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Built site for AMR@3.0.1.9036: 4171d5b
This commit is contained in:
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2
404.html
2
404.html
@@ -31,7 +31,7 @@
|
||||
|
||||
<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">
|
||||
|
||||
15
CLAUDE.html
15
CLAUDE.html
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
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@@ -73,7 +73,7 @@
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||||
<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>
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||||
<span></span>
|
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<span><span class="co"># Code coverage report</span></span>
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<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>
|
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<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>
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||||
<p>From the shell:</p>
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||||
<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>
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<span id="cb2-2"><a href="#cb2-2" tabindex="-1"></a><span class="ex">R</span> CMD check AMR</span></code></pre></div>
|
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@@ -229,11 +229,14 @@ _pkgdown.yml # pkgdown website configuration</code></pre>
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<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>
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<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>
|
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<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>
|
||||
<strong><code>DESCRIPTION</code></strong> — the <code>Version:</code> field</li>
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<ol style="list-style-type: decimal"><li><p><strong><code>DESCRIPTION</code></strong> — the <code>Version:</code> field</p></li>
|
||||
<li>
|
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<strong><code>NEWS.md</code></strong> — the top-level heading <code># AMR <version></code>
|
||||
</li>
|
||||
<p><strong><code>NEWS.md</code></strong> — <strong>only replace line 1</strong> (the <code># AMR <version></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>
|
||||
<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>
|
||||
</div>
|
||||
<div class="section level4">
|
||||
|
||||
15
CLAUDE.md
15
CLAUDE.md
@@ -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):
|
||||
|
||||
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
|
||||
back to reading the current version from `DESCRIPTION` and adding 1 to
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
|
||||
@@ -30,7 +30,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
@@ -91,7 +91,7 @@
|
||||
website update since they are based on randomly created values and the
|
||||
page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
|
||||
Markdown</a>. However, the methodology remains unchanged. This page was
|
||||
generated on 18 March 2026.</p>
|
||||
generated on 20 March 2026.</p>
|
||||
<div class="section level2">
|
||||
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
|
||||
</h2>
|
||||
@@ -147,21 +147,21 @@ make the structure of your data generally look like this:</p>
|
||||
</tr></thead>
|
||||
<tbody>
|
||||
<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">Escherichia coli</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
</tr>
|
||||
<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">Escherichia coli</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
</tr>
|
||||
<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">Escherichia coli</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>
|
||||
<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"><-</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">#> <span style="color: #0000BB;">ℹ Retrieved values from the `microorganisms.codes` data set for "ESCCOL",</span></span></span>
|
||||
<span><span class="co"><span style="color: #0000BB;">#> "KLEPNE", "STAAUR", and "STRPNE".</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #0000BB;">ℹ Microorganism translation was uncertain for four microorganisms. Run</span></span></span>
|
||||
<span><span class="co"><span style="color: #0000BB;">#> `mo_uncertainties()` to review these uncertainties, or use</span></span></span>
|
||||
<span><span class="co"><span style="color: #0000BB;">#> `add_custom_microorganisms()` to add custom entries.</span></span></span></code></pre></div>
|
||||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> Retrieved values from the `microorganisms.codes` data set for "ESCCOL",</span></span>
|
||||
<span><span class="co">#> "KLEPNE", "STAAUR", and "STRPNE".</span></span>
|
||||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> Microorganism translation was uncertain for four microorganisms. Run</span></span>
|
||||
<span><span class="co">#> `mo_uncertainties()` (`?AMR::mo_uncertainties()`) to review these</span></span>
|
||||
<span><span class="co">#> uncertainties, or use `add_custom_microorganisms()`</span></span>
|
||||
<span><span class="co">#> (`?AMR::add_custom_microorganisms()`) to add custom entries.</span></span></code></pre></div>
|
||||
<p>Apparently, there was some uncertainty about the translation to
|
||||
taxonomic codes. Let’s check this:</p>
|
||||
<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>
|
||||
<span><span class="co">#> <span style="color: #0000BB;">Matching scores are based on the resemblance between the input and the full</span></span></span>
|
||||
<span><span class="co"><span style="color: #0000BB;">#> taxonomic name, and the pathogenicity in humans. See `?mo_matching_score`.</span></span></span>
|
||||
<span><span class="co">#> <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">#> </span></span>
|
||||
<span><span class="co">#> <span style="color: #B2B2B2;">--------------------------------------------------------------------------------</span></span></span>
|
||||
<span><span class="co">#> "E. coli" -> <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">#> 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"><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>
|
||||
<span><span class="co"><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>
|
||||
<span><span class="co">#> <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"><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>
|
||||
<span><span class="co"><span style="font-style: italic;">#> 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="color: #B2B2B2;">--------------------------------------------------------------------------------</span></span></span>
|
||||
<span><span class="co">#> "K. pneumoniae" -> <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">#> 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"><span style="font-style: italic;">#> 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">#> <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"><span style="color: #0000BB;">#> (</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">#> <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"><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 style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.361</span>)</span></span>
|
||||
<span><span class="co">#> <span style="color: #B2B2B2;">--------------------------------------------------------------------------------</span></span></span>
|
||||
<span><span class="co">#> "S. aureus" -> <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">#> 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"><span style="font-style: italic;">#> 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">#> <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">#> <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">#> <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">#> <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">#> <span style="color: #B2B2B2;">--------------------------------------------------------------------------------</span></span></span>
|
||||
<span><span class="co">#> "S. pneumoniae" -> <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">#> 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"><span style="font-style: italic;">#> 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">#> <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"><span style="color: #0000BB;">#> (</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"><span style="font-style: italic;">#> 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"><span style="font-style: italic;">#> 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"><span style="font-style: italic;">#> periodonticum</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.519</span>)</span></span>
|
||||
<span><span class="co">#> </span></span>
|
||||
