% CI</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>
@@ -524,9 +524,9 @@ Adhering to previously described approaches (see Source) and especially the Baye
<span class="r-in"><span> antimicrobials <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="antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="antimicrobial_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>,</span></span> <span class="r-in"><span> antimicrobials <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="antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="antimicrobial_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> syndromic_group <span class="op">=</span> <span class="st">"ward"</span></span></span> <span class="r-in"><span> syndromic_group <span class="op">=</span> <span class="st">"ward"</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: #00BBBB;">ℹ</span> For `?aminoglycosides()` using columns <span style="color: #00BB00; font-weight: bold;">GEN</span> (gentamicin), <span style="color: #00BB00; font-weight: bold;">TOB</span> (tobramycin),</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns <span style="color: #00BB00; font-weight: bold;">GEN</span> (gentamicin), <span style="color: #00BB00; font-weight: bold;">TOB</span> (tobramycin), <span style="color: #00BB00; font-weight: bold;">AMK</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00; font-weight: bold;">AMK</span> (amikacin), and <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin)</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> (amikacin), and <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram: 14 × 8</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram: 14 × 8</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Type: Non-WISCA with 95% CI</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Type: Non-WISCA with 95% CI</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> `Syndromic Group` Pathogen Amikacin Gentamicin Imipenem Kanamycin Meropenem</span> <span class="r-out co"><span class="r-pr">#&gt;</span> `Syndromic Group` Pathogen Amikacin Gentamicin Imipenem Kanamycin Meropenem</span>
@@ -551,7 +551,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># now define a data set with only E. coli</span></span></span> <span class="r-in"><span><span class="co"># now define a data set with only E. coli</span></span></span>
<span class="r-in"><span><span class="va">ex1</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu"><a href="mo_property.html">mo_genus</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"Escherichia"</span><span class="op">)</span>, <span class="op">]</span></span></span> <span class="r-in"><span><span class="va">ex1</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu"><a href="mo_property.html">mo_genus</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"Escherichia"</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Using column '<span style="font-weight: bold;">mo</span>' as input for `?mo_genus()`</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Using column <span style="color: #00BB00; font-weight: bold;">mo</span> as input for `mo_genus()`</span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># with a custom language, though this will be determined automatically</span></span></span> <span class="r-in"><span><span class="co"># with a custom language, though this will be determined automatically</span></span></span>
<span class="r-in"><span><span class="co"># (i.e., this table will be in Spanish on Spanish systems)</span></span></span> <span class="r-in"><span><span class="co"># (i.e., this table will be in Spanish on Spanish systems)</span></span></span>
@@ -563,8 +563,8 @@ Adhering to previously described approaches (see Source) and especially the Baye
<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> language <span class="op">=</span> <span class="st">"es"</span></span></span> <span class="r-in"><span> language <span class="op">=</span> <span class="st">"es"</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: #00BBBB;">ℹ</span> For `?aminoglycosides()` using columns <span style="color: #00BB00; font-weight: bold;">GEN</span> (gentamicin), <span style="color: #00BB00; font-weight: bold;">TOB</span> (tobramycin),</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns <span style="color: #00BB00; font-weight: bold;">GEN</span> (gentamicin), <span style="color: #00BB00; font-weight: bold;">TOB</span> (tobramycin), <span style="color: #00BB00; font-weight: bold;">AMK</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00; font-weight: bold;">AMK</span> (amikacin), and <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin)</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> (amikacin), and <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram: 2 × 5</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram: 2 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Type: Non-WISCA with 95% CI</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Type: Non-WISCA with 95% CI</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>
@@ -603,7 +603,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
<span class="r-in"><span> syndromic_group <span class="op">=</span> <span class="st">"ward"</span>,</span></span> <span class="r-in"><span> syndromic_group <span class="op">=</span> <span class="st">"ward"</span>,</span></span>
<span class="r-in"><span> wisca <span class="op">=</span> <span class="cn">TRUE</span></span></span> <span class="r-in"><span> wisca <span class="op">=</span> <span class="cn">TRUE</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: #00BBBB;">ℹ</span> For `?ureidopenicillins()` using column <span style="color: #00BB00; font-weight: bold;">TZP</span> (piperacillin/tazobactam)</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `ureidopenicillins()` using column <span style="color: #00BB00; font-weight: bold;">TZP</span> (piperacillin/tazobactam)</span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># in an Rmd file, you would just need to return `ureido` in a chunk,</span></span></span> <span class="r-in"><span><span class="co"># in an Rmd file, you would just need to return `ureido` in a chunk,</span></span></span>
<span class="r-in"><span><span class="co"># but to be explicit here:</span></span></span> <span class="r-in"><span><span class="co"># but to be explicit here:</span></span></span>

28
reference/antibiogram.md
View File

@@ -598,9 +598,9 @@ example_isolates
antibiogram(example_isolates, antibiogram(example_isolates,
antimicrobials = c(aminoglycosides(), carbapenems()) antimicrobials = c(aminoglycosides(), carbapenems())
) )
#> ℹ For `?aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), #> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK
#> AMK (amikacin), and KAN (kanamycin) #> (amikacin), and KAN (kanamycin)
#> ℹ For `?carbapenems()` using columns IPM (imipenem) and MEM (meropenem) #> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> # An Antibiogram: 10 × 7 #> # An Antibiogram: 10 × 7
#> # Type: Non-WISCA with 95% CI #> # Type: Non-WISCA with 95% CI
#> Pathogen Amikacin Gentamicin Imipenem Kanamycin Meropenem Tobramycin #> Pathogen Amikacin Gentamicin Imipenem Kanamycin Meropenem Tobramycin
@@ -623,8 +623,8 @@ antibiogram(example_isolates,
ab_transform = "atc", ab_transform = "atc",
mo_transform = "gramstain" mo_transform = "gramstain"
) )
#> ℹ For `?aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), #> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK
#> AMK (amikacin), and KAN (kanamycin) #> (amikacin), and KAN (kanamycin)
#> # An Antibiogram: 2 × 5 #> # An Antibiogram: 2 × 5
#> # Type: Non-WISCA with 95% CI #> # Type: Non-WISCA with 95% CI
#> Pathogen J01GB01 J01GB03 J01GB04 J01GB06 #> Pathogen J01GB01 J01GB03 J01GB04 J01GB06
@@ -639,7 +639,7 @@ antibiogram(example_isolates,
ab_transform = "name", ab_transform = "name",
mo_transform = "name" mo_transform = "name"
) )
#> ℹ For `?carbapenems()` using columns IPM (imipenem) and MEM (meropenem) #> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> # An Antibiogram: 5 × 3 #> # An Antibiogram: 5 × 3
#> # Type: Non-WISCA with 95% CI #> # Type: Non-WISCA with 95% CI
#> Pathogen Imipenem Meropenem #> Pathogen Imipenem Meropenem
@@ -677,7 +677,7 @@ antibiogram(example_isolates,
antimicrobials = ureidopenicillins() + c("", "GEN", "tobra"), antimicrobials = ureidopenicillins() + c("", "GEN", "tobra"),
mo_transform = "gramstain" mo_transform = "gramstain"
) )
#> ℹ For `?ureidopenicillins()` using column TZP (piperacillin/tazobactam) #> ℹ For `ureidopenicillins()` using column TZP (piperacillin/tazobactam)
#> # An Antibiogram: 2 × 4 #> # An Antibiogram: 2 × 4
#> # Type: Non-WISCA with 95% CI #> # Type: Non-WISCA with 95% CI
#> Pathogen Piperacillin/tazobac…¹ Piperacillin/tazobac…² Piperacillin/tazobac…³ #> Pathogen Piperacillin/tazobac…¹ Piperacillin/tazobac…² Piperacillin/tazobac…³
@@ -714,9 +714,9 @@ antibiogram(example_isolates,
antimicrobials = c(aminoglycosides(), carbapenems()), antimicrobials = c(aminoglycosides(), carbapenems()),
syndromic_group = "ward" syndromic_group = "ward"
) )
#> ℹ For `?aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), #> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK
#> AMK (amikacin), and KAN (kanamycin) #> (amikacin), and KAN (kanamycin)
#> ℹ For `?carbapenems()` using columns IPM (imipenem) and MEM (meropenem) #> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> # An Antibiogram: 14 × 8 #> # An Antibiogram: 14 × 8
#> # Type: Non-WISCA with 95% CI #> # Type: Non-WISCA with 95% CI
#> `Syndromic Group` Pathogen Amikacin Gentamicin Imipenem Kanamycin Meropenem #> `Syndromic Group` Pathogen Amikacin Gentamicin Imipenem Kanamycin Meropenem
@@ -741,7 +741,7 @@ antibiogram(example_isolates,
# now define a data set with only E. coli # now define a data set with only E. coli
ex1 <- example_isolates[which(mo_genus() == "Escherichia"), ] ex1 <- example_isolates[which(mo_genus() == "Escherichia"), ]
#> ℹ Using column 'mo' as input for `?mo_genus()` #> ℹ Using column mo as input for `mo_genus()`
# with a custom language, though this will be determined automatically # with a custom language, though this will be determined automatically
# (i.e., this table will be in Spanish on Spanish systems) # (i.e., this table will be in Spanish on Spanish systems)
@@ -753,8 +753,8 @@ antibiogram(ex1,
), ),
language = "es" language = "es"
) )
#> ℹ For `?aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), #> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK
#> AMK (amikacin), and KAN (kanamycin) #> (amikacin), and KAN (kanamycin)
#> # An Antibiogram: 2 × 5 #> # An Antibiogram: 2 × 5
#> # Type: Non-WISCA with 95% CI #> # Type: Non-WISCA with 95% CI
#> `Grupo sindrómico` Patógeno Amikacina Gentamicina Tobramicina #> `Grupo sindrómico` Patógeno Amikacina Gentamicina Tobramicina
@@ -793,7 +793,7 @@ ureido <- antibiogram(example_isolates,
syndromic_group = "ward", syndromic_group = "ward",
wisca = TRUE wisca = TRUE
) )
#> ℹ For `?ureidopenicillins()` using column TZP (piperacillin/tazobactam) #> ℹ For `ureidopenicillins()` using column TZP (piperacillin/tazobactam)
# in an Rmd file, you would just need to return `ureido` in a chunk, # in an Rmd file, you would just need to return `ureido` in a chunk,
# but to be explicit here: # but to be explicit here:

290
reference/antimicrobial_selectors.html
View File

@@ -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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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">
@@ -275,16 +275,16 @@ my_data_with_all_these_columns %&amp;gt;%
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2,000 × 46</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2,000 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span> <span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </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;"> 1</span> 2002-01-02 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2002-01-03 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </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;"> 2</span> 2002-01-03 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2002-01-16 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2002-01-16 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2002-01-17 858515 79 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </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> 2002-01-17 858515 79 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #949494;"> 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-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;,</span></span>
@@ -296,7 +296,7 @@ my_data_with_all_these_columns %&amp;gt;%
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># you can use the selectors separately to retrieve all possible antimicrobials:</span></span></span> <span class="r-in"><span><span class="co"># you can use the selectors separately to retrieve all possible antimicrobials:</span></span></span>
<span class="r-in"><span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> in `?carbapenems()`: Imipenem/EDTA (<span style="color: #00BB00;">IPE</span>) and meropenem/nacubactam (<span style="color: #00BB00;">MNC</span>) are</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> in `carbapenems()`: Imipenem/EDTA (<span style="color: #00BB00; font-weight: bold;">IPE</span>) and meropenem/nacubactam (<span style="color: #00BB00; font-weight: bold;">MNC</span>) are</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> not included since `only_treatable = TRUE`.</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> not included since `only_treatable = TRUE`.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> This <span style="color: #0000BB;">&lt;ab&gt;</span> vector was retrieved using `carbapenems()`, which should normally</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> This <span style="color: #0000BB;">&lt;ab&gt;</span> vector was retrieved using `carbapenems()`, which should normally</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> be used inside a <span style="color: #0000BB;">dplyr</span> verb or <span style="color: #0000BB;">&lt;data.frame&gt;</span> call, e.g.:</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> be used inside a <span style="color: #0000BB;">dplyr</span> verb or <span style="color: #0000BB;">&lt;data.frame&gt;</span> call, e.g.:</span>
@@ -404,44 +404,44 @@ my_data_with_all_these_columns %&amp;gt;%
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># select columns 'IPM' (imipenem) and 'MEM' (meropenem)</span></span></span> <span class="r-in"><span><span class="co"># select columns 'IPM' (imipenem) and 'MEM' (meropenem)</span></span></span>
<span class="r-in"><span><span class="va">example_isolates</span><span class="op">[</span>, <span class="fu">carbapenems</span><span class="op">(</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">carbapenems</span><span class="op">(</span><span class="op">)</span><span class="op">]</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2,000 × 2</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2,000 × 2</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> IPM MEM </span> <span class="r-out co"><span class="r-pr">#&gt;</span> IPM MEM </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</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;"> 1</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</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;"> 2</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</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;"> 3</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</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;"> 4</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</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;"> 5</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</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;"> 6</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</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;"> 7</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</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;"> 8</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</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;"> 9</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> 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: #B2B2B2;"> NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> 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"># select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB'</span></span></span> <span class="r-in"><span><span class="co"># select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB'</span></span></span>
<span class="r-in"><span><span class="va">example_isolates</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="st">"mo"</span>, <span class="fu">aminoglycosides</span><span class="op">(</span><span class="op">)</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"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"mo"</span>, <span class="fu">aminoglycosides</span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">]</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?aminoglycosides()` using columns <span style="color: #00BB00; font-weight: bold;">GEN</span> (gentamicin), <span style="color: #00BB00; font-weight: bold;">TOB</span> (tobramycin),</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns <span style="color: #00BB00; font-weight: bold;">GEN</span> (gentamicin), <span style="color: #00BB00; font-weight: bold;">TOB</span> (tobramycin), <span style="color: #00BB00; font-weight: bold;">AMK</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00; font-weight: bold;">AMK</span> (amikacin), and <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin)</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> (amikacin), and <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2,000 × 5</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2,000 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo GEN TOB AMK KAN </span> <span class="r-out co"><span class="r-pr">#&gt;</span> mo GEN TOB AMK KAN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #B2B2B2;"> NA</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;"> 1</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #B2B2B2;"> NA</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;"> 2</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #B2B2B2;"> NA</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;"> 3</span> <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #B2B2B2;"> NA</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;"> 4</span> <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #B2B2B2;"> NA</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;"> 5</span> <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #B2B2B2;"> NA</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;"> 6</span> <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <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> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <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> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #B2B2B2;"> NA</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;"> 9</span> <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #B2B2B2;"> NA</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: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> 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"># select only antimicrobials with DDDs for oral treatment</span></span></span> <span class="r-in"><span><span class="co"># select only antimicrobials with DDDs for oral treatment</span></span></span>
<span class="r-in"><span><span class="va">example_isolates</span><span class="op">[</span>, <span class="fu">administrable_per_os</span><span class="op">(</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">administrable_per_os</span><span class="op">(</span><span class="op">)</span><span class="op">]</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?administrable_per_os()` using columns <span style="color: #00BB00; font-weight: bold;">OXA</span> (oxacillin), <span style="color: #00BB00; font-weight: bold;">FLC</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `administrable_per_os()` using columns <span style="color: #00BB00; font-weight: bold;">OXA</span> (oxacillin), <span style="color: #00BB00; font-weight: bold;">FLC</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (flucloxacillin), <span style="color: #00BB00; font-weight: bold;">AMX</span> (amoxicillin), <span style="color: #00BB00; font-weight: bold;">AMC</span> (amoxicillin/clavulanic acid), <span style="color: #00BB00; font-weight: bold;">AMP</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> (flucloxacillin), <span style="color: #00BB00; font-weight: bold;">AMX</span> (amoxicillin), <span style="color: #00BB00; font-weight: bold;">AMC</span> (amoxicillin/clavulanic acid), <span style="color: #00BB00; font-weight: bold;">AMP</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (ampicillin), <span style="color: #00BB00; font-weight: bold;">CXM</span> (cefuroxime), <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin), <span style="color: #00BB00; font-weight: bold;">TMP</span> (trimethoprim), <span style="color: #00BB00; font-weight: bold;">NIT</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> (ampicillin), <span style="color: #00BB00; font-weight: bold;">CXM</span> (cefuroxime), <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin), <span style="color: #00BB00; font-weight: bold;">TMP</span> (trimethoprim), <span style="color: #00BB00; font-weight: bold;">NIT</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (nitrofurantoin), <span style="color: #00BB00; font-weight: bold;">FOS</span> (fosfomycin), <span style="color: #00BB00; font-weight: bold;">LNZ</span> (linezolid), <span style="color: #00BB00; font-weight: bold;">CIP</span> (ciprofloxacin), <span style="color: #00BB00; font-weight: bold;">MFX</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> (nitrofurantoin), <span style="color: #00BB00; font-weight: bold;">FOS</span> (fosfomycin), <span style="color: #00BB00; font-weight: bold;">LNZ</span> (linezolid), <span style="color: #00BB00; font-weight: bold;">CIP</span> (ciprofloxacin), <span style="color: #00BB00; font-weight: bold;">MFX</span></span>
@@ -451,36 +451,36 @@ my_data_with_all_these_columns %&amp;gt;%
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2,000 × 23</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2,000 × 23</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> OXA FLC AMX AMC AMP CXM KAN TMP NIT FOS LNZ CIP MFX </span> <span class="r-out co"><span class="r-pr">#&gt;</span> OXA FLC AMX AMC AMP CXM KAN TMP NIT FOS LNZ CIP MFX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFD787;"> I </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFD787;"> I </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </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;"> 1</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #AFFFD7;"> I </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #AFFFD7;"> I </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFD787;"> I </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFD787;"> I </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </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;"> 2</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #AFFFD7;"> I </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #AFFFD7;"> I </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </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 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;"> 3</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </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 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;"> 4</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</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;"> 5</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</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;"> 6</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</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;"> 7</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</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;"> 8</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </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 style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #B2B2B2;"> NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #949494;"> 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 style="color: #080808; background-color: #5FD7AF;"> S </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 style="color: #080808; background-color: #5FD7AF;"> S </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: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #949494;"> 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-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 10 more variables: VAN &lt;sir&gt;, TCY &lt;sir&gt;, DOX &lt;sir&gt;, ERY &lt;sir&gt;, CLI &lt;sir&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 10 more variables: VAN &lt;sir&gt;, TCY &lt;sir&gt;, DOX &lt;sir&gt;, ERY &lt;sir&gt;, CLI &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># AZM &lt;sir&gt;, MTR &lt;sir&gt;, CHL &lt;sir&gt;, COL &lt;sir&gt;, RIF &lt;sir&gt;</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># AZM &lt;sir&gt;, MTR &lt;sir&gt;, CHL &lt;sir&gt;, COL &lt;sir&gt;, RIF &lt;sir&gt;</span></span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># filter using any() or all()</span></span></span> <span class="r-in"><span><span class="co"># filter using any() or all()</span></span></span>
<span class="r-in"><span><span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</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"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 55 × 46</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 55 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span> <span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2004-06-09 529296 69 M ICU <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FACM <span style="color: #B2B2B2;"> NA</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;"> 1</span> 2004-06-09 529296 69 M ICU <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FACM <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2004-06-09 529296 69 M ICU <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FACM <span style="color: #B2B2B2;"> NA</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;"> 2</span> 2004-06-09 529296 69 M ICU <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FACM <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2004-11-03 D65308 80 F ICU <span style="color: #949494;">B_</span>STNTR<span style="color: #949494;">_</span>MLTP <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2004-11-03 D65308 80 F ICU <span style="color: #949494;">B_</span>STNTR<span style="color: #949494;">_</span>MLTP <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2005-04-21 452212 82 F ICU <span style="color: #949494;">B_</span>ENTRC <span style="color: #B2B2B2;"> NA</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;"> 4</span> 2005-04-21 452212 82 F ICU <span style="color: #949494;">B_</span>ENTRC <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2005-04-22 452212 82 F ICU <span style="color: #949494;">B_</span>ENTRC <span style="color: #B2B2B2;"> NA</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;"> 5</span> 2005-04-22 452212 82 F ICU <span style="color: #949494;">B_</span>ENTRC <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2005-04-22 452212 82 F ICU <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FACM <span style="color: #B2B2B2;"> NA</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;"> 6</span> 2005-04-22 452212 82 F ICU <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FACM <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2007-02-21 8BBC46 61 F Clinical <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FACM <span style="color: #B2B2B2;"> NA</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;"> 7</span> 2007-02-21 8BBC46 61 F Clinical <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FACM <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2007-12-15 401043 72 M Clinical <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FACM <span style="color: #B2B2B2;"> NA</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;"> 8</span> 2007-12-15 401043 72 M Clinical <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FACM <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2008-01-22 1710B8 82 M Clinical <span style="color: #949494;">B_</span>PROTS<span style="color: #949494;">_</span>MRBL <span style="color: #080808; background-color: #FF5F5F;"> R </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;"> 9</span> 2008-01-22 1710B8 82 M Clinical <span style="color: #949494;">B_</span>PROTS<span style="color: #949494;">_</span>MRBL <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2008-01-22 1710B8 82 M Clinical <span style="color: #949494;">B_</span>PROTS<span style="color: #949494;">_</span>MRBL <span style="color: #080808; background-color: #FF5F5F;"> R </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> 2008-01-22 1710B8 82 M Clinical <span style="color: #949494;">B_</span>PROTS<span style="color: #949494;">_</span>MRBL <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 45 more rows</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 45 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;,</span></span>
@@ -489,20 +489,20 @@ my_data_with_all_these_columns %&amp;gt;%
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># TCY &lt;sir&gt;, TGC &lt;sir&gt;, DOX &lt;sir&gt;, ERY &lt;sir&gt;, CLI &lt;sir&gt;, AZM &lt;sir&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># TCY &lt;sir&gt;, TGC &lt;sir&gt;, DOX &lt;sir&gt;, ERY &lt;sir&gt;, CLI &lt;sir&gt;, AZM &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># IPM &lt;sir&gt;, MEM &lt;sir&gt;, MTR &lt;sir&gt;, CHL &lt;sir&gt;, COL &lt;sir&gt;, MUP &lt;sir&gt;, …</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># IPM &lt;sir&gt;, MEM &lt;sir&gt;, MTR &lt;sir&gt;, CHL &lt;sir&gt;, COL &lt;sir&gt;, MUP &lt;sir&gt;, …</span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">example_isolates</span>, <span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">example_isolates</span>, <span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 55 × 46</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 55 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span> <span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2004-06-09 529296 69 M ICU <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FACM <span style="color: #B2B2B2;"> NA</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;"> 1</span> 2004-06-09 529296 69 M ICU <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FACM <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2004-06-09 529296 69 M ICU <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FACM <span style="color: #B2B2B2;"> NA</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;"> 2</span> 2004-06-09 529296 69 M ICU <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FACM <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2004-11-03 D65308 80 F ICU <span style="color: #949494;">B_</span>STNTR<span style="color: #949494;">_</span>MLTP <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2004-11-03 D65308 80 F ICU <span style="color: #949494;">B_</span>STNTR<span style="color: #949494;">_</span>MLTP <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2005-04-21 452212 82 F ICU <span style="color: #949494;">B_</span>ENTRC <span style="color: #B2B2B2;"> NA</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;"> 4</span> 2005-04-21 452212 82 F ICU <span style="color: #949494;">B_</span>ENTRC <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2005-04-22 452212 82 F ICU <span style="color: #949494;">B_</span>ENTRC <span style="color: #B2B2B2;"> NA</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;"> 5</span> 2005-04-22 452212 82 F ICU <span style="color: #949494;">B_</span>ENTRC <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2005-04-22 452212 82 F ICU <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FACM <span style="color: #B2B2B2;"> NA</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;"> 6</span> 2005-04-22 452212 82 F ICU <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FACM <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2007-02-21 8BBC46 61 F Clinical <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FACM <span style="color: #B2B2B2;"> NA</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;"> 7</span> 2007-02-21 8BBC46 61 F Clinical <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FACM <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2007-12-15 401043 72 M Clinical <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FACM <span style="color: #B2B2B2;"> NA</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;"> 8</span> 2007-12-15 401043 72 M Clinical <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FACM <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2008-01-22 1710B8 82 M Clinical <span style="color: #949494;">B_</span>PROTS<span style="color: #949494;">_</span>MRBL <span style="color: #080808; background-color: #FF5F5F;"> R </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;"> 9</span> 2008-01-22 1710B8 82 M Clinical <span style="color: #949494;">B_</span>PROTS<span style="color: #949494;">_</span>MRBL <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2008-01-22 1710B8 82 M Clinical <span style="color: #949494;">B_</span>PROTS<span style="color: #949494;">_</span>MRBL <span style="color: #080808; background-color: #FF5F5F;"> R </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> 2008-01-22 1710B8 82 M Clinical <span style="color: #949494;">B_</span>PROTS<span style="color: #949494;">_</span>MRBL <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 45 more rows</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 45 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;,</span></span>
@@ -513,21 +513,21 @@ my_data_with_all_these_columns %&amp;gt;%
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># filter on any or all results in the carbapenem columns (i.e., IPM, MEM):</span></span></span> <span class="r-in"><span><span class="co"># filter on any or all results in the carbapenem columns (i.e., IPM, MEM):</span></span></span>
<span class="r-in"><span><span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</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"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Filtering any of columns '<span style="font-weight: bold;">IPM</span>' and '<span style="font-weight: bold;">MEM</span>' to contain value "S", "I" or "R"</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Filtering any of columns '<span style="font-weight: bold;">IPM</span>' and '<span style="font-weight: bold;">MEM</span>' to contain value "S", "I" or "R"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 962 × 46</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 962 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span> <span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2002-01-19 738003 71 M Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </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;"> 1</span> 2002-01-19 738003 71 M Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2002-01-19 738003 71 M Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </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;"> 2</span> 2002-01-19 738003 71 M Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2002-01-22 F35553 50 M ICU <span style="color: #949494;">B_</span>PROTS<span style="color: #949494;">_</span>MRBL <span style="color: #080808; background-color: #FF5F5F;"> R </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;"> 3</span> 2002-01-22 F35553 50 M ICU <span style="color: #949494;">B_</span>PROTS<span style="color: #949494;">_</span>MRBL <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2002-01-22 F35553 50 M ICU <span style="color: #949494;">B_</span>PROTS<span style="color: #949494;">_</span>MRBL <span style="color: #080808; background-color: #FF5F5F;"> R </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;"> 4</span> 2002-01-22 F35553 50 M ICU <span style="color: #949494;">B_</span>PROTS<span style="color: #949494;">_</span>MRBL <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2002-02-05 067927 45 F ICU <span style="color: #949494;">B_</span>SERRT<span style="color: #949494;">_</span>MRCS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2002-02-05 067927 45 F ICU <span style="color: #949494;">B_</span>SERRT<span style="color: #949494;">_</span>MRCS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2002-02-05 067927 45 F ICU <span style="color: #949494;">B_</span>SERRT<span style="color: #949494;">_</span>MRCS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2002-02-05 067927 45 F ICU <span style="color: #949494;">B_</span>SERRT<span style="color: #949494;">_</span>MRCS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2002-02-05 067927 45 F ICU <span style="color: #949494;">B_</span>SERRT<span style="color: #949494;">_</span>MRCS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2002-02-05 067927 45 F ICU <span style="color: #949494;">B_</span>SERRT<span style="color: #949494;">_</span>MRCS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2002-02-27 066895 85 F Clinical <span style="color: #949494;">B_</span>KLBSL<span style="color: #949494;">_</span>PNMN <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2002-02-27 066895 85 F Clinical <span style="color: #949494;">B_</span>KLBSL<span style="color: #949494;">_</span>PNMN <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2002-02-27 066895 85 F Clinical <span style="color: #949494;">B_</span>KLBSL<span style="color: #949494;">_</span>PNMN <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2002-02-27 066895 85 F Clinical <span style="color: #949494;">B_</span>KLBSL<span style="color: #949494;">_</span>PNMN <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2002-03-08 4FC193 69 M Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2002-03-08 4FC193 69 M Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 952 more rows</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 952 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;,</span></span>
@@ -536,21 +536,21 @@ my_data_with_all_these_columns %&amp;gt;%
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># TCY &lt;sir&gt;, TGC &lt;sir&gt;, DOX &lt;sir&gt;, ERY &lt;sir&gt;, CLI &lt;sir&gt;, AZM &lt;sir&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># TCY &lt;sir&gt;, TGC &lt;sir&gt;, DOX &lt;sir&gt;, ERY &lt;sir&gt;, CLI &lt;sir&gt;, AZM &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># IPM &lt;sir&gt;, MEM &lt;sir&gt;, MTR &lt;sir&gt;, CHL &lt;sir&gt;, COL &lt;sir&gt;, MUP &lt;sir&gt;, …</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># IPM &lt;sir&gt;, MEM &lt;sir&gt;, MTR &lt;sir&gt;, CHL &lt;sir&gt;, COL &lt;sir&gt;, MUP &lt;sir&gt;, …</span></span>
<span class="r-in"><span><span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</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"><a href="https://rdrr.io/r/base/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Filtering all of columns '<span style="font-weight: bold;">IPM</span>' and '<span style="font-weight: bold;">MEM</span>' to contain value "S", "I" or "R"</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Filtering all of columns '<span style="font-weight: bold;">IPM</span>' and '<span style="font-weight: bold;">MEM</span>' to contain value "S", "I" or "R"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 756 × 46</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 756 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span> <span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2002-04-14 F30196 73 M Outpat… <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>GRPB <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2002-04-14 F30196 73 M Outpat… <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>GRPB <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2003-04-08 114570 74 M ICU <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PYGN <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2003-04-08 114570 74 M ICU <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PYGN <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2003-04-08 114570 74 M ICU <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>GRPA <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2003-04-08 114570 74 M ICU <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>GRPA <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2003-04-08 114570 74 M ICU <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>GRPA <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2003-04-08 114570 74 M ICU <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>GRPA <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2003-08-14 F71508 0 F Clinic… <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>GRPB <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2003-08-14 F71508 0 F Clinic… <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>GRPB <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2003-10-16 650870 63 F ICU <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2003-10-16 650870 63 F ICU <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2003-10-20 F35553 52 M ICU <span style="color: #949494;">B_</span>ENTRBC<span style="color: #949494;">_</span>CLOC <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2003-10-20 F35553 52 M ICU <span style="color: #949494;">B_</span>ENTRBC<span style="color: #949494;">_</span>CLOC <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2003-10-20 F35553 52 M ICU <span style="color: #949494;">B_</span>ENTRBC<span style="color: #949494;">_</span>CLOC <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2003-10-20 F35553 52 M ICU <span style="color: #949494;">B_</span>ENTRBC<span style="color: #949494;">_</span>CLOC <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2003-11-04 2FC253 87 F ICU <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </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;"> 9</span> 2003-11-04 2FC253 87 F ICU <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2003-11-04 2FC253 87 F ICU <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </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> 2003-11-04 2FC253 87 F ICU <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 746 more rows</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 746 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;,</span></span>
