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2026-03-20 16:11:30 +00:00
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2
404.html
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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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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">

15
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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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">
@@ -73,7 +73,7 @@
<span><span class="fu">pkgdown</span><span class="fu">::</span><span class="fu"><a href="https://pkgdown.r-lib.org/reference/build_site.html" class="external-link">build_site</a></span><span class="op">(</span><span class="op">)</span></span> <span><span class="fu">pkgdown</span><span class="fu">::</span><span class="fu"><a href="https://pkgdown.r-lib.org/reference/build_site.html" class="external-link">build_site</a></span><span class="op">(</span><span class="op">)</span></span>
<span></span> <span></span>
<span><span class="co"># Code coverage report</span></span> <span><span class="co"># Code coverage report</span></span>
<span><span class="fu">covr</span><span class="fu">::</span><span class="fu">package_coverage</span><span class="op">(</span><span class="op">)</span></span></code></pre></div> <span><span class="fu">covr</span><span class="fu">::</span><span class="fu"><a href="http://covr.r-lib.org/reference/package_coverage.html" class="external-link">package_coverage</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<p>From the shell:</p> <p>From the shell:</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" tabindex="-1"></a><span class="co"># CRAN check from parent directory</span></span> <div class="sourceCode" id="cb2"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" tabindex="-1"></a><span class="co"># CRAN check from parent directory</span></span>
<span id="cb2-2"><a href="#cb2-2" tabindex="-1"></a><span class="ex">R</span> CMD check AMR</span></code></pre></div> <span id="cb2-2"><a href="#cb2-2" tabindex="-1"></a><span class="ex">R</span> CMD check AMR</span></code></pre></div>
@@ -229,11 +229,14 @@ _pkgdown.yml # pkgdown website configuration</code></pre>
<span id="cb5-5"><a href="#cb5-5" tabindex="-1"></a><span class="va">currentversion</span><span class="op">=</span><span class="st">"</span><span class="va">${currenttag}</span><span class="st">.</span><span class="va">$((currentcommit</span> <span class="op">+</span> <span class="dv">9001</span> <span class="op">+</span> <span class="dv">1</span><span class="va">))</span><span class="st">"</span></span> <span id="cb5-5"><a href="#cb5-5" tabindex="-1"></a><span class="va">currentversion</span><span class="op">=</span><span class="st">"</span><span class="va">${currenttag}</span><span class="st">.</span><span class="va">$((currentcommit</span> <span class="op">+</span> <span class="dv">9001</span> <span class="op">+</span> <span class="dv">1</span><span class="va">))</span><span class="st">"</span></span>
<span id="cb5-6"><a href="#cb5-6" tabindex="-1"></a><span class="bu">echo</span> <span class="st">"</span><span class="va">$currentversion</span><span class="st">"</span></span></code></pre></div> <span id="cb5-6"><a href="#cb5-6" tabindex="-1"></a><span class="bu">echo</span> <span class="st">"</span><span class="va">$currentversion</span><span class="st">"</span></span></code></pre></div>
<p>The <code>+ 1</code> accounts for the fact that this PR’s squash commit is not yet on the default branch. Set <strong>both</strong> of these files to the resulting version string (and only once per PR, even across multiple commits):</p> <p>The <code>+ 1</code> accounts for the fact that this PR’s squash commit is not yet on the default branch. Set <strong>both</strong> of these files to the resulting version string (and only once per PR, even across multiple commits):</p>
<ol style="list-style-type: decimal"><li> <ol style="list-style-type: decimal"><li><p><strong><code>DESCRIPTION</code></strong> — the <code>Version:</code> field</p></li>
<strong><code>DESCRIPTION</code></strong> — the <code>Version:</code> field</li>
<li> <li>
<strong><code>NEWS.md</code></strong> — the top-level heading <code># AMR &lt;version&gt;</code> <p><strong><code>NEWS.md</code></strong> — <strong>only replace line 1</strong> (the <code># AMR &lt;version&gt;</code> heading) with the new version number; do <strong>not</strong> create a new section. <code>NEWS.md</code> is a <strong>continuous log</strong> for the entire current <code>x.y.z.9nnn</code> development series: all changes since the last stable release accumulate under that single heading. After updating line 1, append the new change as a bullet under the appropriate sub-heading (<code>### New</code>, <code>### Fixes</code>, or <code>### Updates</code>).</p>
</li> <p>Style rules for <code>NEWS.md</code> entries:</p>
<ul><li>Be <strong>extremely concise</strong> — one short line per item</li>
<li>Do <strong>not</strong> end with a full stop (period)</li>
<li>No verbose explanations; just the essential fact</li>
</ul></li>
</ol><p>If <code>git describe</code> fails (e.g. no tags exist in the environment), fall back to reading the current version from <code>DESCRIPTION</code> and adding 1 to the last numeric component — but only if no bump has already been made in this PR.</p> </ol><p>If <code>git describe</code> fails (e.g. no tags exist in the environment), fall back to reading the current version from <code>DESCRIPTION</code> and adding 1 to the last numeric component — but only if no bump has already been made in this PR.</p>
</div> </div>
<div class="section level4"> <div class="section level4">

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CLAUDE.md
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@@ -188,7 +188,20 @@ on the default branch. Set **both** of these files to the resulting
version string (and only once per PR, even across multiple commits): version string (and only once per PR, even across multiple commits):
1. **`DESCRIPTION`** — the `Version:` field 1. **`DESCRIPTION`** — the `Version:` field
2. **`NEWS.md`** — the top-level heading `# AMR <version>`
2. **`NEWS.md`** — **only replace line 1** (the `# AMR <version>`
heading) with the new version number; do **not** create a new
section. `NEWS.md` is a **continuous log** for the entire current
`x.y.z.9nnn` development series: all changes since the last stable
release accumulate under that single heading. After updating line 1,
append the new change as a bullet under the appropriate sub-heading
(`### New`, `### Fixes`, or `### Updates`).
Style rules for `NEWS.md` entries:
- Be **extremely concise** — one short line per item
- Do **not** end with a full stop (period)
- No verbose explanations; just the essential fact
If `git describe` fails (e.g. no tags exist in the environment), fall If `git describe` fails (e.g. no tags exist in the environment), fall
back to reading the current version from `DESCRIPTION` and adding 1 to back to reading the current version from `DESCRIPTION` and adding 1 to

2
LICENSE-text.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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">

160
articles/AMR.html
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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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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 18 March 2026.</p> generated on 20 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">2026-03-18</td> <td align="center">2026-03-20</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">2026-03-18</td> <td align="center">2026-03-20</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">2026-03-18</td> <td align="center">2026-03-20</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>
@@ -263,56 +263,54 @@ user input can be used:</p>
<p>Now we can thus clean our data:</p> <p>Now we can thus clean our data:</p>
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">our_data</span><span class="op">$</span><span class="va">bacteria</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="va">our_data</span><span class="op">$</span><span class="va">bacteria</span>, info <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> <code class="sourceCode R"><span><span class="va">our_data</span><span class="op">$</span><span class="va">bacteria</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="va">our_data</span><span class="op">$</span><span class="va">bacteria</span>, info <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
<span><span class="co">#&gt; <span style="color: #0000BB;">ℹ Retrieved values from the `microorganisms.codes` data set for "ESCCOL",</span></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"><span style="color: #0000BB;">#&gt; "KLEPNE", "STAAUR", and "STRPNE".</span></span></span> <span><span class="co">#&gt; "KLEPNE", "STAAUR", and "STRPNE".</span></span>
<span><span class="co">#&gt; <span style="color: #0000BB;">ℹ Microorganism translation was uncertain for four microorganisms. Run</span></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"><span style="color: #0000BB;">#&gt; `mo_uncertainties()` to review these uncertainties, or use</span></span></span> <span><span class="co">#&gt; `mo_uncertainties()` (`?AMR::mo_uncertainties()`) to review these</span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; `add_custom_microorganisms()` to add custom entries.</span></span></span></code></pre></div> <span><span class="co">#&gt; uncertainties, or use `add_custom_microorganisms()`</span></span>
<span><span class="co">#&gt; (`?AMR::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; <span style="color: #0000BB;">Matching scores are based on the resemblance between the input and the full</span></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"><span style="color: #0000BB;">#&gt; taxonomic name, and the pathogenicity in humans. See `?mo_matching_score`.</span></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; <span style="color: #0000BB;">Colour keys: </span><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; (`?AMR::mo_matching_score()`).</span></span>
<span><span class="co">#&gt; </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; "E. coli" -&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>
<span><span class="co">#&gt; Also matched: <span style="font-style: italic;">Enterococcus crotali</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFFF87;">0.650</span>), <span style="font-style: italic;">Escherichia coli coli</span></span></span> <span><span class="co">#&gt; Also matched: <span style="font-style: italic;">Enterococcus crotali</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFFF87;">0.650</span>), <span style="font-style: italic;">Escherichia coli coli</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.643</span>),</span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; (</span><span style="color: #080808; background-color: #FFD787;">0.643</span>), <span style="font-style: italic;">Escherichia coli expressing</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.611</span>), <span style="font-style: italic;">Enterobacter cowanii</span></span></span> <span><span class="co">#&gt; <span style="font-style: italic;">Escherichia coli expressing</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.611</span>), <span style="font-style: italic;">Enterobacter cowanii</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.600</span>), <span style="font-style: italic;">Enterococcus</span></span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; (</span><span style="color: #080808; background-color: #FFD787;">0.600</span>), <span style="font-style: italic;">Enterococcus columbae</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.595</span>), <span style="font-style: italic;">Enterococcus camelliae</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.591</span>),</span></span> <span><span class="co">#&gt; <span style="font-style: italic;">columbae</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.595</span>), <span style="font-style: italic;">Enterococcus camelliae</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.591</span>), <span style="font-style: italic;">Enterococcus casseliflavus</span></span></span>
<span><span class="co">#&gt; <span style="font-style: italic;">Enterococcus casseliflavus</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.577</span>), <span style="font-style: italic;">Enterobacter cloacae cloacae</span></span></span> <span><span class="co">#&gt; <span style="color: #0000BB;">(</span><span style="color: #080808; background-color: #FFD787;">0.577</span>), <span style="font-style: italic;">Enterobacter cloacae cloacae</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.571</span>), <span style="font-style: italic;">Enterobacter cloacae</span> complex</span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; (</span><span style="color: #080808; background-color: #FFD787;">0.571</span>), <span style="font-style: italic;">Enterobacter cloacae</span> complex<span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.571</span>), and <span style="font-style: italic;">Enterobacter cloacae</span></span></span> <span><span class="co">#&gt; <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>
<span><span class="co"><span style="font-style: italic;">#&gt; dissolvens</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.565</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;">"K. pneumoniae"</span> -&gt; <span style="font-weight: bold; font-style: italic;">Klebsiella pneumoniae</span> (B_KLBSL_PNMN, <span style="color: #080808; background-color: #5FD7AF;">0.786</span>)</span></span>
<span><span class="co">#&gt; "K. pneumoniae" -&gt; <span style="font-weight: bold; font-style: italic;">Klebsiella pneumoniae</span> (B_KLBSL_PNMN, <span style="color: #080808; background-color: #5FD7AF;">0.786</span>)</span></span> <span><span class="co">#&gt; Also matched: <span style="font-style: italic;">Klebsiella pneumoniae</span> complex<span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFFF87;">0.707</span>), <span style="font-style: italic;">Klebsiella pneumoniae</span></span></span>
<span><span class="co">#&gt; Also matched: <span style="font-style: italic;">Klebsiella pneumoniae</span> complex<span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFFF87;">0.707</span>), <span style="font-style: italic;">Klebsiella</span></span></span> <span><span class="co">#&gt; <span style="font-style: italic;">ozaenae</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFFF87;">0.707</span>), <span style="font-style: italic;">Klebsiella pneumoniae pneumoniae</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFFF87;">0.688</span>), <span style="font-style: italic;">Klebsiella</span></span></span>
<span><span class="co"><span style="font-style: italic;">#&gt; pneumoniae ozaenae</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFFF87;">0.707</span>), <span style="font-style: italic;">Klebsiella pneumoniae pneumoniae</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFFF87;">0.688</span>),</span></span> <span><span class="co">#&gt; <span style="font-style: italic;">pneumoniae rhinoscleromatis</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFFF87;">0.658</span>), <span style="font-style: italic;">Klebsiella pasteurii</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.500</span>), <span style="font-style: italic;">Klebsiella</span></span></span>
<span><span class="co">#&gt; <span style="font-style: italic;">Klebsiella pneumoniae rhinoscleromatis</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFFF87;">0.658</span>), <span style="font-style: italic;">Klebsiella pasteurii</span></span></span> <span><span class="co">#&gt; <span style="font-style: italic;">planticola</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.500</span>), <span style="font-style: italic;">Kingella potus</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.400</span>), <span style="font-style: italic;">Kluyveromyces pseudotropicale</span></span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; (</span><span style="color: #080808; background-color: #FF5F5F;">0.500</span>), <span style="font-style: italic;">Klebsiella planticola</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.500</span>), <span style="font-style: italic;">Kingella potus</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.400</span>),</span></span> <span><span class="co">#&gt; <span style="color: #0000BB;">(</span><span style="color: #080808; background-color: #FF5F5F;">0.386</span>), <span style="font-style: italic;">Kluyveromyces pseudotropicalis</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.363</span>), and <span style="font-style: italic;">Kosakonia pseudosacchari</span></span></span>
<span><span class="co">#&gt; <span style="font-style: italic;">Kluyveromyces pseudotropicale</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.386</span>), <span style="font-style: italic;">Kluyveromyces pseudotropicalis</span></span></span> <span><span class="co">#&gt; <span style="color: #0000BB;">(</span><span style="color: #080808; background-color: #FF5F5F;">0.361</span>)</span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; (</span><span style="color: #080808; background-color: #FF5F5F;">0.363</span>), and <span style="font-style: italic;">Kosakonia pseudosacchari</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.361</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;">"S. aureus"</span> -&gt; <span style="font-weight: bold; font-style: italic;">Staphylococcus aureus</span> (B_STPHY_AURS, <span style="color: #080808; background-color: #FFFF87;">0.690</span>)</span></span>
<span><span class="co">#&gt; "S. aureus" -&gt; <span style="font-weight: bold; font-style: italic;">Staphylococcus aureus</span> (B_STPHY_AURS, <span style="color: #080808; background-color: #FFFF87;">0.690</span>)</span></span> <span><span class="co">#&gt; Also matched: <span style="font-style: italic;">Staphylococcus aureus aureus</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.643</span>), <span style="font-style: italic;">Staphylococcus argenteus</span></span></span>
<span><span class="co">#&gt; Also matched: <span style="font-style: italic;">Staphylococcus aureus aureus</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.643</span>), <span style="font-style: italic;">Staphylococcus</span></span></span> <span><span class="co">#&gt; <span style="color: #0000BB;">(</span><span style="color: #080808; background-color: #FFD787;">0.625</span>), <span style="font-style: italic;">Staphylococcus aureus anaerobius</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.625</span>), <span style="font-style: italic;">Staphylococcus auricularis</span></span></span>
<span><span class="co"><span style="font-style: italic;">#&gt; argenteus</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.625</span>), <span style="font-style: italic;">Staphylococcus aureus anaerobius</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.625</span>),</span></span> <span><span class="co">#&gt; <span style="color: #0000BB;">(</span><span style="color: #080808; background-color: #FFD787;">0.615</span>), <span style="font-style: italic;">Salmonella</span> Aurelianis<span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.595</span>), <span style="font-style: italic;">Salmonella</span> Aarhus<span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.588</span>), <span style="font-style: italic;">Salmonella</span></span></span>
<span><span class="co">#&gt; <span style="font-style: italic;">Staphylococcus auricularis</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.615</span>), <span style="font-style: italic;">Salmonella</span> Aurelianis<span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.595</span>),</span></span> <span><span class="co">#&gt; Amounderness<span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.587</span>), <span style="font-style: italic;">Staphylococcus argensis</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.587</span>), <span style="font-style: italic;">Streptococcus australis</span></span></span>
<span><span class="co">#&gt; <span style="font-style: italic;">Salmonella</span> Aarhus<span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.588</span>), <span style="font-style: italic;">Salmonella</span> Amounderness<span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.587</span>),</span></span> <span><span class="co">#&gt; <span style="color: #0000BB;">(</span><span style="color: #080808; background-color: #FFD787;">0.587</span>), and <span style="font-style: italic;">Salmonella choleraesuis arizonae</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.562</span>)</span></span>
<span><span class="co">#&gt; <span style="font-style: italic;">Staphylococcus argensis</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.587</span>), <span style="font-style: italic;">Streptococcus australis</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.587</span>), and</span></span> <span><span class="co">#&gt; <span style="color: #B2B2B2;">-------------------------------------------------------------------------------</span></span></span>
<span><span class="co">#&gt; <span style="font-style: italic;">Salmonella choleraesuis arizonae</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.562</span>)</span></span> <span><span class="co">#&gt; <span style="color: #0000BB;">"S. pneumoniae"</span> -&gt; <span style="font-weight: bold; font-style: italic;">Streptococcus pneumoniae</span> (B_STRPT_PNMN, <span style="color: #080808; background-color: #5FD7AF;">0.750</span>)</span></span>
<span><span class="co">#&gt; <span style="color: #B2B2B2;">--------------------------------------------------------------------------------</span></span></span> <span><span class="co">#&gt; Also matched: <span style="font-style: italic;">Streptococcus pseudopneumoniae</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFFF87;">0.700</span>), <span style="font-style: italic;">Streptococcus phocae</span></span></span>
<span><span class="co">#&gt; "S. pneumoniae" -&gt; <span style="font-weight: bold; font-style: italic;">Streptococcus pneumoniae</span> (B_STRPT_PNMN, <span style="color: #080808; background-color: #5FD7AF;">0.750</span>)</span></span> <span><span class="co">#&gt; <span style="font-style: italic;">salmonis</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.552</span>), <span style="font-style: italic;">Serratia proteamaculans quinovora</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.545</span>), <span style="font-style: italic;">Streptococcus</span></span></span>
<span><span class="co">#&gt; Also matched: <span style="font-style: italic;">Streptococcus pseudopneumoniae</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFFF87;">0.700</span>), <span style="font-style: italic;">Streptococcus</span></span></span> <span><span class="co">#&gt; <span style="font-style: italic;">pseudoporcinus</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.536</span>), <span style="font-style: italic;">Staphylococcus piscifermentans</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.533</span>), <span style="font-style: italic;">Staphylococcus</span></span></span>
<span><span class="co"><span style="font-style: italic;">#&gt; phocae salmonis</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.552</span>), <span style="font-style: italic;">Serratia proteamaculans quinovora</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.545</span>),</span></span> <span><span class="co">#&gt; <span style="font-style: italic;">pseudintermedius</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.532</span>), <span style="font-style: italic;">Serratia proteamaculans proteamaculans</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.526</span>),</span></span>
<span><span class="co">#&gt; <span style="font-style: italic;">Streptococcus pseudoporcinus</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.536</span>), <span style="font-style: italic;">Staphylococcus piscifermentans</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"><span style="color: #0000BB;">#&gt; (</span><span style="color: #080808; background-color: #FF5F5F;">0.533</span>), <span style="font-style: italic;">Staphylococcus pseudintermedius</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.532</span>), <span style="font-style: italic;">Serratia</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"><span style="font-style: italic;">#&gt; proteamaculans proteamaculans</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.526</span>), <span style="font-style: italic;">Streptococcus gallolyticus</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"><span style="font-style: italic;">#&gt; 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>), and <span style="font-style: italic;">Streptococcus</span></span></span> <span><span class="co">#&gt; `print(mo_uncertainties(), n = ...)` (`?AMR::mo_uncertainties()`) to view</span></span>
<span><span class="co"><span style="font-style: italic;">#&gt; periodonticum</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.519</span>)</span></span> <span><span class="co">#&gt; more entries, or save `mo_uncertainties()` (`?AMR::mo_uncertainties()`) to an</span></span>
<span><span class="co">#&gt; </span></span> <span><span class="co">#&gt; object.</span></span></code></pre></div>
<span><span class="co"><span style="color: #0000BB;">#&gt; Only the first 10 other matches of each record are shown. Run</span></span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; `print(mo_uncertainties(), n = ...)` to view more entries, or save</span></span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; `mo_uncertainties()` to an object.</span></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">
@@ -399,16 +397,15 @@ the methods on the <code><a href="../reference/first_isolate.html">first_isolate
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<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: #BB0000;">ℹ Determining first isolates using an episode length of </span><span style="color: #BB0000; 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: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">bacteria</span><span style="color: #0000BB;">' as input for `col_mo`.</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: #0000BB;">ℹ Column '</span><span style="color: #0000BB; font-weight: bold;">first</span><span style="color: #0000BB;">' is SIR eligible (despite only having empty values), since</span></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"><span style="color: #0000BB;">#&gt; it seems to be cefozopran (ZOP)</span></span></span> <span><span class="co">#&gt; seems to be cefozopran (ZOP)</span></span>
<span><span class="co">#&gt; <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">date</span><span style="color: #0000BB;">' as input for `col_date`.</span></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: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">patient_id</span><span style="color: #0000BB;">' as input for `col_patient_id`.</span></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: #BB0000;">ℹ Basing inclusion on all antimicrobial results, using a points threshold</span></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"><span style="color: #BB0000;">#&gt; of 2</span></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; <span style="color: #BBBBBB;">=&gt; Found </span><span style="color: #BBBBBB; font-weight: bold;">2,724 'phenotype-based' first isolates</span><span style="color: #BBBBBB;"> (90.8% of total where a</span></span></span> <span><span class="co">#&gt; microbial ID was available)</span></span></code></pre></div>
<span><span class="co"><span style="color: #BBBBBB;">#&gt; microbial ID was available)</span></span></span></code></pre></div>
<p>So only 91% is suitable for resistance analysis! We can now filter on <p>So only 91% is suitable for resistance analysis! We can now filter on
it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the
<code>dplyr</code> package:</p> <code>dplyr</code> package:</p>
@@ -525,7 +522,7 @@ 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: #0000BB;">ℹ For `aminoglycosides()` using column '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin)</span></span></span> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using column '<span style="font-weight: bold;">GEN</span>' (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>
<span><span class="co">#&gt; <span style="color: #949494; font-style: italic;">&lt;date&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;sir&gt;</span></span></span>
@@ -543,8 +540,8 @@ 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: #0000BB;">ℹ For `betalactams()` using columns '</span><span style="color: #0000BB; font-weight: bold;">AMX</span><span style="color: #0000BB;">' (amoxicillin) and '</span><span style="color: #0000BB; font-weight: bold;">AMC</span><span style="color: #0000BB;">'</span></span></span> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `betalactams()` using columns '<span style="font-weight: bold;">AMX</span>' (amoxicillin) and '<span style="font-weight: bold;">AMC</span>'</span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; (amoxicillin/clavulanic acid)</span></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>
@@ -580,7 +577,7 @@ 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: #0000BB;">ℹ For `aminoglycosides()` using column '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin)</span></span></span> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using column '<span style="font-weight: bold;">GEN</span>' (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>
<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>
@@ -598,8 +595,8 @@ 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: #0000BB;">ℹ For `betalactams()` using columns '</span><span style="color: #0000BB; font-weight: bold;">AMX</span><span style="color: #0000BB;">' (amoxicillin) and '</span><span style="color: #0000BB; font-weight: bold;">AMC</span><span style="color: #0000BB;">'</span></span></span> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `betalactams()` using columns '<span style="font-weight: bold;">AMX</span>' (amoxicillin) and '<span style="font-weight: bold;">AMC</span>'</span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; (amoxicillin/clavulanic acid)</span></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>
<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>
@@ -617,8 +614,8 @@ 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: #0000BB;">ℹ For `betalactams()` using columns '</span><span style="color: #0000BB; font-weight: bold;">AMX</span><span style="color: #0000BB;">' (amoxicillin) and '</span><span style="color: #0000BB; font-weight: bold;">AMC</span><span style="color: #0000BB;">'</span></span></span> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `betalactams()` using columns '<span style="font-weight: bold;">AMX</span>' (amoxicillin) and '<span style="font-weight: bold;">AMC</span>'</span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; (amoxicillin/clavulanic acid)</span></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>
<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>
@@ -699,9 +696,9 @@ 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: #0000BB;">ℹ For `aminoglycosides()` using columns '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin), '</span><span style="color: #0000BB; font-weight: bold;">TOB</span><span style="color: #0000BB;">'</span></span></span> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns '<span style="font-weight: bold;">GEN</span>' (gentamicin), '<span style="font-weight: bold;">TOB</span>' (tobramycin),</span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; (tobramycin), '</span><span style="color: #0000BB; font-weight: bold;">AMK</span><span style="color: #0000BB;">' (amikacin), and '</span><span style="color: #0000BB; font-weight: bold;">KAN</span><span style="color: #0000BB;">' (kanamycin)</span></span></span> <span><span class="co">#&gt; '<span style="font-weight: bold;">AMK</span>' (amikacin), and '<span style="font-weight: bold;">KAN</span>' (kanamycin)</span></span>
<span><span class="co">#&gt; <span style="color: #0000BB;">ℹ For `carbapenems()` using columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem) and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span></span></code></pre></div> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns '<span style="font-weight: bold;">IPM</span>' (imipenem) and '<span style="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%">
@@ -830,8 +827,8 @@ 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: #0000BB;">ℹ For `aminoglycosides()` using columns '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin), '</span><span style="color: #0000BB; font-weight: bold;">TOB</span><span style="color: #0000BB;">'</span></span></span> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns '<span style="font-weight: bold;">GEN</span>' (gentamicin), '<span style="font-weight: bold;">TOB</span>' (tobramycin),</span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; (tobramycin), '</span><span style="color: #0000BB; font-weight: bold;">AMK</span><span style="color: #0000BB;">' (amikacin), and '</span><span style="color: #0000BB; font-weight: bold;">KAN</span><span style="color: #0000BB;">' (kanamycin)</span></span></span></code></pre></div> <span><span class="co">#&gt; '<span style="font-weight: bold;">AMK</span>' (amikacin), and '<span style="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%">
@@ -956,9 +953,9 @@ 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: #0000BB;">ℹ For `aminoglycosides()` using columns '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin), '</span><span style="color: #0000BB; font-weight: bold;">TOB</span><span style="color: #0000BB;">'</span></span></span> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns '<span style="font-weight: bold;">GEN</span>' (gentamicin), '<span style="font-weight: bold;">TOB</span>' (tobramycin),</span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; (tobramycin), '</span><span style="color: #0000BB; font-weight: bold;">AMK</span><span style="color: #0000BB;">' (amikacin), and '</span><span style="color: #0000BB; font-weight: bold;">KAN</span><span style="color: #0000BB;">' (kanamycin)</span></span></span> <span><span class="co">#&gt; '<span style="font-weight: bold;">AMK</span>' (amikacin), and '<span style="font-weight: bold;">KAN</span>' (kanamycin)</span></span>
<span><span class="co">#&gt; <span style="color: #0000BB;">ℹ For `carbapenems()` using columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem) and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span></span></code></pre></div> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns '<span style="font-weight: bold;">IPM</span>' (imipenem) and '<span style="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%">
@@ -1285,10 +1282,11 @@ 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: #0000BB;">ℹ `resistance()` assumes the EUCAST guideline and thus considers the 'I'</span></span></span> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> `resistance()` (`?AMR::resistance()`) assumes the EUCAST guideline and thus</span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; category susceptible. Set the `guideline` argument or the `AMR_guideline`</span></span></span> <span><span class="co">#&gt; considers the 'I' category susceptible. Set the `guideline` argument or the</span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; option to either "CLSI" or "EUCAST", see `?AMR-options`.</span></span></span> <span><span class="co">#&gt; `AMR_guideline` option to either "CLSI" or "EUCAST", see AMR-options</span></span>
<span><span class="co">#&gt; <span style="color: #0000BB;">ℹ This message will be shown once per session.</span></span></span> <span><span class="co">#&gt; (`?AMR::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; [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
<code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, both from the <code>dplyr</code> package:</p> <code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, both from the <code>dplyr</code> package:</p>