<span><span class="co"><span style="color: #0000BB;">#> Only the first 10 other matches of each record are shown. Run</span></span></span>
|
||||
<span><span class="co"><span style="color: #0000BB;">#> `print(mo_uncertainties(), n = ...)` to view more entries, or save</span></span></span>
|
||||
<span><span class="co"><span style="color: #0000BB;">#> `mo_uncertainties()` to an object.</span></span></span></code></pre></div>
|
||||
<span><span class="co">#> Matching scores are based on the resemblance between the input and the full</span></span>
|
||||
<span><span class="co">#> taxonomic name, and the pathogenicity in humans. See `mo_matching_score()`</span></span>
|
||||
<span><span class="co">#> (`?AMR::mo_matching_score()`).</span></span>
|
||||
<span><span class="co">#> 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">#> <span style="color: #B2B2B2;">-------------------------------------------------------------------------------</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #0000BB;">"E. coli"</span> -> <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">#> 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="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="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">#> <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;">(</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="color: #B2B2B2;">-------------------------------------------------------------------------------</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #0000BB;">"K. pneumoniae"</span> -> <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">#> 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">#> <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;">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">#> <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;">(</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">#> <span style="color: #0000BB;">(</span><span style="color: #080808; background-color: #FF5F5F;">0.361</span>)</span></span>
|
||||
<span><span class="co">#> <span style="color: #B2B2B2;">-------------------------------------------------------------------------------</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #0000BB;">"S. aureus"</span> -> <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">#> 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">#> <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="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">#> 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">#> <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">#> <span style="color: #B2B2B2;">-------------------------------------------------------------------------------</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #0000BB;">"S. pneumoniae"</span> -> <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">#> 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">#> <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">#> <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;">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">#> <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">#> 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="color: #00BBBB;">ℹ</span> Only the first 10 other matches of each record are shown. Run</span></span>
|
||||
<span><span class="co">#> `print(mo_uncertainties(), n = ...)` (`?AMR::mo_uncertainties()`) to view</span></span>
|
||||
<span><span class="co">#> more entries, or save `mo_uncertainties()` (`?AMR::mo_uncertainties()`) to an</span></span>
|
||||
<span><span class="co">#> object.</span></span></code></pre></div>
|
||||
<p>That’s all good.</p>
|
||||
</div>
|
||||
<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">
|
||||
<code class="sourceCode R"><span><span class="va">our_data</span> <span class="op"><-</span> <span class="va">our_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</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="co">#> <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">#> <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">#> <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"><span style="color: #0000BB;">#> it seems to be cefozopran (ZOP)</span></span></span>
|
||||
<span><span class="co">#> <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">#> <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">#> <span style="color: #BB0000;">ℹ Basing inclusion on all antimicrobial results, using a points threshold</span></span></span>
|
||||
<span><span class="co"><span style="color: #BB0000;">#> of 2</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #BBBBBB;">=> 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"><span style="color: #BBBBBB;">#> microbial ID was available)</span></span></span></code></pre></div>
|
||||
<span><span class="co">#> <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">#> <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">#> <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">#> seems to be cefozopran (ZOP)</span></span>
|
||||
<span><span class="co">#> <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">#> <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">#> <span style="color: #00BBBB;">ℹ</span> Basing inclusion on all antimicrobial results, using a points threshold of 2</span></span>
|
||||
<span><span class="co">#> => 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">#> microbial ID was available)</span></span></code></pre></div>
|
||||
<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
|
||||
<code>dplyr</code> package:</p>
|
||||
@@ -525,7 +522,7 @@ in:</p>
|
||||
<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">%>%</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="co">#> <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">#> <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using column '<span style="font-weight: bold;">GEN</span>' (gentamicin)</span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 2,724 × 2</span></span></span>
|
||||
<span><span class="co">#> date GEN </span></span>
|
||||
<span><span class="co">#> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><sir></span></span></span>
|
||||
@@ -543,8 +540,8 @@ in:</p>
|
||||
<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">%>%</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="co">#> <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"><span style="color: #0000BB;">#> (amoxicillin/clavulanic acid)</span></span></span>
|
||||
<span><span class="co">#> <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">#> (amoxicillin/clavulanic acid)</span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 2,724 × 3</span></span></span>
|
||||
<span><span class="co">#> bacteria AMX AMC </span></span>
|
||||
<span><span class="co">#> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></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="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</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="co">#> <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">#> <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using column '<span style="font-weight: bold;">GEN</span>' (gentamicin)</span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 981 × 9</span></span></span>
|
||||
<span><span class="co">#> patient_id hospital date bacteria AMX AMC CIP GEN first</span></span>
|
||||
<span><span class="co">#> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><lgl></span></span></span>
|
||||
@@ -598,8 +595,8 @@ in:</p>
|
||||
<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">%>%</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="co">#> <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"><span style="color: #0000BB;">#> (amoxicillin/clavulanic acid)</span></span></span>
|
||||
<span><span class="co">#> <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">#> (amoxicillin/clavulanic acid)</span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 462 × 9</span></span></span>
|
||||
<span><span class="co">#> patient_id hospital date bacteria AMX AMC CIP GEN first</span></span>
|
||||
<span><span class="co">#> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><lgl></span></span></span>
|
||||
@@ -617,8 +614,8 @@ in:</p>
|
||||
<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="co">#> <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"><span style="color: #0000BB;">#> (amoxicillin/clavulanic acid)</span></span></span>
|
||||
<span><span class="co">#> <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">#> (amoxicillin/clavulanic acid)</span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 462 × 9</span></span></span>
|
||||
<span><span class="co">#> patient_id hospital date bacteria AMX AMC CIP GEN first</span></span>
|
||||
<span><span class="co">#> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><lgl></span></span></span>
|
||||
@@ -699,9 +696,9 @@ previously mentioned antibiotic class selectors:</p>
|
||||
<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>
|
||||