@@ -561,18 +561,18 @@ my_data_with_all_these_columns %&amp;gt;%
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># filter with multiple antimicrobial selectors using c()</span></span></span> <span class="r-in"><span><span class="co"># filter with multiple antimicrobial selectors using c()</span></span></span>
<span class="r-in"><span><span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span>, <span class="fu">aminoglycosides</span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</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"><a href="https://rdrr.io/r/base/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span>, <span class="fu">aminoglycosides</span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?aminoglycosides()` using columns <span style="color: #00BB00; font-weight: bold;">GEN</span> (gentamicin), <span style="color: #00BB00; font-weight: bold;">TOB</span> (tobramycin),</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns <span style="color: #00BB00; font-weight: bold;">GEN</span> (gentamicin), <span style="color: #00BB00; font-weight: bold;">TOB</span> (tobramycin), <span style="color: #00BB00; font-weight: bold;">AMK</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00; font-weight: bold;">AMK</span> (amikacin), and <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin)</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> (amikacin), and <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 26 × 46</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 26 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span> <span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2004-11-03 D65308 80 F ICU <span style="color: #949494;">B_</span>STNTR<span style="color: #949494;">_</span>MLTP <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2004-11-03 D65308 80 F ICU <span style="color: #949494;">B_</span>STNTR<span style="color: #949494;">_</span>MLTP <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2005-04-22 452212 82 F ICU <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FACM <span style="color: #B2B2B2;"> NA</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;"> 2</span> 2005-04-22 452212 82 F ICU <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FACM <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2007-02-21 8BBC46 61 F Clinical <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FACM <span style="color: #B2B2B2;"> NA</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;"> 3</span> 2007-02-21 8BBC46 61 F Clinical <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FACM <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2007-12-15 401043 72 M Clinical <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FACM <span style="color: #B2B2B2;"> NA</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;"> 4</span> 2007-12-15 401043 72 M Clinical <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FACM <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2008-12-06 501361 43 F Clinical <span style="color: #949494;">B_</span>STNTR<span style="color: #949494;">_</span>MLTP <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2008-12-06 501361 43 F Clinical <span style="color: #949494;">B_</span>STNTR<span style="color: #949494;">_</span>MLTP <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2011-05-09 207325 82 F ICU <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FACM <span style="color: #B2B2B2;"> NA</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;"> 6</span> 2011-05-09 207325 82 F ICU <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FACM <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2012-03-12 582258 80 M ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>CONS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2012-03-12 582258 80 M ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>CONS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2012-05-19 C25552 89 F Outpati… <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>CONS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2012-05-19 C25552 89 F Outpati… <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>CONS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2012-07-17 F05015 83 M ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>CONS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2012-07-17 F05015 83 M ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>CONS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
@@ -587,23 +587,23 @@ my_data_with_all_these_columns %&amp;gt;%
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># filter + select in one go: get penicillins in carbapenem-resistant strains</span></span></span> <span class="r-in"><span><span class="co"># filter + select in one go: get penicillins in carbapenem-resistant strains</span></span></span>
<span class="r-in"><span><span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span>, <span class="fu">penicillins</span><span class="op">(</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"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span>, <span class="fu">penicillins</span><span class="op">(</span><span class="op">)</span><span class="op">]</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?penicillins()` using columns <span style="color: #00BB00; font-weight: bold;">PEN</span> (benzylpenicillin), <span style="color: #00BB00; font-weight: bold;">OXA</span> (oxacillin),</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `penicillins()` using columns <span style="color: #00BB00; font-weight: bold;">PEN</span> (benzylpenicillin), <span style="color: #00BB00; font-weight: bold;">OXA</span> (oxacillin),</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00; font-weight: bold;">FLC</span> (flucloxacillin), <span style="color: #00BB00; font-weight: bold;">AMX</span> (amoxicillin), <span style="color: #00BB00; font-weight: bold;">AMC</span> (amoxicillin/clavulanic acid),</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00; font-weight: bold;">FLC</span> (flucloxacillin), <span style="color: #00BB00; font-weight: bold;">AMX</span> (amoxicillin), <span style="color: #00BB00; font-weight: bold;">AMC</span> (amoxicillin/clavulanic acid),</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00; font-weight: bold;">AMP</span> (ampicillin), and <span style="color: #00BB00; font-weight: bold;">TZP</span> (piperacillin/tazobactam)</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00; font-weight: bold;">AMP</span> (ampicillin), and <span style="color: #00BB00; font-weight: bold;">TZP</span> (piperacillin/tazobactam)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 55 × 7</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 55 × 7</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> PEN OXA FLC AMX AMC AMP TZP </span> <span class="r-out co"><span class="r-pr">#&gt;</span> PEN OXA FLC AMX AMC AMP TZP </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</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;"> 1</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</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;"> 2</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</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: #080808; background-color: #5FD7AF;"> S </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</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: #080808; background-color: #5FD7AF;"> S </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 45 more rows</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 45 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"># You can combine selectors with '&amp;' to be more specific. For example,</span></span></span> <span class="r-in"><span><span class="co"># You can combine selectors with '&amp;' to be more specific. For example,</span></span></span>
@@ -612,10 +612,10 @@ my_data_with_all_these_columns %&amp;gt;%
<span class="r-in"><span><span class="co"># drugs are both omitted since benzylpenicillin is not administrable per os</span></span></span> <span class="r-in"><span><span class="co"># drugs are both omitted since benzylpenicillin is not administrable per os</span></span></span>
<span class="r-in"><span><span class="co"># and erythromycin is not a penicillin:</span></span></span> <span class="r-in"><span><span class="co"># and erythromycin is not a penicillin:</span></span></span>
<span class="r-in"><span><span class="va">example_isolates</span><span class="op">[</span>, <span class="fu">penicillins</span><span class="op">(</span><span class="op">)</span> <span class="op">&amp;</span> <span class="fu">administrable_per_os</span><span class="op">(</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">penicillins</span><span class="op">(</span><span class="op">)</span> <span class="op">&amp;</span> <span class="fu">administrable_per_os</span><span class="op">(</span><span class="op">)</span><span class="op">]</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?penicillins()` using columns <span style="color: #00BB00; font-weight: bold;">PEN</span> (benzylpenicillin), <span style="color: #00BB00; font-weight: bold;">OXA</span> (oxacillin),</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `penicillins()` using columns <span style="color: #00BB00; font-weight: bold;">PEN</span> (benzylpenicillin), <span style="color: #00BB00; font-weight: bold;">OXA</span> (oxacillin),</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00; font-weight: bold;">FLC</span> (flucloxacillin), <span style="color: #00BB00; font-weight: bold;">AMX</span> (amoxicillin), <span style="color: #00BB00; font-weight: bold;">AMC</span> (amoxicillin/clavulanic acid),</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00; font-weight: bold;">FLC</span> (flucloxacillin), <span style="color: #00BB00; font-weight: bold;">AMX</span> (amoxicillin), <span style="color: #00BB00; font-weight: bold;">AMC</span> (amoxicillin/clavulanic acid),</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00; font-weight: bold;">AMP</span> (ampicillin), and <span style="color: #00BB00; font-weight: bold;">TZP</span> (piperacillin/tazobactam)</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00; font-weight: bold;">AMP</span> (ampicillin), and <span style="color: #00BB00; font-weight: bold;">TZP</span> (piperacillin/tazobactam)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?administrable_per_os()` using columns <span style="color: #00BB00; font-weight: bold;">OXA</span> (oxacillin), <span style="color: #00BB00; font-weight: bold;">FLC</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `administrable_per_os()` using columns <span style="color: #00BB00; font-weight: bold;">OXA</span> (oxacillin), <span style="color: #00BB00; font-weight: bold;">FLC</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (flucloxacillin), <span style="color: #00BB00; font-weight: bold;">AMX</span> (amoxicillin), <span style="color: #00BB00; font-weight: bold;">AMC</span> (amoxicillin/clavulanic acid), <span style="color: #00BB00; font-weight: bold;">AMP</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> (flucloxacillin), <span style="color: #00BB00; font-weight: bold;">AMX</span> (amoxicillin), <span style="color: #00BB00; font-weight: bold;">AMC</span> (amoxicillin/clavulanic acid), <span style="color: #00BB00; font-weight: bold;">AMP</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (ampicillin), <span style="color: #00BB00; font-weight: bold;">CXM</span> (cefuroxime), <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin), <span style="color: #00BB00; font-weight: bold;">TMP</span> (trimethoprim), <span style="color: #00BB00; font-weight: bold;">NIT</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> (ampicillin), <span style="color: #00BB00; font-weight: bold;">CXM</span> (cefuroxime), <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin), <span style="color: #00BB00; font-weight: bold;">TMP</span> (trimethoprim), <span style="color: #00BB00; font-weight: bold;">NIT</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (nitrofurantoin), <span style="color: #00BB00; font-weight: bold;">FOS</span> (fosfomycin), <span style="color: #00BB00; font-weight: bold;">LNZ</span> (linezolid), <span style="color: #00BB00; font-weight: bold;">CIP</span> (ciprofloxacin), <span style="color: #00BB00; font-weight: bold;">MFX</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> (nitrofurantoin), <span style="color: #00BB00; font-weight: bold;">FOS</span> (fosfomycin), <span style="color: #00BB00; font-weight: bold;">LNZ</span> (linezolid), <span style="color: #00BB00; font-weight: bold;">CIP</span> (ciprofloxacin), <span style="color: #00BB00; font-weight: bold;">MFX</span></span>
@@ -625,23 +625,23 @@ my_data_with_all_these_columns %&amp;gt;%
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2,000 × 5</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2,000 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> OXA FLC AMX AMC AMP </span> <span class="r-out co"><span class="r-pr">#&gt;</span> OXA FLC AMX AMC AMP </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFD787;"> I </span> <span style="color: #B2B2B2;"> NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #AFFFD7;"> I </span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFD787;"> I </span> <span style="color: #B2B2B2;"> NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #AFFFD7;"> I </span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </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;"> 3</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </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;"> 4</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </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;"> 5</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </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;"> 6</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </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;"> 9</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> 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: #BCBCBC;">10</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> 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 `antimicrobials` 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>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?amr_selector(oral_ddd &gt; 1 &amp; oral_units == "g")` using columns <span style="color: #00BB00; font-weight: bold;">OXA</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `amr_selector(oral_ddd &gt; 1 &amp; oral_units == "g")` using columns <span style="color: #00BB00; font-weight: bold;">OXA</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (oxacillin), <span style="color: #00BB00; font-weight: bold;">FLC</span> (flucloxacillin), <span style="color: #00BB00; font-weight: bold;">AMX</span> (amoxicillin), <span style="color: #00BB00; font-weight: bold;">AMC</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> (oxacillin), <span style="color: #00BB00; font-weight: bold;">FLC</span> (flucloxacillin), <span style="color: #00BB00; font-weight: bold;">AMX</span> (amoxicillin), <span style="color: #00BB00; font-weight: bold;">AMC</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (amoxicillin/clavulanic acid), <span style="color: #00BB00; font-weight: bold;">AMP</span> (ampicillin), <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin), <span style="color: #00BB00; font-weight: bold;">FOS</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> (amoxicillin/clavulanic acid), <span style="color: #00BB00; font-weight: bold;">AMP</span> (ampicillin), <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin), <span style="color: #00BB00; font-weight: bold;">FOS</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (fosfomycin), <span style="color: #00BB00; font-weight: bold;">LNZ</span> (linezolid), <span style="color: #00BB00; font-weight: bold;">VAN</span> (vancomycin), <span style="color: #00BB00; font-weight: bold;">ERY</span> (erythromycin), <span style="color: #00BB00; font-weight: bold;">CLI</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> (fosfomycin), <span style="color: #00BB00; font-weight: bold;">LNZ</span> (linezolid), <span style="color: #00BB00; font-weight: bold;">VAN</span> (vancomycin), <span style="color: #00BB00; font-weight: bold;">ERY</span> (erythromycin), <span style="color: #00BB00; font-weight: bold;">CLI</span></span>
@@ -649,16 +649,16 @@ my_data_with_all_these_columns %&amp;gt;%
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2,000 × 13</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2,000 × 13</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> OXA FLC AMX AMC AMP KAN FOS LNZ VAN ERY CLI MTR CHL </span> <span class="r-out co"><span class="r-pr">#&gt;</span> OXA FLC AMX AMC AMP KAN FOS LNZ VAN ERY CLI MTR CHL </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFD787;"> I </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </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;"> 1</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #AFFFD7;"> I </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFD787;"> I </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </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;"> 2</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #AFFFD7;"> I </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </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;"> 3</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </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;"> 4</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </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;"> 5</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </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;"> 6</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </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;"> 7</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </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;"> 8</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </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;"> 9</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> 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 style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </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: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> 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></span> <span class="r-in"><span></span></span>
@@ -685,17 +685,17 @@ my_data_with_all_these_columns %&amp;gt;%
<span class="r-msg co"><span class="r-pr">#&gt;</span> The following objects are masked from ‘package:AMR’:</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> The following objects are masked from ‘package:AMR’:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span> <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> %like%, like</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> %like%, like</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>It should never be needed to print an antimicrobial selector class. Are you</span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>It should never be needed to print an antimicrobial selector class. Are you</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> using <span style="color: #0000BB;">data.table</span>? Then add the argument `with = FALSE`, see our examples at</span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> using <span style="color: #0000BB;">data.table</span>? Then add the argument `with = FALSE`, see our examples at</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> `?amr_selector()`.</span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> `amr_selector()`.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;amr_selector&gt;</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;amr_selector&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] IPM MEM</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] IPM MEM</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://r-datatable.com" class="external-link">"data.table"</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://r-datatable.com" class="external-link">"data.table"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="co"># so `with = FALSE` is required</span></span></span> <span class="r-in"><span> <span class="co"># so `with = FALSE` is required</span></span></span>
<span class="r-in"><span> <span class="va">dt</span><span class="op">[</span>, <span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span>, with <span class="op">=</span> <span class="cn">FALSE</span><span class="op">]</span></span></span> <span class="r-in"><span> <span class="va">dt</span><span class="op">[</span>, <span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span>, with <span class="op">=</span> <span class="cn">FALSE</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: #00BBBB;">ℹ</span> For `?carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> IPM MEM</span> <span class="r-out co"><span class="r-pr">#&gt;</span> IPM MEM</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> &lt;sir&gt; &lt;sir&gt;</span> <span class="r-out co"><span class="r-pr">#&gt;</span> &lt;sir&gt; &lt;sir&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1: &lt;NA&gt; &lt;NA&gt;</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 1: &lt;NA&gt; &lt;NA&gt;</span>
@@ -714,8 +714,8 @@ my_data_with_all_these_columns %&amp;gt;%
<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://r-datatable.com" class="external-link">"data.table"</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://r-datatable.com" class="external-link">"data.table"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="va">dt</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="st">"mo"</span>, <span class="fu">aminoglycosides</span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">]</span></span></span> <span class="r-in"><span> <span class="va">dt</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="st">"mo"</span>, <span class="fu">aminoglycosides</span><span class="op">(</span><span class="op">)</span><span class="op">)</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: #00BBBB;">ℹ</span> For `?aminoglycosides()` using columns <span style="color: #00BB00; font-weight: bold;">GEN</span> (gentamicin), <span style="color: #00BB00; font-weight: bold;">TOB</span> (tobramycin),</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns <span style="color: #00BB00; font-weight: bold;">GEN</span> (gentamicin), <span style="color: #00BB00; font-weight: bold;">TOB</span> (tobramycin), <span style="color: #00BB00; font-weight: bold;">AMK</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00; font-weight: bold;">AMK</span> (amikacin), and <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin)</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> (amikacin), and <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo GEN TOB AMK KAN</span> <span class="r-out co"><span class="r-pr">#&gt;</span> mo GEN TOB AMK KAN</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> &lt;mo&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt;</span> <span class="r-out co"><span class="r-pr">#&gt;</span> &lt;mo&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1: B_ESCHR_COLI &lt;NA&gt; &lt;NA&gt; &lt;NA&gt; &lt;NA&gt;</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 1: B_ESCHR_COLI &lt;NA&gt; &lt;NA&gt; &lt;NA&gt; &lt;NA&gt;</span>
@@ -732,9 +732,9 @@ my_data_with_all_these_columns %&amp;gt;%
<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://r-datatable.com" class="external-link">"data.table"</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://r-datatable.com" class="external-link">"data.table"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="va">dt</span><span class="op">[</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span>, <span class="fu">aminoglycosides</span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">]</span></span></span> <span class="r-in"><span> <span class="va">dt</span><span class="op">[</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span>, <span class="fu">aminoglycosides</span><span class="op">(</span><span class="op">)</span><span class="op">)</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: #00BBBB;">ℹ</span> For `?carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?aminoglycosides()` using columns <span style="color: #00BB00; font-weight: bold;">GEN</span> (gentamicin), <span style="color: #00BB00; font-weight: bold;">TOB</span> (tobramycin),</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns <span style="color: #00BB00; font-weight: bold;">GEN</span> (gentamicin), <span style="color: #00BB00; font-weight: bold;">TOB</span> (tobramycin), <span style="color: #00BB00; font-weight: bold;">AMK</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00; font-weight: bold;">AMK</span> (amikacin), and <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin)</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> (amikacin), and <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> IPM MEM GEN TOB AMK KAN</span> <span class="r-out co"><span class="r-pr">#&gt;</span> IPM MEM GEN TOB AMK KAN</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> &lt;sir&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt;</span> <span class="r-out co"><span class="r-pr">#&gt;</span> &lt;sir&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1: &lt;NA&gt; &lt;NA&gt; &lt;NA&gt; &lt;NA&gt; &lt;NA&gt; &lt;NA&gt;</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 1: &lt;NA&gt; &lt;NA&gt; &lt;NA&gt; &lt;NA&gt; &lt;NA&gt; &lt;NA&gt;</span>
@@ -753,7 +753,7 @@ my_data_with_all_these_columns %&amp;gt;%
<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://r-datatable.com" class="external-link">"data.table"</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://r-datatable.com" class="external-link">"data.table"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="va">dt</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"S"</span><span class="op">)</span>, <span class="op">]</span></span></span> <span class="r-in"><span> <span class="va">dt</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"S"</span><span class="op">)</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: #00BBBB;">ℹ</span> For `?carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC</span> <span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> &lt;Date&gt; &lt;char&gt; &lt;num&gt; &lt;char&gt; &lt;char&gt; &lt;mo&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt;</span> <span class="r-out co"><span class="r-pr">#&gt;</span> &lt;Date&gt; &lt;char&gt; &lt;num&gt; &lt;char&gt; &lt;char&gt; &lt;mo&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1: 2002-01-19 738003 71 M Clinical B_ESCHR_COLI R &lt;NA&gt; &lt;NA&gt;</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 1: 2002-01-19 738003 71 M Clinical B_ESCHR_COLI R &lt;NA&gt; &lt;NA&gt;</span>
@@ -822,8 +822,8 @@ my_data_with_all_these_columns %&amp;gt;%
<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://r-datatable.com" class="external-link">"data.table"</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://r-datatable.com" class="external-link">"data.table"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="va">dt</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"S"</span><span class="op">)</span>, <span class="fu">penicillins</span><span class="op">(</span><span class="op">)</span>, with <span class="op">=</span> <span class="cn">FALSE</span><span class="op">]</span></span></span> <span class="r-in"><span> <span class="va">dt</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"S"</span><span class="op">)</span>, <span class="fu">penicillins</span><span class="op">(</span><span class="op">)</span>, with <span class="op">=</span> <span class="cn">FALSE</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: #00BBBB;">ℹ</span> For `?carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?penicillins()` using columns <span style="color: #00BB00; font-weight: bold;">PEN</span> (benzylpenicillin), <span style="color: #00BB00; font-weight: bold;">OXA</span> (oxacillin),</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `penicillins()` using columns <span style="color: #00BB00; font-weight: bold;">PEN</span> (benzylpenicillin), <span style="color: #00BB00; font-weight: bold;">OXA</span> (oxacillin),</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00; font-weight: bold;">FLC</span> (flucloxacillin), <span style="color: #00BB00; font-weight: bold;">AMX</span> (amoxicillin), <span style="color: #00BB00; font-weight: bold;">AMC</span> (amoxicillin/clavulanic acid),</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00; font-weight: bold;">FLC</span> (flucloxacillin), <span style="color: #00BB00; font-weight: bold;">AMX</span> (amoxicillin), <span style="color: #00BB00; font-weight: bold;">AMC</span> (amoxicillin/clavulanic acid),</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00; font-weight: bold;">AMP</span> (ampicillin), and <span style="color: #00BB00; font-weight: bold;">TZP</span> (piperacillin/tazobactam)</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00; font-weight: bold;">AMP</span> (ampicillin), and <span style="color: #00BB00; font-weight: bold;">TZP</span> (piperacillin/tazobactam)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> PEN OXA FLC AMX AMC AMP TZP</span> <span class="r-out co"><span class="r-pr">#&gt;</span> PEN OXA FLC AMX AMC AMP TZP</span>