106
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@@ -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 18 March 2026. methodology remains unchanged. This page was generated on 20 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 |
|:----------:|:----------:|:----------------:|:---:|:---:| |:----------:|:----------:|:----------------:|:---:|:---:|
| 2026-03-18 | abcd | Escherichia coli | S | S | | 2026-03-20 | abcd | Escherichia coli | S | S |
| 2026-03-18 | abcd | Escherichia coli | S | R | | 2026-03-20 | abcd | Escherichia coli | S | R |
| 2026-03-18 | efgh | Escherichia coli | R | S | | 2026-03-20 | efgh | Escherichia coli | R | S |
### Needed R packages ### Needed R packages
@@ -169,8 +169,9 @@ 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()` (`?AMR::mo_uncertainties()`) to review these
#> `add_custom_microorganisms()` to add custom entries. #> uncertainties, or use `add_custom_microorganisms()`
#> (`?AMR::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
@@ -179,46 +180,43 @@ 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()`
#> (`?AMR::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)
#> Also matched: Enterococcus crotali (0.650), Escherichia coli coli #> Also matched: Enterococcus crotali (0.650), Escherichia coli coli (0.643),
#> (0.643), Escherichia coli expressing (0.611), Enterobacter cowanii #> Escherichia coli expressing (0.611), Enterobacter cowanii (0.600), Enterococcus
#> (0.600), Enterococcus columbae (0.595), Enterococcus camelliae (0.591), #> columbae (0.595), Enterococcus camelliae (0.591), Enterococcus casseliflavus
#> Enterococcus casseliflavus (0.577), Enterobacter cloacae cloacae #> (0.577), Enterobacter cloacae cloacae (0.571), Enterobacter cloacae complex
#> (0.571), Enterobacter cloacae complex (0.571), and Enterobacter cloacae #> (0.571), and Enterobacter cloacae dissolvens (0.565)
#> dissolvens (0.565) #> -------------------------------------------------------------------------------
#> --------------------------------------------------------------------------------
#> "K. pneumoniae" -> Klebsiella pneumoniae (B_KLBSL_PNMN, 0.786) #> "K. pneumoniae" -> Klebsiella pneumoniae (B_KLBSL_PNMN, 0.786)
#> Also matched: Klebsiella pneumoniae complex (0.707), Klebsiella #> Also matched: Klebsiella pneumoniae complex (0.707), Klebsiella pneumoniae
#> pneumoniae ozaenae (0.707), Klebsiella pneumoniae pneumoniae (0.688), #> ozaenae (0.707), Klebsiella pneumoniae pneumoniae (0.688), Klebsiella
#> Klebsiella pneumoniae rhinoscleromatis (0.658), Klebsiella pasteurii #> pneumoniae rhinoscleromatis (0.658), Klebsiella pasteurii (0.500), Klebsiella
#> (0.500), Klebsiella planticola (0.500), Kingella potus (0.400), #> planticola (0.500), Kingella potus (0.400), Kluyveromyces pseudotropicale
#> Kluyveromyces pseudotropicale (0.386), Kluyveromyces pseudotropicalis #> (0.386), Kluyveromyces pseudotropicalis (0.363), and Kosakonia pseudosacchari
#> (0.363), and Kosakonia pseudosacchari (0.361) #> (0.361)
#> -------------------------------------------------------------------------------- #> -------------------------------------------------------------------------------
#> "S. aureus" -> Staphylococcus aureus (B_STPHY_AURS, 0.690) #> "S. aureus" -> Staphylococcus aureus (B_STPHY_AURS, 0.690)
#> Also matched: Staphylococcus aureus aureus (0.643), Staphylococcus #> Also matched: Staphylococcus aureus aureus (0.643), Staphylococcus argenteus
#> argenteus (0.625), Staphylococcus aureus anaerobius (0.625), #> (0.625), Staphylococcus aureus anaerobius (0.625), Staphylococcus auricularis
#> Staphylococcus auricularis (0.615), Salmonella Aurelianis (0.595), #> (0.615), Salmonella Aurelianis (0.595), Salmonella Aarhus (0.588), Salmonella
#> Salmonella Aarhus (0.588), Salmonella Amounderness (0.587), #> Amounderness (0.587), Staphylococcus argensis (0.587), Streptococcus australis
#> Staphylococcus argensis (0.587), Streptococcus australis (0.587), and #> (0.587), and Salmonella choleraesuis arizonae (0.562)
#> Salmonella choleraesuis arizonae (0.562) #> -------------------------------------------------------------------------------
#> --------------------------------------------------------------------------------
#> "S. pneumoniae" -> Streptococcus pneumoniae (B_STRPT_PNMN, 0.750) #> "S. pneumoniae" -> Streptococcus pneumoniae (B_STRPT_PNMN, 0.750)
#> Also matched: Streptococcus pseudopneumoniae (0.700), Streptococcus #> Also matched: Streptococcus pseudopneumoniae (0.700), Streptococcus phocae
#> phocae salmonis (0.552), Serratia proteamaculans quinovora (0.545), #> salmonis (0.552), Serratia proteamaculans quinovora (0.545), Streptococcus
#> Streptococcus pseudoporcinus (0.536), Staphylococcus piscifermentans #> pseudoporcinus (0.536), Staphylococcus piscifermentans (0.533), Staphylococcus
#> (0.533), Staphylococcus pseudintermedius (0.532), Serratia #> pseudintermedius (0.532), Serratia proteamaculans proteamaculans (0.526),
#> proteamaculans proteamaculans (0.526), Streptococcus gallolyticus #> Streptococcus gallolyticus pasteurianus (0.526), Salmonella Portanigra (0.524),
#> pasteurianus (0.526), Salmonella Portanigra (0.524), and Streptococcus #> and Streptococcus periodonticum (0.519)
#> periodonticum (0.519) #> ℹ Only the first 10 other matches of each record are shown. Run
#> #> `print(mo_uncertainties(), n = ...)` (`?AMR::mo_uncertainties()`) to view
#> Only the first 10 other matches of each record are shown. Run #> more entries, or save `mo_uncertainties()` (`?AMR::mo_uncertainties()`) to an
#> `print(mo_uncertainties(), n = ...)` to view more entries, or save #> object.
#> `mo_uncertainties()` to an object.
``` ```
That’s all good. That’s all good.
@@ -317,12 +315,11 @@ 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 #> ℹ Column 'first' is SIR eligible (despite only having empty values), since it
#> 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 #> ℹ Basing inclusion on all antimicrobial results, using a points threshold of 2
#> 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)
``` ```
@@ -628,8 +625,8 @@ 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' #> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB' (tobramycin),
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin) #> 'AMK' (amikacin), and 'KAN' (kanamycin)
#> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
``` ```
@@ -667,8 +664,8 @@ 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' #> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB' (tobramycin),
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin) #> 'AMK' (amikacin), and 'KAN' (kanamycin)
``` ```
| Patógeno | Amikacina | Gentamicina | Kanamicina | Tobramicina | | Patógeno | Amikacina | Gentamicina | Kanamicina | Tobramicina |
@@ -711,8 +708,8 @@ 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' #> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB' (tobramycin),
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin) #> 'AMK' (amikacin), and 'KAN' (kanamycin)
#> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
``` ```
@@ -844,9 +841,10 @@ 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()` (`?AMR::resistance()`) assumes the EUCAST guideline and thus
#> category susceptible. Set the `guideline` argument or the `AMR_guideline` #> considers the 'I' category susceptible. Set the `guideline` argument or the
#> option to either "CLSI" or "EUCAST", see `?AMR-options`. #> `AMR_guideline` option to either "CLSI" or "EUCAST", see AMR-options
#> (`?AMR::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
``` ```

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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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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">

62
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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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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">
@@ -179,14 +179,14 @@ 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: #0000BB;">ℹ For `aminoglycosides()` using columns '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin), '</span><span style="color: #0000BB; font-weight: bold;">TOB</span><span style="color: #0000BB;">'</span></span></span> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns '<span style="font-weight: bold;">GEN</span>' (gentamicin), '<span style="font-weight: bold;">TOB</span>' (tobramycin),</span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; (tobramycin), '</span><span style="color: #0000BB; font-weight: bold;">AMK</span><span style="color: #0000BB;">' (amikacin), and '</span><span style="color: #0000BB; font-weight: bold;">KAN</span><span style="color: #0000BB;">' (kanamycin)</span></span></span> <span><span class="co">#&gt; '<span style="font-weight: bold;">AMK</span>' (amikacin), and '<span style="font-weight: bold;">KAN</span>' (kanamycin)</span></span>
<span><span class="co">#&gt; <span style="color: #0000BB;">ℹ For `betalactams()` using columns '</span><span style="color: #0000BB; font-weight: bold;">PEN</span><span style="color: #0000BB;">' (benzylpenicillin), '</span><span style="color: #0000BB; font-weight: bold;">OXA</span><span style="color: #0000BB;">'</span></span></span> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `betalactams()` using columns '<span style="font-weight: bold;">PEN</span>' (benzylpenicillin), '<span style="font-weight: bold;">OXA</span>'</span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; (oxacillin), '</span><span style="color: #0000BB; font-weight: bold;">FLC</span><span style="color: #0000BB;">' (flucloxacillin), '</span><span style="color: #0000BB; font-weight: bold;">AMX</span><span style="color: #0000BB;">' (amoxicillin), '</span><span style="color: #0000BB; font-weight: bold;">AMC</span><span style="color: #0000BB;">'</span></span></span> <span><span class="co">#&gt; (oxacillin), '<span style="font-weight: bold;">FLC</span>' (flucloxacillin), '<span style="font-weight: bold;">AMX</span>' (amoxicillin), '<span style="font-weight: bold;">AMC</span>'</span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; (amoxicillin/clavulanic acid), '</span><span style="color: #0000BB; font-weight: bold;">AMP</span><span style="color: #0000BB;">' (ampicillin), '</span><span style="color: #0000BB; font-weight: bold;">TZP</span><span style="color: #0000BB;">'</span></span></span> <span><span class="co">#&gt; (amoxicillin/clavulanic acid), '<span style="font-weight: bold;">AMP</span>' (ampicillin), '<span style="font-weight: bold;">TZP</span>'</span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; (piperacillin/tazobactam), '</span><span style="color: #0000BB; font-weight: bold;">CZO</span><span style="color: #0000BB;">' (cefazolin), '</span><span style="color: #0000BB; font-weight: bold;">FEP</span><span style="color: #0000BB;">' (cefepime), '</span><span style="color: #0000BB; font-weight: bold;">CXM</span><span style="color: #0000BB;">'</span></span></span> <span><span class="co">#&gt; (piperacillin/tazobactam), '<span style="font-weight: bold;">CZO</span>' (cefazolin), '<span style="font-weight: bold;">FEP</span>' (cefepime), '<span style="font-weight: bold;">CXM</span>'</span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; (cefuroxime), '</span><span style="color: #0000BB; font-weight: bold;">FOX</span><span style="color: #0000BB;">' (cefoxitin), '</span><span style="color: #0000BB; font-weight: bold;">CTX</span><span style="color: #0000BB;">' (cefotaxime), '</span><span style="color: #0000BB; font-weight: bold;">CAZ</span><span style="color: #0000BB;">' (ceftazidime),</span></span></span> <span><span class="co">#&gt; (cefuroxime), '<span style="font-weight: bold;">FOX</span>' (cefoxitin), '<span style="font-weight: bold;">CTX</span>' (cefotaxime), '<span style="font-weight: bold;">CAZ</span>' (ceftazidime),</span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; '</span><span style="color: #0000BB; font-weight: bold;">CRO</span><span style="color: #0000BB;">' (ceftriaxone), '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem), and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span></span></code></pre></div> <span><span class="co">#&gt; '<span style="font-weight: bold;">CRO</span>' (ceftriaxone), '<span style="font-weight: bold;">IPM</span>' (imipenem), and '<span style="font-weight: bold;">MEM</span>' (meropenem)</span></span></code></pre></div>
<p><strong>Explanation:</strong></p> <p><strong>Explanation:</strong></p>
<ul> <ul>
<li> <li>
@@ -227,26 +227,37 @@ 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: #0000BB;">ℹ For `aminoglycosides()` using columns '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin), '</span><span style="color: #0000BB; font-weight: bold;">TOB</span><span style="color: #0000BB;">'</span></span></span> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns '<span style="font-weight: bold;">GEN</span>' (gentamicin), '<span style="font-weight: bold;">TOB</span>' (tobramycin),</span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; (tobramycin), '</span><span style="color: #0000BB; font-weight: bold;">AMK</span><span style="color: #0000BB;">' (amikacin), and '</span><span style="color: #0000BB; font-weight: bold;">KAN</span><span style="color: #0000BB;">' (kanamycin)</span></span></span> <span><span class="co">#&gt; '<span style="font-weight: bold;">AMK</span>' (amikacin), and '<span style="font-weight: bold;">KAN</span>' (kanamycin)</span></span>
<span><span class="co">#&gt; <span style="color: #0000BB;">ℹ For `betalactams()` using columns '</span><span style="color: #0000BB; font-weight: bold;">PEN</span><span style="color: #0000BB;">' (benzylpenicillin), '</span><span style="color: #0000BB; font-weight: bold;">OXA</span><span style="color: #0000BB;">'</span></span></span> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `betalactams()` using columns '<span style="font-weight: bold;">PEN</span>' (benzylpenicillin), '<span style="font-weight: bold;">OXA</span>'</span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; (oxacillin), '</span><span style="color: #0000BB; font-weight: bold;">FLC</span><span style="color: #0000BB;">' (flucloxacillin), '</span><span style="color: #0000BB; font-weight: bold;">AMX</span><span style="color: #0000BB;">' (amoxicillin), '</span><span style="color: #0000BB; font-weight: bold;">AMC</span><span style="color: #0000BB;">'</span></span></span> <span><span class="co">#&gt; (oxacillin), '<span style="font-weight: bold;">FLC</span>' (flucloxacillin), '<span style="font-weight: bold;">AMX</span>' (amoxicillin), '<span style="font-weight: bold;">AMC</span>'</span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; (amoxicillin/clavulanic acid), '</span><span style="color: #0000BB; font-weight: bold;">AMP</span><span style="color: #0000BB;">' (ampicillin), '</span><span style="color: #0000BB; font-weight: bold;">TZP</span><span style="color: #0000BB;">'</span></span></span> <span><span class="co">#&gt; (amoxicillin/clavulanic acid), '<span style="font-weight: bold;">AMP</span>' (ampicillin), '<span style="font-weight: bold;">TZP</span>'</span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; (piperacillin/tazobactam), '</span><span style="color: #0000BB; font-weight: bold;">CZO</span><span style="color: #0000BB;">' (cefazolin), '</span><span style="color: #0000BB; font-weight: bold;">FEP</span><span style="color: #0000BB;">' (cefepime), '</span><span style="color: #0000BB; font-weight: bold;">CXM</span><span style="color: #0000BB;">'</span></span></span> <span><span class="co">#&gt; (piperacillin/tazobactam), '<span style="font-weight: bold;">CZO</span>' (cefazolin), '<span style="font-weight: bold;">FEP</span>' (cefepime), '<span style="font-weight: bold;">CXM</span>'</span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; (cefuroxime), '</span><span style="color: #0000BB; font-weight: bold;">FOX</span><span style="color: #0000BB;">' (cefoxitin), '</span><span style="color: #0000BB; font-weight: bold;">CTX</span><span style="color: #0000BB;">' (cefotaxime), '</span><span style="color: #0000BB; font-weight: bold;">CAZ</span><span style="color: #0000BB;">' (ceftazidime),</span></span></span> <span><span class="co">#&gt; (cefuroxime), '<span style="font-weight: bold;">FOX</span>' (cefoxitin), '<span style="font-weight: bold;">CTX</span>' (cefotaxime), '<span style="font-weight: bold;">CAZ</span>' (ceftazidime),</span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; '</span><span style="color: #0000BB; font-weight: bold;">CRO</span><span style="color: #0000BB;">' (ceftriaxone), '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem), and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span></span> <span><span class="co">#&gt; '<span style="font-weight: bold;">CRO</span>' (ceftriaxone), '<span style="font-weight: bold;">IPM</span>' (imipenem), and '<span style="font-weight: bold;">MEM</span>' (meropenem)</span></span>
<span><span class="co">#&gt; </span></span>
<span><span class="co">#&gt; </span></span> <span><span class="co">#&gt; </span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">Recipe</span> <span style="color: #00BBBB;">──────────────────────────────────────────────────────────────────────</span></span></span> <span><span class="co">#&gt; <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">Recipe</span> <span style="color: #00BBBB;">──────────────────────────────────────────────────────────────────────</span></span></span>
<span><span class="co">#&gt; </span></span> <span><span class="co">#&gt; </span></span>
<span><span class="co">#&gt; ── Inputs</span></span> <span><span class="co">#&gt; </span></span>
<span><span class="co">#&gt; </span></span>
<span><span class="co">#&gt; ── Inputs </span></span>
<span><span class="co">#&gt; </span></span>
<span><span class="co">#&gt; Number of variables by role</span></span> <span><span class="co">#&gt; Number of variables by role</span></span>
<span><span class="co">#&gt; </span></span>
<span><span class="co">#&gt; outcome: 1</span></span> <span><span class="co">#&gt; outcome: 1</span></span>
<span><span class="co">#&gt; predictor: 20</span></span> <span><span class="co">#&gt; predictor: 20</span></span>
<span><span class="co">#&gt; </span></span> <span><span class="co">#&gt; </span></span>
<span><span class="co">#&gt; ── Training information</span></span> <span><span class="co">#&gt; </span></span>
<span><span class="co">#&gt; </span></span>
<span><span class="co">#&gt; ── Training information </span></span>
<span><span class="co">#&gt; </span></span>
<span><span class="co">#&gt; Training data contained 1968 data points and no incomplete rows.</span></span> <span><span class="co">#&gt; Training data contained 1968 data points and no incomplete rows.</span></span>
<span><span class="co">#&gt; </span></span> <span><span class="co">#&gt; </span></span>
<span><span class="co">#&gt; ── Operations</span></span> <span><span class="co">#&gt; </span></span>
<span><span class="co">#&gt; </span></span>
<span><span class="co">#&gt; ── Operations </span></span>
<span><span class="co">#&gt; </span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">•</span> Correlation filter on: <span style="color: #0000BB;">AMX</span> <span style="color: #0000BB;">CTX</span> | <span style="font-style: italic;">Trained</span></span></span></code></pre></div> <span><span class="co">#&gt; <span style="color: #00BBBB;">•</span> Correlation filter on: <span style="color: #0000BB;">AMX</span> <span style="color: #0000BB;">CTX</span> | <span style="font-style: italic;">Trained</span></span></span></code></pre></div>
<p><strong>Explanation:</strong></p> <p><strong>Explanation:</strong></p>
<ul> <ul>
@@ -737,11 +748,12 @@ 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: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">mo</span><span style="color: #0000BB;">' as input for `col_mo`.</span></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: #0000BB;">ℹ `resistance()` assumes the EUCAST guideline and thus considers the 'I'</span></span></span> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> `resistance()` (`?AMR::resistance()`) assumes the EUCAST guideline and thus</span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; category susceptible. Set the `guideline` argument or the `AMR_guideline`</span></span></span> <span><span class="co">#&gt; considers the 'I' category susceptible. Set the `guideline` argument or the</span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; option to either "CLSI" or "EUCAST", see `?AMR-options`.</span></span></span> <span><span class="co">#&gt; `AMR_guideline` option to either "CLSI" or "EUCAST", see AMR-options</span></span>
<span><span class="co">#&gt; <span style="color: #0000BB;">ℹ This message will be shown once per session.</span></span></span> <span><span class="co">#&gt; (`?AMR::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> <span></span>
<span><span class="va">data_time</span></span> <span><span class="va">data_time</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 32 × 5</span></span></span> <span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 32 × 5</span></span></span>