<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">#> <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"><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>
|
||||
<span><span class="co">#> <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">#> <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="font-weight: bold;">AMK</span>' (amikacin), and '<span style="font-weight: bold;">KAN</span>' (kanamycin)</span></span>
|
||||
<span><span class="co">#> <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">
|
||||
<colgroup>
|
||||
<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> 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><span class="co">#> <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"><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></code></pre></div>
|
||||
<span><span class="co">#> <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="font-weight: bold;">AMK</span>' (amikacin), and '<span style="font-weight: bold;">KAN</span>' (kanamycin)</span></span></code></pre></div>
|
||||
<table class="table">
|
||||
<colgroup>
|
||||
<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>
|
||||
<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><span class="co">#> <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"><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>
|
||||
<span><span class="co">#> <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">#> <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="font-weight: bold;">AMK</span>' (amikacin), and '<span style="font-weight: bold;">KAN</span>' (kanamycin)</span></span>
|
||||
<span><span class="co">#> <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">
|
||||
<colgroup>
|
||||
<col width="10%">
|
||||
@@ -1285,10 +1282,11 @@ I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equa
|
||||
own:</p>
|
||||
<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">%>%</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">#> <span style="color: #0000BB;">ℹ `resistance()` assumes the EUCAST guideline and thus considers the 'I'</span></span></span>
|
||||
<span><span class="co"><span style="color: #0000BB;">#> category susceptible. Set the `guideline` argument or the `AMR_guideline`</span></span></span>
|
||||
<span><span class="co"><span style="color: #0000BB;">#> option to either "CLSI" or "EUCAST", see `?AMR-options`.</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #0000BB;">ℹ This message will be shown once per session.</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> `resistance()` (`?AMR::resistance()`) assumes the EUCAST guideline and thus</span></span>
|
||||
<span><span class="co">#> considers the 'I' category susceptible. Set the `guideline` argument or the</span></span>
|
||||
<span><span class="co">#> `AMR_guideline` option to either "CLSI" or "EUCAST", see AMR-options</span></span>
|
||||
<span><span class="co">#> (`?AMR::AMR-options`).</span></span>
|
||||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> This message will be shown once per session.</span></span>
|
||||
<span><span class="co">#> [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
|
||||
<code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
|
||||
|
||||
108
articles/AMR.md
108
articles/AMR.md
@@ -3,7 +3,7 @@
|
||||
**Note:** values on this page will change with every website update
|
||||
since they are based on randomly created values and the page was written
|
||||
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
|
||||
|
||||
@@ -51,9 +51,9 @@ structure of your data generally look like this:
|
||||
|
||||
| date | patient_id | mo | AMX | CIP |
|
||||
|:----------:|:----------:|:----------------:|:---:|:---:|
|
||||
| 2026-03-18 | abcd | Escherichia coli | S | S |
|
||||
| 2026-03-18 | abcd | Escherichia coli | S | R |
|
||||
| 2026-03-18 | efgh | Escherichia coli | R | S |
|
||||
| 2026-03-20 | abcd | Escherichia coli | S | S |
|
||||
| 2026-03-20 | abcd | Escherichia coli | S | R |
|
||||
| 2026-03-20 | efgh | Escherichia coli | R | S |
|
||||
|
||||
### 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",
|
||||
#> "KLEPNE", "STAAUR", and "STRPNE".
|
||||
#> ℹ Microorganism translation was uncertain for four microorganisms. Run
|
||||
#> `mo_uncertainties()` to review these uncertainties, or use
|
||||
#> `add_custom_microorganisms()` to add custom entries.
|
||||
#> `mo_uncertainties()` (`?AMR::mo_uncertainties()`) to review these
|
||||
#> uncertainties, or use `add_custom_microorganisms()`
|
||||
#> (`?AMR::add_custom_microorganisms()`) to add custom entries.
|
||||
```
|
||||
|
||||
Apparently, there was some uncertainty about the translation to
|
||||
@@ -179,46 +180,43 @@ taxonomic codes. Let’s check this:
|
||||
``` r
|
||||
mo_uncertainties()
|
||||
#> 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
|
||||
#>
|
||||
#> --------------------------------------------------------------------------------
|
||||
#> -------------------------------------------------------------------------------
|
||||
#> "E. coli" -> Escherichia coli (B_ESCHR_COLI, 0.688)
|
||||
#> Also matched: Enterococcus crotali (0.650), Escherichia coli coli
|
||||
#> (0.643), Escherichia coli expressing (0.611), Enterobacter cowanii
|
||||
#> (0.600), Enterococcus columbae (0.595), Enterococcus camelliae (0.591),
|
||||
#> Enterococcus casseliflavus (0.577), Enterobacter cloacae cloacae
|
||||
#> (0.571), Enterobacter cloacae complex (0.571), and Enterobacter cloacae
|
||||
#> dissolvens (0.565)
|
||||
#> --------------------------------------------------------------------------------
|
||||
#> Also matched: Enterococcus crotali (0.650), Escherichia coli coli (0.643),
|
||||
#> Escherichia coli expressing (0.611), Enterobacter cowanii (0.600), Enterococcus
|
||||
#> columbae (0.595), Enterococcus camelliae (0.591), Enterococcus casseliflavus
|
||||
#> (0.577), Enterobacter cloacae cloacae (0.571), Enterobacter cloacae complex
|
||||
#> (0.571), and Enterobacter cloacae dissolvens (0.565)
|
||||
#> -------------------------------------------------------------------------------
|
||||
#> "K. pneumoniae" -> Klebsiella pneumoniae (B_KLBSL_PNMN, 0.786)
|
||||
#> Also matched: Klebsiella pneumoniae complex (0.707), Klebsiella
|
||||
#> pneumoniae ozaenae (0.707), Klebsiella pneumoniae pneumoniae (0.688),
|
||||
#> Klebsiella pneumoniae rhinoscleromatis (0.658), Klebsiella pasteurii
|
||||
#> (0.500), Klebsiella planticola (0.500), Kingella potus (0.400),
|
||||
#> Kluyveromyces pseudotropicale (0.386), Kluyveromyces pseudotropicalis
|
||||
#> (0.363), and Kosakonia pseudosacchari (0.361)
|
||||
#> --------------------------------------------------------------------------------
|
||||
#> Also matched: Klebsiella pneumoniae complex (0.707), Klebsiella pneumoniae
|
||||
#> ozaenae (0.707), Klebsiella pneumoniae pneumoniae (0.688), Klebsiella
|
||||
#> pneumoniae rhinoscleromatis (0.658), Klebsiella pasteurii (0.500), Klebsiella
|
||||
#> planticola (0.500), Kingella potus (0.400), Kluyveromyces pseudotropicale
|
||||
#> (0.386), Kluyveromyces pseudotropicalis (0.363), and Kosakonia pseudosacchari
|
||||
#> (0.361)
|
||||
#> -------------------------------------------------------------------------------
|
||||
#> "S. aureus" -> Staphylococcus aureus (B_STPHY_AURS, 0.690)
|
||||
#> Also matched: Staphylococcus aureus aureus (0.643), Staphylococcus
|
||||
#> argenteus (0.625), Staphylococcus aureus anaerobius (0.625),
|
||||
#> Staphylococcus auricularis (0.615), Salmonella Aurelianis (0.595),
|
||||
#> Salmonella Aarhus (0.588), Salmonella Amounderness (0.587),
|
||||
#> Staphylococcus argensis (0.587), Streptococcus australis (0.587), and
|
||||
#> Salmonella choleraesuis arizonae (0.562)
|
||||
#> --------------------------------------------------------------------------------
|
||||
#> Also matched: Staphylococcus aureus aureus (0.643), Staphylococcus argenteus
|
||||
#> (0.625), Staphylococcus aureus anaerobius (0.625), Staphylococcus auricularis
|
||||
#> (0.615), Salmonella Aurelianis (0.595), Salmonella Aarhus (0.588), Salmonella
|
||||
#> Amounderness (0.587), Staphylococcus argensis (0.587), Streptococcus australis
|
||||
#> (0.587), and Salmonella choleraesuis arizonae (0.562)
|
||||
#> -------------------------------------------------------------------------------
|
||||
#> "S. pneumoniae" -> Streptococcus pneumoniae (B_STRPT_PNMN, 0.750)
|
||||
#> Also matched: Streptococcus pseudopneumoniae (0.700), Streptococcus
|
||||
#> phocae salmonis (0.552), Serratia proteamaculans quinovora (0.545),
|
||||
#> Streptococcus pseudoporcinus (0.536), Staphylococcus piscifermentans
|
||||
#> (0.533), Staphylococcus pseudintermedius (0.532), Serratia
|
||||
#> proteamaculans proteamaculans (0.526), Streptococcus gallolyticus
|
||||
#> pasteurianus (0.526), Salmonella Portanigra (0.524), and Streptococcus
|
||||
#> periodonticum (0.519)
|
||||
#>
|
||||
#> Only the first 10 other matches of each record are shown. Run
|
||||
#> `print(mo_uncertainties(), n = ...)` to view more entries, or save
|
||||
#> `mo_uncertainties()` to an object.