56
reference/antimicrobial_selectors.md
View File

@@ -669,7 +669,7 @@ example_isolates
# you can use the selectors separately to retrieve all possible antimicrobials: # you can use the selectors separately to retrieve all possible antimicrobials:
carbapenems() carbapenems()
#> ℹ in `?carbapenems()`: Imipenem/EDTA (IPE) and meropenem/nacubactam (MNC) are #> ℹ in `carbapenems()`: Imipenem/EDTA (IPE) and meropenem/nacubactam (MNC) are
#> not included since `only_treatable = TRUE`. #> not included since `only_treatable = TRUE`.
#> ℹ This <ab> vector was retrieved using `carbapenems()`, which should normally #> ℹ This <ab> vector was retrieved using `carbapenems()`, which should normally
#> be used inside a dplyr verb or <data.frame> call, e.g.: #> be used inside a dplyr verb or <data.frame> call, e.g.:
@@ -777,7 +777,7 @@ identical(x, y) && identical(y, z)
# select columns 'IPM' (imipenem) and 'MEM' (meropenem) # select columns 'IPM' (imipenem) and 'MEM' (meropenem)
example_isolates[, carbapenems()] example_isolates[, carbapenems()]
#> ℹ For `?carbapenems()` using columns IPM (imipenem) and MEM (meropenem) #> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> # A tibble: 2,000 × 2 #> # A tibble: 2,000 × 2
#> IPM MEM #> IPM MEM
#> <sir> <sir> #> <sir> <sir>
@@ -795,8 +795,8 @@ example_isolates[, carbapenems()]
# select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB' # select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB'
example_isolates[, c("mo", aminoglycosides())] example_isolates[, c("mo", aminoglycosides())]
#> ℹ For `?aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), #> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK
#> AMK (amikacin), and KAN (kanamycin) #> (amikacin), and KAN (kanamycin)
#> # A tibble: 2,000 × 5 #> # A tibble: 2,000 × 5
#> mo GEN TOB AMK KAN #> mo GEN TOB AMK KAN
#> <mo> <sir> <sir> <sir> <sir> #> <mo> <sir> <sir> <sir> <sir>
@@ -814,7 +814,7 @@ example_isolates[, c("mo", aminoglycosides())]
# select only antimicrobials with DDDs for oral treatment # select only antimicrobials with DDDs for oral treatment
example_isolates[, administrable_per_os()] example_isolates[, administrable_per_os()]
#> ℹ For `?administrable_per_os()` using columns OXA (oxacillin), FLC #> ℹ For `administrable_per_os()` using columns OXA (oxacillin), FLC
#> (flucloxacillin), AMX (amoxicillin), AMC (amoxicillin/clavulanic acid), AMP #> (flucloxacillin), AMX (amoxicillin), AMC (amoxicillin/clavulanic acid), AMP
#> (ampicillin), CXM (cefuroxime), KAN (kanamycin), TMP (trimethoprim), NIT #> (ampicillin), CXM (cefuroxime), KAN (kanamycin), TMP (trimethoprim), NIT
#> (nitrofurantoin), FOS (fosfomycin), LNZ (linezolid), CIP (ciprofloxacin), MFX #> (nitrofurantoin), FOS (fosfomycin), LNZ (linezolid), CIP (ciprofloxacin), MFX
@@ -840,7 +840,7 @@ example_isolates[, administrable_per_os()]
# filter using any() or all() # filter using any() or all()
example_isolates[any(carbapenems() == "R"), ] example_isolates[any(carbapenems() == "R"), ]
#> ℹ For `?carbapenems()` using columns IPM (imipenem) and MEM (meropenem) #> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> # A tibble: 55 × 46 #> # A tibble: 55 × 46
#> date patient age gender ward mo PEN OXA FLC AMX #> date patient age gender ward mo PEN OXA FLC AMX
#> <date> <chr> <dbl> <chr> <chr> <mo> <sir> <sir> <sir> <sir> #> <date> <chr> <dbl> <chr> <chr> <mo> <sir> <sir> <sir> <sir>
@@ -862,7 +862,7 @@ example_isolates[any(carbapenems() == "R"), ]
#> # TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>, #> # TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>,
#> # IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, … #> # IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, …
subset(example_isolates, any(carbapenems() == "R")) subset(example_isolates, any(carbapenems() == "R"))
#> ℹ For `?carbapenems()` using columns IPM (imipenem) and MEM (meropenem) #> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> # A tibble: 55 × 46 #> # A tibble: 55 × 46
#> date patient age gender ward mo PEN OXA FLC AMX #> date patient age gender ward mo PEN OXA FLC AMX
#> <date> <chr> <dbl> <chr> <chr> <mo> <sir> <sir> <sir> <sir> #> <date> <chr> <dbl> <chr> <chr> <mo> <sir> <sir> <sir> <sir>
@@ -886,7 +886,7 @@ subset(example_isolates, any(carbapenems() == "R"))
# filter on any or all results in the carbapenem columns (i.e., IPM, MEM): # filter on any or all results in the carbapenem columns (i.e., IPM, MEM):
example_isolates[any(carbapenems()), ] example_isolates[any(carbapenems()), ]
#> ℹ For `?carbapenems()` using columns IPM (imipenem) and MEM (meropenem) #> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> ℹ Filtering any of columns 'IPM' and 'MEM' to contain value "S", "I" or "R" #> ℹ Filtering any of columns 'IPM' and 'MEM' to contain value "S", "I" or "R"
#> # A tibble: 962 × 46 #> # A tibble: 962 × 46
#> date patient age gender ward mo PEN OXA FLC AMX #> date patient age gender ward mo PEN OXA FLC AMX
@@ -909,7 +909,7 @@ example_isolates[any(carbapenems()), ]
#> # TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>, #> # TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>,
#> # IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, … #> # IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, …
example_isolates[all(carbapenems()), ] example_isolates[all(carbapenems()), ]
#> ℹ For `?carbapenems()` using columns IPM (imipenem) and MEM (meropenem) #> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> ℹ Filtering all of columns 'IPM' and 'MEM' to contain value "S", "I" or "R" #> ℹ Filtering all of columns 'IPM' and 'MEM' to contain value "S", "I" or "R"
#> # A tibble: 756 × 46 #> # A tibble: 756 × 46
#> date patient age gender ward mo PEN OXA FLC AMX #> date patient age gender ward mo PEN OXA FLC AMX
@@ -934,9 +934,9 @@ example_isolates[all(carbapenems()), ]
# filter with multiple antimicrobial selectors using c() # filter with multiple antimicrobial selectors using c()
example_isolates[all(c(carbapenems(), aminoglycosides()) == "R"), ] example_isolates[all(c(carbapenems(), aminoglycosides()) == "R"), ]
#> ℹ For `?carbapenems()` using columns IPM (imipenem) and MEM (meropenem) #> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> ℹ For `?aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), #> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK
#> AMK (amikacin), and KAN (kanamycin) #> (amikacin), and KAN (kanamycin)
#> # A tibble: 26 × 46 #> # A tibble: 26 × 46
#> date patient age gender ward mo PEN OXA FLC AMX #> date patient age gender ward mo PEN OXA FLC AMX
#> <date> <chr> <dbl> <chr> <chr> <mo> <sir> <sir> <sir> <sir> #> <date> <chr> <dbl> <chr> <chr> <mo> <sir> <sir> <sir> <sir>
@@ -960,8 +960,8 @@ example_isolates[all(c(carbapenems(), aminoglycosides()) == "R"), ]
# filter + select in one go: get penicillins in carbapenem-resistant strains # filter + select in one go: get penicillins in carbapenem-resistant strains
example_isolates[any(carbapenems() == "R"), penicillins()] example_isolates[any(carbapenems() == "R"), penicillins()]
#> ℹ For `?carbapenems()` using columns IPM (imipenem) and MEM (meropenem) #> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> ℹ For `?penicillins()` using columns PEN (benzylpenicillin), OXA (oxacillin), #> ℹ For `penicillins()` using columns PEN (benzylpenicillin), OXA (oxacillin),
#> FLC (flucloxacillin), AMX (amoxicillin), AMC (amoxicillin/clavulanic acid), #> FLC (flucloxacillin), AMX (amoxicillin), AMC (amoxicillin/clavulanic acid),
#> AMP (ampicillin), and TZP (piperacillin/tazobactam) #> AMP (ampicillin), and TZP (piperacillin/tazobactam)
#> # A tibble: 55 × 7 #> # A tibble: 55 × 7
@@ -985,10 +985,10 @@ example_isolates[any(carbapenems() == "R"), penicillins()]
# drugs are both omitted since benzylpenicillin is not administrable per os # drugs are both omitted since benzylpenicillin is not administrable per os
# and erythromycin is not a penicillin: # and erythromycin is not a penicillin:
example_isolates[, penicillins() & administrable_per_os()] example_isolates[, penicillins() & administrable_per_os()]
#> ℹ For `?penicillins()` using columns PEN (benzylpenicillin), OXA (oxacillin), #> ℹ For `penicillins()` using columns PEN (benzylpenicillin), OXA (oxacillin),
#> FLC (flucloxacillin), AMX (amoxicillin), AMC (amoxicillin/clavulanic acid), #> FLC (flucloxacillin), AMX (amoxicillin), AMC (amoxicillin/clavulanic acid),
#> AMP (ampicillin), and TZP (piperacillin/tazobactam) #> AMP (ampicillin), and TZP (piperacillin/tazobactam)
#> ℹ For `?administrable_per_os()` using columns OXA (oxacillin), FLC #> ℹ For `administrable_per_os()` using columns OXA (oxacillin), FLC
#> (flucloxacillin), AMX (amoxicillin), AMC (amoxicillin/clavulanic acid), AMP #> (flucloxacillin), AMX (amoxicillin), AMC (amoxicillin/clavulanic acid), AMP
#> (ampicillin), CXM (cefuroxime), KAN (kanamycin), TMP (trimethoprim), NIT #> (ampicillin), CXM (cefuroxime), KAN (kanamycin), TMP (trimethoprim), NIT
#> (nitrofurantoin), FOS (fosfomycin), LNZ (linezolid), CIP (ciprofloxacin), MFX #> (nitrofurantoin), FOS (fosfomycin), LNZ (linezolid), CIP (ciprofloxacin), MFX
@@ -1014,7 +1014,7 @@ example_isolates[, penicillins() & administrable_per_os()]
# very flexible. For instance, to select antimicrobials with an oral DDD # very flexible. For instance, to select antimicrobials with an oral DDD
# of at least 1 gram: # of at least 1 gram:
example_isolates[, amr_selector(oral_ddd > 1 & oral_units == "g")] example_isolates[, amr_selector(oral_ddd > 1 & oral_units == "g")]
#> ℹ For `?amr_selector(oral_ddd > 1 & oral_units == "g")` using columns OXA #> ℹ For `amr_selector(oral_ddd > 1 & oral_units == "g")` using columns OXA
#> (oxacillin), FLC (flucloxacillin), AMX (amoxicillin), AMC #> (oxacillin), FLC (flucloxacillin), AMX (amoxicillin), AMC
#> (amoxicillin/clavulanic acid), AMP (ampicillin), KAN (kanamycin), FOS #> (amoxicillin/clavulanic acid), AMP (ampicillin), KAN (kanamycin), FOS
#> (fosfomycin), LNZ (linezolid), VAN (vancomycin), ERY (erythromycin), CLI #> (fosfomycin), LNZ (linezolid), VAN (vancomycin), ERY (erythromycin), CLI
@@ -1058,17 +1058,17 @@ if (require("data.table")) {
#> The following objects are masked from ‘package:AMR’: #> The following objects are masked from ‘package:AMR’:
#> #>
#> %like%, like #> %like%, like
#> ℹ For `?carbapenems()` using columns IPM (imipenem) and MEM (meropenem) #> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> Warning: It should never be needed to print an antimicrobial selector class. Are you #> Warning: It should never be needed to print an antimicrobial selector class. Are you
#> using data.table? Then add the argument `with = FALSE`, see our examples at #> using data.table? Then add the argument `with = FALSE`, see our examples at
#> `?amr_selector()`. #> `amr_selector()`.
#> Class <amr_selector> #> Class <amr_selector>
#> [1] IPM MEM #> [1] IPM MEM
if (require("data.table")) { if (require("data.table")) {
# so `with = FALSE` is required # so `with = FALSE` is required
dt[, carbapenems(), with = FALSE] dt[, carbapenems(), with = FALSE]
} }
#> ℹ For `?carbapenems()` using columns IPM (imipenem) and MEM (meropenem) #> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> IPM MEM #> IPM MEM
#> <sir> <sir> #> <sir> <sir>
#> 1: <NA> <NA> #> 1: <NA> <NA>
@@ -1087,8 +1087,8 @@ if (require("data.table")) {
if (require("data.table")) { if (require("data.table")) {
dt[, c("mo", aminoglycosides())] dt[, c("mo", aminoglycosides())]
} }
#> ℹ For `?aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), #> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK
#> AMK (amikacin), and KAN (kanamycin) #> (amikacin), and KAN (kanamycin)
#> mo GEN TOB AMK KAN #> mo GEN TOB AMK KAN
#> <mo> <sir> <sir> <sir> <sir> #> <mo> <sir> <sir> <sir> <sir>
#> 1: B_ESCHR_COLI <NA> <NA> <NA> <NA> #> 1: B_ESCHR_COLI <NA> <NA> <NA> <NA>
@@ -1105,9 +1105,9 @@ if (require("data.table")) {
if (require("data.table")) { if (require("data.table")) {
dt[, c(carbapenems(), aminoglycosides())] dt[, c(carbapenems(), aminoglycosides())]
} }
#> ℹ For `?carbapenems()` using columns IPM (imipenem) and MEM (meropenem) #> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> ℹ For `?aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), #> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK
#> AMK (amikacin), and KAN (kanamycin) #> (amikacin), and KAN (kanamycin)
#> IPM MEM GEN TOB AMK KAN #> IPM MEM GEN TOB AMK KAN
#> <sir> <sir> <sir> <sir> <sir> <sir> #> <sir> <sir> <sir> <sir> <sir> <sir>
#> 1: <NA> <NA> <NA> <NA> <NA> <NA> #> 1: <NA> <NA> <NA> <NA> <NA> <NA>
@@ -1126,7 +1126,7 @@ if (require("data.table")) {
if (require("data.table")) { if (require("data.table")) {
dt[any(carbapenems() == "S"), ] dt[any(carbapenems() == "S"), ]
} }
#> ℹ For `?carbapenems()` using columns IPM (imipenem) and MEM (meropenem) #> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> date patient age gender ward mo PEN OXA FLC #> date patient age gender ward mo PEN OXA FLC
#> <Date> <char> <num> <char> <char> <mo> <sir> <sir> <sir> #> <Date> <char> <num> <char> <char> <mo> <sir> <sir> <sir>
#> 1: 2002-01-19 738003 71 M Clinical B_ESCHR_COLI R <NA> <NA> #> 1: 2002-01-19 738003 71 M Clinical B_ESCHR_COLI R <NA> <NA>
@@ -1195,8 +1195,8 @@ if (require("data.table")) {
if (require("data.table")) { if (require("data.table")) {
dt[any(carbapenems() == "S"), penicillins(), with = FALSE] dt[any(carbapenems() == "S"), penicillins(), with = FALSE]
} }
#> ℹ For `?carbapenems()` using columns IPM (imipenem) and MEM (meropenem) #> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> ℹ For `?penicillins()` using columns PEN (benzylpenicillin), OXA (oxacillin), #> ℹ For `penicillins()` using columns PEN (benzylpenicillin), OXA (oxacillin),
#> FLC (flucloxacillin), AMX (amoxicillin), AMC (amoxicillin/clavulanic acid), #> FLC (flucloxacillin), AMX (amoxicillin), AMC (amoxicillin/clavulanic acid),
#> AMP (ampicillin), and TZP (piperacillin/tazobactam) #> AMP (ampicillin), and TZP (piperacillin/tazobactam)
#> PEN OXA FLC AMX AMC AMP TZP #> PEN OXA FLC AMX AMC AMP TZP

2
reference/antimicrobials.html
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@@ -9,7 +9,7 @@ The antibiotics data set has been renamed to antimicrobials. The old name will b
<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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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/as.ab.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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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">
@@ -191,16 +191,16 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2,000 × 46</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2,000 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo J01CE01 J01CF04 J01CF05</span> <span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo J01CE01 J01CF04 J01CF05</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </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;"> 1</span> 2002-01-02 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2002-01-03 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </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;"> 2</span> 2002-01-03 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2002-01-16 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2002-01-16 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2002-01-17 858515 79 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2002-01-17 858515 79 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </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-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 37 more variables: J01CA04 &lt;sir&gt;, J01CR02 &lt;sir&gt;, J01CA01 &lt;sir&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 37 more variables: J01CA04 &lt;sir&gt;, J01CR02 &lt;sir&gt;, J01CA01 &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># J01CR05 &lt;sir&gt;, J01DB04 &lt;sir&gt;, J01DE01 &lt;sir&gt;, J01DC02 &lt;sir&gt;, J01DC01 &lt;sir&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># J01CR05 &lt;sir&gt;, J01DB04 &lt;sir&gt;, J01DE01 &lt;sir&gt;, J01DC02 &lt;sir&gt;, J01DC01 &lt;sir&gt;,</span></span>

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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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/as.disk.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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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/as.mic.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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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/as.mo.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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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
reference/as.sir.html
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@@ -9,7 +9,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</small>
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@@ -351,16 +351,16 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2,000 × 46</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2,000 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span> <span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </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;"> 1</span> 2002-01-02 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2002-01-03 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </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;"> 2</span> 2002-01-03 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2002-01-16 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2002-01-16 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2002-01-17 858515 79 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </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> 2002-01-17 858515 79 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #949494;"> 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-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;,</span></span>
@@ -424,10 +424,10 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4 × 18</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4 × 18</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index method ab_given mo_given host_given input_given</span> <span class="r-out co"><span class="r-pr">#&gt;</span> datetime index method ab_given mo_given host_given input_given</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;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;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;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> 2026-03-22 <span style="color: #949494;">21:27:17</span> 1 MIC amoxicillin Escherich… human 8 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2026-03-24 <span style="color: #949494;">12:30:17</span> 1 MIC amoxicillin Escherich… human 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2026-03-22 <span style="color: #949494;">21:27:17</span> 1 MIC cipro Escherich… human 0.256 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2026-03-24 <span style="color: #949494;">12:30:17</span> 1 MIC cipro Escherich… human 0.256 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2026-03-22 <span style="color: #949494;">21:27:18</span> 1 DISK tobra Escherich… human 16 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2026-03-24 <span style="color: #949494;">12:30:18</span> 1 DISK tobra Escherich… human 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2026-03-22 <span style="color: #949494;">21:27:18</span> 1 DISK genta Escherich… human 18 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2026-03-24 <span style="color: #949494;">12:30:18</span> 1 DISK genta Escherich… human 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 11 more variables: ab &lt;ab&gt;, mo &lt;mo&gt;, host &lt;chr&gt;, input &lt;chr&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 11 more variables: ab &lt;ab&gt;, mo &lt;mo&gt;, host &lt;chr&gt;, input &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># outcome &lt;sir&gt;, 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;"># outcome &lt;sir&gt;, 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;"># breakpoint_S_R &lt;chr&gt;, site &lt;chr&gt;</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># breakpoint_S_R &lt;chr&gt;, site &lt;chr&gt;</span></span>
@@ -435,15 +435,14 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<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="co"># using parallel computing, which is available in base R:</span></span></span> <span class="r-in"><span><span class="co"># using parallel computing, which is available in base R:</span></span></span>
<span class="r-in"><span><span class="fu">as.sir</span><span class="op">(</span><span class="va">df_wide</span>, parallel <span class="op">=</span> <span class="cn">TRUE</span>, info <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu">as.sir</span><span class="op">(</span><span class="va">df_wide</span>, parallel <span class="op">=</span> <span class="cn">TRUE</span>, info <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Returning a previously coerced value for an antimicrobial. Run</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Run `sir_interpretation_history()` afterwards to retrieve a logbook with all</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> `?ab_reset_session()` to reset this. This note will be shown once per</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> details of the breakpoint interpretations.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> session.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span> <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Running in parallel mode using 3 out of 4 cores, on columns '<span style="font-weight: bold;">amoxicillin</span>',</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> Processing columns:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> '<span style="font-weight: bold;">cipro</span>', '<span style="font-weight: bold;">tobra</span>', '<span style="font-weight: bold;">genta</span>', and '<span style="font-weight: bold;">ERY</span>'...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #5FD7AF;">DONE</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span> <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Run `?sir_interpretation_history()` to retrieve a logbook with all details of</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #5FD7AF;">­ONE</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Run `sir_interpretation_history()` to retrieve a logbook with all details of</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> the breakpoint interpretations.</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> the breakpoint interpretations.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> microorganism amoxicillin cipro tobra genta ERY</span> <span class="r-out co"><span class="r-pr">#&gt;</span> microorganism amoxicillin cipro tobra genta ERY</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 Escherichia coli S I S S R</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 1 Escherichia coli S I S S R</span>
@@ -556,7 +555,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<span class="r-in"><span> <span class="va">df_wide</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">df_wide</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_all.html" class="external-link">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">cipro</span><span class="op">:</span><span class="va">genta</span><span class="op">)</span>, <span class="va">as.sir</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, uti <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">cipro</span><span class="op">:</span><span class="va">genta</span><span class="op">)</span>, <span class="va">as.sir</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, uti <span class="op">=</span> <span class="cn">TRUE</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: #00BBBB;">ℹ</span> For `?aminopenicillins()` using column <span style="color: #00BB00; font-weight: bold;">amoxicillin</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `aminopenicillins()` using column <span style="color: #00BB00; font-weight: bold;">amoxicillin</span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>There was 1 warning in `mutate()`.</span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>There was 1 warning in `mutate()`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In argument: `across(...)`.</span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In argument: `across(...)`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> Caused by warning:</span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> Caused by warning:</span>
@@ -582,11 +581,6 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<span class="r-wrn co"><span class="r-pr">#&gt;</span> Caused by warning:</span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> Caused by warning:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> Some MICs were converted to the nearest higher log2 level, following the CLSI</span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> Some MICs were converted to the nearest higher log2 level, following the CLSI</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> interpretation guideline.</span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> interpretation guideline.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: '<span style="font-weight: bold;">antibiotic</span>' (TESTAB, test Antibiotic), <span style="font-weight: bold;">CLSI 2025</span>...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: '<span style="font-weight: bold;">antibiotic</span>' (TESTAB, test Antibiotic), <span style="font-weight: bold;">CLSI</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="font-weight: bold;">2025</span>...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: '<span style="font-weight: bold;">antibiotic</span>' (TESTAB, test Antibiotic), <span style="font-weight: bold;">CLSI</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="font-weight: bold;">2025</span>...</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>There was 1 warning in `mutate()`.</span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>There was 1 warning in `mutate()`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In argument: `cipro = (function (x, ...) ...`.</span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In argument: `cipro = (function (x, ...) ...`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> Caused by warning:</span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> Caused by warning:</span>
@@ -627,7 +621,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<span class="r-in"><span><span class="co"># For CLEANING existing SIR values -------------------------------------</span></span></span> <span class="r-in"><span><span class="co"># For CLEANING existing SIR values -------------------------------------</span></span></span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">as.sir</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="st">"S"</span>, <span class="st">"SDD"</span>, <span class="st">"I"</span>, <span class="st">"R"</span>, <span class="st">"NI"</span>, <span class="st">"A"</span>, <span class="st">"B"</span>, <span class="st">"C"</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu">as.sir</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="st">"S"</span>, <span class="st">"SDD"</span>, <span class="st">"I"</span>, <span class="st">"R"</span>, <span class="st">"NI"</span>, <span class="st">"A"</span>, <span class="st">"B"</span>, <span class="st">"C"</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in `?as.sir()`: 3 results truncated (38%) that were invalid antimicrobial</span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in `as.sir()`: 3 results truncated (38%) that were invalid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> interpretations: "A", "B", and "C"</span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> interpretations: "A", "B", and "C"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;sir&gt;</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] S SDD I R NI &lt;NA&gt; &lt;NA&gt; &lt;NA&gt;</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] S SDD I R NI &lt;NA&gt; &lt;NA&gt; &lt;NA&gt;</span>
@@ -636,11 +630,11 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] S</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] S</span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">as.sir</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="fl">1</span>, <span class="fl">2</span>, <span class="fl">3</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu">as.sir</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="fl">1</span>, <span class="fl">2</span>, <span class="fl">3</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> `?as.sir()`: Interpreting input value 1 as "S", 2 as "I", and 3 as "R"</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> `as.sir()`: Interpreting input value 1 as "S", 2 as "I", and 3 as "R"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;sir&gt;</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] S I R</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] S I R</span>
<span class="r-in"><span><span class="fu">as.sir</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="fl">1</span>, <span class="fl">2</span>, <span class="fl">3</span><span class="op">)</span>, S <span class="op">=</span> <span class="fl">3</span>, I <span class="op">=</span> <span class="fl">2</span>, R <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu">as.sir</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="fl">1</span>, <span class="fl">2</span>, <span class="fl">3</span><span class="op">)</span>, S <span class="op">=</span> <span class="fl">3</span>, I <span class="op">=</span> <span class="fl">2</span>, R <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> `?as.sir()`: Interpreting input value 1 as "R", 2 as "I", and 3 as "S"</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> `as.sir()`: Interpreting input value 1 as "R", 2 as "I", and 3 as "S"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;sir&gt;</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] R I S</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] R I S</span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
@@ -679,16 +673,16 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2,000 × 46</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2,000 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span> <span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </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;"> 1</span> 2002-01-02 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2002-01-03 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </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;"> 2</span> 2002-01-03 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2002-01-16 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2002-01-16 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2002-01-17 858515 79 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </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> 2002-01-17 858515 79 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #949494;"> 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-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;,</span></span>