26
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@@ -94,8 +94,8 @@ 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' #> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB' (tobramycin),
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin) #> 'AMK' (amikacin), and 'KAN' (kanamycin)
#> ℹ For `betalactams()` using columns 'PEN' (benzylpenicillin), 'OXA' #> ℹ For `betalactams()` using columns 'PEN' (benzylpenicillin), 'OXA'
#> (oxacillin), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC' #> (oxacillin), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC'
#> (amoxicillin/clavulanic acid), 'AMP' (ampicillin), 'TZP' #> (amoxicillin/clavulanic acid), 'AMP' (ampicillin), 'TZP'
@@ -144,8 +144,8 @@ a training set using `prep()`:
``` r ``` r
prep(resistance_recipe) prep(resistance_recipe)
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB' #> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB' (tobramycin),
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin) #> 'AMK' (amikacin), and 'KAN' (kanamycin)
#> ℹ For `betalactams()` using columns 'PEN' (benzylpenicillin), 'OXA' #> ℹ For `betalactams()` using columns 'PEN' (benzylpenicillin), 'OXA'
#> (oxacillin), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC' #> (oxacillin), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC'
#> (amoxicillin/clavulanic acid), 'AMP' (ampicillin), 'TZP' #> (amoxicillin/clavulanic acid), 'AMP' (ampicillin), 'TZP'
@@ -153,17 +153,28 @@ prep(resistance_recipe)
#> (cefuroxime), 'FOX' (cefoxitin), 'CTX' (cefotaxime), 'CAZ' (ceftazidime), #> (cefuroxime), 'FOX' (cefoxitin), 'CTX' (cefotaxime), 'CAZ' (ceftazidime),
#> 'CRO' (ceftriaxone), 'IPM' (imipenem), and 'MEM' (meropenem) #> 'CRO' (ceftriaxone), 'IPM' (imipenem), and 'MEM' (meropenem)
#> #>
#>
#> ── Recipe ────────────────────────────────────────────────────────────────────── #> ── Recipe ──────────────────────────────────────────────────────────────────────
#> #>
#>
#>
#> ── Inputs #> ── Inputs
#>
#> Number of variables by role #> Number of variables by role
#>
#> outcome: 1 #> outcome: 1
#> predictor: 20 #> predictor: 20
#> #>
#>
#>
#> ── Training information #> ── Training information
#>
#> Training data contained 1968 data points and no incomplete rows. #> Training data contained 1968 data points and no incomplete rows.
#> #>
#>
#>
#> ── Operations #> ── Operations
#>
#> • Correlation filter on: AMX CTX | Trained #> • Correlation filter on: AMX CTX | Trained
``` ```
@@ -636,9 +647,10 @@ data_time <- example_isolates %>%
.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()` (`?AMR::resistance()`) assumes the EUCAST guideline and thus
#> category susceptible. Set the `guideline` argument or the `AMR_guideline` #> considers the 'I' category susceptible. Set the `guideline` argument or the
#> option to either "CLSI" or "EUCAST", see `?AMR-options`. #> `AMR_guideline` option to either "CLSI" or "EUCAST", see AMR-options
#> (`?AMR::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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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">

15
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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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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">
@@ -163,10 +163,11 @@ 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: #0000BB;">ℹ `resistance()` assumes the EUCAST guideline and thus considers the 'I'</span></span></span> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> `resistance()` (`?AMR::resistance()`) assumes the EUCAST guideline and thus</span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; category susceptible. Set the `guideline` argument or the `AMR_guideline`</span></span></span> <span><span class="co">#&gt; considers the 'I' category susceptible. Set the `guideline` argument or the</span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; option to either "CLSI" or "EUCAST", see `?AMR-options`.</span></span></span> <span><span class="co">#&gt; `AMR_guideline` option to either "CLSI" or "EUCAST", see AMR-options</span></span>
<span><span class="co">#&gt; <span style="color: #0000BB;">ℹ This message will be shown once per session.</span></span></span> <span><span class="co">#&gt; (`?AMR::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> <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>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 6 × 10</span></span></span> <span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 6 × 10</span></span></span>
@@ -188,8 +189,8 @@ that contain numeric values in all selected variables, so we now only
need to do:</p> need to do:</p>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">pca_result</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/pca.html">pca</a></span><span class="op">(</span><span class="va">resistance_data</span><span class="op">)</span></span> <code class="sourceCode R"><span><span class="va">pca_result</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/pca.html">pca</a></span><span class="op">(</span><span class="va">resistance_data</span><span class="op">)</span></span>
<span><span class="co">#&gt; <span style="color: #0000BB;">ℹ Columns selected for PCA: "</span><span style="color: #0000BB; font-weight: bold;">AMC</span><span style="color: #0000BB;">", "</span><span style="color: #0000BB; font-weight: bold;">CAZ</span><span style="color: #0000BB;">", "</span><span style="color: #0000BB; font-weight: bold;">CTX</span><span style="color: #0000BB;">", "</span><span style="color: #0000BB; font-weight: bold;">CXM</span><span style="color: #0000BB;">", "</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">", "</span><span style="color: #0000BB; font-weight: bold;">SXT</span><span style="color: #0000BB;">",</span></span></span> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Columns selected for PCA: "<span style="font-weight: bold;">AMC</span>", "<span style="font-weight: bold;">CAZ</span>", "<span style="font-weight: bold;">CTX</span>", "<span style="font-weight: bold;">CXM</span>", "<span style="font-weight: bold;">GEN</span>", "<span style="font-weight: bold;">SXT</span>", "<span style="font-weight: bold;">TMP</span>",</span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; "</span><span style="color: #0000BB; font-weight: bold;">TMP</span><span style="color: #0000BB;">", and "</span><span style="color: #0000BB; font-weight: bold;">TOB</span><span style="color: #0000BB;">". Total observations available: 7.</span></span></span></code></pre></div> <span><span class="co">#&gt; and "<span style="font-weight: bold;">TOB</span>". Total observations available: 7.</span></span></code></pre></div>
<p>The result can be reviewed with the good old <code><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary()</a></code> <p>The result can be reviewed with the good old <code><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary()</a></code>
function:</p> function:</p>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">

11
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@@ -78,9 +78,10 @@ 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()` (`?AMR::resistance()`) assumes the EUCAST guideline and thus
#> category susceptible. Set the `guideline` argument or the `AMR_guideline` #> considers the 'I' category susceptible. Set the `guideline` argument or the
#> option to either "CLSI" or "EUCAST", see `?AMR-options`. #> `AMR_guideline` option to either "CLSI" or "EUCAST", see AMR-options
#> (`?AMR::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)
@@ -104,8 +105,8 @@ variables, so we now only need to do:
``` r ``` r
pca_result <- pca(resistance_data) pca_result <- pca(resistance_data)
#> ℹ Columns selected for PCA: "AMC", "CAZ", "CTX", "CXM", "GEN", "SXT", #> ℹ Columns selected for PCA: "AMC", "CAZ", "CTX", "CXM", "GEN", "SXT", "TMP",
#> "TMP", and "TOB". Total observations available: 7. #> and "TOB". Total observations available: 7.
``` ```
The result can be reviewed with the good old The result can be reviewed with the good old

11
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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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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">
@@ -255,10 +255,11 @@ 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: #0000BB;">ℹ `susceptibility()` assumes the EUCAST guideline and thus considers the</span></span></span> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> `susceptibility()` (`?AMR::susceptibility()`) assumes the EUCAST guideline</span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; 'I' category susceptible. Set the `guideline` argument or the</span></span></span> <span><span class="co">#&gt; and thus considers the 'I' category susceptible. Set the `guideline` argument</span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; `AMR_guideline` option to either "CLSI" or "EUCAST", see `?AMR-options`.</span></span></span> <span><span class="co">#&gt; or the `AMR_guideline` option to either "CLSI" or "EUCAST", see AMR-options</span></span>
<span><span class="co">#&gt; <span style="color: #0000BB;">ℹ This message will be shown once per session.</span></span></span></code></pre></div> <span><span class="co">#&gt; (`?AMR::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>
<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>
Length: 500<br> Length: 500<br>

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@@ -101,9 +101,10 @@ 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 `susceptibility()` (`?AMR::susceptibility()`) assumes the EUCAST guideline
#> 'I' category susceptible. Set the `guideline` argument or the #> and thus considers the 'I' category susceptible. Set the `guideline` argument
#> `AMR_guideline` option to either "CLSI" or "EUCAST", see `?AMR-options`. #> or the `AMR_guideline` option to either "CLSI" or "EUCAST", see AMR-options
#> (`?AMR::AMR-options`).
#> ℹ This message will be shown once per session. #> ℹ This message will be shown once per session.
``` ```

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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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

4
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@@ -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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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">18 March 2026</h4> <h4 data-toc-skip class="date">20 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>

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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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">

13
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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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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="3.0.1.9035" id="amr-3019035">AMR 3.0.1.9035<a class="anchor" aria-label="anchor" href="#amr-3019035"></a></h2> <h2 class="pkg-version" data-toc-text="3.0.1.9036" id="amr-3019036">AMR 3.0.1.9036<a class="anchor" aria-label="anchor" href="#amr-3019036"></a></h2>
<div class="section level4"> <div class="section level4">
<h4 id="new-3-0-1-9035">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9035"></a></h4> <h4 id="new-3-0-1-9036">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9036"></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>
@@ -83,7 +83,7 @@
<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-3-0-1-9035">Fixes<a class="anchor" aria-label="anchor" href="#fixes-3-0-1-9035"></a></h4> <h4 id="fixes-3-0-1-9036">Fixes<a class="anchor" aria-label="anchor" href="#fixes-3-0-1-9036"></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>
@@ -96,8 +96,9 @@
<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-3-0-1-9035">Updates<a class="anchor" aria-label="anchor" href="#updates-3-0-1-9035"></a></h4> <h4 id="updates-3-0-1-9036">Updates<a class="anchor" aria-label="anchor" href="#updates-3-0-1-9036"></a></h4>
<ul><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>
<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>
<li> <li>
<code><a href="../reference/proportion.html">susceptibility()</a></code> and <code><a href="../reference/proportion.html">resistance()</a></code> gained the argument <code>guideline</code>, which defaults to EUCAST, for interpreting the ‘I’ category correctly.</li> <code><a href="../reference/proportion.html">susceptibility()</a></code> and <code><a href="../reference/proportion.html">resistance()</a></code> gained the argument <code>guideline</code>, which defaults to EUCAST, for interpreting the ‘I’ category correctly.</li>

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@@ -1,6 +1,6 @@
# Changelog # Changelog
## AMR 3.0.1.9035 ## AMR 3.0.1.9036
#### New #### New
@@ -81,6 +81,10 @@
#### Updates #### Updates
- Extensive `cli` integration for better message handling and clickable
links in messages and warnings
([\#191](https://github.com/msberends/AMR/issues/191),
[\#265](https://github.com/msberends/AMR/issues/265))
- [`mdro()`](https://amr-for-r.org/reference/mdro.md) now infers - [`mdro()`](https://amr-for-r.org/reference/mdro.md) now infers
resistance for a *missing* base drug column from an *available* resistance for a *missing* base drug column from an *available*
corresponding drug+inhibitor combination showing resistance (e.g., corresponding drug+inhibitor combination showing resistance (e.g.,

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: 2026-03-18T09:40Z last_built: 2026-03-20T16:06Z
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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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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@@ -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>
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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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</small>
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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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</small>
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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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</small>
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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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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">

9
reference/add_custom_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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -111,7 +111,7 @@
<span class="r-in"><span> group <span class="op">=</span> <span class="st">"Test Group"</span></span></span> <span class="r-in"><span> group <span class="op">=</span> <span class="st">"Test Group"</span></span></span>
<span class="r-in"><span> <span class="op">)</span></span></span> <span class="r-in"><span> <span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span> <span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Added one record to the internal `antimicrobials` data set.</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Added one record to the internal `antimicrobials` data set.</span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># "testab" is now a new antibiotic:</span></span></span> <span class="r-in"><span><span class="co"># "testab" is now a new antibiotic:</span></span></span>
<span class="r-in"><span><span class="fu"><a href="as.ab.html">as.ab</a></span><span class="op">(</span><span class="st">"testab"</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="as.ab.html">as.ab</a></span><span class="op">(</span><span class="st">"testab"</span><span class="op">)</span></span></span>
@@ -180,7 +180,7 @@
<span class="r-in"><span> group <span class="op">=</span> <span class="st">"Beta-lactams/penicillins"</span></span></span> <span class="r-in"><span> group <span class="op">=</span> <span class="st">"Beta-lactams/penicillins"</span></span></span>
<span class="r-in"><span> <span class="op">)</span></span></span> <span class="r-in"><span> <span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span> <span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Added one record to the internal `antimicrobials` data set.</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Added one record to the internal `antimicrobials` data set.</span>
<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_atc</a></span><span class="op">(</span><span class="st">"Co-fluampicil"</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_atc</a></span><span class="op">(</span><span class="st">"Co-fluampicil"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "J01CR50"</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "J01CR50"</span>
<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_name</a></span><span class="op">(</span><span class="st">"J01CR50"</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_name</a></span><span class="op">(</span><span class="st">"J01CR50"</span><span class="op">)</span></span></span>
@@ -197,8 +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: #0000BB;">ℹ For `betalactams()` using columns '</span><span style="color: #0000BB; font-weight: bold;">coflu</span><span style="color: #0000BB;">' (co-fluampicil) and</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="font-weight: bold;">coflu</span>' (co-fluampicil) and '<span style="font-weight: bold;">ampicillin</span>'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> '</span><span style="color: #0000BB; font-weight: bold;">ampicillin</span><span style="color: #0000BB;">'</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>

3
reference/add_custom_antimicrobials.md
View File

@@ -185,8 +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 #> ℹ For `betalactams()` using columns 'coflu' (co-fluampicil) and 'ampicillin'
#> 'ampicillin'
#> coflu ampicillin #> coflu ampicillin
#> 1 S R #> 1 S R
# } # }

13
reference/add_custom_microorganisms.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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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">
@@ -109,8 +109,8 @@
<span class="r-in"><span> species <span class="op">=</span> <span class="st">"asburiae/cloacae"</span></span></span> <span class="r-in"><span> species <span class="op">=</span> <span class="st">"asburiae/cloacae"</span></span></span>
<span class="r-in"><span> <span class="op">)</span></span></span> <span class="r-in"><span> <span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span> <span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Added </span><span style="color: #0000BB; font-style: italic;">Enterobacter asburiae/cloacae</span><span style="color: #0000BB;"> to the internal `microorganisms` data</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Added <span style="font-style: italic;">Enterobacter asburiae/cloacae</span> to the internal `microorganisms` data</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> set.</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> set.</span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># E. asburiae/cloacae is now a new microorganism:</span></span></span> <span class="r-in"><span><span class="co"># E. asburiae/cloacae is now a new microorganism:</span></span></span>
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"Enterobacter asburiae/cloacae"</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"Enterobacter asburiae/cloacae"</span><span class="op">)</span></span></span>
@@ -204,8 +204,7 @@
<span class="r-in"><span> SPECIES <span class="op">=</span> <span class="st">"SPECIES"</span></span></span> <span class="r-in"><span> SPECIES <span class="op">=</span> <span class="st">"SPECIES"</span></span></span>
<span class="r-in"><span> <span class="op">)</span></span></span> <span class="r-in"><span> <span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span> <span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Added </span><span style="color: #0000BB; font-style: italic;">Bacteroides/Parabacteroides</span><span style="color: #0000BB;"> to the internal `microorganisms` data</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Added <span style="font-style: italic;">Bacteroides/Parabacteroides</span> to the internal `microorganisms` data set.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> set.</span></span>
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"BACTEROIDES / PARABACTEROIDES"</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"BACTEROIDES / PARABACTEROIDES"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Bacteroides/Parabacteroides"</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Bacteroides/Parabacteroides"</span>
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_rank</a></span><span class="op">(</span><span class="st">"BACTEROIDES / PARABACTEROIDES"</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_rank</a></span><span class="op">(</span><span class="st">"BACTEROIDES / PARABACTEROIDES"</span><span class="op">)</span></span></span>
@@ -224,8 +223,8 @@
<span class="r-in"><span> subspecies <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">"complex"</span>, <span class="st">""</span><span class="op">)</span></span></span> <span class="r-in"><span> subspecies <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">"complex"</span>, <span class="st">""</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-in"><span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Added </span><span style="color: #0000BB; font-style: italic;">Citrobacter braakii</span><span style="color: #0000BB;"> complex and </span><span style="color: #0000BB; font-style: italic;">Citrobacter freundii</span><span style="color: #0000BB;"> complex to the</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Added <span style="font-style: italic;">Citrobacter braakii</span> complex and <span style="font-style: italic;">Citrobacter freundii</span> complex to the</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> internal `microorganisms` data set.</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> internal `microorganisms` data set.</span>
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_name</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="st">"C. freundii complex"</span>, <span class="st">"C. braakii complex"</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_name</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="st">"C. freundii complex"</span>, <span class="st">"C. braakii complex"</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Citrobacter freundii complex" "Citrobacter braakii complex" </span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Citrobacter freundii complex" "Citrobacter braakii complex" </span>
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_species</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="st">"C. freundii complex"</span>, <span class="st">"C. braakii complex"</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_species</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="st">"C. freundii complex"</span>, <span class="st">"C. braakii complex"</span><span class="op">)</span><span class="op">)</span></span></span>

3
reference/add_custom_microorganisms.md
View File

@@ -193,8 +193,7 @@ add_custom_microorganisms(
SPECIES = "SPECIES" SPECIES = "SPECIES"
) )
) )
#> ℹ Added Bacteroides/Parabacteroides to the internal `microorganisms` data #> ℹ Added Bacteroides/Parabacteroides to the internal `microorganisms` data set.
#> set.
mo_name("BACTEROIDES / PARABACTEROIDES") mo_name("BACTEROIDES / PARABACTEROIDES")
#> [1] "Bacteroides/Parabacteroides" #> [1] "Bacteroides/Parabacteroides"
mo_rank("BACTEROIDES / PARABACTEROIDES") mo_rank("BACTEROIDES / PARABACTEROIDES")

22
reference/age.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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 26.71507 0</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 1 1999-06-30 26 26.72055 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1968-01-29 58 58.13151 31</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 2 1968-01-29 58 58.13699 31</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1965-12-05 60 60.28219 34</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 3 1965-12-05 60 60.28767 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1980-03-01 46 46.04658 19</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 4 1980-03-01 46 46.05205 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1949-11-01 76 76.37534 50</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 5 1949-11-01 76 76.38082 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1947-02-14 79 79.08767 52</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 6 1947-02-14 79 79.09315 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1940-02-19 86 86.07397 59</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 7 1940-02-19 86 86.07945 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1988-01-10 38 38.18356 11</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 8 1988-01-10 38 38.18904 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1997-08-27 28 28.55616 2</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 9 1997-08-27 28 28.56164 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1978-01-26 48 48.13973 21</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 10 1978-01-26 48 48.14521 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 26.71507 0 #> 1 1999-06-30 26 26.72055 0
#> 2 1968-01-29 58 58.13151 31 #> 2 1968-01-29 58 58.13699 31
#> 3 1965-12-05 60 60.28219 34 #> 3 1965-12-05 60 60.28767 34
#> 4 1980-03-01 46 46.04658 19 #> 4 1980-03-01 46 46.05205 19
#> 5 1949-11-01 76 76.37534 50 #> 5 1949-11-01 76 76.38082 50
#> 6 1947-02-14 79 79.08767 52 #> 6 1947-02-14 79 79.09315 52
#> 7 1940-02-19 86 86.07397 59 #> 7 1940-02-19 86 86.07945 59
#> 8 1988-01-10 38 38.18356 11 #> 8 1988-01-10 38 38.18904 11
#> 9 1997-08-27 28 28.55616 2 #> 9 1997-08-27 28 28.56164 2
#> 10 1978-01-26 48 48.13973 21 #> 10 1978-01-26 48 48.14521 21
``` ```