|
||||
#> Also matched: Streptococcus pseudopneumoniae (0.700), Streptococcus phocae
|
||||
#> salmonis (0.552), Serratia proteamaculans quinovora (0.545), Streptococcus
|
||||
#> pseudoporcinus (0.536), Staphylococcus piscifermentans (0.533), Staphylococcus
|
||||
#> pseudintermedius (0.532), Serratia proteamaculans proteamaculans (0.526),
|
||||
#> Streptococcus gallolyticus pasteurianus (0.526), Salmonella Portanigra (0.524),
|
||||
#> and Streptococcus 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
|
||||
#> more entries, or save `mo_uncertainties()` (`?AMR::mo_uncertainties()`) to an
|
||||
#> object.
|
||||
```
|
||||
|
||||
That’s all good.
|
||||
@@ -317,14 +315,13 @@ our_data <- our_data %>%
|
||||
mutate(first = first_isolate(info = TRUE))
|
||||
#> ℹ Determining first isolates using an episode length of 365 days
|
||||
#> ℹ Using column 'bacteria' as input for `col_mo`.
|
||||
#> ℹ Column 'first' is SIR eligible (despite only having empty values), since
|
||||
#> it seems to be cefozopran (ZOP)
|
||||
#> ℹ Column 'first' is SIR eligible (despite only having empty values), since it
|
||||
#> seems to be cefozopran (ZOP)
|
||||
#> ℹ Using column 'date' as input for `col_date`.
|
||||
#> ℹ Using column 'patient_id' as input for `col_patient_id`.
|
||||
#> ℹ Basing inclusion on all antimicrobial results, using a points threshold
|
||||
#> of 2
|
||||
#> ℹ Basing inclusion on all antimicrobial results, using a points threshold of 2
|
||||
#> => Found 2,724 'phenotype-based' first isolates (90.8% of total where a
|
||||
#> microbial ID was available)
|
||||
#> microbial ID was available)
|
||||
```
|
||||
|
||||
So only 91% is suitable for resistance analysis! We can now filter on it
|
||||
@@ -628,8 +625,8 @@ antibiotic class selectors:
|
||||
``` r
|
||||
antibiogram(example_isolates,
|
||||
antibiotics = c(aminoglycosides(), carbapenems()))
|
||||
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'
|
||||
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
|
||||
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB' (tobramycin),
|
||||
#> 'AMK' (amikacin), and 'KAN' (kanamycin)
|
||||
#> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
|
||||
```
|
||||
|
||||
@@ -667,8 +664,8 @@ antibiogram(example_isolates,
|
||||
antibiotics = aminoglycosides(),
|
||||
ab_transform = "name",
|
||||
language = "es")
|
||||
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'
|
||||
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
|
||||
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB' (tobramycin),
|
||||
#> 'AMK' (amikacin), and 'KAN' (kanamycin)
|
||||
```
|
||||
|
||||
| Patógeno | Amikacina | Gentamicina | Kanamicina | Tobramicina |
|
||||
@@ -711,8 +708,8 @@ on certain columns:
|
||||
antibiogram(example_isolates,
|
||||
antibiotics = c(aminoglycosides(), carbapenems()),
|
||||
syndromic_group = "ward")
|
||||
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'
|
||||
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
|
||||
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB' (tobramycin),
|
||||
#> 'AMK' (amikacin), and 'KAN' (kanamycin)
|
||||
#> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
|
||||
```
|
||||
|
||||
@@ -844,9 +841,10 @@ These functions can be used on their own:
|
||||
|
||||
``` r
|
||||
our_data_1st %>% resistance(AMX)
|
||||
#> ℹ `resistance()` assumes the EUCAST guideline and thus considers the 'I'
|
||||
#> category susceptible. Set the `guideline` argument or the `AMR_guideline`
|
||||
#> option to either "CLSI" or "EUCAST", see `?AMR-options`.
|
||||
#> ℹ `resistance()` (`?AMR::resistance()`) assumes the EUCAST guideline and thus
|
||||
#> considers the 'I' category susceptible. Set the `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.