34
reference/as.sir.md
View File

@@ -660,10 +660,10 @@ sir_interpretation_history()
#> # A tibble: 4 × 18 #> # A tibble: 4 × 18
#> datetime index method ab_given mo_given host_given input_given #> datetime index method ab_given mo_given host_given input_given
#> <dttm> <int> <chr> <chr> <chr> <chr> <chr> #> <dttm> <int> <chr> <chr> <chr> <chr> <chr>
#> 1 2026-03-22 21:27:17 1 MIC amoxicillin Escherich… human 8 #> 1 2026-03-24 12:30:17 1 MIC amoxicillin Escherich… human 8
#> 2 2026-03-22 21:27:17 1 MIC cipro Escherich… human 0.256 #> 2 2026-03-24 12:30:17 1 MIC cipro Escherich… human 0.256
#> 3 2026-03-22 21:27:18 1 DISK tobra Escherich… human 16 #> 3 2026-03-24 12:30:18 1 DISK tobra Escherich… human 16
#> 4 2026-03-22 21:27:18 1 DISK genta Escherich… human 18 #> 4 2026-03-24 12:30:18 1 DISK genta Escherich… human 18
#> # ℹ 11 more variables: ab <ab>, mo <mo>, host <chr>, input <chr>, #> # ℹ 11 more variables: ab <ab>, mo <mo>, host <chr>, input <chr>,
#> # outcome <sir>, notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>, #> # outcome <sir>, notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,
#> # breakpoint_S_R <chr>, site <chr> #> # breakpoint_S_R <chr>, site <chr>
@@ -671,15 +671,14 @@ sir_interpretation_history()
# \donttest{ # \donttest{
# using parallel computing, which is available in base R: # using parallel computing, which is available in base R:
as.sir(df_wide, parallel = TRUE, info = TRUE) as.sir(df_wide, parallel = TRUE, info = TRUE)
#> ℹ Returning a previously coerced value for an antimicrobial. Run #> ℹ Run `sir_interpretation_history()` afterwards to retrieve a logbook with all
#> `?ab_reset_session()` to reset this. This note will be shown once per #> details of the breakpoint interpretations.
#> session.
#> #>
#> Running in parallel mode using 3 out of 4 cores, on columns 'amoxicillin', #> Processing columns:
#> 'cipro', 'tobra', 'genta', and 'ERY'...
#> DONE
#> #>
#> ℹ Run `?sir_interpretation_history()` to retrieve a logbook with all details of #> ­ONE
#>
#> ℹ Run `sir_interpretation_history()` to retrieve a logbook with all details of
#> the breakpoint interpretations. #> the breakpoint interpretations.
#> microorganism amoxicillin cipro tobra genta ERY #> microorganism amoxicillin cipro tobra genta ERY
#> 1 Escherichia coli S I S S R #> 1 Escherichia coli S I S S R
@@ -792,7 +791,7 @@ if (require("dplyr")) {
df_wide %>% df_wide %>%
mutate_at(vars(cipro:genta), as.sir, mo = "E. coli", uti = TRUE) mutate_at(vars(cipro:genta), as.sir, mo = "E. coli", uti = TRUE)
} }
#> ℹ For `?aminopenicillins()` using column amoxicillin #> ℹ For `aminopenicillins()` using column amoxicillin
#> Warning: There was 1 warning in `mutate()`. #> Warning: There was 1 warning in `mutate()`.
#> ℹ In argument: `across(...)`. #> ℹ In argument: `across(...)`.
#> Caused by warning: #> Caused by warning:
@@ -818,11 +817,6 @@ if (require("dplyr")) {
#> Caused by warning: #> Caused by warning:
#> ! Some MICs were converted to the nearest higher log2 level, following the CLSI #> ! Some MICs were converted to the nearest higher log2 level, following the CLSI
#> interpretation guideline. #> interpretation guideline.
#> Interpreting MIC values: 'antibiotic' (TESTAB, test Antibiotic), CLSI 2025...
#> Interpreting disk diffusion zones: 'antibiotic' (TESTAB, test Antibiotic), CLSI
#> 2025...
#> Interpreting disk diffusion zones: 'antibiotic' (TESTAB, test Antibiotic), CLSI
#> 2025...
#> Warning: There was 1 warning in `mutate()`. #> Warning: There was 1 warning in `mutate()`.
#> ℹ In argument: `cipro = (function (x, ...) ...`. #> ℹ In argument: `cipro = (function (x, ...) ...`.
#> Caused by warning: #> Caused by warning:
@@ -863,7 +857,7 @@ as.sir(
# For CLEANING existing SIR values ------------------------------------- # For CLEANING existing SIR values -------------------------------------
as.sir(c("S", "SDD", "I", "R", "NI", "A", "B", "C")) as.sir(c("S", "SDD", "I", "R", "NI", "A", "B", "C"))
#> Warning: in `?as.sir()`: 3 results truncated (38%) that were invalid antimicrobial #> Warning: in `as.sir()`: 3 results truncated (38%) that were invalid antimicrobial
#> interpretations: "A", "B", and "C" #> interpretations: "A", "B", and "C"
#> Class <sir> #> Class <sir>
#> [1] S SDD I R NI <NA> <NA> <NA> #> [1] S SDD I R NI <NA> <NA> <NA>
@@ -872,11 +866,11 @@ as.sir("<= 0.002; S") # will return "S"
#> [1] S #> [1] S
as.sir(c(1, 2, 3)) as.sir(c(1, 2, 3))
#> ℹ `?as.sir()`: Interpreting input value 1 as "S", 2 as "I", and 3 as "R" #> ℹ `as.sir()`: Interpreting input value 1 as "S", 2 as "I", and 3 as "R"
#> Class <sir> #> Class <sir>
#> [1] S I R #> [1] S I R
as.sir(c(1, 2, 3), S = 3, I = 2, R = 1) as.sir(c(1, 2, 3), S = 3, I = 2, R = 1)
#> ℹ `?as.sir()`: Interpreting input value 1 as "R", 2 as "I", and 3 as "S" #> ℹ `as.sir()`: Interpreting input value 1 as "R", 2 as "I", and 3 as "S"
#> Class <sir> #> Class <sir>
#> [1] R I S #> [1] R I S

6
reference/atc_online.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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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">
@@ -135,10 +135,10 @@
<span class="r-in"><span> <span class="fu">atc_online_property</span><span class="op">(</span><span class="st">"J01CA04"</span>, property <span class="op">=</span> <span class="st">"groups"</span><span class="op">)</span> <span class="co"># search hierarchical groups of amoxicillin</span></span></span> <span class="r-in"><span> <span class="fu">atc_online_property</span><span class="op">(</span><span class="st">"J01CA04"</span>, property <span class="op">=</span> <span class="st">"groups"</span><span class="op">)</span> <span class="co"># search hierarchical groups of amoxicillin</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> Loading required namespace: rvest</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> Loading required namespace: rvest</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> `?atc_online_property()`: no properties found for ATC QG51AA03. Please check</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> `atc_online_property()`: no properties found for ATC QG51AA03. Please check</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB; font-style: italic;">&lt;https://atcddd.fhi.no/atcvet/atcvet_index/?code=QG51AA03&amp;showdescription=no</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB; font-style: italic;">&lt;https://atcddd.fhi.no/atcvet/atcvet_index/?code=QG51AA03&amp;showdescription=no</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB; font-style: italic;">this WHOCC webpage&gt;</span>.</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB; font-style: italic;">this WHOCC webpage&gt;</span>.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> `?atc_online_property()`: no properties found for ATC QJ01CA04. Please check</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> `atc_online_property()`: no properties found for ATC QJ01CA04. Please check</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB; font-style: italic;">&lt;https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01CA04&amp;showdescription=no</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB; font-style: italic;">&lt;https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01CA04&amp;showdescription=no</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB; font-style: italic;">this WHOCC webpage&gt;</span>.</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB; font-style: italic;">this WHOCC webpage&gt;</span>.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "ANTIINFECTIVES FOR SYSTEMIC USE" </span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "ANTIINFECTIVES FOR SYSTEMIC USE" </span>

4
reference/atc_online.md
View File

@@ -117,10 +117,10 @@ if (requireNamespace("curl") && requireNamespace("rvest") && requireNamespace("x
atc_online_property("J01CA04", property = "groups") # search hierarchical groups of amoxicillin atc_online_property("J01CA04", property = "groups") # search hierarchical groups of amoxicillin
} }
#> Loading required namespace: rvest #> Loading required namespace: rvest
#> ℹ `?atc_online_property()`: no properties found for ATC QG51AA03. Please check #> ℹ `atc_online_property()`: no properties found for ATC QG51AA03. Please check
#> <https://atcddd.fhi.no/atcvet/atcvet_index/?code=QG51AA03&showdescription=no #> <https://atcddd.fhi.no/atcvet/atcvet_index/?code=QG51AA03&showdescription=no
#> this WHOCC webpage>. #> this WHOCC webpage>.
#> ℹ `?atc_online_property()`: no properties found for ATC QJ01CA04. Please check #> ℹ `atc_online_property()`: no properties found for ATC QJ01CA04. Please check
#> <https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01CA04&showdescription=no #> <https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01CA04&showdescription=no
#> this WHOCC webpage>. #> this WHOCC webpage>.
#> [1] "ANTIINFECTIVES FOR SYSTEMIC USE" #> [1] "ANTIINFECTIVES FOR SYSTEMIC USE"

2
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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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/av_property.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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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/availability.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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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">
@@ -82,9 +82,9 @@
<div class="section level2"> <div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">availability</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span></span></span> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">availability</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> `?resistance()` assumes the EUCAST guideline and thus considers the 'I'</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> `resistance()` assumes the EUCAST guideline and thus considers the 'I'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> category susceptible. Set the `guideline` argument or the `AMR_guideline`</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> category susceptible. Set the `guideline` argument or the `AMR_guideline`</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> option to either "CLSI" or "EUCAST", see AMR-options.</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> option to either "CLSI" or "EUCAST", see `?AMR-options`.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> This message will be shown once per session.</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> This message will be shown once per session.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> count available visual_availabilty resistant visual_resistance</span> <span class="r-out co"><span class="r-pr">#&gt;</span> count available visual_availabilty resistant visual_resistance</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date 2000 100.0% |####################| </span> <span class="r-out co"><span class="r-pr">#&gt;</span> date 2000 100.0% |####################| </span>