2
reference/age_groups.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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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
reference/amr_course.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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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">
@@ -50,7 +50,7 @@
</div> </div>
<div class="ref-description section level2"> <div class="ref-description section level2">
<p>Downloads and unpacks a GitHub repository containing course materials, using <code>usethis::use_course()</code>. This is a convenience wrapper intended for use in educational settings, such as workshops or tutorials associated with the AMR package.</p> <p>Downloads and unpacks a GitHub repository containing course materials, using <code><a href="https://usethis.r-lib.org/reference/zip-utils.html" class="external-link">usethis::use_course()</a></code>. This is a convenience wrapper intended for use in educational settings, such as workshops or tutorials associated with the AMR package.</p>
</div> </div>
<div class="section level2"> <div class="section level2">
@@ -71,21 +71,21 @@
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt> <dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>Additional arguments passed on to <code>usethis::use_course()</code>.</p></dd> <dd><p>Additional arguments passed on to <code><a href="https://usethis.r-lib.org/reference/zip-utils.html" class="external-link">usethis::use_course()</a></code>.</p></dd>
</dl></div> </dl></div>
<div class="section level2"> <div class="section level2">
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
<p>Called for its side effect. <code>usethis::use_course()</code> will prompt the user to choose a destination and open the extracted project. Returns invisibly whatever <code>usethis::use_course()</code> returns.</p> <p>Called for its side effect. <code><a href="https://usethis.r-lib.org/reference/zip-utils.html" class="external-link">usethis::use_course()</a></code> will prompt the user to choose a destination and open the extracted project. Returns invisibly whatever <code><a href="https://usethis.r-lib.org/reference/zip-utils.html" class="external-link">usethis::use_course()</a></code> returns.</p>
</div> </div>
<div class="section level2"> <div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p>This function constructs a ZIP archive URL from the provided <code>github_repo</code> and <code>branch</code>, then delegates to <code>usethis::use_course()</code> to handle the download and extraction.</p> <p>This function constructs a ZIP archive URL from the provided <code>github_repo</code> and <code>branch</code>, then delegates to <code><a href="https://usethis.r-lib.org/reference/zip-utils.html" class="external-link">usethis::use_course()</a></code> to handle the download and extraction.</p>
<p>The function is designed for interactive use in course or workshop settings and is not intended for use in non-interactive or automated pipelines.</p> <p>The function is designed for interactive use in course or workshop settings and is not intended for use in non-interactive or automated pipelines.</p>
</div> </div>
<div class="section level2"> <div class="section level2">
<h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2> <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
<div class="dont-index"><p><code>usethis::use_course()</code></p></div> <div class="dont-index"><p><code><a href="https://usethis.r-lib.org/reference/zip-utils.html" class="external-link">usethis::use_course()</a></code></p></div>
</div> </div>
<div class="section level2"> <div class="section level2">

26
reference/amr_course.md
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@@ -1,9 +1,10 @@
# Download and Unpack an AMR Course Repository # Download and Unpack an AMR Course Repository
Downloads and unpacks a GitHub repository containing course materials, Downloads and unpacks a GitHub repository containing course materials,
using `usethis::use_course()`. This is a convenience wrapper intended using
for use in educational settings, such as workshops or tutorials [`usethis::use_course()`](https://usethis.r-lib.org/reference/zip-utils.html).
associated with the AMR package. This is a convenience wrapper intended for use in educational settings,
such as workshops or tutorials associated with the AMR package.
## Usage ## Usage
@@ -25,19 +26,24 @@ amr_course(github_repo, branch = "main", ...)
- ...: - ...:
Additional arguments passed on to `usethis::use_course()`. Additional arguments passed on to
[`usethis::use_course()`](https://usethis.r-lib.org/reference/zip-utils.html).
## Value ## Value
Called for its side effect. `usethis::use_course()` will prompt the user Called for its side effect.
to choose a destination and open the extracted project. Returns [`usethis::use_course()`](https://usethis.r-lib.org/reference/zip-utils.html)
invisibly whatever `usethis::use_course()` returns. will prompt the user to choose a destination and open the extracted
project. Returns invisibly whatever
[`usethis::use_course()`](https://usethis.r-lib.org/reference/zip-utils.html)
returns.
## Details ## Details
This function constructs a ZIP archive URL from the provided This function constructs a ZIP archive URL from the provided
`github_repo` and `branch`, then delegates to `usethis::use_course()` to `github_repo` and `branch`, then delegates to
handle the download and extraction. [`usethis::use_course()`](https://usethis.r-lib.org/reference/zip-utils.html)
to handle the download and extraction.
The function is designed for interactive use in course or workshop The function is designed for interactive use in course or workshop
settings and is not intended for use in non-interactive or automated settings and is not intended for use in non-interactive or automated
@@ -45,7 +51,7 @@ pipelines.
## See also ## See also
`usethis::use_course()` [`usethis::use_course()`](https://usethis.r-lib.org/reference/zip-utils.html)
## Examples ## Examples

30
reference/antibiogram.html
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@@ -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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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">
@@ -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: #0000BB;">ℹ For `aminoglycosides()` using columns '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin), '</span><span style="color: #0000BB; font-weight: bold;">TOB</span><span style="color: #0000BB;">'</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns '<span style="font-weight: bold;">GEN</span>' (gentamicin), '<span style="font-weight: bold;">TOB</span>' (tobramycin),</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> (tobramycin), '</span><span style="color: #0000BB; font-weight: bold;">AMK</span><span style="color: #0000BB;">' (amikacin), and '</span><span style="color: #0000BB; font-weight: bold;">KAN</span><span style="color: #0000BB;">' (kanamycin)</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> '<span style="font-weight: bold;">AMK</span>' (amikacin), and '<span style="font-weight: bold;">KAN</span>' (kanamycin)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ For `carbapenems()` using columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem) and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns '<span style="font-weight: bold;">IPM</span>' (imipenem) and '<span style="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: #0000BB;">ℹ For `aminoglycosides()` using columns '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin), '</span><span style="color: #0000BB; font-weight: bold;">TOB</span><span style="color: #0000BB;">'</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns '<span style="font-weight: bold;">GEN</span>' (gentamicin), '<span style="font-weight: bold;">TOB</span>' (tobramycin),</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> (tobramycin), '</span><span style="color: #0000BB; font-weight: bold;">AMK</span><span style="color: #0000BB;">' (amikacin), and '</span><span style="color: #0000BB; font-weight: bold;">KAN</span><span style="color: #0000BB;">' (kanamycin)</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> '<span style="font-weight: bold;">AMK</span>' (amikacin), and '<span style="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: #0000BB;">ℹ For `carbapenems()` using columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem) and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns '<span style="font-weight: bold;">IPM</span>' (imipenem) and '<span style="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: #0000BB;">ℹ For `ureidopenicillins()` using column '</span><span style="color: #0000BB; font-weight: bold;">TZP</span><span style="color: #0000BB;">' (piperacillin/tazobactam)</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="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: #0000BB;">ℹ For `aminoglycosides()` using columns '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin), '</span><span style="color: #0000BB; font-weight: bold;">TOB</span><span style="color: #0000BB;">'</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns '<span style="font-weight: bold;">GEN</span>' (gentamicin), '<span style="font-weight: bold;">TOB</span>' (tobramycin),</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> (tobramycin), '</span><span style="color: #0000BB; font-weight: bold;">AMK</span><span style="color: #0000BB;">' (amikacin), and '</span><span style="color: #0000BB; font-weight: bold;">KAN</span><span style="color: #0000BB;">' (kanamycin)</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> '<span style="font-weight: bold;">AMK</span>' (amikacin), and '<span style="font-weight: bold;">KAN</span>' (kanamycin)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ For `carbapenems()` using columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem) and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns '<span style="font-weight: bold;">IPM</span>' (imipenem) and '<span style="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: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">mo</span><span style="color: #0000BB;">' as input for `mo_genus()`</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()` (`?AMR::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: #0000BB;">ℹ For `aminoglycosides()` using columns '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin), '</span><span style="color: #0000BB; font-weight: bold;">TOB</span><span style="color: #0000BB;">'</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns '<span style="font-weight: bold;">GEN</span>' (gentamicin), '<span style="font-weight: bold;">TOB</span>' (tobramycin),</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> (tobramycin), '</span><span style="color: #0000BB; font-weight: bold;">AMK</span><span style="color: #0000BB;">' (amikacin), and '</span><span style="color: #0000BB; font-weight: bold;">KAN</span><span style="color: #0000BB;">' (kanamycin)</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> '<span style="font-weight: bold;">AMK</span>' (amikacin), and '<span style="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: #0000BB;">ℹ For `ureidopenicillins()` using column '</span><span style="color: #0000BB; font-weight: bold;">TZP</span><span style="color: #0000BB;">' (piperacillin/tazobactam)</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="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>

18
reference/antibiogram.md
View File

@@ -598,8 +598,8 @@ example_isolates
antibiogram(example_isolates, antibiogram(example_isolates,
antimicrobials = c(aminoglycosides(), carbapenems()) antimicrobials = c(aminoglycosides(), carbapenems())
) )
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB' #> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB' (tobramycin),
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin) #> 'AMK' (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
@@ -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' #> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB' (tobramycin),
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin) #> 'AMK' (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
@@ -714,8 +714,8 @@ 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' #> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB' (tobramycin),
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin) #> 'AMK' (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
@@ -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()` (`?AMR::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' #> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB' (tobramycin),
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin) #> 'AMK' (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