|
||||
#> [1] 0.4203377
|
||||
```
|
||||
|
||||
@@ -30,7 +30,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
|
||||
@@ -30,7 +30,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
@@ -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">%>%</a></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="co">#> <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"><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>
|
||||
<span><span class="co">#> <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"><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>
|
||||
<span><span class="co"><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;">TZP</span><span style="color: #0000BB;">'</span></span></span>
|
||||
<span><span class="co"><span style="color: #0000BB;">#> (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"><span style="color: #0000BB;">#> (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"><span style="color: #0000BB;">#> '</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">#> <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="font-weight: bold;">AMK</span>' (amikacin), and '<span style="font-weight: bold;">KAN</span>' (kanamycin)</span></span>
|
||||
<span><span class="co">#> <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">#> (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">#> (amoxicillin/clavulanic acid), '<span style="font-weight: bold;">AMP</span>' (ampicillin), '<span style="font-weight: bold;">TZP</span>'</span></span>
|
||||
<span><span class="co">#> (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">#> (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="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>
|
||||
<ul>
|
||||
<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>
|
||||
<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>
|
||||
<span><span class="co">#> <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"><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>
|
||||
<span><span class="co">#> <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"><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>
|
||||
<span><span class="co"><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;">TZP</span><span style="color: #0000BB;">'</span></span></span>
|
||||
<span><span class="co"><span style="color: #0000BB;">#> (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"><span style="color: #0000BB;">#> (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"><span style="color: #0000BB;">#> '</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">#> <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="font-weight: bold;">AMK</span>' (amikacin), and '<span style="font-weight: bold;">KAN</span>' (kanamycin)</span></span>
|
||||
<span><span class="co">#> <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">#> (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">#> (amoxicillin/clavulanic acid), '<span style="font-weight: bold;">AMP</span>' (ampicillin), '<span style="font-weight: bold;">TZP</span>'</span></span>
|
||||
<span><span class="co">#> (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">#> (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="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">#> </span></span>
|
||||
<span><span class="co">#> </span></span>
|
||||
<span><span class="co">#> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">Recipe</span> <span style="color: #00BBBB;">──────────────────────────────────────────────────────────────────────</span></span></span>
|
||||
<span><span class="co">#> </span></span>
|
||||
<span><span class="co">#> ── Inputs</span></span>
|
||||
<span><span class="co">#> </span></span>
|
||||
<span><span class="co">#> </span></span>
|
||||
<span><span class="co">#> ── Inputs </span></span>
|
||||
<span><span class="co">#> </span></span>
|
||||
<span><span class="co">#> Number of variables by role</span></span>
|
||||
<span><span class="co">#> </span></span>
|
||||
<span><span class="co">#> outcome: 1</span></span>
|
||||
<span><span class="co">#> predictor: 20</span></span>
|
||||
<span><span class="co">#> </span></span>
|
||||
<span><span class="co">#> ── Training information</span></span>
|
||||
<span><span class="co">#> </span></span>
|
||||
<span><span class="co">#> </span></span>
|
||||
<span><span class="co">#> ── Training information </span></span>
|
||||
<span><span class="co">#> </span></span>
|
||||
<span><span class="co">#> Training data contained 1968 data points and no incomplete rows.</span></span>
|
||||
<span><span class="co">#> </span></span>
|
||||
<span><span class="co">#> ── Operations</span></span>
|
||||
<span><span class="co">#> </span></span>
|
||||
<span><span class="co">#> </span></span>
|
||||
<span><span class="co">#> ── Operations </span></span>
|
||||
<span><span class="co">#> </span></span>
|
||||
<span><span class="co">#> <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>
|
||||
<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> .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">%>%</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">&</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">&</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">#> <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">#> <span style="color: #0000BB;">ℹ `resistance()` assumes the EUCAST guideline and thus considers the 'I'</span></span></span>
|
||||
<span><span class="co"><span style="color: #0000BB;">#> category susceptible. Set the `guideline` argument or the `AMR_guideline`</span></span></span>
|
||||
<span><span class="co"><span style="color: #0000BB;">#> option to either "CLSI" or "EUCAST", see `?AMR-options`.</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #0000BB;">ℹ This message will be shown once per session.</span></span></span>
|
||||
<span><span class="co">#> <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">#> <span style="color: #00BBBB;">ℹ</span> `resistance()` (`?AMR::resistance()`) assumes the EUCAST guideline and thus</span></span>
|
||||
<span><span class="co">#> considers the 'I' category susceptible. Set the `guideline` argument or the</span></span>
|
||||
<span><span class="co">#> `AMR_guideline` option to either "CLSI" or "EUCAST", see AMR-options</span></span>
|
||||
<span><span class="co">#> (`?AMR::AMR-options`).</span></span>
|
||||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> This message will be shown once per session.</span></span>
|
||||
<span></span>
|
||||
<span><span class="va">data_time</span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 32 × 5</span></span></span>
|
||||
|
||||
@@ -94,8 +94,8 @@ data <- example_isolates %>%
|
||||
mo = as.factor(mo_gramstain(mo))) %>%
|
||||
# drop NAs - the ones without a Gramstain (fungi, etc.)
|
||||
drop_na()
|
||||
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'
|
||||
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
|
||||
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB' (tobramycin),
|
||||
#> 'AMK' (amikacin), and 'KAN' (kanamycin)
|
||||
#> ℹ For `betalactams()` using columns 'PEN' (benzylpenicillin), 'OXA'
|
||||
#> (oxacillin), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC'
|
||||
#> (amoxicillin/clavulanic acid), 'AMP' (ampicillin), 'TZP'
|
||||
@@ -144,8 +144,8 @@ a training set using `prep()`:
|
||||
|
||||
``` r
|
||||
prep(resistance_recipe)
|
||||
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'
|
||||
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
|
||||
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB' (tobramycin),
|
||||
#> 'AMK' (amikacin), and 'KAN' (kanamycin)
|
||||
#> ℹ For `betalactams()` using columns 'PEN' (benzylpenicillin), 'OXA'
|
||||
#> (oxacillin), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC'
|
||||
#> (amoxicillin/clavulanic acid), 'AMP' (ampicillin), 'TZP'
|
||||
@@ -153,17 +153,28 @@ prep(resistance_recipe)
|
||||
#> (cefuroxime), 'FOX' (cefoxitin), 'CTX' (cefotaxime), 'CAZ' (ceftazidime),
|
||||
#> 'CRO' (ceftriaxone), 'IPM' (imipenem), and 'MEM' (meropenem)
|
||||
#>
|
||||
#>
|
||||
#> ── Recipe ──────────────────────────────────────────────────────────────────────
|
||||
#>
|
||||
#> ── Inputs
|
||||
#>
|
||||
#>
|
||||
#> ── Inputs
|
||||
#>
|
||||
#> Number of variables by role
|
||||
#>
|
||||
#> outcome: 1
|
||||
#> predictor: 20
|
||||
#>
|
||||
#> ── Training information
|
||||
#>
|
||||
#>
|
||||
#> ── Training information
|
||||
#>
|
||||
#> Training data contained 1968 data points and no incomplete rows.