4
reference/availability.md
View File

@@ -41,9 +41,9 @@ calculated with
``` r ``` r
availability(example_isolates) availability(example_isolates)
#> ℹ `?resistance()` assumes the EUCAST guideline and thus considers the 'I' #> ℹ `resistance()` assumes the EUCAST guideline and thus considers the 'I'
#> category susceptible. Set the `guideline` argument or the `AMR_guideline` #> category susceptible. Set the `guideline` argument or the `AMR_guideline`
#> option to either "CLSI" or "EUCAST", see AMR-options. #> option to either "CLSI" or "EUCAST", see `?AMR-options`.
#> ℹ This message will be shown once per session. #> ℹ This message will be shown once per session.
#> count available visual_availabilty resistant visual_resistance #> count available visual_availabilty resistant visual_resistance
#> date 2000 100.0% |####################| #> date 2000 100.0% |####################|

22
reference/bug_drug_combinations.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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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">
@@ -142,16 +142,16 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2,000 × 46</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2,000 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span> <span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </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;"> 1</span> 2002-01-02 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2002-01-03 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </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;"> 2</span> 2002-01-03 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2002-01-16 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2002-01-16 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2002-01-17 858515 79 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </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> 2002-01-17 858515 79 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #949494;"> 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-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;,</span></span>

2
reference/clinical_breakpoints.html
View File

@@ -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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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">

20
reference/count.html
View File

@@ -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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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">
@@ -174,15 +174,15 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># base R ------------------------------------------------------------</span></span></span> <span class="r-in"><span><span class="co"># base R ------------------------------------------------------------</span></span></span>
<span class="r-in"><span><span class="fu">count_resistant</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span> <span class="co"># counts "R"</span></span></span> <span class="r-in"><span><span class="fu">count_resistant</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span> <span class="co"># counts "R"</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> `?count_resistant()` assumes the EUCAST guideline and thus considers the 'I'</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> `count_resistant()` assumes the EUCAST guideline and thus considers the 'I'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> category susceptible. Set the `guideline` argument or the `AMR_guideline`</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> category susceptible. Set the `guideline` argument or the `AMR_guideline`</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> option to either "CLSI" or "EUCAST", see AMR-options.</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> option to either "CLSI" or "EUCAST", see `?AMR-options`.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> This message will be shown once per session.</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> This message will be shown once per session.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 804</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 804</span>
<span class="r-in"><span><span class="fu">count_susceptible</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span> <span class="co"># counts "S" and "I"</span></span></span> <span class="r-in"><span><span class="fu">count_susceptible</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span> <span class="co"># counts "S" and "I"</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> `?count_susceptible()` assumes the EUCAST guideline and thus considers the</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> `count_susceptible()` assumes the EUCAST guideline and thus considers the 'I'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'I' category susceptible. Set the `guideline` argument or the `AMR_guideline`</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> category susceptible. Set the `guideline` argument or the `AMR_guideline`</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> option to either "CLSI" or "EUCAST", see AMR-options.</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> option to either "CLSI" or "EUCAST", see `?AMR-options`.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> This message will be shown once per session.</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> This message will be shown once per session.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 546</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 546</span>
<span class="r-in"><span><span class="fu">count_all</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span> <span class="co"># counts "S", "I" and "R"</span></span></span> <span class="r-in"><span><span class="fu">count_all</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span> <span class="co"># counts "S", "I" and "R"</span></span></span>
@@ -213,9 +213,9 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<span class="r-in"><span><span class="fu">count_susceptible</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu">count_susceptible</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 546</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 546</span>
<span class="r-in"><span><span class="fu"><a href="proportion.html">susceptibility</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span> <span class="op">*</span> <span class="fu">n_sir</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="proportion.html">susceptibility</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span> <span class="op">*</span> <span class="fu">n_sir</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> `?susceptibility()` assumes the EUCAST guideline and thus considers the 'I'</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> `susceptibility()` assumes the EUCAST guideline and thus considers the 'I'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> category susceptible. Set the `guideline` argument or the `AMR_guideline`</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> category susceptible. Set the `guideline` argument or the `AMR_guideline`</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> option to either "CLSI" or "EUCAST", see AMR-options.</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> option to either "CLSI" or "EUCAST", see `?AMR-options`.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> This message will be shown once per session.</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> This message will be shown once per session.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 546</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 546</span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
@@ -262,8 +262,8 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">ward</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span> <span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">ward</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="fu">count_df</span><span class="op">(</span>translate <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span> <span class="r-in"><span> <span class="fu">count_df</span><span class="op">(</span>translate <span class="op">=</span> <span class="cn">FALSE</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: #00BBBB;">ℹ</span> For `?aminoglycosides()` using columns <span style="color: #00BB00; font-weight: bold;">GEN</span> (gentamicin), <span style="color: #00BB00; font-weight: bold;">TOB</span> (tobramycin),</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns <span style="color: #00BB00; font-weight: bold;">GEN</span> (gentamicin), <span style="color: #00BB00; font-weight: bold;">TOB</span> (tobramycin), <span style="color: #00BB00; font-weight: bold;">AMK</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00; font-weight: bold;">AMK</span> (amikacin), and <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin)</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> (amikacin), and <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 12 × 4</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 12 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward antibiotic interpretation value</span> <span class="r-out co"><span class="r-pr">#&gt;</span> ward antibiotic interpretation value</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;ord&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&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;ord&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span>

18
reference/count.md
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@@ -188,15 +188,15 @@ calculate microbial resistance and susceptibility.
# base R ------------------------------------------------------------ # base R ------------------------------------------------------------
count_resistant(example_isolates$AMX) # counts "R" count_resistant(example_isolates$AMX) # counts "R"
#> ℹ `?count_resistant()` assumes the EUCAST guideline and thus considers the 'I' #> ℹ `count_resistant()` assumes the EUCAST guideline and thus considers the 'I'
#> category susceptible. Set the `guideline` argument or the `AMR_guideline` #> category susceptible. Set the `guideline` argument or the `AMR_guideline`
#> option to either "CLSI" or "EUCAST", see AMR-options. #> option to either "CLSI" or "EUCAST", see `?AMR-options`.
#> ℹ This message will be shown once per session. #> ℹ This message will be shown once per session.
#> [1] 804 #> [1] 804
count_susceptible(example_isolates$AMX) # counts "S" and "I" count_susceptible(example_isolates$AMX) # counts "S" and "I"
#> ℹ `?count_susceptible()` assumes the EUCAST guideline and thus considers the #> ℹ `count_susceptible()` assumes the EUCAST guideline and thus considers the 'I'
#> 'I' category susceptible. Set the `guideline` argument or the `AMR_guideline` #> category susceptible. Set the `guideline` argument or the `AMR_guideline`
#> option to either "CLSI" or "EUCAST", see AMR-options. #> option to either "CLSI" or "EUCAST", see `?AMR-options`.
#> ℹ This message will be shown once per session. #> ℹ This message will be shown once per session.
#> [1] 546 #> [1] 546
count_all(example_isolates$AMX) # counts "S", "I" and "R" count_all(example_isolates$AMX) # counts "S", "I" and "R"
@@ -227,9 +227,9 @@ n_sir(example_isolates$AMX)
count_susceptible(example_isolates$AMX) count_susceptible(example_isolates$AMX)
#> [1] 546 #> [1] 546
susceptibility(example_isolates$AMX) * n_sir(example_isolates$AMX) susceptibility(example_isolates$AMX) * n_sir(example_isolates$AMX)
#> ℹ `?susceptibility()` assumes the EUCAST guideline and thus considers the 'I' #> ℹ `susceptibility()` assumes the EUCAST guideline and thus considers the 'I'
#> category susceptible. Set the `guideline` argument or the `AMR_guideline` #> category susceptible. Set the `guideline` argument or the `AMR_guideline`
#> option to either "CLSI" or "EUCAST", see AMR-options. #> option to either "CLSI" or "EUCAST", see `?AMR-options`.
#> ℹ This message will be shown once per session. #> ℹ This message will be shown once per session.
#> [1] 546 #> [1] 546
@@ -276,8 +276,8 @@ if (require("dplyr")) {
group_by(ward) %>% group_by(ward) %>%
count_df(translate = FALSE) count_df(translate = FALSE)
} }
#> ℹ For `?aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), #> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK
#> AMK (amikacin), and KAN (kanamycin) #> (amikacin), and KAN (kanamycin)
#> # A tibble: 12 × 4 #> # A tibble: 12 × 4
#> ward antibiotic interpretation value #> ward antibiotic interpretation value
#> <chr> <chr> <ord> <int> #> <chr> <chr> <ord> <int>

2
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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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">

5
reference/custom_mdro_guideline.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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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">
@@ -245,8 +245,7 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> Results will be of class 'factor', with ordered levels: Negative &lt; Custom MDRO 1 &lt; Custom MDRO 2</span> <span class="r-out co"><span class="r-pr">#&gt;</span> Results will be of class 'factor', with ordered levels: Negative &lt; Custom MDRO 1 &lt; Custom MDRO 2</span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">out</span> <span class="op">&lt;-</span> <span class="fu"><a href="mdro.html">mdro</a></span><span class="op">(</span><span class="va">example_isolates</span>, guideline <span class="op">=</span> <span class="va">my_guideline</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="va">out</span> <span class="op">&lt;-</span> <span class="fu"><a href="mdro.html">mdro</a></span><span class="op">(</span><span class="va">example_isolates</span>, guideline <span class="op">=</span> <span class="va">my_guideline</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?cephalosporins_2nd()` using columns <span style="color: #00BB00; font-weight: bold;">CXM</span> (cefuroxime) and <span style="color: #00BB00; font-weight: bold;">FOX</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `cephalosporins_2nd()` using columns <span style="color: #00BB00; font-weight: bold;">CXM</span> (cefuroxime) and <span style="color: #00BB00; font-weight: bold;">FOX</span> (cefoxitin)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (cefoxitin)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Assuming a filter on all 2 cephalosporins_2nd. Wrap around `all()` or `any()`</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Assuming a filter on all 2 cephalosporins_2nd. Wrap around `all()` or `any()`</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> to prevent this note.</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> to prevent this note.</span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/table.html" class="external-link">table</a></span><span class="op">(</span><span class="va">out</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/table.html" class="external-link">table</a></span><span class="op">(</span><span class="va">out</span><span class="op">)</span></span></span>

3
reference/custom_mdro_guideline.md
View File

@@ -526,8 +526,7 @@ my_guideline
#> Results will be of class 'factor', with ordered levels: Negative < Custom MDRO 1 < Custom MDRO 2 #> Results will be of class 'factor', with ordered levels: Negative < Custom MDRO 1 < Custom MDRO 2
out <- mdro(example_isolates, guideline = my_guideline) out <- mdro(example_isolates, guideline = my_guideline)
#> ℹ For `?cephalosporins_2nd()` using columns CXM (cefuroxime) and FOX #> ℹ For `cephalosporins_2nd()` using columns CXM (cefuroxime) and FOX (cefoxitin)
#> (cefoxitin)
#> ℹ Assuming a filter on all 2 cephalosporins_2nd. Wrap around `all()` or `any()` #> ℹ Assuming a filter on all 2 cephalosporins_2nd. Wrap around `all()` or `any()`
#> to prevent this note. #> to prevent this note.
table(out) table(out)

2
reference/dosage.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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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/esbl_isolates.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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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">
@@ -75,16 +75,16 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 500 × 19</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 500 × 19</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> esbl genus AMC AMP TZP CXM FOX CTX CAZ GEN TOB TMP SXT</span> <span class="r-out co"><span class="r-pr">#&gt;</span> esbl genus AMC AMP TZP CXM FOX CTX CAZ GEN TOB TMP SXT</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> FALSE Esch… 32 32 4 64 64 8<span style="color: #555555;">.00</span> 8<span style="color: #555555;">.00</span> 1 1 16<span style="color: #555555;">.0</span> 20</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> FALSE Esch… 32 32 4 64 64 8<span style="color: #949494;">.00</span> 8<span style="color: #949494;">.00</span> 1 1 16<span style="color: #949494;">.0</span> 20</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> FALSE Esch… 32 32 4 64 64 4<span style="color: #555555;">.00</span> 8<span style="color: #555555;">.00</span> 1 1 16<span style="color: #555555;">.0</span> 320</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> FALSE Esch… 32 32 4 64 64 4<span style="color: #949494;">.00</span> 8<span style="color: #949494;">.00</span> 1 1 16<span style="color: #949494;">.0</span> 320</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> FALSE Esch… 4 2 64 8 4 8<span style="color: #555555;">.00</span> 0.12 16 16 0.5 20</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> FALSE Esch… 4 2 64 8 4 8<span style="color: #949494;">.00</span> 0.12 16 16 0.5 20</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> FALSE Kleb… 32 32 16 64 64 8<span style="color: #555555;">.00</span> 8<span style="color: #555555;">.00</span> 1 1 0.5 20</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> FALSE Kleb… 32 32 16 64 64 8<span style="color: #949494;">.00</span> 8<span style="color: #949494;">.00</span> 1 1 0.5 20</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> FALSE Esch… 32 32 4 4 4 0.25 2<span style="color: #555555;">.00</span> 1 1 16<span style="color: #555555;">.0</span> 320</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> FALSE Esch… 32 32 4 4 4 0.25 2<span style="color: #949494;">.00</span> 1 1 16<span style="color: #949494;">.0</span> 320</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> FALSE Citr… 32 32 16 64 64 64<span style="color: #555555;">.00</span> 32<span style="color: #555555;">.00</span> 1 1 0.5 20</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> FALSE Citr… 32 32 16 64 64 64<span style="color: #949494;">.00</span> 32<span style="color: #949494;">.00</span> 1 1 0.5 20</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> FALSE Morg… 32 32 4 64 64 16<span style="color: #555555;">.00</span> 2<span style="color: #555555;">.00</span> 1 1 0.5 20</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> FALSE Morg… 32 32 4 64 64 16<span style="color: #949494;">.00</span> 2<span style="color: #949494;">.00</span> 1 1 0.5 20</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> FALSE Prot… 16 32 4 1 4 8<span style="color: #555555;">.00</span> 0.12 1 1 16<span style="color: #555555;">.0</span> 320</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> FALSE Prot… 16 32 4 1 4 8<span style="color: #949494;">.00</span> 0.12 1 1 16<span style="color: #949494;">.0</span> 320</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> FALSE Ente… 32 32 8 64 64 32<span style="color: #555555;">.00</span> 4<span style="color: #555555;">.00</span> 1 1 0.5 20</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> FALSE Ente… 32 32 8 64 64 32<span style="color: #949494;">.00</span> 4<span style="color: #949494;">.00</span> 1 1 0.5 20</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> FALSE Citr… 32 32 32 64 64 8<span style="color: #555555;">.00</span> 64<span style="color: #555555;">.00</span> 1 1 16<span style="color: #555555;">.0</span> 320</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> FALSE Citr… 32 32 32 64 64 8<span style="color: #949494;">.00</span> 64<span style="color: #949494;">.00</span> 1 1 16<span style="color: #949494;">.0</span> 320</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 490 more rows</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 490 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 6 more variables: NIT &lt;mic&gt;, FOS &lt;mic&gt;, CIP &lt;mic&gt;, IPM &lt;mic&gt;, MEM &lt;mic&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 6 more variables: NIT &lt;mic&gt;, FOS &lt;mic&gt;, CIP &lt;mic&gt;, IPM &lt;mic&gt;, MEM &lt;mic&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># COL &lt;mic&gt;</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># COL &lt;mic&gt;</span></span>

22
reference/example_isolates.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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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">
@@ -83,16 +83,16 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2,000 × 46</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2,000 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span> <span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </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;"> 1</span> 2002-01-02 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2002-01-03 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </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;"> 2</span> 2002-01-03 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2002-01-16 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2002-01-16 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2002-01-17 858515 79 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </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> 2002-01-17 858515 79 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #949494;"> 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-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;,</span></span>

2
reference/example_isolates_unclean.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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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/export_ncbi_biosample.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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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">

98
reference/first_isolate.html
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@@ -9,7 +9,7 @@
<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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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">
@@ -211,25 +211,25 @@
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">example_isolates</span><span class="op">[</span><span class="fu">first_isolate</span><span class="op">(</span>info <span class="op">=</span> <span class="cn">TRUE</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">first_isolate</span><span class="op">(</span>info <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Determining first isolates using an episode length of <span style="font-weight: bold;">365 days</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Determining first isolates using an episode length of <span style="font-weight: bold;">365 days</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Using column '<span style="font-weight: bold;">date</span>' as input for `col_date`.</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Using column <span style="color: #00BB00; font-weight: bold;">date</span> as input for `col_date`.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Using column '<span style="font-weight: bold;">patient</span>' as input for `col_patient_id`.</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Using column <span style="color: #00BB00; font-weight: bold;">patient</span> as input for `col_patient_id`.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Basing inclusion on all antimicrobial results, using a points threshold of 2</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Basing inclusion on all antimicrobial results, using a points threshold of 2</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Excluding 16 isolates with a microbial ID 'UNKNOWN' (in column '<span style="font-weight: bold;">mo</span>')</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Excluding 16 isolates with a microbial ID 'UNKNOWN' (in column <span style="color: #00BB00; font-weight: bold;">mo</span>)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Found <span style="font-weight: bold;">1,387 'phenotype-based' first isolates</span> (69.4% of total where a</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Found <span style="font-weight: bold;">1,387 'phenotype-based' first isolates</span> (69.4% of total where a</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> microbial ID was available)</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> microbial ID was available)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 1,387 × 46</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 1,387 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span> <span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </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;"> 1</span> 2002-01-02 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2002-01-16 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2002-01-16 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2002-01-17 858515 79 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #B2B2B2;"> NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2002-01-17 858515 79 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2002-01-17 495616 67 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #B2B2B2;"> NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2002-01-17 495616 67 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2002-01-19 738003 71 M Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </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;"> 7</span> 2002-01-19 738003 71 M Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2002-01-21 462081 75 F Clinical <span style="color: #949494;">B_</span>CTRBC<span style="color: #949494;">_</span>FRND <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2002-01-21 462081 75 F Clinical <span style="color: #949494;">B_</span>CTRBC<span style="color: #949494;">_</span>FRND <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2002-01-22 F35553 50 M ICU <span style="color: #949494;">B_</span>PROTS<span style="color: #949494;">_</span>MRBL <span style="color: #080808; background-color: #FF5F5F;"> R </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;"> 9</span> 2002-01-22 F35553 50 M ICU <span style="color: #949494;">B_</span>PROTS<span style="color: #949494;">_</span>MRBL <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2002-02-03 481442 76 M ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>CONS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </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> 2002-02-03 481442 76 M ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>CONS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 1,377 more rows</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 1,377 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;,</span></span>
@@ -240,20 +240,20 @@
<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="co"># get all first Gram-negatives</span></span></span> <span class="r-in"><span><span class="co"># get all first Gram-negatives</span></span></span>
<span class="r-in"><span><span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu">first_isolate</span><span class="op">(</span>info <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span> <span class="op">&amp;</span> <span class="fu"><a href="mo_property.html">mo_is_gram_negative</a></span><span class="op">(</span><span class="op">)</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"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu">first_isolate</span><span class="op">(</span>info <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span> <span class="op">&amp;</span> <span class="fu"><a href="mo_property.html">mo_is_gram_negative</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Using column '<span style="font-weight: bold;">mo</span>' as input for `?mo_is_gram_negative()`</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Using column <span style="color: #00BB00; font-weight: bold;">mo</span> as input for `mo_is_gram_negative()`</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 441 × 46</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 441 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span> <span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </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;"> 1</span> 2002-01-02 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2002-01-19 738003 71 M Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </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;"> 2</span> 2002-01-19 738003 71 M Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2002-01-21 462081 75 F Clinical <span style="color: #949494;">B_</span>CTRBC<span style="color: #949494;">_</span>FRND <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2002-01-21 462081 75 F Clinical <span style="color: #949494;">B_</span>CTRBC<span style="color: #949494;">_</span>FRND <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2002-01-22 F35553 50 M ICU <span style="color: #949494;">B_</span>PROTS<span style="color: #949494;">_</span>MRBL <span style="color: #080808; background-color: #FF5F5F;"> R </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;"> 4</span> 2002-01-22 F35553 50 M ICU <span style="color: #949494;">B_</span>PROTS<span style="color: #949494;">_</span>MRBL <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2002-02-05 067927 45 F ICU <span style="color: #949494;">B_</span>SERRT<span style="color: #949494;">_</span>MRCS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2002-02-05 067927 45 F ICU <span style="color: #949494;">B_</span>SERRT<span style="color: #949494;">_</span>MRCS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2002-02-27 066895 85 F Clinical <span style="color: #949494;">B_</span>KLBSL<span style="color: #949494;">_</span>PNMN <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2002-02-27 066895 85 F Clinical <span style="color: #949494;">B_</span>KLBSL<span style="color: #949494;">_</span>PNMN <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2002-03-08 4FC193 69 M Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2002-03-08 4FC193 69 M Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2002-03-16 4FC193 69 M Clinical <span style="color: #949494;">B_</span>PSDMN<span style="color: #949494;">_</span>AERG <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2002-03-16 4FC193 69 M Clinical <span style="color: #949494;">B_</span>PSDMN<span style="color: #949494;">_</span>AERG <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2002-04-01 496896 46 F ICU <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </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;"> 9</span> 2002-04-01 496896 46 F ICU <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2002-04-23 EE2510 69 F ICU <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </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> 2002-04-23 EE2510 69 F ICU <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 431 more rows</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 431 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;,</span></span>
@@ -269,22 +269,22 @@
<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: #00BBBB;">ℹ</span> Determining first isolates using an episode length of <span style="font-weight: bold;">365 days</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Determining first isolates using an episode length of <span style="font-weight: bold;">365 days</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Basing inclusion on all antimicrobial results, using a points threshold of 2</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Basing inclusion on all antimicrobial results, using a points threshold of 2</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Excluding 16 isolates with a microbial ID 'UNKNOWN' (in column '<span style="font-weight: bold;">mo</span>')</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Excluding 16 isolates with a microbial ID 'UNKNOWN' (in column <span style="color: #00BB00; font-weight: bold;">mo</span>)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Found <span style="font-weight: bold;">1,387 'phenotype-based' first isolates</span> (69.4% of total where a</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Found <span style="font-weight: bold;">1,387 'phenotype-based' first isolates</span> (69.4% of total where a</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> microbial ID was available)</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> microbial ID was available)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 1,387 × 46</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 1,387 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span> <span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </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;"> 1</span> 2002-01-02 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2002-01-16 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2002-01-16 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2002-01-17 858515 79 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #B2B2B2;"> NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2002-01-17 858515 79 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2002-01-17 495616 67 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #B2B2B2;"> NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2002-01-17 495616 67 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2002-01-19 738003 71 M Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </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;"> 7</span> 2002-01-19 738003 71 M Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2002-01-21 462081 75 F Clinical <span style="color: #949494;">B_</span>CTRBC<span style="color: #949494;">_</span>FRND <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2002-01-21 462081 75 F Clinical <span style="color: #949494;">B_</span>CTRBC<span style="color: #949494;">_</span>FRND <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2002-01-22 F35553 50 M ICU <span style="color: #949494;">B_</span>PROTS<span style="color: #949494;">_</span>MRBL <span style="color: #080808; background-color: #FF5F5F;"> R </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;"> 9</span> 2002-01-22 F35553 50 M ICU <span style="color: #949494;">B_</span>PROTS<span style="color: #949494;">_</span>MRBL <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2002-02-03 481442 76 M ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>CONS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </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> 2002-02-03 481442 76 M ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>CONS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 1,377 more rows</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 1,377 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;,</span></span>
@@ -300,16 +300,16 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 1,387 × 46</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 1,387 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span> <span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </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;"> 1</span> 2002-01-02 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2002-01-16 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2002-01-16 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2002-01-17 858515 79 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #B2B2B2;"> NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2002-01-17 858515 79 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2002-01-17 495616 67 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #B2B2B2;"> NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2002-01-17 495616 67 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2002-01-19 738003 71 M Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </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;"> 7</span> 2002-01-19 738003 71 M Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2002-01-21 462081 75 F Clinical <span style="color: #949494;">B_</span>CTRBC<span style="color: #949494;">_</span>FRND <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2002-01-21 462081 75 F Clinical <span style="color: #949494;">B_</span>CTRBC<span style="color: #949494;">_</span>FRND <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2002-01-22 F35553 50 M ICU <span style="color: #949494;">B_</span>PROTS<span style="color: #949494;">_</span>MRBL <span style="color: #080808; background-color: #FF5F5F;"> R </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;"> 9</span> 2002-01-22 F35553 50 M ICU <span style="color: #949494;">B_</span>PROTS<span style="color: #949494;">_</span>MRBL <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2002-02-03 481442 76 M ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>CONS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </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> 2002-02-03 481442 76 M ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>CONS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 1,377 more rows</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 1,377 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;,</span></span>
@@ -327,15 +327,15 @@
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Determining first isolates using an episode length of <span style="font-weight: bold;">365 days</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Determining first isolates using an episode length of <span style="font-weight: bold;">365 days</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Basing inclusion on all antimicrobial results, using a points threshold of 2</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Basing inclusion on all antimicrobial results, using a points threshold of 2</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Group: ward = "Clinical"</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> Group: ward = "Clinical"</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Excluding 9 isolates with a microbial ID 'UNKNOWN' (in column '<span style="font-weight: bold;">mo</span>')</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Excluding 9 isolates with a microbial ID 'UNKNOWN' (in column <span style="color: #00BB00; font-weight: bold;">mo</span>)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Found <span style="font-weight: bold;">865 'phenotype-based' first isolates</span> (70.1% of total where a microbial</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Found <span style="font-weight: bold;">865 'phenotype-based' first isolates</span> (70.1% of total where a microbial</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ID was available)</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> ID was available)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Group: ward = "ICU"</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> Group: ward = "ICU"</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Excluding 6 isolates with a microbial ID 'UNKNOWN' (in column '<span style="font-weight: bold;">mo</span>')</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Excluding 6 isolates with a microbial ID 'UNKNOWN' (in column <span style="color: #00BB00; font-weight: bold;">mo</span>)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Found <span style="font-weight: bold;">452 'phenotype-based' first isolates</span> (70.0% of total where a microbial</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Found <span style="font-weight: bold;">452 'phenotype-based' first isolates</span> (70.0% of total where a microbial</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ID was available)</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> ID was available)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Group: ward = "Outpatient"</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> Group: ward = "Outpatient"</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Excluding 1 isolates with a microbial ID 'UNKNOWN' (in column '<span style="font-weight: bold;">mo</span>')</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Excluding 1 isolates with a microbial ID 'UNKNOWN' (in column <span style="color: #00BB00; font-weight: bold;">mo</span>)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Found <span style="font-weight: bold;">99 'phenotype-based' first isolates</span> (82.5% of total where a microbial</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Found <span style="font-weight: bold;">99 'phenotype-based' first isolates</span> (82.5% of total where a microbial</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ID was available)</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> ID was available)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2,000 × 5</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2,000 × 5</span></span>

16
reference/first_isolate.md
View File

@@ -330,10 +330,10 @@ method is applied at default.
example_isolates[first_isolate(info = TRUE), ] example_isolates[first_isolate(info = TRUE), ]
#> ℹ Determining first isolates using an episode length of 365 days #> ℹ Determining first isolates using an episode length of 365 days
#> ℹ Using column 'date' as input for `col_date`. #> ℹ Using column date as input for `col_date`.
#> ℹ Using column 'patient' as input for `col_patient_id`. #> ℹ Using column patient as input for `col_patient_id`.
#> ℹ Basing inclusion on all antimicrobial results, using a points threshold of 2 #> ℹ Basing inclusion on all antimicrobial results, using a points threshold of 2
#> ℹ Excluding 16 isolates with a microbial ID 'UNKNOWN' (in column 'mo') #> ℹ Excluding 16 isolates with a microbial ID 'UNKNOWN' (in column mo)
#> => Found 1,387 'phenotype-based' first isolates (69.4% of total where a #> => Found 1,387 'phenotype-based' first isolates (69.4% of total where a
#> microbial ID was available) #> microbial ID was available)
#> # A tibble: 1,387 × 46 #> # A tibble: 1,387 × 46
@@ -359,7 +359,7 @@ example_isolates[first_isolate(info = TRUE), ]
# \donttest{ # \donttest{
# get all first Gram-negatives # get all first Gram-negatives
example_isolates[which(first_isolate(info = FALSE) & mo_is_gram_negative()), ] example_isolates[which(first_isolate(info = FALSE) & mo_is_gram_negative()), ]
#> ℹ Using column 'mo' as input for `?mo_is_gram_negative()` #> ℹ Using column mo as input for `mo_is_gram_negative()`
#> # A tibble: 441 × 46 #> # A tibble: 441 × 46
#> date patient age gender ward mo PEN OXA FLC AMX #> date patient age gender ward mo PEN OXA FLC AMX
#> <date> <chr> <dbl> <chr> <chr> <mo> <sir> <sir> <sir> <sir> #> <date> <chr> <dbl> <chr> <chr> <mo> <sir> <sir> <sir> <sir>
@@ -388,7 +388,7 @@ if (require("dplyr")) {
} }
#> ℹ Determining first isolates using an episode length of 365 days #> ℹ Determining first isolates using an episode length of 365 days
#> ℹ Basing inclusion on all antimicrobial results, using a points threshold of 2 #> ℹ Basing inclusion on all antimicrobial results, using a points threshold of 2
#> ℹ Excluding 16 isolates with a microbial ID 'UNKNOWN' (in column 'mo') #> ℹ Excluding 16 isolates with a microbial ID 'UNKNOWN' (in column mo)
#> => Found 1,387 'phenotype-based' first isolates (69.4% of total where a #> => Found 1,387 'phenotype-based' first isolates (69.4% of total where a
#> microbial ID was available) #> microbial ID was available)
#> # A tibble: 1,387 × 46 #> # A tibble: 1,387 × 46
@@ -446,15 +446,15 @@ if (require("dplyr")) {
#> ℹ Determining first isolates using an episode length of 365 days #> ℹ Determining first isolates using an episode length of 365 days
#> ℹ Basing inclusion on all antimicrobial results, using a points threshold of 2 #> ℹ Basing inclusion on all antimicrobial results, using a points threshold of 2
#> Group: ward = "Clinical" #> Group: ward = "Clinical"
#> ℹ Excluding 9 isolates with a microbial ID 'UNKNOWN' (in column 'mo') #> ℹ Excluding 9 isolates with a microbial ID 'UNKNOWN' (in column mo)
#> => Found 865 'phenotype-based' first isolates (70.1% of total where a microbial #> => Found 865 'phenotype-based' first isolates (70.1% of total where a microbial
#> ID was available) #> ID was available)
#> Group: ward = "ICU" #> Group: ward = "ICU"
#> ℹ Excluding 6 isolates with a microbial ID 'UNKNOWN' (in column 'mo') #> ℹ Excluding 6 isolates with a microbial ID 'UNKNOWN' (in column mo)
#> => Found 452 'phenotype-based' first isolates (70.0% of total where a microbial #> => Found 452 'phenotype-based' first isolates (70.0% of total where a microbial
#> ID was available) #> ID was available)
#> Group: ward = "Outpatient" #> Group: ward = "Outpatient"
#> ℹ Excluding 1 isolates with a microbial ID 'UNKNOWN' (in column 'mo') #> ℹ Excluding 1 isolates with a microbial ID 'UNKNOWN' (in column mo)
#> => Found 99 'phenotype-based' first isolates (82.5% of total where a microbial #> => Found 99 'phenotype-based' first isolates (82.5% of total where a microbial
#> ID was available) #> ID was available)
#> # A tibble: 2,000 × 5 #> # A tibble: 2,000 × 5

2
reference/g.test.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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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
reference/get_episode.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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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">
@@ -174,7 +174,7 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 1 × 46</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 1 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span> <span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2003-01-06 894506 83 M ICU <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2003-01-06 894506 83 M ICU <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># TOB &lt;sir&gt;, AMK &lt;sir&gt;, KAN &lt;sir&gt;, TMP &lt;sir&gt;, SXT &lt;sir&gt;, NIT &lt;sir&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># TOB &lt;sir&gt;, AMK &lt;sir&gt;, KAN &lt;sir&gt;, TMP &lt;sir&gt;, SXT &lt;sir&gt;, NIT &lt;sir&gt;,</span></span>

2
reference/ggplot_pca.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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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
reference/ggplot_sir.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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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">
@@ -285,7 +285,7 @@
<span class="r-in"><span> datalabels <span class="op">=</span> <span class="cn">FALSE</span></span></span> <span class="r-in"><span> datalabels <span class="op">=</span> <span class="cn">FALSE</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: #00BBBB;">ℹ</span> Using column '<span style="font-weight: bold;">mo</span>' as input for `?mo_is_gram_negative()`</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Using column <span style="color: #00BB00; font-weight: bold;">mo</span> as input for `mo_is_gram_negative()`</span>
<span class="r-plt img"><img src="ggplot_sir-10.png" alt="" width="700" height="433"></span> <span class="r-plt img"><img src="ggplot_sir-10.png" alt="" width="700" height="433"></span>
<span class="r-in"><span><span class="co"># }</span></span></span> <span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div> </code></pre></div>

2
reference/ggplot_sir.md
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@@ -295,7 +295,7 @@ if (require("ggplot2") && require("dplyr")) {
datalabels = FALSE datalabels = FALSE
) )
} }
#> ℹ Using column 'mo' as input for `?mo_is_gram_negative()` #> ℹ Using column mo as input for `mo_is_gram_negative()`
# } # }
``` ```