136
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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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">
@@ -296,15 +296,15 @@ 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: #0000BB;">ℹ in `carbapenems()`: Imipenem/EDTA (`IPE`) and meropenem/nacubactam</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> in `carbapenems()` (`?AMR::carbapenems()`): Imipenem/EDTA (`IPE`) and</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> (`MNC`) are not included since `only_treatable = TRUE`.</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> meropenem/nacubactam (`MNC`) are not included since `only_treatable = TRUE`.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ This 'ab' vector was retrieved using `carbapenems()`, which should</span></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: #0000BB;"> normally be used inside a `dplyr` verb or `data.frame` call, e.g.:</span></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> <span style="color: #0000BB;"> • your_data %&gt;% select(carbapenems())</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> • your_data <span style="color: #D7AF00;">%&gt;%</span> <span style="font-weight: bold;">select</span><span style="color: #D7AF00;">(</span><span style="font-weight: bold;">carbapenems</span><span style="color: #BBBB00;">()</span><span style="color: #D7AF00;">)</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> • your_data %&gt;% select(column_a, column_b, carbapenems())</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> • your_data <span style="color: #D7AF00;">%&gt;%</span> <span style="font-weight: bold;">select</span><span style="color: #D7AF00;">(</span>column_a, column_b, <span style="font-weight: bold;">carbapenems</span><span style="color: #BBBB00;">()</span><span style="color: #D7AF00;">)</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> • your_data %&gt;% filter(any(carbapenems() == "R"))</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> • your_data <span style="color: #D7AF00;">%&gt;%</span> <span style="font-weight: bold;">filter</span><span style="color: #D7AF00;">(</span><span style="font-weight: bold;">any</span><span style="color: #BBBB00;">(</span><span style="font-weight: bold;">carbapenems</span><span style="color: #0000BB;">()</span> <span style="color: #D7AF00;">==</span> <span style="color: #00AFAF;">"R"</span><span style="color: #BBBB00;">)</span><span style="color: #D7AF00;">)</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> • your_data[, carbapenems()]</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> • your_data<span style="color: #D7AF00;">[</span>, <span style="font-weight: bold;">carbapenems</span><span style="color: #BBBB00;">()</span><span style="color: #D7AF00;">]</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> • your_data[, c("column_a", "column_b", carbapenems())]</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> • your_data<span style="color: #D7AF00;">[</span>, <span style="font-weight: bold;">c</span><span style="color: #BBBB00;">(</span><span style="color: #00AFAF;">"column_a"</span>, <span style="color: #00AFAF;">"column_b"</span>, <span style="font-weight: bold;">carbapenems</span><span style="color: #0000BB;">()</span><span style="color: #BBBB00;">)</span><span style="color: #D7AF00;">]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'ab'</span> <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'ab'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] BIA DOR ETP IMR IPM MEM MEV PAN RIA RIT RZM TAN TBP</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] BIA DOR ETP IMR IPM MEM MEV PAN RIA RIT RZM TAN TBP</span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
@@ -404,7 +404,7 @@ 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"># 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: #0000BB;">ℹ For `carbapenems()` using columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem) and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns '<span style="font-weight: bold;">IPM</span>' (imipenem) and '<span style="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>
@@ -422,8 +422,8 @@ 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 '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: #0000BB;">ℹ For `aminoglycosides()` using columns '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin), '</span><span style="color: #0000BB; font-weight: bold;">TOB</span><span style="color: #0000BB;">'</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns '<span style="font-weight: bold;">GEN</span>' (gentamicin), '<span style="font-weight: bold;">TOB</span>' (tobramycin),</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> (tobramycin), '</span><span style="color: #0000BB; font-weight: bold;">AMK</span><span style="color: #0000BB;">' (amikacin), and '</span><span style="color: #0000BB; font-weight: bold;">KAN</span><span style="color: #0000BB;">' (kanamycin)</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> '<span style="font-weight: bold;">AMK</span>' (amikacin), and '<span style="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>
@@ -441,15 +441,14 @@ 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 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: #0000BB;">ℹ For `administrable_per_os()` using columns '</span><span style="color: #0000BB; font-weight: bold;">OXA</span><span style="color: #0000BB;">' (oxacillin), '</span><span style="color: #0000BB; font-weight: bold;">FLC</span><span style="color: #0000BB;">'</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="font-weight: bold;">OXA</span>' (oxacillin), '<span style="font-weight: bold;">FLC</span>'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> (flucloxacillin), '</span><span style="color: #0000BB; font-weight: bold;">AMX</span><span style="color: #0000BB;">' (amoxicillin), '</span><span style="color: #0000BB; font-weight: bold;">AMC</span><span style="color: #0000BB;">' (amoxicillin/clavulanic acid),</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> (flucloxacillin), '<span style="font-weight: bold;">AMX</span>' (amoxicillin), '<span style="font-weight: bold;">AMC</span>' (amoxicillin/clavulanic acid),</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> '</span><span style="color: #0000BB; font-weight: bold;">AMP</span><span style="color: #0000BB;">' (ampicillin), '</span><span style="color: #0000BB; font-weight: bold;">CXM</span><span style="color: #0000BB;">' (cefuroxime), '</span><span style="color: #0000BB; font-weight: bold;">KAN</span><span style="color: #0000BB;">' (kanamycin), '</span><span style="color: #0000BB; font-weight: bold;">TMP</span><span style="color: #0000BB;">'</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> '<span style="font-weight: bold;">AMP</span>' (ampicillin), '<span style="font-weight: bold;">CXM</span>' (cefuroxime), '<span style="font-weight: bold;">KAN</span>' (kanamycin), '<span style="font-weight: bold;">TMP</span>'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> (trimethoprim), '</span><span style="color: #0000BB; font-weight: bold;">NIT</span><span style="color: #0000BB;">' (nitrofurantoin), '</span><span style="color: #0000BB; font-weight: bold;">FOS</span><span style="color: #0000BB;">' (fosfomycin), '</span><span style="color: #0000BB; font-weight: bold;">LNZ</span><span style="color: #0000BB;">'</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> (trimethoprim), '<span style="font-weight: bold;">NIT</span>' (nitrofurantoin), '<span style="font-weight: bold;">FOS</span>' (fosfomycin), '<span style="font-weight: bold;">LNZ</span>'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> (linezolid), '</span><span style="color: #0000BB; font-weight: bold;">CIP</span><span style="color: #0000BB;">' (ciprofloxacin), '</span><span style="color: #0000BB; font-weight: bold;">MFX</span><span style="color: #0000BB;">' (moxifloxacin), '</span><span style="color: #0000BB; font-weight: bold;">VAN</span><span style="color: #0000BB;">'</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> (linezolid), '<span style="font-weight: bold;">CIP</span>' (ciprofloxacin), '<span style="font-weight: bold;">MFX</span>' (moxifloxacin), '<span style="font-weight: bold;">VAN</span>' (vancomycin),</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> (vancomycin), '</span><span style="color: #0000BB; font-weight: bold;">TCY</span><span style="color: #0000BB;">' (tetracycline), '</span><span style="color: #0000BB; font-weight: bold;">DOX</span><span style="color: #0000BB;">' (doxycycline), '</span><span style="color: #0000BB; font-weight: bold;">ERY</span><span style="color: #0000BB;">'</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> '<span style="font-weight: bold;">TCY</span>' (tetracycline), '<span style="font-weight: bold;">DOX</span>' (doxycycline), '<span style="font-weight: bold;">ERY</span>' (erythromycin), '<span style="font-weight: bold;">CLI</span>'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> (erythromycin), '</span><span style="color: #0000BB; font-weight: bold;">CLI</span><span style="color: #0000BB;">' (clindamycin), '</span><span style="color: #0000BB; font-weight: bold;">AZM</span><span style="color: #0000BB;">' (azithromycin), '</span><span style="color: #0000BB; font-weight: bold;">MTR</span><span style="color: #0000BB;">'</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> (clindamycin), '<span style="font-weight: bold;">AZM</span>' (azithromycin), '<span style="font-weight: bold;">MTR</span>' (metronidazole), '<span style="font-weight: bold;">CHL</span>'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> (metronidazole), '</span><span style="color: #0000BB; font-weight: bold;">CHL</span><span style="color: #0000BB;">' (chloramphenicol), '</span><span style="color: #0000BB; font-weight: bold;">COL</span><span style="color: #0000BB;">' (colistin), and '</span><span style="color: #0000BB; font-weight: bold;">RIF</span><span style="color: #0000BB;">'</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> (chloramphenicol), '<span style="font-weight: bold;">COL</span>' (colistin), and '<span style="font-weight: bold;">RIF</span>' (rifampicin)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> (rifampicin)</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> <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>
@@ -469,7 +468,7 @@ 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"># 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: #0000BB;">ℹ For `carbapenems()` using columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem) and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns '<span style="font-weight: bold;">IPM</span>' (imipenem) and '<span style="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>
@@ -491,7 +490,7 @@ 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: #0000BB;">ℹ For `carbapenems()` using columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem) and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns '<span style="font-weight: bold;">IPM</span>' (imipenem) and '<span style="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>
@@ -515,8 +514,8 @@ 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: #0000BB;">ℹ For `carbapenems()` using columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem) and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns '<span style="font-weight: bold;">IPM</span>' (imipenem) and '<span style="font-weight: bold;">MEM</span>' (meropenem)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Filtering any of columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' to contain value "S", "I" or "R"</span></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>
@@ -538,8 +537,8 @@ 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: #0000BB;">ℹ For `carbapenems()` using columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem) and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns '<span style="font-weight: bold;">IPM</span>' (imipenem) and '<span style="font-weight: bold;">MEM</span>' (meropenem)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Filtering all of columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' to contain value "S", "I" or "R"</span></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>
@@ -563,9 +562,9 @@ 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: #0000BB;">ℹ For `carbapenems()` using columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem) and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns '<span style="font-weight: bold;">IPM</span>' (imipenem) and '<span style="font-weight: bold;">MEM</span>' (meropenem)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ For `aminoglycosides()` using columns '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin), '</span><span style="color: #0000BB; font-weight: bold;">TOB</span><span style="color: #0000BB;">'</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns '<span style="font-weight: bold;">GEN</span>' (gentamicin), '<span style="font-weight: bold;">TOB</span>' (tobramycin),</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> (tobramycin), '</span><span style="color: #0000BB; font-weight: bold;">AMK</span><span style="color: #0000BB;">' (amikacin), and '</span><span style="color: #0000BB; font-weight: bold;">KAN</span><span style="color: #0000BB;">' (kanamycin)</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> '<span style="font-weight: bold;">AMK</span>' (amikacin), and '<span style="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>
@@ -589,11 +588,11 @@ 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: #0000BB;">ℹ For `carbapenems()` using columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem) and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns '<span style="font-weight: bold;">IPM</span>' (imipenem) and '<span style="font-weight: bold;">MEM</span>' (meropenem)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ For `penicillins()` using columns '</span><span style="color: #0000BB; font-weight: bold;">PEN</span><span style="color: #0000BB;">' (benzylpenicillin), '</span><span style="color: #0000BB; font-weight: bold;">OXA</span><span style="color: #0000BB;">'</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="font-weight: bold;">PEN</span>' (benzylpenicillin), '<span style="font-weight: bold;">OXA</span>'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> (oxacillin), '</span><span style="color: #0000BB; font-weight: bold;">FLC</span><span style="color: #0000BB;">' (flucloxacillin), '</span><span style="color: #0000BB; font-weight: bold;">AMX</span><span style="color: #0000BB;">' (amoxicillin), '</span><span style="color: #0000BB; font-weight: bold;">AMC</span><span style="color: #0000BB;">'</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> (oxacillin), '<span style="font-weight: bold;">FLC</span>' (flucloxacillin), '<span style="font-weight: bold;">AMX</span>' (amoxicillin), '<span style="font-weight: bold;">AMC</span>'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> (amoxicillin/clavulanic acid), '</span><span style="color: #0000BB; font-weight: bold;">AMP</span><span style="color: #0000BB;">' (ampicillin), and '</span><span style="color: #0000BB; font-weight: bold;">TZP</span><span style="color: #0000BB;">'</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> (amoxicillin/clavulanic acid), '<span style="font-weight: bold;">AMP</span>' (ampicillin), and '<span style="font-weight: bold;">TZP</span>'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> (piperacillin/tazobactam)</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</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>
@@ -615,19 +614,18 @@ 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: #0000BB;">ℹ For `penicillins()` using columns '</span><span style="color: #0000BB; font-weight: bold;">PEN</span><span style="color: #0000BB;">' (benzylpenicillin), '</span><span style="color: #0000BB; font-weight: bold;">OXA</span><span style="color: #0000BB;">'</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="font-weight: bold;">PEN</span>' (benzylpenicillin), '<span style="font-weight: bold;">OXA</span>'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> (oxacillin), '</span><span style="color: #0000BB; font-weight: bold;">FLC</span><span style="color: #0000BB;">' (flucloxacillin), '</span><span style="color: #0000BB; font-weight: bold;">AMX</span><span style="color: #0000BB;">' (amoxicillin), '</span><span style="color: #0000BB; font-weight: bold;">AMC</span><span style="color: #0000BB;">'</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> (oxacillin), '<span style="font-weight: bold;">FLC</span>' (flucloxacillin), '<span style="font-weight: bold;">AMX</span>' (amoxicillin), '<span style="font-weight: bold;">AMC</span>'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> (amoxicillin/clavulanic acid), '</span><span style="color: #0000BB; font-weight: bold;">AMP</span><span style="color: #0000BB;">' (ampicillin), and '</span><span style="color: #0000BB; font-weight: bold;">TZP</span><span style="color: #0000BB;">'</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> (amoxicillin/clavulanic acid), '<span style="font-weight: bold;">AMP</span>' (ampicillin), and '<span style="font-weight: bold;">TZP</span>'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> (piperacillin/tazobactam)</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> (piperacillin/tazobactam)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ For `administrable_per_os()` using columns '</span><span style="color: #0000BB; font-weight: bold;">OXA</span><span style="color: #0000BB;">' (oxacillin), '</span><span style="color: #0000BB; font-weight: bold;">FLC</span><span style="color: #0000BB;">'</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="font-weight: bold;">OXA</span>' (oxacillin), '<span style="font-weight: bold;">FLC</span>'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> (flucloxacillin), '</span><span style="color: #0000BB; font-weight: bold;">AMX</span><span style="color: #0000BB;">' (amoxicillin), '</span><span style="color: #0000BB; font-weight: bold;">AMC</span><span style="color: #0000BB;">' (amoxicillin/clavulanic acid),</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> (flucloxacillin), '<span style="font-weight: bold;">AMX</span>' (amoxicillin), '<span style="font-weight: bold;">AMC</span>' (amoxicillin/clavulanic acid),</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> '</span><span style="color: #0000BB; font-weight: bold;">AMP</span><span style="color: #0000BB;">' (ampicillin), '</span><span style="color: #0000BB; font-weight: bold;">CXM</span><span style="color: #0000BB;">' (cefuroxime), '</span><span style="color: #0000BB; font-weight: bold;">KAN</span><span style="color: #0000BB;">' (kanamycin), '</span><span style="color: #0000BB; font-weight: bold;">TMP</span><span style="color: #0000BB;">'</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> '<span style="font-weight: bold;">AMP</span>' (ampicillin), '<span style="font-weight: bold;">CXM</span>' (cefuroxime), '<span style="font-weight: bold;">KAN</span>' (kanamycin), '<span style="font-weight: bold;">TMP</span>'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> (trimethoprim), '</span><span style="color: #0000BB; font-weight: bold;">NIT</span><span style="color: #0000BB;">' (nitrofurantoin), '</span><span style="color: #0000BB; font-weight: bold;">FOS</span><span style="color: #0000BB;">' (fosfomycin), '</span><span style="color: #0000BB; font-weight: bold;">LNZ</span><span style="color: #0000BB;">'</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> (trimethoprim), '<span style="font-weight: bold;">NIT</span>' (nitrofurantoin), '<span style="font-weight: bold;">FOS</span>' (fosfomycin), '<span style="font-weight: bold;">LNZ</span>'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> (linezolid), '</span><span style="color: #0000BB; font-weight: bold;">CIP</span><span style="color: #0000BB;">' (ciprofloxacin), '</span><span style="color: #0000BB; font-weight: bold;">MFX</span><span style="color: #0000BB;">' (moxifloxacin), '</span><span style="color: #0000BB; font-weight: bold;">VAN</span><span style="color: #0000BB;">'</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> (linezolid), '<span style="font-weight: bold;">CIP</span>' (ciprofloxacin), '<span style="font-weight: bold;">MFX</span>' (moxifloxacin), '<span style="font-weight: bold;">VAN</span>' (vancomycin),</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> (vancomycin), '</span><span style="color: #0000BB; font-weight: bold;">TCY</span><span style="color: #0000BB;">' (tetracycline), '</span><span style="color: #0000BB; font-weight: bold;">DOX</span><span style="color: #0000BB;">' (doxycycline), '</span><span style="color: #0000BB; font-weight: bold;">ERY</span><span style="color: #0000BB;">'</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> '<span style="font-weight: bold;">TCY</span>' (tetracycline), '<span style="font-weight: bold;">DOX</span>' (doxycycline), '<span style="font-weight: bold;">ERY</span>' (erythromycin), '<span style="font-weight: bold;">CLI</span>'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> (erythromycin), '</span><span style="color: #0000BB; font-weight: bold;">CLI</span><span style="color: #0000BB;">' (clindamycin), '</span><span style="color: #0000BB; font-weight: bold;">AZM</span><span style="color: #0000BB;">' (azithromycin), '</span><span style="color: #0000BB; font-weight: bold;">MTR</span><span style="color: #0000BB;">'</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> (clindamycin), '<span style="font-weight: bold;">AZM</span>' (azithromycin), '<span style="font-weight: bold;">MTR</span>' (metronidazole), '<span style="font-weight: bold;">CHL</span>'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> (metronidazole), '</span><span style="color: #0000BB; font-weight: bold;">CHL</span><span style="color: #0000BB;">' (chloramphenicol), '</span><span style="color: #0000BB; font-weight: bold;">COL</span><span style="color: #0000BB;">' (colistin), and '</span><span style="color: #0000BB; font-weight: bold;">RIF</span><span style="color: #0000BB;">'</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> (chloramphenicol), '<span style="font-weight: bold;">COL</span>' (colistin), and '<span style="font-weight: bold;">RIF</span>' (rifampicin)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> (rifampicin)</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> <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>
@@ -647,11 +645,11 @@ my_data_with_all_these_columns %&amp;gt;%
<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: #0000BB;">ℹ For `amr_selector(oral_ddd &gt; 1 &amp; oral_units == "g")` using columns '</span><span style="color: #0000BB; font-weight: bold;">OXA</span><span style="color: #0000BB;">'</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="font-weight: bold;">OXA</span>'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> (oxacillin), '</span><span style="color: #0000BB; font-weight: bold;">FLC</span><span style="color: #0000BB;">' (flucloxacillin), '</span><span style="color: #0000BB; font-weight: bold;">AMX</span><span style="color: #0000BB;">' (amoxicillin), '</span><span style="color: #0000BB; font-weight: bold;">AMC</span><span style="color: #0000BB;">'</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> (oxacillin), '<span style="font-weight: bold;">FLC</span>' (flucloxacillin), '<span style="font-weight: bold;">AMX</span>' (amoxicillin), '<span style="font-weight: bold;">AMC</span>'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> (amoxicillin/clavulanic acid), '</span><span style="color: #0000BB; font-weight: bold;">AMP</span><span style="color: #0000BB;">' (ampicillin), '</span><span style="color: #0000BB; font-weight: bold;">KAN</span><span style="color: #0000BB;">' (kanamycin), '</span><span style="color: #0000BB; font-weight: bold;">FOS</span><span style="color: #0000BB;">'</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> (amoxicillin/clavulanic acid), '<span style="font-weight: bold;">AMP</span>' (ampicillin), '<span style="font-weight: bold;">KAN</span>' (kanamycin), '<span style="font-weight: bold;">FOS</span>'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> (fosfomycin), '</span><span style="color: #0000BB; font-weight: bold;">LNZ</span><span style="color: #0000BB;">' (linezolid), '</span><span style="color: #0000BB; font-weight: bold;">VAN</span><span style="color: #0000BB;">' (vancomycin), '</span><span style="color: #0000BB; font-weight: bold;">ERY</span><span style="color: #0000BB;">' (erythromycin),</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> (fosfomycin), '<span style="font-weight: bold;">LNZ</span>' (linezolid), '<span style="font-weight: bold;">VAN</span>' (vancomycin), '<span style="font-weight: bold;">ERY</span>' (erythromycin),</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> '</span><span style="color: #0000BB; font-weight: bold;">CLI</span><span style="color: #0000BB;">' (clindamycin), '</span><span style="color: #0000BB; font-weight: bold;">MTR</span><span style="color: #0000BB;">' (metronidazole), and '</span><span style="color: #0000BB; font-weight: bold;">CHL</span><span style="color: #0000BB;">' (chloramphenicol)</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> '<span style="font-weight: bold;">CLI</span>' (clindamycin), '<span style="font-weight: bold;">MTR</span>' (metronidazole), and '<span style="font-weight: bold;">CHL</span>' (chloramphenicol)</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> <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>
@@ -691,17 +689,17 @@ 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: #0000BB;">ℹ For `carbapenems()` using columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem) and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns '<span style="font-weight: bold;">IPM</span>' (imipenem) and '<span style="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 data.table? 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()` (`?AMR::amr_selector()`).</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'amr_selector'</span> <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'amr_selector'</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: #0000BB;">ℹ For `carbapenems()` using columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem) and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns '<span style="font-weight: bold;">IPM</span>' (imipenem) and '<span style="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>
@@ -720,8 +718,8 @@ 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: #0000BB;">ℹ For `aminoglycosides()` using columns '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin), '</span><span style="color: #0000BB; font-weight: bold;">TOB</span><span style="color: #0000BB;">'</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns '<span style="font-weight: bold;">GEN</span>' (gentamicin), '<span style="font-weight: bold;">TOB</span>' (tobramycin),</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> (tobramycin), '</span><span style="color: #0000BB; font-weight: bold;">AMK</span><span style="color: #0000BB;">' (amikacin), and '</span><span style="color: #0000BB; font-weight: bold;">KAN</span><span style="color: #0000BB;">' (kanamycin)</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> '<span style="font-weight: bold;">AMK</span>' (amikacin), and '<span style="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>
@@ -738,9 +736,9 @@ 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: #0000BB;">ℹ For `carbapenems()` using columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem) and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns '<span style="font-weight: bold;">IPM</span>' (imipenem) and '<span style="font-weight: bold;">MEM</span>' (meropenem)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ For `aminoglycosides()` using columns '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin), '</span><span style="color: #0000BB; font-weight: bold;">TOB</span><span style="color: #0000BB;">'</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns '<span style="font-weight: bold;">GEN</span>' (gentamicin), '<span style="font-weight: bold;">TOB</span>' (tobramycin),</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> (tobramycin), '</span><span style="color: #0000BB; font-weight: bold;">AMK</span><span style="color: #0000BB;">' (amikacin), and '</span><span style="color: #0000BB; font-weight: bold;">KAN</span><span style="color: #0000BB;">' (kanamycin)</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> '<span style="font-weight: bold;">AMK</span>' (amikacin), and '<span style="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>
@@ -759,7 +757,7 @@ 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: #0000BB;">ℹ For `carbapenems()` using columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem) and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns '<span style="font-weight: bold;">IPM</span>' (imipenem) and '<span style="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>
@@ -828,11 +826,11 @@ 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: #0000BB;">ℹ For `carbapenems()` using columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem) and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns '<span style="font-weight: bold;">IPM</span>' (imipenem) and '<span style="font-weight: bold;">MEM</span>' (meropenem)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ For `penicillins()` using columns '</span><span style="color: #0000BB; font-weight: bold;">PEN</span><span style="color: #0000BB;">' (benzylpenicillin), '</span><span style="color: #0000BB; font-weight: bold;">OXA</span><span style="color: #0000BB;">'</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="font-weight: bold;">PEN</span>' (benzylpenicillin), '<span style="font-weight: bold;">OXA</span>'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> (oxacillin), '</span><span style="color: #0000BB; font-weight: bold;">FLC</span><span style="color: #0000BB;">' (flucloxacillin), '</span><span style="color: #0000BB; font-weight: bold;">AMX</span><span style="color: #0000BB;">' (amoxicillin), '</span><span style="color: #0000BB; font-weight: bold;">AMC</span><span style="color: #0000BB;">'</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> (oxacillin), '<span style="font-weight: bold;">FLC</span>' (flucloxacillin), '<span style="font-weight: bold;">AMX</span>' (amoxicillin), '<span style="font-weight: bold;">AMC</span>'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> (amoxicillin/clavulanic acid), '</span><span style="color: #0000BB; font-weight: bold;">AMP</span><span style="color: #0000BB;">' (ampicillin), and '</span><span style="color: #0000BB; font-weight: bold;">TZP</span><span style="color: #0000BB;">'</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> (amoxicillin/clavulanic acid), '<span style="font-weight: bold;">AMP</span>' (ampicillin), and '<span style="font-weight: bold;">TZP</span>'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> (piperacillin/tazobactam)</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</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>
<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; &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; &lt;sir&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1: R &lt;NA&gt; &lt;NA&gt; &lt;NA&gt; I &lt;NA&gt; &lt;NA&gt;</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 1: R &lt;NA&gt; &lt;NA&gt; &lt;NA&gt; I &lt;NA&gt; &lt;NA&gt;</span>