|
||||
#>
|
||||
#> ── Operations
|
||||
#>
|
||||
#>
|
||||
#> ── Operations
|
||||
#>
|
||||
#> • Correlation filter on: AMX CTX | Trained
|
||||
```
|
||||
|
||||
@@ -636,9 +647,10 @@ data_time <- example_isolates %>%
|
||||
.groups = "drop") %>%
|
||||
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 `resistance()` assumes the EUCAST guideline and thus considers the 'I'
|
||||
#> category susceptible. Set the `guideline` argument or the `AMR_guideline`
|
||||
#> option to either "CLSI" or "EUCAST", see `?AMR-options`.
|
||||
#> ℹ `resistance()` (`?AMR::resistance()`) assumes the EUCAST guideline and thus
|
||||
#> considers the 'I' category susceptible. Set the `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.
|
||||
|
||||
data_time
|
||||
|
||||
@@ -30,7 +30,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
|
||||
@@ -30,7 +30,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
@@ -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">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="co">#> <span style="color: #0000BB;">ℹ `resistance()` assumes the EUCAST guideline and thus considers the 'I'</span></span></span>
|
||||
<span><span class="co"><span style="color: #0000BB;">#> category susceptible. Set the `guideline` argument or the `AMR_guideline`</span></span></span>
|
||||
<span><span class="co"><span style="color: #0000BB;">#> option to either "CLSI" or "EUCAST", see `?AMR-options`.</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #0000BB;">ℹ This message will be shown once per session.</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> `resistance()` (`?AMR::resistance()`) assumes the EUCAST guideline and thus</span></span>
|
||||
<span><span class="co">#> considers the 'I' category susceptible. Set the `guideline` argument or the</span></span>
|
||||
<span><span class="co">#> `AMR_guideline` option to either "CLSI" or "EUCAST", see AMR-options</span></span>
|
||||
<span><span class="co">#> (`?AMR::AMR-options`).</span></span>
|
||||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> This message will be shown once per session.</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="co">#> <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>
|
||||
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="va">pca_result</span> <span class="op"><-</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">#> <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"><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></code></pre></div>
|
||||
<span><span class="co">#> <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">#> 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>
|
||||
function:</p>
|
||||
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
|
||||
|
||||
@@ -78,9 +78,10 @@ resistance_data <- example_isolates %>%
|
||||
order, genus, AMC, CXM, CTX,
|
||||
CAZ, GEN, TOB, TMP, SXT
|
||||
) # and select only relevant columns
|
||||
#> ℹ `resistance()` assumes the EUCAST guideline and thus considers the 'I'
|
||||
#> category susceptible. Set the `guideline` argument or the `AMR_guideline`
|
||||
#> option to either "CLSI" or "EUCAST", see `?AMR-options`.
|
||||
#> ℹ `resistance()` (`?AMR::resistance()`) assumes the EUCAST guideline and thus
|
||||
#> considers the 'I' category susceptible. Set the `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.
|
||||
|
||||
head(resistance_data)
|
||||
@@ -104,8 +105,8 @@ variables, so we now only need to do:
|
||||
|
||||
``` r
|
||||
pca_result <- pca(resistance_data)
|
||||
#> ℹ Columns selected for PCA: "AMC", "CAZ", "CTX", "CXM", "GEN", "SXT",
|
||||
#> "TMP", and "TOB". Total observations available: 7.
|
||||
#> ℹ Columns selected for PCA: "AMC", "CAZ", "CTX", "CXM", "GEN", "SXT", "TMP",
|
||||
#> and "TOB". Total observations available: 7.
|
||||
```
|
||||
|
||||
The result can be reviewed with the good old
|
||||
|
||||
@@ -30,7 +30,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
@@ -255,10 +255,11 @@ Longest: 40</p>
|
||||
<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="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</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">#> <span style="color: #0000BB;">ℹ `susceptibility()` assumes the EUCAST guideline and thus considers the</span></span></span>
|
||||
<span><span class="co"><span style="color: #0000BB;">#> 'I' category susceptible. Set the `guideline` argument or the</span></span></span>
|
||||
<span><span class="co"><span style="color: #0000BB;">#> `AMR_guideline` option to either "CLSI" or "EUCAST", see `?AMR-options`.</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #0000BB;">ℹ This message will be shown once per session.</span></span></span></code></pre></div>
|
||||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> `susceptibility()` (`?AMR::susceptibility()`) assumes the EUCAST guideline</span></span>
|
||||
<span><span class="co">#> and thus considers the 'I' category susceptible. Set the `guideline` argument</span></span>
|
||||
<span><span class="co">#> or the `AMR_guideline` option to either "CLSI" or "EUCAST", see AMR-options</span></span>
|
||||
<span><span class="co">#> (`?AMR::AMR-options`).</span></span>
|
||||
<span><span class="co">#> <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>Class: factor > ordered > sir (numeric)<br>
|
||||
Length: 500<br>
|
||||
|
||||
@@ -101,9 +101,10 @@ Longest: 40
|
||||
# our transformed antibiotic columns
|
||||
# amoxicillin/clavulanic acid (J01CR02) as an example
|
||||
data %>% freq(AMC_ND2)
|
||||
#> ℹ `susceptibility()` assumes the EUCAST guideline and thus considers the
|
||||
#> 'I' category susceptible. Set the `guideline` argument or the
|
||||
#> `AMR_guideline` option to either "CLSI" or "EUCAST", see `?AMR-options`.
|
||||
#> ℹ `susceptibility()` (`?AMR::susceptibility()`) assumes the EUCAST guideline
|
||||
#> and thus considers the 'I' category susceptible. Set the `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.