10
reference/guess_ab_col.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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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">
@@ -101,12 +101,10 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "tetr"</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "tetr"</span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">guess_ab_col</span><span class="op">(</span><span class="va">df</span>, <span class="st">"J01AA07"</span>, verbose <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu">guess_ab_col</span><span class="op">(</span><span class="va">df</span>, <span class="st">"J01AA07"</span>, verbose <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Auto-guessing columns suitable for analysis</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK.</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> OK.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Using column '<span style="font-weight: bold;">amox</span>' as input for AMX (amoxicillin).</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Using column <span style="color: #00BB00; font-weight: bold;">amox</span> as input for AMX (amoxicillin).</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Using column '<span style="font-weight: bold;">tetr</span>' as input for TCY (tetracycline).</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Using column <span style="color: #00BB00; font-weight: bold;">tetr</span> as input for TCY (tetracycline).</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Using column '<span style="font-weight: bold;">tetr</span>' as input for J01AA07 (tetracycline).</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Using column <span style="color: #00BB00; font-weight: bold;">tetr</span> as input for J01AA07 (tetracycline).</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "tetr"</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "tetr"</span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># WHONET codes</span></span></span> <span class="r-in"><span><span class="co"># WHONET codes</span></span></span>

8
reference/guess_ab_col.md
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@@ -61,12 +61,10 @@ guess_ab_col(df, "J01AA07") # ATC code of tetracycline
#> [1] "tetr" #> [1] "tetr"
guess_ab_col(df, "J01AA07", verbose = TRUE) guess_ab_col(df, "J01AA07", verbose = TRUE)
#> Auto-guessing columns suitable for analysis
#> ...
#> OK. #> OK.
#> ℹ Using column 'amox' as input for AMX (amoxicillin). #> ℹ Using column amox as input for AMX (amoxicillin).
#> ℹ Using column 'tetr' as input for TCY (tetracycline). #> ℹ Using column tetr as input for TCY (tetracycline).
#> ℹ Using column 'tetr' as input for J01AA07 (tetracycline). #> ℹ Using column tetr as input for J01AA07 (tetracycline).
#> [1] "tetr" #> [1] "tetr"
# WHONET codes # WHONET codes

2
reference/index.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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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/interpretive_rules.html
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@@ -9,7 +9,7 @@ To improve the interpretation of the antibiogram before CLSI/EUCAST interpretive
<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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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">
@@ -228,7 +228,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># apply EUCAST rules: some results wil be changed</span></span></span> <span class="r-in"><span><span class="co"># apply EUCAST rules: some results wil be changed</span></span></span>
<span class="r-in"><span><span class="va">b</span> <span class="op">&lt;-</span> <span class="fu">eucast_rules</span><span class="op">(</span><span class="va">a</span>, overwrite <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="va">b</span> <span class="op">&lt;-</span> <span class="fu">eucast_rules</span><span class="op">(</span><span class="va">a</span>, overwrite <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in `?eucast_rules()`: not all columns with antimicrobial results are of class</span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in `eucast_rules()`: not all columns with antimicrobial results are of class</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">&lt;sir&gt;</span>. Transform them on beforehand, e.g.: - x <span style="color: #D7AF00;">%&gt;%</span> <span style="font-weight: bold;">as.sir</span><span style="color: #D7AF00;">(</span>CXM<span style="color: #D7AF00;">:</span>AMX<span style="color: #D7AF00;">)</span> - x <span style="color: #D7AF00;">%&gt;%</span></span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">&lt;sir&gt;</span>. Transform them on beforehand, e.g.: - x <span style="color: #D7AF00;">%&gt;%</span> <span style="font-weight: bold;">as.sir</span><span style="color: #D7AF00;">(</span>CXM<span style="color: #D7AF00;">:</span>AMX<span style="color: #D7AF00;">)</span> - x <span style="color: #D7AF00;">%&gt;%</span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="font-weight: bold;">mutate_if</span><span style="color: #D7AF00;">(</span>is_sir_eligible, as.sir<span style="color: #D7AF00;">)</span> - x <span style="color: #D7AF00;">%&gt;%</span></span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="font-weight: bold;">mutate_if</span><span style="color: #D7AF00;">(</span>is_sir_eligible, as.sir<span style="color: #D7AF00;">)</span> - x <span style="color: #D7AF00;">%&gt;%</span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="font-weight: bold;">mutate</span><span style="color: #D7AF00;">(</span><span style="font-weight: bold;">across</span><span style="color: #BBBB00;">(</span><span style="font-weight: bold;">where</span><span style="color: #0000BB;">(</span>is_sir_eligible<span style="color: #0000BB;">)</span>, as.sir<span style="color: #BBBB00;">)</span><span style="color: #D7AF00;">)</span></span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="font-weight: bold;">mutate</span><span style="color: #D7AF00;">(</span><span style="font-weight: bold;">across</span><span style="color: #BBBB00;">(</span><span style="font-weight: bold;">where</span><span style="color: #0000BB;">(</span>is_sir_eligible<span style="color: #0000BB;">)</span>, as.sir<span style="color: #BBBB00;">)</span><span style="color: #D7AF00;">)</span></span>
@@ -245,7 +245,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<span class="r-in"><span><span class="co"># do not apply EUCAST rules, but rather get a data.frame</span></span></span> <span class="r-in"><span><span class="co"># do not apply EUCAST rules, but rather get a data.frame</span></span></span>
<span class="r-in"><span><span class="co"># containing all details about the transformations:</span></span></span> <span class="r-in"><span><span class="co"># containing all details about the transformations:</span></span></span>
<span class="r-in"><span><span class="va">c</span> <span class="op">&lt;-</span> <span class="fu">eucast_rules</span><span class="op">(</span><span class="va">a</span>, overwrite <span class="op">=</span> <span class="cn">TRUE</span>, verbose <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="va">c</span> <span class="op">&lt;-</span> <span class="fu">eucast_rules</span><span class="op">(</span><span class="va">a</span>, overwrite <span class="op">=</span> <span class="cn">TRUE</span>, verbose <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in `?eucast_rules()`: not all columns with antimicrobial results are of class</span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in `eucast_rules()`: not all columns with antimicrobial results are of class</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">&lt;sir&gt;</span>. Transform them on beforehand, e.g.: - x <span style="color: #D7AF00;">%&gt;%</span> <span style="font-weight: bold;">as.sir</span><span style="color: #D7AF00;">(</span>CXM<span style="color: #D7AF00;">:</span>AMX<span style="color: #D7AF00;">)</span> - x <span style="color: #D7AF00;">%&gt;%</span></span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">&lt;sir&gt;</span>. Transform them on beforehand, e.g.: - x <span style="color: #D7AF00;">%&gt;%</span> <span style="font-weight: bold;">as.sir</span><span style="color: #D7AF00;">(</span>CXM<span style="color: #D7AF00;">:</span>AMX<span style="color: #D7AF00;">)</span> - x <span style="color: #D7AF00;">%&gt;%</span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="font-weight: bold;">mutate_if</span><span style="color: #D7AF00;">(</span>is_sir_eligible, as.sir<span style="color: #D7AF00;">)</span> - x <span style="color: #D7AF00;">%&gt;%</span></span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="font-weight: bold;">mutate_if</span><span style="color: #D7AF00;">(</span>is_sir_eligible, as.sir<span style="color: #D7AF00;">)</span> - x <span style="color: #D7AF00;">%&gt;%</span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="font-weight: bold;">mutate</span><span style="color: #D7AF00;">(</span><span style="font-weight: bold;">across</span><span style="color: #BBBB00;">(</span><span style="font-weight: bold;">where</span><span style="color: #0000BB;">(</span>is_sir_eligible<span style="color: #0000BB;">)</span>, as.sir<span style="color: #BBBB00;">)</span><span style="color: #D7AF00;">)</span></span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="font-weight: bold;">mutate</span><span style="color: #D7AF00;">(</span><span style="font-weight: bold;">across</span><span style="color: #BBBB00;">(</span><span style="font-weight: bold;">where</span><span style="color: #0000BB;">(</span>is_sir_eligible<span style="color: #0000BB;">)</span>, as.sir<span style="color: #BBBB00;">)</span><span style="color: #D7AF00;">)</span></span>

4
reference/interpretive_rules.md
View File

@@ -306,7 +306,7 @@ head(a)
# apply EUCAST rules: some results wil be changed # apply EUCAST rules: some results wil be changed
b <- eucast_rules(a, overwrite = TRUE) b <- eucast_rules(a, overwrite = TRUE)
#> Warning: in `?eucast_rules()`: not all columns with antimicrobial results are of class #> Warning: in `eucast_rules()`: not all columns with antimicrobial results are of class
#> <sir>. Transform them on beforehand, e.g.: - x %>% as.sir(CXM:AMX) - x %>% #> <sir>. Transform them on beforehand, e.g.: - x %>% as.sir(CXM:AMX) - x %>%
#> mutate_if(is_sir_eligible, as.sir) - x %>% #> mutate_if(is_sir_eligible, as.sir) - x %>%
#> mutate(across(where(is_sir_eligible), as.sir)) #> mutate(across(where(is_sir_eligible), as.sir))
@@ -323,7 +323,7 @@ head(b)
# do not apply EUCAST rules, but rather get a data.frame # do not apply EUCAST rules, but rather get a data.frame
# containing all details about the transformations: # containing all details about the transformations:
c <- eucast_rules(a, overwrite = TRUE, verbose = TRUE) c <- eucast_rules(a, overwrite = TRUE, verbose = TRUE)
#> Warning: in `?eucast_rules()`: not all columns with antimicrobial results are of class #> Warning: in `eucast_rules()`: not all columns with antimicrobial results are of class
#> <sir>. Transform them on beforehand, e.g.: - x %>% as.sir(CXM:AMX) - x %>% #> <sir>. Transform them on beforehand, e.g.: - x %>% as.sir(CXM:AMX) - x %>%
#> mutate_if(is_sir_eligible, as.sir) - x %>% #> mutate_if(is_sir_eligible, as.sir) - x %>%
#> mutate(across(where(is_sir_eligible), as.sir)) #> mutate(across(where(is_sir_eligible), as.sir))

2
reference/intrinsic_resistant.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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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/italicise_taxonomy.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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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
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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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/key_antimicrobials.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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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/kurtosis.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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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">

46
reference/like.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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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">
@@ -133,20 +133,20 @@
<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="co"># get isolates whose name start with 'Entero' (case-insensitive)</span></span></span> <span class="r-in"><span><span class="co"># get isolates whose name start with 'Entero' (case-insensitive)</span></span></span>
<span class="r-in"><span><span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu"><a href="mo_property.html">mo_name</a></span><span class="op">(</span><span class="op">)</span> <span class="op">%like%</span> <span class="st">"^entero"</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"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu"><a href="mo_property.html">mo_name</a></span><span class="op">(</span><span class="op">)</span> <span class="op">%like%</span> <span class="st">"^entero"</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Using column '<span style="font-weight: bold;">mo</span>' as input for `?mo_name()`</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Using column <span style="color: #00BB00; font-weight: bold;">mo</span> as input for `mo_name()`</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 106 × 46</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 106 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span> <span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2002-02-21 4FC193 69 M Clinic… <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FACM <span style="color: #B2B2B2;"> NA</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;"> 1</span> 2002-02-21 4FC193 69 M Clinic… <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FACM <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2002-04-08 130252 78 M ICU <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FCLS <span style="color: #B2B2B2;"> NA</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;"> 2</span> 2002-04-08 130252 78 M ICU <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FCLS <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2002-06-23 798871 82 M Clinic… <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FCLS <span style="color: #B2B2B2;"> NA</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;"> 3</span> 2002-06-23 798871 82 M Clinic… <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FCLS <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2002-06-23 798871 82 M Clinic… <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FCLS <span style="color: #B2B2B2;"> NA</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;"> 4</span> 2002-06-23 798871 82 M Clinic… <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FCLS <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2003-04-20 6BC362 62 M ICU <span style="color: #949494;">B_</span>ENTRC <span style="color: #B2B2B2;"> NA</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;"> 5</span> 2003-04-20 6BC362 62 M ICU <span style="color: #949494;">B_</span>ENTRC <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2003-04-21 6BC362 62 M ICU <span style="color: #949494;">B_</span>ENTRC <span style="color: #B2B2B2;"> NA</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;"> 6</span> 2003-04-21 6BC362 62 M ICU <span style="color: #949494;">B_</span>ENTRC <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2003-08-13 F35553 52 M ICU <span style="color: #949494;">B_</span>ENTRBC<span style="color: #949494;">_</span>CLOC <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2003-08-13 F35553 52 M ICU <span style="color: #949494;">B_</span>ENTRBC<span style="color: #949494;">_</span>CLOC <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2003-08-13 F35553 52 M ICU <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FCLS <span style="color: #B2B2B2;"> NA</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;"> 8</span> 2003-08-13 F35553 52 M ICU <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FCLS <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2003-09-05 F35553 52 M ICU <span style="color: #949494;">B_</span>ENTRC <span style="color: #B2B2B2;"> NA</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;"> 9</span> 2003-09-05 F35553 52 M ICU <span style="color: #949494;">B_</span>ENTRC <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2003-09-05 F35553 52 M ICU <span style="color: #949494;">B_</span>ENTRBC<span style="color: #949494;">_</span>CLOC <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2003-09-05 F35553 52 M ICU <span style="color: #949494;">B_</span>ENTRBC<span style="color: #949494;">_</span>CLOC <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 96 more rows</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 96 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;,</span></span>
@@ -159,20 +159,20 @@
<span class="r-in"><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">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/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="mo_property.html">mo_name</a></span><span class="op">(</span><span class="op">)</span> <span class="op">%like%</span> <span class="st">"^ent"</span><span class="op">)</span></span></span> <span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="mo_property.html">mo_name</a></span><span class="op">(</span><span class="op">)</span> <span class="op">%like%</span> <span class="st">"^ent"</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: #00BBBB;">ℹ</span> Using column '<span style="font-weight: bold;">mo</span>' as input for `?mo_name()`</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Using column <span style="color: #00BB00; font-weight: bold;">mo</span> as input for `mo_name()`</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 106 × 46</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 106 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span> <span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2002-02-21 4FC193 69 M Clinic… <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FACM <span style="color: #B2B2B2;"> NA</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;"> 1</span> 2002-02-21 4FC193 69 M Clinic… <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FACM <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2002-04-08 130252 78 M ICU <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FCLS <span style="color: #B2B2B2;"> NA</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;"> 2</span> 2002-04-08 130252 78 M ICU <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FCLS <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2002-06-23 798871 82 M Clinic… <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FCLS <span style="color: #B2B2B2;"> NA</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;"> 3</span> 2002-06-23 798871 82 M Clinic… <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FCLS <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2002-06-23 798871 82 M Clinic… <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FCLS <span style="color: #B2B2B2;"> NA</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;"> 4</span> 2002-06-23 798871 82 M Clinic… <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FCLS <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2003-04-20 6BC362 62 M ICU <span style="color: #949494;">B_</span>ENTRC <span style="color: #B2B2B2;"> NA</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;"> 5</span> 2003-04-20 6BC362 62 M ICU <span style="color: #949494;">B_</span>ENTRC <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2003-04-21 6BC362 62 M ICU <span style="color: #949494;">B_</span>ENTRC <span style="color: #B2B2B2;"> NA</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;"> 6</span> 2003-04-21 6BC362 62 M ICU <span style="color: #949494;">B_</span>ENTRC <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2003-08-13 F35553 52 M ICU <span style="color: #949494;">B_</span>ENTRBC<span style="color: #949494;">_</span>CLOC <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2003-08-13 F35553 52 M ICU <span style="color: #949494;">B_</span>ENTRBC<span style="color: #949494;">_</span>CLOC <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2003-08-13 F35553 52 M ICU <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FCLS <span style="color: #B2B2B2;"> NA</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;"> 8</span> 2003-08-13 F35553 52 M ICU <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FCLS <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2003-09-05 F35553 52 M ICU <span style="color: #949494;">B_</span>ENTRC <span style="color: #B2B2B2;"> NA</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;"> 9</span> 2003-09-05 F35553 52 M ICU <span style="color: #949494;">B_</span>ENTRC <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2003-09-05 F35553 52 M ICU <span style="color: #949494;">B_</span>ENTRBC<span style="color: #949494;">_</span>CLOC <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2003-09-05 F35553 52 M ICU <span style="color: #949494;">B_</span>ENTRBC<span style="color: #949494;">_</span>CLOC <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 96 more rows</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 96 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;,</span></span>