44
reference/antimicrobial_selectors.md
View File

@@ -669,10 +669,10 @@ 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 #> ℹ in `carbapenems()` (`?AMR::carbapenems()`): Imipenem/EDTA (`IPE`) and
#> (`MNC`) are not included since `only_treatable = TRUE`. #> meropenem/nacubactam (`MNC`) are not included since `only_treatable = TRUE`.
#> ℹ This 'ab' vector was retrieved using `carbapenems()`, which should #> ℹ This <ab> vector was retrieved using `carbapenems()`, which should normally
#> 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.:
#> • your_data %>% select(carbapenems()) #> • your_data %>% select(carbapenems())
#> • your_data %>% select(column_a, column_b, carbapenems()) #> • your_data %>% select(column_a, column_b, carbapenems())
#> • your_data %>% filter(any(carbapenems() == "R")) #> • your_data %>% filter(any(carbapenems() == "R"))
@@ -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' #> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB' (tobramycin),
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin) #> 'AMK' (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>
@@ -818,11 +818,10 @@ example_isolates[, administrable_per_os()]
#> (flucloxacillin), 'AMX' (amoxicillin), 'AMC' (amoxicillin/clavulanic acid), #> (flucloxacillin), 'AMX' (amoxicillin), 'AMC' (amoxicillin/clavulanic acid),
#> 'AMP' (ampicillin), 'CXM' (cefuroxime), 'KAN' (kanamycin), 'TMP' #> 'AMP' (ampicillin), 'CXM' (cefuroxime), 'KAN' (kanamycin), 'TMP'
#> (trimethoprim), 'NIT' (nitrofurantoin), 'FOS' (fosfomycin), 'LNZ' #> (trimethoprim), 'NIT' (nitrofurantoin), 'FOS' (fosfomycin), 'LNZ'
#> (linezolid), 'CIP' (ciprofloxacin), 'MFX' (moxifloxacin), 'VAN' #> (linezolid), 'CIP' (ciprofloxacin), 'MFX' (moxifloxacin), 'VAN' (vancomycin),
#> (vancomycin), 'TCY' (tetracycline), 'DOX' (doxycycline), 'ERY' #> 'TCY' (tetracycline), 'DOX' (doxycycline), 'ERY' (erythromycin), 'CLI'
#> (erythromycin), 'CLI' (clindamycin), 'AZM' (azithromycin), 'MTR' #> (clindamycin), 'AZM' (azithromycin), 'MTR' (metronidazole), 'CHL'
#> (metronidazole), 'CHL' (chloramphenicol), 'COL' (colistin), and 'RIF' #> (chloramphenicol), 'COL' (colistin), and 'RIF' (rifampicin)
#> (rifampicin)
#> # A tibble: 2,000 × 23 #> # A tibble: 2,000 × 23
#> OXA FLC AMX AMC AMP CXM KAN TMP NIT FOS LNZ CIP MFX #> OXA FLC AMX AMC AMP CXM KAN TMP NIT FOS LNZ CIP MFX
#> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> #> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir>
@@ -937,8 +936,8 @@ 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' #> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB' (tobramycin),
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin) #> 'AMK' (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>
@@ -996,11 +995,10 @@ example_isolates[, penicillins() & administrable_per_os()]
#> (flucloxacillin), 'AMX' (amoxicillin), 'AMC' (amoxicillin/clavulanic acid), #> (flucloxacillin), 'AMX' (amoxicillin), 'AMC' (amoxicillin/clavulanic acid),
#> 'AMP' (ampicillin), 'CXM' (cefuroxime), 'KAN' (kanamycin), 'TMP' #> 'AMP' (ampicillin), 'CXM' (cefuroxime), 'KAN' (kanamycin), 'TMP'
#> (trimethoprim), 'NIT' (nitrofurantoin), 'FOS' (fosfomycin), 'LNZ' #> (trimethoprim), 'NIT' (nitrofurantoin), 'FOS' (fosfomycin), 'LNZ'
#> (linezolid), 'CIP' (ciprofloxacin), 'MFX' (moxifloxacin), 'VAN' #> (linezolid), 'CIP' (ciprofloxacin), 'MFX' (moxifloxacin), 'VAN' (vancomycin),
#> (vancomycin), 'TCY' (tetracycline), 'DOX' (doxycycline), 'ERY' #> 'TCY' (tetracycline), 'DOX' (doxycycline), 'ERY' (erythromycin), 'CLI'
#> (erythromycin), 'CLI' (clindamycin), 'AZM' (azithromycin), 'MTR' #> (clindamycin), 'AZM' (azithromycin), 'MTR' (metronidazole), 'CHL'
#> (metronidazole), 'CHL' (chloramphenicol), 'COL' (colistin), and 'RIF' #> (chloramphenicol), 'COL' (colistin), and 'RIF' (rifampicin)
#> (rifampicin)
#> # A tibble: 2,000 × 5 #> # A tibble: 2,000 × 5
#> OXA FLC AMX AMC AMP #> OXA FLC AMX AMC AMP
#> <sir> <sir> <sir> <sir> <sir> #> <sir> <sir> <sir> <sir> <sir>
@@ -1067,7 +1065,7 @@ if (require("data.table")) {
#> 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()` (`?AMR::amr_selector()`).
#> Class 'amr_selector' #> Class 'amr_selector'
#> [1] IPM MEM #> [1] IPM MEM
if (require("data.table")) { if (require("data.table")) {
@@ -1093,8 +1091,8 @@ 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' #> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB' (tobramycin),
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin) #> 'AMK' (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>
@@ -1112,8 +1110,8 @@ 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' #> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB' (tobramycin),
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin) #> 'AMK' (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>

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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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.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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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.av.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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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/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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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">
@@ -322,8 +322,8 @@
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="st">"ESCO"</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="st">"ESCO"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Gram-negative"</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Gram-negative"</span>
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span><span class="st">"ESCCOL"</span>, ab <span class="op">=</span> <span class="st">"vanco"</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span><span class="st">"ESCCOL"</span>, ab <span class="op">=</span> <span class="st">"vanco"</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Determining intrinsic resistance based on 'EUCAST Expected Resistant</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Determining intrinsic resistance based on 'EUCAST Expected Resistant</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> Phenotypes' v1.2 (2023). </span><span style="color: #BB0000;">This note will be shown once per session.</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> Phenotypes' v1.2 (2023). <span style="color: #BB0000;">This note will be shown once per session.</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE</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>

78
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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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">
@@ -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> 2026-03-18 <span style="color: #949494;">09:41:20</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> 2026-03-20 <span style="color: #949494;">16:07:38</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> 2026-03-18 <span style="color: #949494;">09:41:20</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> 2026-03-20 <span style="color: #949494;">16:07:38</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> 2026-03-18 <span style="color: #949494;">09:41:21</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> 2026-03-20 <span style="color: #949494;">16:07:39</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> 2026-03-18 <span style="color: #949494;">09:41:21</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> 2026-03-20 <span style="color: #949494;">16:07:39</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>
@@ -435,17 +435,16 @@ 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: #0000BB;">ℹ Returning previously coerced values for various antimicrobials. Run</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: #0000BB;"> `ab_reset_session()` to reset this. This note will be shown once per</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> `ab_reset_session()` (`?AMR::ab_reset_session()`) to reset this. This note</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> session.</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> will be shown once per 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> <span style="color: #0000BB;">Running in parallel mode using 3 out of 4 cores, on columns '</span><span style="color: #0000BB; font-weight: bold;">amoxicillin</span><span style="color: #0000BB;">',</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> <span style="color: #0000BB;">'</span><span style="color: #0000BB; font-weight: bold;">cipro</span><span style="color: #0000BB;">', '</span><span style="color: #0000BB; font-weight: bold;">tobra</span><span style="color: #0000BB;">', '</span><span style="color: #0000BB; font-weight: bold;">genta</span><span style="color: #0000BB;">', and '</span><span style="color: #0000BB; font-weight: bold;">ERY</span><span style="color: #0000BB;">'...</span></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 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> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Run `sir_interpretation_history()` (`?AMR::sir_interpretation_history()`) to</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">ℹ Run `sir_interpretation_history()` to retrieve a logbook with all details</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> retrieve a logbook with all details of the breakpoint interpretations.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;"> of the breakpoint interpretations.</span></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>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
@@ -557,48 +556,47 @@ 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: #0000BB;">ℹ For `aminopenicillins()` using column '</span><span style="color: #0000BB; font-weight: bold;">amoxicillin</span><span style="color: #0000BB;">'</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="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>
<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</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> CLSI interpretation guideline.</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> <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>
<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</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> CLSI interpretation guideline.</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> <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>
<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</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> CLSI interpretation guideline.</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> <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: `mics = (function (x, ...) ...`.</span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In argument: `mics = (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>
<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</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> CLSI interpretation guideline.</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> <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>
<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</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> CLSI 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> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">antibiotic</span><span style="color: #0000BB;">' (TESTAB, test Antibiotic), </span><span style="color: #0000BB; font-weight: bold;">CLSI</span></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> <span style="color: #0000BB; font-weight: bold;">2025</span><span style="color: #0000BB;">...</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="color: #0000BB;">Interpreting disk diffusion zones: '</span><span style="color: #0000BB; font-weight: bold;">antibiotic</span><span style="color: #0000BB;">' (TESTAB, test Antibiotic),</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> <span style="color: #0000BB; font-weight: bold;">CLSI 2025</span><span style="color: #0000BB;">...</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="color: #0000BB;">Interpreting disk diffusion zones: '</span><span style="color: #0000BB; font-weight: bold;">antibiotic</span><span style="color: #0000BB;">' (TESTAB, test Antibiotic),</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> <span style="color: #0000BB; font-weight: bold;">CLSI 2025</span><span style="color: #0000BB;">...</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>
<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</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> CLSI interpretation guideline.</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> <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>
<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</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> CLSI interpretation guideline.</span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> interpretation guideline.</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 8 &lt;NA&gt; S S R</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 1 Escherichia coli 8 &lt;NA&gt; S S R</span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
@@ -629,8 +627,8 @@ 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()` (`?AMR::as.sir()`): 3 results truncated (38%) that were invalid</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> antimicrobial interpretations: "A", "B", and "C"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span> <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</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>
<span class="r-in"><span><span class="fu">as.sir</span><span class="op">(</span><span class="st">"&lt;= 0.002; S"</span><span class="op">)</span> <span class="co"># will return "S"</span></span></span> <span class="r-in"><span><span class="fu">as.sir</span><span class="op">(</span><span class="st">"&lt;= 0.002; S"</span><span class="op">)</span> <span class="co"># will return "S"</span></span></span>
@@ -638,11 +636,13 @@ 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: #0000BB;">ℹ in `as.sir()`: Interpreting input value 1 as "S", 2 as "I", and 3 as "R"</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> in `as.sir()` (`?AMR::as.sir()`): Interpreting input value 1 as "S", 2 as</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "I", and 3 as "R"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span> <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</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: #0000BB;">ℹ in `as.sir()`: Interpreting input value 1 as "R", 2 as "I", and 3 as "S"</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> in `as.sir()` (`?AMR::as.sir()`): Interpreting input value 1 as "R", 2 as</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "I", and 3 as "S"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span> <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</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>

66
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 2026-03-18 09:41:20 1 MIC amoxicillin Escherich… human 8 #> 1 2026-03-20 16:07:38 1 MIC amoxicillin Escherich… human 8
#> 2 2026-03-18 09:41:20 1 MIC cipro Escherich… human 0.256 #> 2 2026-03-20 16:07:38 1 MIC cipro Escherich… human 0.256
#> 3 2026-03-18 09:41:21 1 DISK tobra Escherich… human 16 #> 3 2026-03-20 16:07:39 1 DISK tobra Escherich… human 16
#> 4 2026-03-18 09:41:21 1 DISK genta Escherich… human 18 #> 4 2026-03-20 16:07:39 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>
@@ -671,17 +671,16 @@ 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 previously coerced values for various antimicrobials. Run #> ℹ Returning a previously coerced value for an antimicrobial. Run
#> `ab_reset_session()` to reset this. This note will be shown once per #> `ab_reset_session()` (`?AMR::ab_reset_session()`) to reset this. This note
#> session. #> will be shown once per session.
#> #>
#> Running in parallel mode using 3 out of 4 cores, on columns 'amoxicillin', #> Running in parallel mode using 3 out of 4 cores, on columns 'amoxicillin',
#> 'cipro', 'tobra', 'genta', and 'ERY'... #> 'cipro', 'tobra', 'genta', and 'ERY'...
#> DONE #> DONE
#> #>
#> #> ℹ Run `sir_interpretation_history()` (`?AMR::sir_interpretation_history()`) to
#> ℹ Run `sir_interpretation_history()` to retrieve a logbook with all details #> retrieve a logbook with all details of the breakpoint interpretations.
#> of 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
@@ -797,44 +796,43 @@ if (require("dplyr")) {
#> 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:
#> ! Some MICs were converted to the nearest higher log2 level, following the #> ! Some MICs were converted to the nearest higher log2 level, following the CLSI
#> CLSI interpretation guideline. #> interpretation guideline.
#> 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:
#> ! Some MICs were converted to the nearest higher log2 level, following the #> ! Some MICs were converted to the nearest higher log2 level, following the CLSI
#> CLSI interpretation guideline. #> interpretation guideline.
#> 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:
#> ! Some MICs were converted to the nearest higher log2 level, following the #> ! Some MICs were converted to the nearest higher log2 level, following the CLSI
#> CLSI interpretation guideline. #> interpretation guideline.
#> Warning: There was 1 warning in `mutate()`. #> Warning: There was 1 warning in `mutate()`.
#> ℹ In argument: `mics = (function (x, ...) ...`. #> ℹ In argument: `mics = (function (x, ...) ...`.
#> Caused by warning: #> Caused by warning:
#> ! Some MICs were converted to the nearest higher log2 level, following the #> ! Some MICs were converted to the nearest higher log2 level, following the CLSI
#> CLSI interpretation guideline. #> interpretation guideline.
#> 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:
#> ! Some MICs were converted to the nearest higher log2 level, following the #> ! Some MICs were converted to the nearest higher log2 level, following the CLSI
#> CLSI interpretation guideline. #> interpretation guideline.
#> Interpreting MIC values: 'antibiotic' (TESTAB, test Antibiotic), CLSI #> 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... #> 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:
#> ! Some MICs were converted to the nearest higher log2 level, following the #> ! Some MICs were converted to the nearest higher log2 level, following the CLSI
#> CLSI interpretation guideline. #> interpretation guideline.
#> 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:
#> ! Some MICs were converted to the nearest higher log2 level, following the #> ! Some MICs were converted to the nearest higher log2 level, following the CLSI
#> CLSI interpretation guideline. #> interpretation guideline.
#> microorganism amoxicillin cipro tobra genta ERY #> microorganism amoxicillin cipro tobra genta ERY
#> 1 Escherichia coli 8 <NA> S S R #> 1 Escherichia coli 8 <NA> S S R
@@ -865,8 +863,8 @@ 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()` (`?AMR::as.sir()`): 3 results truncated (38%) that were invalid
#> interpretations: "A", "B", and "C" #> antimicrobial 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>
as.sir("<= 0.002; S") # will return "S" as.sir("<= 0.002; S") # will return "S"
@@ -874,11 +872,13 @@ 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 in `as.sir()`: Interpreting input value 1 as "S", 2 as "I", and 3 as "R" #> ℹ in `as.sir()` (`?AMR::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 in `as.sir()`: Interpreting input value 1 as "R", 2 as "I", and 3 as "S" #> ℹ in `as.sir()` (`?AMR::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

16
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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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">
@@ -135,12 +135,14 @@
<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: #0000BB;">ℹ in `atc_online_property()`: no properties found for ATC QG51AA03. Please</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> in `atc_online_property()` (`?AMR::atc_online_property()`): no properties</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> check</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> found for ATC QG51AA03. Please check</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> 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;">ℹ in `atc_online_property()`: no properties found for ATC QJ01CA04. Please</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;"> check</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> in `atc_online_property()` (`?AMR::atc_online_property()`): no properties</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> 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> 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;">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>
<span class="r-out co"><span class="r-pr">#&gt;</span> [2] "ANTIBACTERIALS FOR SYSTEMIC USE" </span> <span class="r-out co"><span class="r-pr">#&gt;</span> [2] "ANTIBACTERIALS FOR SYSTEMIC USE" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [3] "BETA-LACTAM ANTIBACTERIALS, PENICILLINS"</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [3] "BETA-LACTAM ANTIBACTERIALS, PENICILLINS"</span>

14
reference/atc_online.md
View File

@@ -117,12 +117,14 @@ 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 in `atc_online_property()`: no properties found for ATC QG51AA03. Please #> ℹ in `atc_online_property()` (`?AMR::atc_online_property()`): no properties
#> check #> 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
#> ℹ in `atc_online_property()`: no properties found for ATC QJ01CA04. Please #> this WHOCC webpage>.
#> check #> ℹ in `atc_online_property()` (`?AMR::atc_online_property()`): no properties
#> https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01CA04&showdescription=no. #> found for ATC QJ01CA04. Please check
#> <https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01CA04&showdescription=no
#> this WHOCC webpage>.
#> [1] "ANTIINFECTIVES FOR SYSTEMIC USE" #> [1] "ANTIINFECTIVES FOR SYSTEMIC USE"
#> [2] "ANTIBACTERIALS FOR SYSTEMIC USE" #> [2] "ANTIBACTERIALS FOR SYSTEMIC USE"
#> [3] "BETA-LACTAM ANTIBACTERIALS, PENICILLINS" #> [3] "BETA-LACTAM ANTIBACTERIALS, PENICILLINS"

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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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">

11
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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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">
@@ -82,10 +82,11 @@
<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: #0000BB;">ℹ `resistance()` assumes the EUCAST guideline and thus considers the 'I'</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> `resistance()` (`?AMR::resistance()`) assumes the EUCAST guideline and thus</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> category susceptible. Set the `guideline` argument or the `AMR_guideline`</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> considers the 'I' category susceptible. Set the `guideline` argument or the</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> option to either "CLSI" or "EUCAST", see `?AMR-options`.</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> `AMR_guideline` option to either "CLSI" or "EUCAST", see AMR-options</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ This message will be shown once per session.</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> (`?AMR::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-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>
<span class="r-out co"><span class="r-pr">#&gt;</span> patient 2000 100.0% |####################| </span> <span class="r-out co"><span class="r-pr">#&gt;</span> patient 2000 100.0% |####################| </span>