|
||||
```
|
||||
|
||||
|
||||
@@ -30,7 +30,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
|
||||
@@ -30,7 +30,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
@@ -80,7 +80,7 @@
|
||||
<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>
|
||||
|
||||
<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>
|
||||
<div class="d-none name"><code>datasets.Rmd</code></div>
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
|
||||
@@ -33,7 +33,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
@@ -49,9 +49,9 @@
|
||||
</div>
|
||||
|
||||
<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">
|
||||
<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>
|
||||
<code><a href="../reference/amr-tidymodels.html">step_mic_log2()</a></code> to transform <code><mic></code> columns with log2, and <code><a href="../reference/amr-tidymodels.html">step_sir_numeric()</a></code> to convert <code><sir></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>
|
||||
</ul></div>
|
||||
<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>
|
||||
<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>
|
||||
@@ -96,8 +96,9 @@
|
||||
<li>Fixed SIR and MIC coercion of combined values, e.g. <code>as.sir("<= 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>
|
||||
<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>
|
||||
<ul><li>
|
||||
<h4 id="updates-3-0-1-9036">Updates<a class="anchor" aria-label="anchor" href="#updates-3-0-1-9036"></a></h4>
|
||||
<ul><li>Extensive <code>cli</code> integration for better message handling and clickable links in messages and warnings (<a href="https://github.com/msberends/AMR/issues/191" class="external-link">#191</a>, <a href="https://github.com/msberends/AMR/issues/265" class="external-link">#265</a>)</li>
|
||||
<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>
|
||||
<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>
|
||||
|
||||
@@ -1,6 +1,6 @@
|
||||
# Changelog
|
||||
|
||||
## AMR 3.0.1.9035
|
||||
## AMR 3.0.1.9036
|
||||
|
||||
#### New
|
||||
|
||||
@@ -81,6 +81,10 @@
|
||||
|
||||
#### 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
|
||||
resistance for a *missing* base drug column from an *available*
|
||||
corresponding drug+inhibitor combination showing resistance (e.g.,
|
||||
|
||||
@@ -10,7 +10,7 @@ articles:
|
||||
PCA: PCA.html
|
||||
WHONET: WHONET.html
|
||||
WISCA: WISCA.html
|
||||
last_built: 2026-03-18T09:40Z
|
||||
last_built: 2026-03-20T16:06Z
|
||||
urls:
|
||||
reference: https://amr-for-r.org/reference
|
||||
article: https://amr-for-r.org/articles
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
|
||||
@@ -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>
|
||||
|
||||
<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">
|
||||
|
||||
@@ -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>
|
||||
|
||||
<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">
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
@@ -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> <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">#></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">#></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 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>
|
||||
@@ -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> <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">#></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">#></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-out co"><span class="r-pr">#></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>
|
||||
@@ -197,8 +197,7 @@
|
||||
<span class="r-out co"><span class="r-pr">#></span> random_column coflu ampicillin</span>
|
||||
<span class="r-out co"><span class="r-pr">#></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-msg co"><span class="r-pr">#></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">#></span> <span style="color: #0000BB;"> '</span><span style="color: #0000BB; font-weight: bold;">ampicillin</span><span style="color: #0000BB;">'</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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-out co"><span class="r-pr">#></span> coflu ampicillin</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 S R</span>
|
||||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||||
|
||||
@@ -185,8 +185,7 @@ x
|
||||
#> random_column coflu ampicillin
|
||||
#> 1 some value S R
|
||||
x[, betalactams()]
|
||||
#> ℹ For `betalactams()` using columns 'coflu' (co-fluampicil) and
|
||||
#> 'ampicillin'
|
||||
#> ℹ For `betalactams()` using columns 'coflu' (co-fluampicil) and 'ampicillin'
|
||||
#> coflu ampicillin
|
||||
#> 1 S R
|
||||
# }
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
@@ -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> <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">#></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">#></span> <span style="color: #0000BB;"> set.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></span> set.</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="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> <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">#></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">#></span> <span style="color: #0000BB;"> set.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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-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">#></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>
|
||||
@@ -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> <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">#></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">#></span> <span style="color: #0000BB;"> internal `microorganisms` data set.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></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-out co"><span class="r-pr">#></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>
|
||||
|
||||
@@ -193,8 +193,7 @@ add_custom_microorganisms(
|
||||
SPECIES = "SPECIES"
|
||||
)
|
||||
)
|
||||
#> ℹ Added Bacteroides/Parabacteroides to the internal `microorganisms` data
|
||||
#> set.
|
||||
#> ℹ Added Bacteroides/Parabacteroides to the internal `microorganisms` data set.
|
||||
mo_name("BACTEROIDES / PARABACTEROIDES")
|
||||
#> [1] "Bacteroides/Parabacteroides"
|
||||
mo_rank("BACTEROIDES / PARABACTEROIDES")
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
@@ -112,16 +112,16 @@
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="va">df</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> birth_date age age_exact age_at_y2k</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 1999-06-30 26 26.71507 0</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 1968-01-29 58 58.13151 31</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 1965-12-05 60 60.28219 34</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 1980-03-01 46 46.04658 19</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 1949-11-01 76 76.37534 50</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 1947-02-14 79 79.08767 52</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 1940-02-19 86 86.07397 59</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 1988-01-10 38 38.18356 11</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 1997-08-27 28 28.55616 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 1978-01-26 48 48.13973 21</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 1999-06-30 26 26.72055 0</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 1968-01-29 58 58.13699 31</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 1965-12-05 60 60.28767 34</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 1980-03-01 46 46.05205 19</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 1949-11-01 76 76.38082 50</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 1947-02-14 79 79.09315 52</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 1940-02-19 86 86.07945 59</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 1988-01-10 38 38.18904 11</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 1997-08-27 28 28.56164 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 1978-01-26 48 48.14521 21</span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
|
||||
|
||||
@@ -81,14 +81,14 @@ df$age_at_y2k <- age(df$birth_date, "2000-01-01")
|
||||
|
||||
df
|
||||
#> birth_date age age_exact age_at_y2k
|
||||
#> 1 1999-06-30 26 26.71507 0
|
||||
#> 2 1968-01-29 58 58.13151 31
|
||||
#> 3 1965-12-05 60 60.28219 34
|
||||
#> 4 1980-03-01 46 46.04658 19
|
||||
#> 5 1949-11-01 76 76.37534 50
|
||||
#> 6 1947-02-14 79 79.08767 52
|
||||
#> 7 1940-02-19 86 86.07397 59
|
||||
#> 8 1988-01-10 38 38.18356 11
|
||||
#> 9 1997-08-27 28 28.55616 2
|
||||
#> 10 1978-01-26 48 48.13973 21
|
||||
#> 1 1999-06-30 26 26.72055 0
|
||||
#> 2 1968-01-29 58 58.13699 31
|
||||
#> 3 1965-12-05 60 60.28767 34
|
||||
#> 4 1980-03-01 46 46.05205 19
|
||||
#> 5 1949-11-01 76 76.38082 50
|
||||
#> 6 1947-02-14 79 79.09315 52
|
||||
#> 7 1940-02-19 86 86.07945 59
|
||||
#> 8 1988-01-10 38 38.18904 11
|
||||
#> 9 1997-08-27 28 28.56164 2
|
||||
#> 10 1978-01-26 48 48.14521 21
|
||||
```
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
@@ -50,7 +50,7 @@
|
||||
</div>
|
||||
|
||||
<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 class="section level2">
|
||||
@@ -71,21 +71,21 @@
|
||||
|
||||
|
||||
<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>
|
||||
<div class="section level2">
|
||||
<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 class="section level2">
|
||||
<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>
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
|
||||
<div class="dont-index"><p><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 class="section level2">
|
||||
|
||||
@@ -1,9 +1,10 @@
|
||||
# Download and Unpack an AMR Course Repository
|
||||
|
||||
Downloads and unpacks a GitHub repository containing course materials,
|
||||
using `usethis::use_course()`. This is a convenience wrapper intended
|
||||
for use in educational settings, such as workshops or tutorials
|
||||
associated with the AMR package.