4
reference/like.md
View File

@@ -114,7 +114,7 @@ a %like% b[1]
# \donttest{ # \donttest{
# get isolates whose name start with 'Entero' (case-insensitive) # get isolates whose name start with 'Entero' (case-insensitive)
example_isolates[which(mo_name() %like% "^entero"), ] example_isolates[which(mo_name() %like% "^entero"), ]
#> ℹ Using column 'mo' as input for `?mo_name()` #> ℹ Using column mo as input for `mo_name()`
#> # A tibble: 106 × 46 #> # A tibble: 106 × 46
#> date patient age gender ward mo PEN OXA FLC AMX #> date patient age gender ward mo PEN OXA FLC AMX
#> <date> <chr> <dbl> <chr> <chr> <mo> <sir> <sir> <sir> <sir> #> <date> <chr> <dbl> <chr> <chr> <mo> <sir> <sir> <sir> <sir>
@@ -140,7 +140,7 @@ if (require("dplyr")) {
example_isolates %>% example_isolates %>%
filter(mo_name() %like% "^ent") filter(mo_name() %like% "^ent")
} }
#> ℹ Using column 'mo' as input for `?mo_name()` #> ℹ Using column mo as input for `mo_name()`
#> # A tibble: 106 × 46 #> # A tibble: 106 × 46
#> date patient age gender ward mo PEN OXA FLC AMX #> date patient age gender ward mo PEN OXA FLC AMX
#> <date> <chr> <dbl> <chr> <chr> <mo> <sir> <sir> <sir> <sir> #> <date> <chr> <dbl> <chr> <chr> <mo> <sir> <sir> <sir> <sir>

6
reference/mdro.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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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">
@@ -210,7 +210,7 @@ Ordered <a href="https://rdrr.io/pkg/data.table/man/fctr.html" class="external-l
<div class="section level2"> <div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <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">out</span> <span class="op">&lt;-</span> <span class="fu">mdro</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span></span></span> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">out</span> <span class="op">&lt;-</span> <span class="fu">mdro</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span></span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in `?mdro()`: NA introduced for isolates where the available percentage of</span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in `mdro()`: NA introduced for isolates where the available percentage of</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> antimicrobial classes was below 50% (set with `pct_required_classes`)</span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> antimicrobial classes was below 50% (set with `pct_required_classes`)</span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/str.html" class="external-link">str</a></span><span class="op">(</span><span class="va">out</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/str.html" class="external-link">str</a></span><span class="op">(</span><span class="va">out</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Ord.factor w/ 4 levels "Negative"&lt;"Multi-drug-resistant (MDR)"&lt;..: NA NA 1 1 1 1 NA NA 1 1 ...</span> <span class="r-out co"><span class="r-pr">#&gt;</span> Ord.factor w/ 4 levels "Negative"&lt;"Multi-drug-resistant (MDR)"&lt;..: NA NA 1 1 1 1 NA NA 1 1 ...</span>
@@ -237,7 +237,7 @@ Ordered <a href="https://rdrr.io/pkg/data.table/man/fctr.html" class="external-l
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>There was 1 warning in `mutate()`.</span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>There was 1 warning in `mutate()`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In argument: `MDRO = mdro()`.</span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In argument: `MDRO = mdro()`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> Caused by warning:</span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> Caused by warning:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> in `?mdro()`: NA introduced for isolates where the available percentage of</span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> in `mdro()`: NA introduced for isolates where the available percentage of</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> antimicrobial classes was below 50% (set with `pct_required_classes`)</span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> antimicrobial classes was below 50% (set with `pct_required_classes`)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 2</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 2</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> MDRO n</span> <span class="r-out co"><span class="r-pr">#&gt;</span> MDRO n</span>

4
reference/mdro.md
View File

@@ -297,7 +297,7 @@ susceptible isolates.
``` r ``` r
out <- mdro(example_isolates) out <- mdro(example_isolates)
#> Warning: in `?mdro()`: NA introduced for isolates where the available percentage of #> Warning: in `mdro()`: NA introduced for isolates where the available percentage of
#> antimicrobial classes was below 50% (set with `pct_required_classes`) #> antimicrobial classes was below 50% (set with `pct_required_classes`)
str(out) str(out)
#> Ord.factor w/ 4 levels "Negative"<"Multi-drug-resistant (MDR)"<..: NA NA 1 1 1 1 NA NA 1 1 ... #> Ord.factor w/ 4 levels "Negative"<"Multi-drug-resistant (MDR)"<..: NA NA 1 1 1 1 NA NA 1 1 ...
@@ -324,7 +324,7 @@ if (require("dplyr")) {
#> Warning: There was 1 warning in `mutate()`. #> Warning: There was 1 warning in `mutate()`.
#> ℹ In argument: `MDRO = mdro()`. #> ℹ In argument: `MDRO = mdro()`.
#> Caused by warning: #> Caused by warning:
#> ! in `?mdro()`: NA introduced for isolates where the available percentage of #> ! in `mdro()`: NA introduced for isolates where the available percentage of
#> antimicrobial classes was below 50% (set with `pct_required_classes`) #> antimicrobial classes was below 50% (set with `pct_required_classes`)
#> # A tibble: 3 × 2 #> # A tibble: 3 × 2
#> MDRO n #> MDRO n

24
reference/mean_amr_distance.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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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">
@@ -205,24 +205,24 @@
<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>dist <span class="op">=</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">.</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></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>dist <span class="op">=</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">.</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></span>
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">mo</span>, <span class="va">dist</span><span class="op">)</span></span></span> <span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">mo</span>, <span class="va">dist</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: #00BBBB;">ℹ</span> Using column '<span style="font-weight: bold;">mo</span>' as input for `?mo_genus()`</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Using column <span style="color: #00BB00; font-weight: bold;">mo</span> as input for `mo_genus()`</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Using column '<span style="font-weight: bold;">mo</span>' as input for `?mo_species()`</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Using column <span style="color: #00BB00; font-weight: bold;">mo</span> as input for `mo_species()`</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Calculating mean AMR distance based on columns "TCY", "IPM", and "MEM"</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Calculating mean AMR distance based on columns "TCY", "IPM", and "MEM"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 63 × 5</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 63 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: mo [4]</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: mo [4]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo TCY IPM MEM dist</span> <span class="r-out co"><span class="r-pr">#&gt;</span> mo TCY IPM MEM dist</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&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: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&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> <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>AVIM <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #B2B2B2;"> NA</span> 0 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>AVIM <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #949494;"> NA</span> 0 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>AVIM <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #B2B2B2;"> NA</span> 0 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>AVIM <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #949494;"> NA</span> 0 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>CSSL <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #BB0000;">NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>CSSL <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #949494;"> NA</span> <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FACM <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #B2B2B2;"> NA</span> -<span style="color: #BB0000;">2.66</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FACM <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #949494;"> NA</span> -<span style="color: #BB0000;">2.66</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FACM <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> -<span style="color: #BB0000;">0.423</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FACM <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> -<span style="color: #BB0000;">0.423</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FACM <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> -<span style="color: #BB0000;">0.423</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FACM <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> -<span style="color: #BB0000;">0.423</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FACM <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> 0.224</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FACM <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> 0.224</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FACM <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> 0.224</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FACM <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> 0.224</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FACM <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> 0.224</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FACM <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> 0.224</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FACM <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> 0.224</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FACM <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> 0.224</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 53 more rows</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 53 more rows</span></span>
</code></pre></div> </code></pre></div>
</div> </div>

6
reference/mean_amr_distance.md
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@@ -180,9 +180,9 @@ if (require("dplyr")) {
mutate(dist = mean_amr_distance(.)) %>% mutate(dist = mean_amr_distance(.)) %>%
arrange(mo, dist) arrange(mo, dist)
} }
#> ℹ Using column 'mo' as input for `?mo_genus()` #> ℹ Using column mo as input for `mo_genus()`
#> ℹ Using column 'mo' as input for `?mo_species()` #> ℹ Using column mo as input for `mo_species()`
#> ℹ For `?carbapenems()` using columns IPM (imipenem) and MEM (meropenem) #> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> ℹ Calculating mean AMR distance based on columns "TCY", "IPM", and "MEM" #> ℹ Calculating mean AMR distance based on columns "TCY", "IPM", and "MEM"
#> # A tibble: 63 × 5 #> # A tibble: 63 × 5
#> # Groups: mo [4] #> # Groups: mo [4]

2
reference/microorganisms.codes.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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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/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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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/microorganisms.html
View File

@@ -9,7 +9,7 @@ This data set is carefully crafted, yet made 100% reproducible from public and a
<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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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">

8
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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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">
@@ -120,7 +120,7 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] B_ESCHR_COLI</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] B_ESCHR_COLI</span>
<span class="r-in"><span><span class="fu"><a href="as.mo.html">mo_uncertainties</a></span><span class="op">(</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="as.mo.html">mo_uncertainties</a></span><span class="op">(</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Matching scores are based on the resemblance between the input and the full</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> Matching scores are based on the resemblance between the input and the full</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> taxonomic name, and the pathogenicity in humans. See `?mo_matching_score()`.</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> taxonomic name, and the pathogenicity in humans. See `mo_matching_score()`.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Colour keys: <span style="color: #080808; background-color: #FF5F5F;"> 0.000-0.549 </span><span style="color: #080808; background-color: #FFD787;"> 0.550-0.649 </span><span style="color: #080808; background-color: #FFFF87;"> 0.650-0.749 </span><span style="color: #080808; background-color: #5FD7AF;"> 0.750-1.000 </span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> Colour keys: <span style="color: #080808; background-color: #FF5F5F;"> 0.000-0.549 </span><span style="color: #080808; background-color: #FFD787;"> 0.550-0.649 </span><span style="color: #080808; background-color: #FFFF87;"> 0.650-0.749 </span><span style="color: #080808; background-color: #5FD7AF;"> 0.750-1.000 </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #B2B2B2;">-------------------------------------------------------------------------------</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #B2B2B2;">-------------------------------------------------------------------------------</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">"E. coli"</span> -&gt; <span style="font-weight: bold; font-style: italic;">Escherichia coli</span> (B_ESCHR_COLI, <span style="color: #080808; background-color: #FFFF87;">0.688</span>)</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">"E. coli"</span> -&gt; <span style="font-weight: bold; font-style: italic;">Escherichia coli</span> (B_ESCHR_COLI, <span style="color: #080808; background-color: #FFFF87;">0.688</span>)</span>
@@ -131,8 +131,8 @@
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">(</span><span style="color: #080808; background-color: #FFD787;">0.571</span>), and <span style="font-style: italic;">Enterobacter cloacae dissolvens</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.565</span>)</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">(</span><span style="color: #080808; background-color: #FFD787;">0.571</span>), and <span style="font-style: italic;">Enterobacter cloacae dissolvens</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.565</span>)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Only the first 10 other matches of each record are shown. Run ``</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Only the first 10 other matches of each record are shown. Run ``</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ?`print(mo_uncertainties(), n = ...)` `` to view more entries, or save</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> `print(mo_uncertainties(), n = ...)` `` to view more entries, or save</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> `?mo_uncertainties()` to an object.</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> `mo_uncertainties()` to an object.</span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">mo_matching_score</span><span class="op">(</span></span></span> <span class="r-in"><span><span class="fu">mo_matching_score</span><span class="op">(</span></span></span>
<span class="r-in"><span> x <span class="op">=</span> <span class="st">"E. coli"</span>,</span></span> <span class="r-in"><span> x <span class="op">=</span> <span class="st">"E. coli"</span>,</span></span>

6
reference/mo_matching_score.md
View File

@@ -190,7 +190,7 @@ as.mo("E. coli")
#> [1] B_ESCHR_COLI #> [1] B_ESCHR_COLI
mo_uncertainties() mo_uncertainties()
#> Matching scores are based on the resemblance between the input and the full #> Matching scores are based on the resemblance between the input and the full
#> taxonomic name, and the pathogenicity in humans. See `?mo_matching_score()`. #> taxonomic name, and the pathogenicity in humans. See `mo_matching_score()`.
#> Colour keys: 0.000-0.549 0.550-0.649 0.650-0.749 0.750-1.000 #> Colour keys: 0.000-0.549 0.550-0.649 0.650-0.749 0.750-1.000
#> ------------------------------------------------------------------------------- #> -------------------------------------------------------------------------------
#> "E. coli" -> Escherichia coli (B_ESCHR_COLI, 0.688) #> "E. coli" -> Escherichia coli (B_ESCHR_COLI, 0.688)
@@ -201,8 +201,8 @@ mo_uncertainties()
#> (0.571), and Enterobacter cloacae dissolvens (0.565) #> (0.571), and Enterobacter cloacae dissolvens (0.565)
#> #>
#> ℹ Only the first 10 other matches of each record are shown. Run `` #> ℹ Only the first 10 other matches of each record are shown. Run ``
#> ?`print(mo_uncertainties(), n = ...)` `` to view more entries, or save #> `print(mo_uncertainties(), n = ...)` `` to view more entries, or save
#> `?mo_uncertainties()` to an object. #> `mo_uncertainties()` to an object.
mo_matching_score( mo_matching_score(
x = "E. coli", x = "E. coli",

12
reference/mo_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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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">
@@ -368,7 +368,7 @@
<span class="r-in"><span><span class="fu">mo_mycobank</span><span class="op">(</span><span class="st">"Candida krusei"</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu">mo_mycobank</span><span class="op">(</span><span class="st">"Candida krusei"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "337013"</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "337013"</span>
<span class="r-in"><span><span class="fu">mo_mycobank</span><span class="op">(</span><span class="st">"Candida krusei"</span>, keep_synonyms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu">mo_mycobank</span><span class="op">(</span><span class="st">"Candida krusei"</span>, keep_synonyms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>`?as.mo()` returned one outdated taxonomic name. Use `keep_synonyms = FALSE` to</span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>`as.mo()` returned one outdated taxonomic name. Use `keep_synonyms = FALSE` to</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> clean the input to currently accepted taxonomic names, or set the R option</span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> clean the input to currently accepted taxonomic names, or set the R option</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> `AMR_keep_synonyms` to `FALSE`. This warning will be shown once per session.</span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> `AMR_keep_synonyms` to `FALSE`. This warning will be shown once per session.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "268707"</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "268707"</span>
@@ -462,8 +462,8 @@
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu">mo_is_gram_positive</span><span class="op">(</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></span> <span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu">mo_is_gram_positive</span><span class="op">(</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></span>
<span class="r-in"><span> <span class="fu"><a href="count.html">count</a></span><span class="op">(</span><span class="fu">mo_genus</span><span class="op">(</span><span class="op">)</span>, sort <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-in"><span> <span class="fu"><a href="count.html">count</a></span><span class="op">(</span><span class="fu">mo_genus</span><span class="op">(</span><span class="op">)</span>, sort <span class="op">=</span> <span class="cn">TRUE</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: #00BBBB;">ℹ</span> Using column '<span style="font-weight: bold;">mo</span>' as input for `?mo_is_gram_positive()`</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Using column <span style="color: #00BB00; font-weight: bold;">mo</span> as input for `mo_is_gram_positive()`</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Using column '<span style="font-weight: bold;">mo</span>' as input for `?mo_genus()`</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Using column <span style="color: #00BB00; font-weight: bold;">mo</span> as input for `mo_genus()`</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 18 × 2</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 18 × 2</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> `mo_genus()` n</span> <span class="r-out co"><span class="r-pr">#&gt;</span> `mo_genus()` n</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;int&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;int&gt;</span></span>
@@ -490,8 +490,8 @@
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu">mo_is_intrinsic_resistant</span><span class="op">(</span>ab <span class="op">=</span> <span class="st">"vanco"</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></span> <span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu">mo_is_intrinsic_resistant</span><span class="op">(</span>ab <span class="op">=</span> <span class="st">"vanco"</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></span>
<span class="r-in"><span> <span class="fu"><a href="count.html">count</a></span><span class="op">(</span><span class="fu">mo_genus</span><span class="op">(</span><span class="op">)</span>, sort <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-in"><span> <span class="fu"><a href="count.html">count</a></span><span class="op">(</span><span class="fu">mo_genus</span><span class="op">(</span><span class="op">)</span>, sort <span class="op">=</span> <span class="cn">TRUE</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: #00BBBB;">ℹ</span> Using column '<span style="font-weight: bold;">mo</span>' as input for `?mo_is_intrinsic_resistant()`</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Using column <span style="color: #00BB00; font-weight: bold;">mo</span> as input for `mo_is_intrinsic_resistant()`</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Using column '<span style="font-weight: bold;">mo</span>' as input for `?mo_genus()`</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Using column <span style="color: #00BB00; font-weight: bold;">mo</span> as input for `mo_genus()`</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 19 × 2</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 19 × 2</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> `mo_genus()` n</span> <span class="r-out co"><span class="r-pr">#&gt;</span> `mo_genus()` n</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;int&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;int&gt;</span></span>

10
reference/mo_property.md
View File

@@ -485,7 +485,7 @@ mo_mycobank("Candida albicans")
mo_mycobank("Candida krusei") mo_mycobank("Candida krusei")
#> [1] "337013" #> [1] "337013"
mo_mycobank("Candida krusei", keep_synonyms = TRUE) mo_mycobank("Candida krusei", keep_synonyms = TRUE)
#> Warning: `?as.mo()` returned one outdated taxonomic name. Use `keep_synonyms = FALSE` to #> Warning: `as.mo()` returned one outdated taxonomic name. Use `keep_synonyms = FALSE` to
#> clean the input to currently accepted taxonomic names, or set the R option #> clean the input to currently accepted taxonomic names, or set the R option
#> `AMR_keep_synonyms` to `FALSE`. This warning will be shown once per session. #> `AMR_keep_synonyms` to `FALSE`. This warning will be shown once per session.
#> [1] "268707" #> [1] "268707"
@@ -579,8 +579,8 @@ if (require("dplyr")) {
filter(mo_is_gram_positive()) %>% filter(mo_is_gram_positive()) %>%
count(mo_genus(), sort = TRUE) count(mo_genus(), sort = TRUE)
} }
#> ℹ Using column 'mo' as input for `?mo_is_gram_positive()` #> ℹ Using column mo as input for `mo_is_gram_positive()`
#> ℹ Using column 'mo' as input for `?mo_genus()` #> ℹ Using column mo as input for `mo_genus()`
#> # A tibble: 18 × 2 #> # A tibble: 18 × 2
#> `mo_genus()` n #> `mo_genus()` n
#> <chr> <int> #> <chr> <int>
@@ -607,8 +607,8 @@ if (require("dplyr")) {
filter(mo_is_intrinsic_resistant(ab = "vanco")) %>% filter(mo_is_intrinsic_resistant(ab = "vanco")) %>%
count(mo_genus(), sort = TRUE) count(mo_genus(), sort = TRUE)
} }
#> ℹ Using column 'mo' as input for `?mo_is_intrinsic_resistant()` #> ℹ Using column mo as input for `mo_is_intrinsic_resistant()`
#> ℹ Using column 'mo' as input for `?mo_genus()` #> ℹ Using column mo as input for `mo_genus()`
#> # A tibble: 19 × 2 #> # A tibble: 19 × 2
#> `mo_genus()` n #> `mo_genus()` n
#> <chr> <int> #> <chr> <int>

2
reference/mo_source.html
View File

@@ -9,7 +9,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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/pca.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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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/plot.html
View File

@@ -9,7 +9,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<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="">3.0.1.9038</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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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