7
reference/availability.md
View File

@@ -41,9 +41,10 @@ calculated with
``` r ``` r
availability(example_isolates) availability(example_isolates)
#> ℹ `resistance()` assumes the EUCAST guideline and thus considers the 'I' #> ℹ `resistance()` (`?AMR::resistance()`) assumes the EUCAST guideline and thus
#> category susceptible. Set the `guideline` argument or the `AMR_guideline` #> considers the 'I' category susceptible. Set the `guideline` argument or the
#> option to either "CLSI" or "EUCAST", see `?AMR-options`. #> `AMR_guideline` option to either "CLSI" or "EUCAST", see AMR-options
#> (`?AMR::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% |####################|

8
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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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">
@@ -172,7 +172,7 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> (unknown species) AMX 15 0 0 1 0 0 0 0 16</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> (unknown species) AMX 15 0 0 1 0 0 0 0 16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">5</span> (unknown species) AZM 3 0 0 3 0 0 0 0 6</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">5</span> (unknown species) AZM 3 0 0 3 0 0 0 0 6</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">6</span> (unknown species) CAZ 0 0 0 0 0 0 0 0 0</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">6</span> (unknown species) CAZ 0 0 0 0 0 0 0 0 0</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Use 'format()' on this result to get a publishable/printable format.</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> Use 'format()' on this result to get a publishable/printable format.</span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/format.html" class="external-link">format</a></span><span class="op">(</span><span class="va">x</span>, translate_ab <span class="op">=</span> <span class="st">"name (atc)"</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/format.html" class="external-link">format</a></span><span class="op">(</span><span class="va">x</span>, translate_ab <span class="op">=</span> <span class="st">"name (atc)"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 39 × 12</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 39 × 12</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Group Drug CoNS `E. coli` `E. faecalis` `K. pneumoniae` `P. aeruginosa`</span> <span class="r-out co"><span class="r-pr">#&gt;</span> Group Drug CoNS `E. coli` `E. faecalis` `K. pneumoniae` `P. aeruginosa`</span>
@@ -209,7 +209,7 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Gram-negative CLI 18 0 1 709 0 0 0 0 728</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Gram-negative CLI 18 0 1 709 0 0 0 0 728</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Gram-negative COL 309 0 0 78 0 0 0 0 387</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Gram-negative COL 309 0 0 78 0 0 0 0 387</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 70 more rows</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 70 more rows</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Use 'format()' on this result to get a publishable/printable format.</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> Use 'format()' on this result to get a publishable/printable format.</span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">bug_drug_combinations</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span> <span class="r-in"><span><span class="fu">bug_drug_combinations</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
<span class="r-in"><span> FUN <span class="op">=</span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="op">{</span></span></span> <span class="r-in"><span> FUN <span class="op">=</span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="op">{</span></span></span>
@@ -233,7 +233,7 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> E. coli CLI 0 0 0 467 0 0 0 0 467</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> E. coli CLI 0 0 0 467 0 0 0 0 467</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> E. coli COL 240 0 0 0 0 0 0 0 240</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> E. coli COL 240 0 0 0 0 0 0 0 240</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 70 more rows</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 70 more rows</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Use 'format()' on this result to get a publishable/printable format.</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> Use 'format()' on this result to get a publishable/printable format.</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>
</div> </div>

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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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">

33
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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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">
@@ -174,16 +174,18 @@ 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: #0000BB;">ℹ `count_resistant()` assumes the EUCAST guideline and thus considers the</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> `count_resistant()` (`?AMR::count_resistant()`) assumes the EUCAST guideline</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> 'I' category susceptible. Set the `guideline` argument or the</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> and thus considers the 'I' category susceptible. Set the `guideline` argument</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> `AMR_guideline` option to either "CLSI" or "EUCAST", see `?AMR-options`.</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> or the `AMR_guideline` option to either "CLSI" or "EUCAST", see AMR-options</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ This message will be shown once per session.</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> (`?AMR::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-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: #0000BB;">ℹ `count_susceptible()` assumes the EUCAST guideline and thus considers the</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> `count_susceptible()` (`?AMR::count_susceptible()`) assumes the EUCAST</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> 'I' category susceptible. Set the `guideline` argument or the</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> guideline and thus considers the 'I' category susceptible. Set the</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> `AMR_guideline` option to either "CLSI" or "EUCAST", see `?AMR-options`.</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> `guideline` argument or the `AMR_guideline` option to either "CLSI" or</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ This message will be shown once per session.</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> "EUCAST", see AMR-options (`?AMR::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-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>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1350</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1350</span>
@@ -213,10 +215,11 @@ 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: #0000BB;">ℹ `susceptibility()` assumes the EUCAST guideline and thus considers the</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> `susceptibility()` (`?AMR::susceptibility()`) assumes the EUCAST guideline</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> 'I' category susceptible. Set the `guideline` argument or the</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> and thus considers the 'I' category susceptible. Set the `guideline` argument</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> `AMR_guideline` option to either "CLSI" or "EUCAST", see `?AMR-options`.</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> or the `AMR_guideline` option to either "CLSI" or "EUCAST", see AMR-options</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ This message will be shown once per session.</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> (`?AMR::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-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>
<span class="r-in"><span><span class="co"># dplyr -------------------------------------------------------------</span></span></span> <span class="r-in"><span><span class="co"># dplyr -------------------------------------------------------------</span></span></span>
@@ -262,8 +265,8 @@ 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: #0000BB;">ℹ For `aminoglycosides()` using columns '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin), '</span><span style="color: #0000BB; font-weight: bold;">TOB</span><span style="color: #0000BB;">'</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns '<span style="font-weight: bold;">GEN</span>' (gentamicin), '<span style="font-weight: bold;">TOB</span>' (tobramycin),</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> (tobramycin), '</span><span style="color: #0000BB; font-weight: bold;">AMK</span><span style="color: #0000BB;">' (amikacin), and '</span><span style="color: #0000BB; font-weight: bold;">KAN</span><span style="color: #0000BB;">' (kanamycin)</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> '<span style="font-weight: bold;">AMK</span>' (amikacin), and '<span style="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>

25
reference/count.md
View File

@@ -188,15 +188,17 @@ 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 `count_resistant()` (`?AMR::count_resistant()`) assumes the EUCAST guideline
#> 'I' category susceptible. Set the `guideline` argument or the #> and thus considers the 'I' category susceptible. Set the `guideline` argument
#> `AMR_guideline` option to either "CLSI" or "EUCAST", see `?AMR-options`. #> or the `AMR_guideline` option to either "CLSI" or "EUCAST", see AMR-options
#> (`?AMR::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()` (`?AMR::count_susceptible()`) assumes the EUCAST
#> 'I' category susceptible. Set the `guideline` argument or the #> guideline and thus considers the 'I' category susceptible. Set the
#> `AMR_guideline` option to either "CLSI" or "EUCAST", see `?AMR-options`. #> `guideline` argument or the `AMR_guideline` option to either "CLSI" or
#> "EUCAST", see AMR-options (`?AMR::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 +229,10 @@ 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 `susceptibility()` (`?AMR::susceptibility()`) assumes the EUCAST guideline
#> 'I' category susceptible. Set the `guideline` argument or the #> and thus considers the 'I' category susceptible. Set the `guideline` argument
#> `AMR_guideline` option to either "CLSI" or "EUCAST", see `?AMR-options`. #> or the `AMR_guideline` option to either "CLSI" or "EUCAST", see AMR-options
#> (`?AMR::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 +279,8 @@ 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' #> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB' (tobramycin),
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin) #> 'AMK' (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>

8
reference/custom_eucast_rules.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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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">
@@ -244,11 +244,7 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">amoxicillin</span> (AMX), <span style="color: #0000BB;">amoxicillin/clavulanic acid</span> (AMC), <span style="color: #0000BB;">ampicillin</span> (AMP)</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">amoxicillin</span> (AMX), <span style="color: #0000BB;">amoxicillin/clavulanic acid</span> (AMC), <span style="color: #0000BB;">ampicillin</span> (AMP)</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-out co"><span class="r-pr">#&gt;</span> 3. <span style="font-weight: bold;">If </span><span style="color: #0000BB;">TZP</span><span style="color: #BBBBBB;"> is </span><span style="color: #080808; background-color: #FF5F5F;"> R </span><span style="font-weight: bold;"> then </span>set to <span style="color: #080808; background-color: #FF5F5F;"> R </span>:</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 3. <span style="font-weight: bold;">If </span><span style="color: #0000BB;">TZP</span><span style="color: #BBBBBB;"> is </span><span style="color: #080808; background-color: #FF5F5F;"> R </span><span style="font-weight: bold;"> then </span>set to <span style="color: #080808; background-color: #FF5F5F;"> R </span>:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">biapenem</span> (BIA), <span style="color: #0000BB;">doripenem</span> (DOR), <span style="color: #0000BB;">ertapenem</span> (ETP), <span style="color: #0000BB;">imipenem</span> (IPM),</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">biapenem</span> (BIA), <span style="color: #0000BB;">doripenem</span> (DOR), <span style="color: #0000BB;">ertapenem</span> (ETP), <span style="color: #0000BB;">imipenem</span> (IPM), <span style="color: #0000BB;">imipenem/EDTA</span> (IPE), <span style="color: #0000BB;">imipenem/relebactam</span> (IMR), <span style="color: #0000BB;">meropenem</span> (MEM), <span style="color: #0000BB;">meropenem/nacubactam</span> (MNC), <span style="color: #0000BB;">meropenem/vaborbactam</span> (MEV), <span style="color: #0000BB;">panipenem</span> (PAN), <span style="color: #0000BB;">razupenem</span> (RZM), <span style="color: #0000BB;">ritipenem</span> (RIT), <span style="color: #0000BB;">ritipenem acoxil</span> (RIA), <span style="color: #0000BB;">taniborbactam</span> (TAN), <span style="color: #0000BB;">tebipenem</span> (TBP)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">imipenem/EDTA</span> (IPE), <span style="color: #0000BB;">imipenem/relebactam</span> (IMR), <span style="color: #0000BB;">meropenem</span> (MEM),</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">meropenem/nacubactam</span> (MNC), <span style="color: #0000BB;">meropenem/vaborbactam</span> (MEV), <span style="color: #0000BB;">panipenem</span> (PAN),</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">razupenem</span> (RZM), <span style="color: #0000BB;">ritipenem</span> (RIT), <span style="color: #0000BB;">ritipenem acoxil</span> (RIA), <span style="color: #0000BB;">taniborbactam</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> (TAN), <span style="color: #0000BB;">tebipenem</span> (TBP)</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>

6
reference/custom_eucast_rules.md
View File

@@ -546,9 +546,5 @@ x2
#> amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), ampicillin (AMP) #> amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), ampicillin (AMP)
#> #>
#> 3. If TZP is R then set to R : #> 3. If TZP is R then set to R :
#> biapenem (BIA), doripenem (DOR), ertapenem (ETP), imipenem (IPM), #> biapenem (BIA), doripenem (DOR), ertapenem (ETP), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), panipenem (PAN), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), taniborbactam (TAN), tebipenem (TBP)
#> imipenem/EDTA (IPE), imipenem/relebactam (IMR), meropenem (MEM),
#> meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), panipenem (PAN),
#> razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), taniborbactam
#> (TAN), tebipenem (TBP)
``` ```

22
reference/custom_mdro_guideline.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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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">
@@ -192,9 +192,9 @@
<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="va">x</span></span></span> <span class="r-in"><span><span class="va">x</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> A set of custom MDRO rules:</span> <span class="r-out co"><span class="r-pr">#&gt;</span> A set of custom MDRO rules:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1. <span style="font-weight: bold;">If </span><span style="color: #0000BB;">CIP</span><span style="color: #BBBBBB;"> is </span><span style="color: #080808; background-color: #FF5F5F;"> R </span><span style="color: #BBBBBB; font-weight: bold;"> and </span><span style="color: #0000BB;">age</span><span style="color: #BBBBBB;"> is higher than </span><span style="color: #0000BB;">60</span><span style="font-weight: bold;"> then: </span><span style="color: #BB0000;">Elderly Type A</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span>   1. <span style="font-weight: bold;">If </span><span style="color: #0000BB;">CIP</span><span style="color: #BBBBBB;"> is </span><span style="color: #080808; background-color: #FF5F5F;"> R </span><span style="color: #BBBBBB; font-weight: bold;"> and </span><span style="color: #0000BB;">age</span><span style="color: #BBBBBB;"> is higher than </span><span style="color: #0000BB;">60</span><span style="font-weight: bold;"> then: </span><span style="color: #BB0000;">Elderly Type A</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2. <span style="font-weight: bold;">If </span><span style="color: #0000BB;">ERY</span><span style="color: #BBBBBB;"> is </span><span style="color: #080808; background-color: #FF5F5F;"> R </span><span style="color: #BBBBBB; font-weight: bold;"> and </span><span style="color: #0000BB;">age</span><span style="color: #BBBBBB;"> is higher than </span><span style="color: #0000BB;">60</span><span style="font-weight: bold;"> then: </span><span style="color: #BB0000;">Elderly Type B</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span>   2. <span style="font-weight: bold;">If </span><span style="color: #0000BB;">ERY</span><span style="color: #BBBBBB;"> is </span><span style="color: #080808; background-color: #FF5F5F;"> R </span><span style="color: #BBBBBB; font-weight: bold;"> and </span><span style="color: #0000BB;">age</span><span style="color: #BBBBBB;"> is higher than </span><span style="color: #0000BB;">60</span><span style="font-weight: bold;"> then: </span><span style="color: #BB0000;">Elderly Type B</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3. <span style="font-weight: bold;">Otherwise: </span><span style="color: #BB0000;">Negative</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span>   3. <span style="font-weight: bold;">Otherwise: </span><span style="color: #BB0000;">Negative</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-out co"><span class="r-pr">#&gt;</span> Unmatched rows will return <span style="color: #BB0000;">NA</span>.</span> <span class="r-out co"><span class="r-pr">#&gt;</span> Unmatched rows will return <span style="color: #BB0000;">NA</span>.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Results will be of class 'factor', with ordered levels: Negative &lt; Elderly Type A &lt; Elderly Type B</span> <span class="r-out co"><span class="r-pr">#&gt;</span> Results will be of class 'factor', with ordered levels: Negative &lt; Elderly Type A &lt; Elderly Type B</span>
@@ -237,18 +237,18 @@
<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="va">my_guideline</span></span></span> <span class="r-in"><span><span class="va">my_guideline</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> A set of custom MDRO rules:</span> <span class="r-out co"><span class="r-pr">#&gt;</span> A set of custom MDRO rules:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1. <span style="font-weight: bold;">If </span><span style="color: #0000BB;">AMX</span><span style="color: #BBBBBB;"> is </span><span style="color: #080808; background-color: #FF5F5F;"> R </span><span style="font-weight: bold;"> then: </span><span style="color: #BB0000;">Custom MDRO 1</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span>   1. <span style="font-weight: bold;">If </span><span style="color: #0000BB;">AMX</span><span style="color: #BBBBBB;"> is </span><span style="color: #080808; background-color: #FF5F5F;"> R </span><span style="font-weight: bold;"> then: </span><span style="color: #BB0000;">Custom MDRO 1</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2. <span style="font-weight: bold;">If </span><span style="color: #BBBBBB;">all of </span><span style="color: #0000BB;">cephalosporins_2nd()</span><span style="color: #BBBBBB;"> is </span><span style="color: #080808; background-color: #FF5F5F;"> R </span><span style="font-weight: bold;"> then: </span><span style="color: #BB0000;">Custom MDRO 2</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span>   2. <span style="font-weight: bold;">If </span><span style="color: #BBBBBB;">all of </span><span style="color: #0000BB;">cephalosporins_2nd()</span><span style="color: #BBBBBB;"> is </span><span style="color: #080808; background-color: #FF5F5F;"> R </span><span style="font-weight: bold;"> then: </span><span style="color: #BB0000;">Custom MDRO 2</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3. <span style="font-weight: bold;">Otherwise: </span><span style="color: #BB0000;">Negative</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span>   3. <span style="font-weight: bold;">Otherwise: </span><span style="color: #BB0000;">Negative</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-out co"><span class="r-pr">#&gt;</span> Unmatched rows will return <span style="color: #BB0000;">NA</span>.</span> <span class="r-out co"><span class="r-pr">#&gt;</span> Unmatched rows will return <span style="color: #BB0000;">NA</span>.</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-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: #0000BB;">ℹ For `cephalosporins_2nd()` using columns '</span><span style="color: #0000BB; font-weight: bold;">CXM</span><span style="color: #0000BB;">' (cefuroxime) and '</span><span style="color: #0000BB; font-weight: bold;">FOX</span><span style="color: #0000BB;">'</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="font-weight: bold;">CXM</span>' (cefuroxime) and '<span style="font-weight: bold;">FOX</span>'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> (cefoxitin)</span></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: #0000BB;">ℹ Assuming a filter on all 2 cephalosporins_2nd. Wrap around `all()` or</span></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: #0000BB;"> `any()` to prevent this note.</span></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>
<span class="r-out co"><span class="r-pr">#&gt;</span> out</span> <span class="r-out co"><span class="r-pr">#&gt;</span> out</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Negative Custom MDRO 1 Custom MDRO 2 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> Negative Custom MDRO 1 Custom MDRO 2 </span>

16
reference/custom_mdro_guideline.md
View File

@@ -473,9 +473,9 @@ x <- custom_mdro_guideline(
) )
x x
#> A set of custom MDRO rules: #> A set of custom MDRO rules:
#> 1. If CIP is R and age is higher than 60 then: Elderly Type A #>   1. If CIP is R and age is higher than 60 then: Elderly Type A
#> 2. If ERY is R and age is higher than 60 then: Elderly Type B #>   2. If ERY is R and age is higher than 60 then: Elderly Type B
#> 3. Otherwise: Negative #>   3. Otherwise: Negative
#> #>
#> Unmatched rows will return NA. #> Unmatched rows will return NA.
#> Results will be of class 'factor', with ordered levels: Negative < Elderly Type A < Elderly Type B #> Results will be of class 'factor', with ordered levels: Negative < Elderly Type A < Elderly Type B
@@ -518,9 +518,9 @@ my_guideline <- custom_mdro_guideline(
) )
my_guideline my_guideline
#> A set of custom MDRO rules: #> A set of custom MDRO rules:
#> 1. If AMX is R then: Custom MDRO 1 #>   1. If AMX is R then: Custom MDRO 1
#> 2. If all of cephalosporins_2nd() is R then: Custom MDRO 2 #>   2. If all of cephalosporins_2nd() is R then: Custom MDRO 2
#> 3. Otherwise: Negative #>   3. Otherwise: Negative
#> #>
#> Unmatched rows will return NA. #> Unmatched rows will return NA.
#> 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
@@ -528,8 +528,8 @@ my_guideline
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 #> ℹ Assuming a filter on all 2 cephalosporins_2nd. Wrap around `all()` or `any()`
#> `any()` to prevent this note. #> to prevent this note.
table(out) table(out)
#> out #> out
#> Negative Custom MDRO 1 Custom MDRO 2 #> Negative Custom MDRO 1 Custom MDRO 2

2
reference/dosage.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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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/esbl_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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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/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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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/example_isolates_unclean.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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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
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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

63
reference/first_isolate.html
View File

@@ -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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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">
@@ -210,14 +210,13 @@
<span class="r-in"><span><span class="co"># See ?example_isolates.</span></span></span> <span class="r-in"><span><span class="co"># See ?example_isolates.</span></span></span>
<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: #BB0000;">ℹ Determining first isolates using an episode length of </span><span style="color: #BB0000; 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: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">date</span><span style="color: #0000BB;">' as input for `col_date`.</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: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">patient</span><span style="color: #0000BB;">' as input for `col_patient_id`.</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;">patient</span>' as input for `col_patient_id`.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #BB0000;">ℹ Basing inclusion on all antimicrobial results, using a points threshold</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: #BB0000;"> of 2</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="font-weight: bold;">mo</span>')</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #BB0000;">ℹ Excluding 16 isolates with a microbial ID 'UNKNOWN' (in column '</span><span style="color: #BB0000; font-weight: bold;">mo</span><span style="color: #BB0000;">')</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> <span style="color: #BBBBBB;">=&gt; Found </span><span style="color: #BBBBBB; font-weight: bold;">1,387 'phenotype-based' first isolates</span><span style="color: #BBBBBB;"> (69.4% of total where a</span></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> <span style="color: #BBBBBB;"> microbial ID was available)</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> <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>
@@ -241,7 +240,8 @@
<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: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">mo</span><span style="color: #0000BB;">' as input for `mo_is_gram_negative()`</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> (`?AMR::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>
@@ -268,12 +268,11 @@
<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">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="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></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="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: #BB0000;">ℹ Determining first isolates using an episode length of </span><span style="color: #BB0000; 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: #BB0000;">ℹ Basing inclusion on all antimicrobial results, using a points threshold</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: #BB0000;"> of 2</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="font-weight: bold;">mo</span>')</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #BB0000;">ℹ Excluding 16 isolates with a microbial ID 'UNKNOWN' (in column '</span><span style="color: #BB0000; font-weight: bold;">mo</span><span style="color: #BB0000;">')</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> <span style="color: #BBBBBB;">=&gt; Found </span><span style="color: #BBBBBB; font-weight: bold;">1,387 'phenotype-based' first isolates</span><span style="color: #BBBBBB;"> (69.4% of total where a</span></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> <span style="color: #BBBBBB;"> microbial ID was available)</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> <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>
@@ -326,24 +325,20 @@
<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>first <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 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>first <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 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/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">ward</span>, <span class="va">date</span>, <span class="va">patient</span>, <span class="va">mo</span>, <span class="va">first</span><span class="op">)</span></span></span> <span class="r-in"><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">ward</span>, <span class="va">date</span>, <span class="va">patient</span>, <span class="va">mo</span>, <span class="va">first</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: #BB0000;">ℹ Determining first isolates using an episode length of </span><span style="color: #BB0000; 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: #BB0000;">ℹ Basing inclusion on all antimicrobial results, using a points threshold</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: #BB0000;"> of 2</span></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> <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: #BB0000;">Group: ward = "Clinical"</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> <span style="color: #BB0000;">ℹ Excluding 9 isolates with a microbial ID 'UNKNOWN' (in column '</span><span style="color: #BB0000; font-weight: bold;">mo</span><span style="color: #BB0000;">')</span></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> <span style="color: #BBBBBB;">=&gt; Found </span><span style="color: #BBBBBB; font-weight: bold;">865 'phenotype-based' first isolates</span><span style="color: #BBBBBB;"> (70.1% of total where a</span></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: #BBBBBB;"> microbial ID was available)</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="font-weight: bold;">mo</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> =&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> <span style="color: #BB0000;">Group: ward = "ICU"</span></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> <span style="color: #BB0000;">ℹ Excluding 6 isolates with a microbial ID 'UNKNOWN' (in column '</span><span style="color: #BB0000; font-weight: bold;">mo</span><span style="color: #BB0000;">')</span></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: #BBBBBB;">=&gt; Found </span><span style="color: #BBBBBB; font-weight: bold;">452 'phenotype-based' first isolates</span><span style="color: #BBBBBB;"> (70.0% of total where a</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="font-weight: bold;">mo</span>')</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #BBBBBB;"> microbial ID was available)</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> </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> <span style="color: #BB0000;">Group: ward = "Outpatient"</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #BB0000;">ℹ Excluding 1 isolates with a microbial ID 'UNKNOWN' (in column '</span><span style="color: #BB0000; font-weight: bold;">mo</span><span style="color: #BB0000;">')</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #BBBBBB;">=&gt; Found </span><span style="color: #BBBBBB; font-weight: bold;">99 'phenotype-based' first isolates</span><span style="color: #BBBBBB;"> (82.5% of total where a</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #BBBBBB;"> microbial ID was available)</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> <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;"># Groups: ward [3]</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: ward [3]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward date patient mo first</span> <span class="r-out co"><span class="r-pr">#&gt;</span> ward date patient mo first</span>

25
reference/first_isolate.md
View File

@@ -332,8 +332,7 @@ 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 #> ℹ Basing inclusion on all antimicrobial results, using a points threshold of 2
#> 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)
@@ -361,6 +360,7 @@ example_isolates[first_isolate(info = TRUE), ]
# 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()`
#> (`?AMR::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>
@@ -388,8 +388,7 @@ if (require("dplyr")) {
filter(first_isolate(info = TRUE)) filter(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 Basing inclusion on all antimicrobial results, using a points threshold #> ℹ Basing inclusion on all antimicrobial results, using a points threshold of 2
#> 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)
@@ -446,23 +445,19 @@ if (require("dplyr")) {
select(ward, date, patient, mo, first) select(ward, date, patient, mo, first)
} }
#> 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 #> ℹ Basing inclusion on all antimicrobial results, using a points threshold of 2
#> 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 #> => Found 865 'phenotype-based' first isolates (70.1% of total where a microbial
#> 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 #> => Found 452 'phenotype-based' first isolates (70.0% of total where a microbial
#> 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 #> => Found 99 'phenotype-based' first isolates (82.5% of total where a microbial
#> microbial ID was available) #> ID was available)
#> # A tibble: 2,000 × 5 #> # A tibble: 2,000 × 5
#> # Groups: ward [3] #> # Groups: ward [3]
#> ward date patient mo first #> ward date patient mo first

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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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/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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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/ggplot_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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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">
@@ -226,8 +226,8 @@
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> Introducing NA: only 14 results available for PEN in group: order =</span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> Introducing NA: only 14 results available for PEN in group: order =</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Enterococcus" (`minimum` = 30).</span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Enterococcus" (`minimum` = 30).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Run `dplyr::last_dplyr_warnings()` to see the 72 remaining warnings.</span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Run `dplyr::last_dplyr_warnings()` to see the 72 remaining warnings.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Columns selected for PCA: "</span><span style="color: #0000BB; font-weight: bold;">AMC</span><span style="color: #0000BB;">", "</span><span style="color: #0000BB; font-weight: bold;">CAZ</span><span style="color: #0000BB;">", "</span><span style="color: #0000BB; font-weight: bold;">CTX</span><span style="color: #0000BB;">", "</span><span style="color: #0000BB; font-weight: bold;">CXM</span><span style="color: #0000BB;">", "</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">", "</span><span style="color: #0000BB; font-weight: bold;">SXT</span><span style="color: #0000BB;">",</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Columns selected for PCA: "<span style="font-weight: bold;">AMC</span>", "<span style="font-weight: bold;">CAZ</span>", "<span style="font-weight: bold;">CTX</span>", "<span style="font-weight: bold;">CXM</span>", "<span style="font-weight: bold;">GEN</span>", "<span style="font-weight: bold;">SXT</span>", "<span style="font-weight: bold;">TMP</span>",</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> "</span><span style="color: #0000BB; font-weight: bold;">TMP</span><span style="color: #0000BB;">", and "</span><span style="color: #0000BB; font-weight: bold;">TOB</span><span style="color: #0000BB;">". Total observations available: 7.</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> and "<span style="font-weight: bold;">TOB</span>". Total observations available: 7.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Groups (n=4, named as 'order'):</span> <span class="r-out co"><span class="r-pr">#&gt;</span> Groups (n=4, named as 'order'):</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Caryophanales" "Enterobacterales" "Lactobacillales" "Pseudomonadales" </span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Caryophanales" "Enterobacterales" "Lactobacillales" "Pseudomonadales" </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>

4
reference/ggplot_pca.md
View File

@@ -217,8 +217,8 @@ if (require("dplyr")) {
#> ! Introducing NA: only 14 results available for PEN in group: order = #> ! Introducing NA: only 14 results available for PEN in group: order =
#> "Lactobacillales", genus = "Enterococcus" (`minimum` = 30). #> "Lactobacillales", genus = "Enterococcus" (`minimum` = 30).
#> ℹ Run `dplyr::last_dplyr_warnings()` to see the 72 remaining warnings. #> ℹ Run `dplyr::last_dplyr_warnings()` to see the 72 remaining warnings.
#> ℹ Columns selected for PCA: "AMC", "CAZ", "CTX", "CXM", "GEN", "SXT", #> ℹ Columns selected for PCA: "AMC", "CAZ", "CTX", "CXM", "GEN", "SXT", "TMP",
#> "TMP", and "TOB". Total observations available: 7. #> and "TOB". Total observations available: 7.
#> Groups (n=4, named as 'order'): #> Groups (n=4, named as 'order'):
#> [1] "Caryophanales" "Enterobacterales" "Lactobacillales" "Pseudomonadales" #> [1] "Caryophanales" "Enterobacterales" "Lactobacillales" "Pseudomonadales"
#> #>

5
reference/ggplot_sir.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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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 +285,8 @@
<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: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">mo</span><span style="color: #0000BB;">' as input for `mo_is_gram_negative()`</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> (`?AMR::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>

1
reference/ggplot_sir.md
View File

@@ -296,6 +296,7 @@ if (require("ggplot2") && require("dplyr")) {
) )
} }
#> ℹ Using column 'mo' as input for `mo_is_gram_negative()` #> ℹ Using column 'mo' as input for `mo_is_gram_negative()`
#> (`?AMR::mo_is_gram_negative()`)
# } # }
``` ```

14
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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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 +101,12 @@
<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> <span style="color: #0000BB;">Auto-guessing columns suitable for analysis</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 style="color: #0000BB;">...</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: #00BB00; font-weight: bold;"> OK.</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> <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">amox</span><span style="color: #0000BB;">' as input for AMX (amoxicillin).</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;">amox</span>' as input for AMX (amoxicillin).</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">tetr</span><span style="color: #0000BB;">' as input for TCY (tetracycline).</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;">tetr</span>' as input for TCY (tetracycline).</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">tetr</span><span style="color: #0000BB;">' as input for J01AA07 (tetracycline).</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;">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>

2
reference/index.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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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">

24
reference/interpretive_rules.html
View File

@@ -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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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">
@@ -228,11 +228,10 @@ 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</span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in `eucast_rules()` (`?AMR::eucast_rules()`): not all columns with</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> class 'sir'. Transform them on beforehand, with e.g.:</span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> antimicrobial results are of class <span style="color: #0000BB;">&lt;sir&gt;</span>. Transform them on beforehand, e.g.: -</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> - x %&gt;% as.sir(CXM:AMX)</span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> 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 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> - x %&gt;% mutate_if(is_sir_eligible, as.sir)</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> - x %&gt;% mutate(across(where(is_sir_eligible), as.sir))</span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><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">b</span><span class="op">)</span></span></span> <span class="r-in"><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">b</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo VAN AMX COL CAZ CXM PEN FOX</span> <span class="r-out co"><span class="r-pr">#&gt;</span> mo VAN AMX COL CAZ CXM PEN FOX</span>
@@ -246,11 +245,10 @@ 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</span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in `eucast_rules()` (`?AMR::eucast_rules()`): not all columns with</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> class 'sir'. Transform them on beforehand, with e.g.:</span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> antimicrobial results are of class <span style="color: #0000BB;">&lt;sir&gt;</span>. Transform them on beforehand, e.g.: -</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> - x %&gt;% as.sir(CXM:AMX)</span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> 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 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> - x %&gt;% mutate_if(is_sir_eligible, as.sir)</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> - x %&gt;% mutate(across(where(is_sir_eligible), as.sir))</span>
<span class="r-in"><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">c</span><span class="op">)</span></span></span> <span class="r-in"><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">c</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> row col mo_fullname old new rule rule_group</span> <span class="r-out co"><span class="r-pr">#&gt;</span> row col mo_fullname old new rule rule_group</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1 AMX Staphylococcus aureus - S Breakpoints</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 1 1 AMX Staphylococcus aureus - S Breakpoints</span>
@@ -278,8 +276,8 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<span class="r-in"><span><span class="co"># Dosage guidelines:</span></span></span> <span class="r-in"><span><span class="co"># Dosage guidelines:</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">eucast_dosage</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">"tobra"</span>, <span class="st">"genta"</span>, <span class="st">"cipro"</span><span class="op">)</span>, <span class="st">"iv"</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu">eucast_dosage</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">"tobra"</span>, <span class="st">"genta"</span>, <span class="st">"cipro"</span><span class="op">)</span>, <span class="st">"iv"</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Dosages for antimicrobial drugs, as meant for 'EUCAST Clinical Breakpoint</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Dosages for antimicrobial drugs, as meant for 'EUCAST Clinical Breakpoint</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> Tables' v15.0 (2025). </span><span style="color: #BB0000;">This note will be shown once per session.</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> Tables' v15.0 (2025). <span style="color: #BB0000;">This note will be shown once per session.</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 5</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ab name standard_dosage high_dosage eucast_version</span> <span class="r-out co"><span class="r-pr">#&gt;</span> ab name standard_dosage high_dosage eucast_version</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;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;dbl&gt;</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;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;dbl&gt;</span></span>

18
reference/interpretive_rules.md
View File

@@ -306,11 +306,10 @@ 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 #> Warning: in `eucast_rules()` (`?AMR::eucast_rules()`): not all columns with
#> class 'sir'. Transform them on beforehand, with e.g.: #> antimicrobial results are of class <sir>. Transform them on beforehand, e.g.: -
#> - x %>% as.sir(CXM:AMX) #> x %>% as.sir(CXM:AMX) - x %>% mutate_if(is_sir_eligible, as.sir) - x %>%
#> - x %>% mutate_if(is_sir_eligible, as.sir) #> mutate(across(where(is_sir_eligible), as.sir))
#> - x %>% mutate(across(where(is_sir_eligible), as.sir))
head(b) head(b)
#> mo VAN AMX COL CAZ CXM PEN FOX #> mo VAN AMX COL CAZ CXM PEN FOX
@@ -324,11 +323,10 @@ 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 #> Warning: in `eucast_rules()` (`?AMR::eucast_rules()`): not all columns with
#> class 'sir'. Transform them on beforehand, with e.g.: #> antimicrobial results are of class <sir>. Transform them on beforehand, e.g.: -
#> - x %>% as.sir(CXM:AMX) #> x %>% as.sir(CXM:AMX) - x %>% mutate_if(is_sir_eligible, as.sir) - x %>%
#> - x %>% mutate_if(is_sir_eligible, as.sir) #> mutate(across(where(is_sir_eligible), as.sir))
#> - x %>% mutate(across(where(is_sir_eligible), as.sir))
head(c) head(c)
#> row col mo_fullname old new rule rule_group #> row col mo_fullname old new rule rule_group
#> 1 1 AMX Staphylococcus aureus - S Breakpoints #> 1 1 AMX Staphylococcus aureus - S Breakpoints

2
reference/intrinsic_resistant.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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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/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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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">
@@ -154,7 +154,7 @@
<span class="r-in"><span> <span class="fu">left_join_microorganisms</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">left_join_microorganisms</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://rdrr.io/r/base/colnames.html" class="external-link">colnames</a></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/colnames.html" class="external-link">colnames</a></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: #BBBBBB;">Joining, by = "mo"</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> Joining, by = "mo"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "date" "patient" "age" </span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "date" "patient" "age" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [4] "gender" "ward" "mo" </span> <span class="r-out co"><span class="r-pr">#&gt;</span> [4] "gender" "ward" "mo" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] "PEN" "OXA" "FLC" </span> <span class="r-out co"><span class="r-pr">#&gt;</span> [7] "PEN" "OXA" "FLC" </span>

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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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/like.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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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">
@@ -133,7 +133,7 @@
<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: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">mo</span><span style="color: #0000BB;">' as input for `mo_name()`</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()` (`?AMR::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>
@@ -159,7 +159,7 @@
<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: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">mo</span><span style="color: #0000BB;">' as input for `mo_name()`</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()` (`?AMR::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>

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()` (`?AMR::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()` (`?AMR::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>

12
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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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">
@@ -210,8 +210,9 @@ 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()` (`?AMR::mdro()`): NA introduced for isolates where the available</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> percentage of antimicrobial classes was below 50% (set with</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> `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>
<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>
@@ -237,8 +238,9 @@ 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()` (`?AMR::mdro()`): NA introduced for isolates where the available</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> percentage of antimicrobial classes was below 50% (set with</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> `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>
<span class="r-out co"><span class="r-pr">#&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;ord&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span>

10
reference/mdro.md
View File

@@ -297,8 +297,9 @@ 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()` (`?AMR::mdro()`): NA introduced for isolates where the available
#> antimicrobial classes was below 50% (set with `pct_required_classes`) #> percentage of 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 ...
table(out) table(out)
@@ -324,8 +325,9 @@ 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()` (`?AMR::mdro()`): NA introduced for isolates where the available
#> antimicrobial classes was below 50% (set with `pct_required_classes`) #> percentage of antimicrobial classes was below 50% (set with
#> `pct_required_classes`)
#> # A tibble: 3 × 2 #> # A tibble: 3 × 2
#> MDRO n #> MDRO n
#> <ord> <int> #> <ord> <int>

20
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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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">
@@ -156,12 +156,12 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I R 28 16 2</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 9 I R 28 16 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J S 22 16 4</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 10 J S 22 16 4</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span></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 "amox", "cipr", "gent", and</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> and "tobr"</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> "tobr"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.52677313 0.16501937 0.34372779 -0.05155946 -0.97765805 0.26901032</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.52677313 0.16501937 0.34372779 -0.05155946 -0.97765805 0.26901032</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.30452889 -0.58337098 0.36899264 -0.36546366</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.30452889 -0.58337098 0.36899264 -0.36546366</span>
<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op">&lt;-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu"><a href="as.mic.html">is.mic</a></span><span class="op">(</span><span class="va">y</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op">&lt;-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu"><a href="as.mic.html">is.mic</a></span><span class="op">(</span><span class="va">y</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: #0000BB;">ℹ Calculating mean AMR distance based on columns "gent" and "tobr"</span></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 "gent" and "tobr"</span>
<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span> <span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance</span> <span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H I 31 &lt;=8 &lt;=1 -1.0808937</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 8 H I 31 &lt;=8 &lt;=1 -1.0808937</span>
@@ -183,8 +183,8 @@
<span class="r-in"><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="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">check_id_C</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">check_id_C</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span> <span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span></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 "amox", "cipr", "gent", and</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> and "tobr"</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> "tobr"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance check_id_C</span> <span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance check_id_C</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 C S 27 16 32 0.34372779 0.00000000</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 1 C S 27 16 32 0.34372779 0.00000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 I R 28 16 2 0.36899264 0.02526485</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 2 I R 28 16 2 0.36899264 0.02526485</span>
@@ -205,10 +205,10 @@
<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: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">mo</span><span style="color: #0000BB;">' as input for `mo_genus()`</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()` (`?AMR::mo_genus()`)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">mo</span><span style="color: #0000BB;">' as input for `mo_species()`</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_species()` (`?AMR::mo_species()`)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ For `carbapenems()` using columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem) and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns '<span style="font-weight: bold;">IPM</span>' (imipenem) and '<span style="font-weight: bold;">MEM</span>' (meropenem)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Calculating mean AMR distance based on columns "TCY", "IPM", and "MEM"</span></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>

12
reference/mean_amr_distance.md
View File

@@ -131,8 +131,8 @@ y
#> 9 I R 28 16 2 #> 9 I R 28 16 2
#> 10 J S 22 16 4 #> 10 J S 22 16 4
mean_amr_distance(y) mean_amr_distance(y)
#> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent", #> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent", and
#> and "tobr" #> "tobr"
#> [1] 0.52677313 0.16501937 0.34372779 -0.05155946 -0.97765805 0.26901032 #> [1] 0.52677313 0.16501937 0.34372779 -0.05155946 -0.97765805 0.26901032
#> [7] 0.30452889 -0.58337098 0.36899264 -0.36546366 #> [7] 0.30452889 -0.58337098 0.36899264 -0.36546366
y$amr_distance <- mean_amr_distance(y, is.mic(y)) y$amr_distance <- mean_amr_distance(y, is.mic(y))
@@ -158,8 +158,8 @@ if (require("dplyr")) {
) %>% ) %>%
arrange(check_id_C) arrange(check_id_C)
} }
#> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent", #> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent", and
#> and "tobr" #> "tobr"
#> id amox cipr gent tobr amr_distance check_id_C #> id amox cipr gent tobr amr_distance check_id_C
#> 1 C S 27 16 32 0.34372779 0.00000000 #> 1 C S 27 16 32 0.34372779 0.00000000
#> 2 I R 28 16 2 0.36899264 0.02526485 #> 2 I R 28 16 2 0.36899264 0.02526485
@@ -180,8 +180,8 @@ 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()` (`?AMR::mo_genus()`)
#> ℹ Using column 'mo' as input for `mo_species()` #> ℹ Using column 'mo' as input for `mo_species()` (`?AMR::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

2
reference/microorganisms.codes.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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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
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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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">

34
reference/mo_matching_score.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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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">
@@ -113,28 +113,28 @@
<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"><a href="as.mo.html">mo_reset_session</a></span><span class="op">(</span><span class="op">)</span></span></span> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="as.mo.html">mo_reset_session</a></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: #0000BB;">ℹ Reset 17 previously matched input values.</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Reset 17 previously matched input values.</span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu"><a href="as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mo'</span> <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mo'</span>
<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-out co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Matching scores are based on the resemblance between the input and the full</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-out co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">taxonomic name, and the pathogenicity in humans. See `?mo_matching_score`.</span></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> <span style="color: #0000BB;">Colour keys: </span><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> (`?AMR::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-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> Also matched: <span style="font-style: italic;">Enterococcus crotali</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFFF87;">0.650</span>), <span style="font-style: italic;">Escherichia coli coli</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.643</span>),</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="font-style: italic;">Escherichia coli expressing</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.611</span>), <span style="font-style: italic;">Enterobacter cowanii</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.600</span>), <span style="font-style: italic;">Enterococcus</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="font-style: italic;">columbae</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.595</span>), <span style="font-style: italic;">Enterococcus camelliae</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.591</span>), <span style="font-style: italic;">Enterococcus casseliflavus</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;">0.577</span>), <span style="font-style: italic;">Enterobacter cloacae cloacae</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.571</span>), <span style="font-style: italic;">Enterobacter cloacae</span> complex</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-out 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: #00BBBB;">ℹ</span> Only the first 10 other matches of each record are shown. Run</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> "E. coli" -&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> `print(mo_uncertainties(), n = ...)` (`?AMR::mo_uncertainties()`) to view</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Also matched: <span style="font-style: italic;">Enterococcus crotali</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFFF87;">0.650</span>), <span style="font-style: italic;">Escherichia coli coli</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> more entries, or save `mo_uncertainties()` (`?AMR::mo_uncertainties()`) to an</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.643</span>), <span style="font-style: italic;">Escherichia coli expressing</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.611</span>), <span style="font-style: italic;">Enterobacter cowanii</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> object.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.600</span>), <span style="font-style: italic;">Enterococcus columbae</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.595</span>), <span style="font-style: italic;">Enterococcus camelliae</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.591</span>),</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="font-style: italic;">Enterococcus casseliflavus</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.577</span>), <span style="font-style: italic;">Enterobacter cloacae cloacae</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.571</span>), <span style="font-style: italic;">Enterobacter cloacae</span> complex<span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.571</span>), and <span style="font-style: italic;">Enterobacter cloacae</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="font-style: italic;"> 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 style="color: #0000BB;">Only the first 10 other matches of each record are shown. Run</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">`print(mo_uncertainties(), n = ...)` to view more entries, or save</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">`mo_uncertainties()` to an object.</span></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>

24
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@@ -190,21 +190,21 @@ 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()`
#> (`?AMR::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)
#> Also matched: Enterococcus crotali (0.650), Escherichia coli coli #> Also matched: Enterococcus crotali (0.650), Escherichia coli coli (0.643),
#> (0.643), Escherichia coli expressing (0.611), Enterobacter cowanii #> Escherichia coli expressing (0.611), Enterobacter cowanii (0.600), Enterococcus
#> (0.600), Enterococcus columbae (0.595), Enterococcus camelliae (0.591), #> columbae (0.595), Enterococcus camelliae (0.591), Enterococcus casseliflavus
#> Enterococcus casseliflavus (0.577), Enterobacter cloacae cloacae #> (0.577), Enterobacter cloacae cloacae (0.571), Enterobacter cloacae complex
#> (0.571), Enterobacter cloacae complex (0.571), and Enterobacter cloacae #> (0.571), and Enterobacter cloacae dissolvens (0.565)
#> dissolvens (0.565)
#> #>
#> 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 = ...)` (`?AMR::mo_uncertainties()`) to view
#> `mo_uncertainties()` to an object. #> more entries, or save `mo_uncertainties()` (`?AMR::mo_uncertainties()`) to an
#> object.
mo_matching_score( mo_matching_score(
x = "E. coli", x = "E. coli",

20
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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="">3.0.1.9035</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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">
@@ -368,10 +368,10 @@
<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>Function `as.mo()` returned one outdated taxonomic name. Use `as.mo(...,</span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>`as.mo()` (`?AMR::as.mo()`) returned one outdated taxonomic name. Use</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> keep_synonyms = FALSE)` to clean the input to currently accepted taxonomic</span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> `keep_synonyms = FALSE` to clean the input to currently accepted taxonomic</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> names, or set the R option `AMR_keep_synonyms` to `FALSE`. This warning</span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> names, or set the R option `AMR_keep_synonyms` to `FALSE`. This warning will be</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> will be shown once per session.</span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> 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>
<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>
@@ -463,8 +463,9 @@
<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: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">mo</span><span style="color: #0000BB;">' as input for `mo_is_gram_positive()`</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: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">mo</span><span style="color: #0000BB;">' as input for `mo_genus()`</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> (`?AMR::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()` (`?AMR::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>
@@ -491,8 +492,9 @@
<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: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">mo</span><span style="color: #0000BB;">' as input for `mo_is_intrinsic_resistant()`</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: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">mo</span><span style="color: #0000BB;">' as input for `mo_genus()`</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> (`?AMR::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()` (`?AMR::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>

14
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@@ -485,10 +485,10 @@ 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: Function `as.mo()` returned one outdated taxonomic name. Use `as.mo(..., #> Warning: `as.mo()` (`?AMR::as.mo()`) returned one outdated taxonomic name. Use
#> keep_synonyms = FALSE)` to clean the input to currently accepted taxonomic #> `keep_synonyms = FALSE` to clean the input to currently accepted taxonomic
#> names, or set the R option `AMR_keep_synonyms` to `FALSE`. This warning #> names, or set the R option `AMR_keep_synonyms` to `FALSE`. This warning will be
#> will be shown once per session. #> shown once per session.
#> [1] "268707" #> [1] "268707"
@@ -581,7 +581,8 @@ if (require("dplyr")) {
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()` #> (`?AMR::mo_is_gram_positive()`)
#> ℹ Using column 'mo' as input for `mo_genus()` (`?AMR::mo_genus()`)
#> # A tibble: 18 × 2 #> # A tibble: 18 × 2
#> `mo_genus()` n #> `mo_genus()` n
#> <chr> <int> #> <chr> <int>
@@ -609,7 +610,8 @@ if (require("dplyr")) {
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()` #> (`?AMR::mo_is_intrinsic_resistant()`)
#> ℹ Using column 'mo' as input for `mo_genus()` (`?AMR::mo_genus()`)
#> # A tibble: 19 × 2 #> # A tibble: 19 × 2
#> `mo_genus()` n #> `mo_genus()` n
#> <chr> <int> #> <chr> <int>

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