|
||||
using
|
||||
[`usethis::use_course()`](https://usethis.r-lib.org/reference/zip-utils.html).
|
||||
This is a convenience wrapper intended for use in educational settings,
|
||||
such as workshops or tutorials associated with the AMR package.
|
||||
|
||||
## 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
|
||||
|
||||
Called for its side effect. `usethis::use_course()` will prompt the user
|
||||
to choose a destination and open the extracted project. Returns
|
||||
invisibly whatever `usethis::use_course()` returns.
|
||||
Called for its side effect.
|
||||
[`usethis::use_course()`](https://usethis.r-lib.org/reference/zip-utils.html)
|
||||
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
|
||||
|
||||
This function constructs a ZIP archive URL from the provided
|
||||
`github_repo` and `branch`, then delegates to `usethis::use_course()` to
|
||||
handle the download and extraction.
|
||||
`github_repo` and `branch`, then delegates to
|
||||
[`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
|
||||
settings and is not intended for use in non-interactive or automated
|
||||
@@ -45,7 +51,7 @@ pipelines.
|
||||
|
||||
## See also
|
||||
|
||||
`usethis::use_course()`
|
||||
[`usethis::use_course()`](https://usethis.r-lib.org/reference/zip-utils.html)
|
||||
|
||||
## Examples
|
||||
|
||||
|
||||
@@ -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>
|
||||
|
||||
<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">
|
||||
@@ -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> 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-msg co"><span class="r-pr">#></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">#></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">#></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">#></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">#></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">#></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">#></span> <span style="color: #949494;"># An Antibiogram: 10 × 7</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Type: Non-WISCA with 95% CI</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></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> 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-msg co"><span class="r-pr">#></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">#></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">#></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">#></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">#></span> <span style="color: #949494;"># An Antibiogram: 2 × 5</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Type: Non-WISCA with 95% CI</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></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> 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-msg co"><span class="r-pr">#></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">#></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">#></span> <span style="color: #949494;"># An Antibiogram: 5 × 3</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Type: Non-WISCA with 95% CI</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></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> 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-msg co"><span class="r-pr">#></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">#></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">#></span> <span style="color: #949494;"># An Antibiogram: 2 × 4</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Type: Non-WISCA with 95% CI</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></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> 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-msg co"><span class="r-pr">#></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">#></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">#></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">#></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">#></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">#></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">#></span> <span style="color: #949494;"># An Antibiogram: 14 × 8</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Type: Non-WISCA with 95% CI</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></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 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"><-</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">#></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">#></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 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>
|
||||
@@ -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> 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-msg co"><span class="r-pr">#></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">#></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">#></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">#></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">#></span> <span style="color: #949494;"># An Antibiogram: 2 × 5</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Type: Non-WISCA with 95% CI</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></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> 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-msg co"><span class="r-pr">#></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">#></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 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>
|
||||
|
||||
@@ -598,8 +598,8 @@ example_isolates
|
||||
antibiogram(example_isolates,
|
||||
antimicrobials = c(aminoglycosides(), carbapenems())
|
||||
)
|
||||
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'
|
||||
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
|
||||
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB' (tobramycin),
|
||||
#> 'AMK' (amikacin), and 'KAN' (kanamycin)
|
||||
#> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
|
||||
#> # An Antibiogram: 10 × 7
|
||||
#> # Type: Non-WISCA with 95% CI
|
||||
@@ -623,8 +623,8 @@ antibiogram(example_isolates,
|
||||
ab_transform = "atc",
|
||||
mo_transform = "gramstain"
|
||||
)
|
||||
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'
|
||||
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
|
||||
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB' (tobramycin),
|
||||
#> 'AMK' (amikacin), and 'KAN' (kanamycin)
|
||||
#> # An Antibiogram: 2 × 5
|
||||
#> # Type: Non-WISCA with 95% CI
|
||||
#> Pathogen J01GB01 J01GB03 J01GB04 J01GB06
|
||||
@@ -714,8 +714,8 @@ antibiogram(example_isolates,
|
||||
antimicrobials = c(aminoglycosides(), carbapenems()),
|
||||
syndromic_group = "ward"
|
||||
)
|
||||
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'
|
||||
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
|
||||
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB' (tobramycin),
|
||||
#> 'AMK' (amikacin), and 'KAN' (kanamycin)
|
||||
#> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
|
||||
#> # An Antibiogram: 14 × 8
|
||||
#> # Type: Non-WISCA with 95% CI
|
||||
@@ -741,7 +741,7 @@ antibiogram(example_isolates,
|
||||
|
||||
# now define a data set with only E. coli
|
||||
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
|
||||
# (i.e., this table will be in Spanish on Spanish systems)
|
||||
@@ -753,8 +753,8 @@ antibiogram(ex1,
|
||||
),
|
||||
language = "es"
|
||||
)
|
||||
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'
|
||||
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
|
||||
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB' (tobramycin),
|
||||
#> 'AMK' (amikacin), and 'KAN' (kanamycin)
|
||||
#> # An Antibiogram: 2 × 5
|
||||
#> # Type: Non-WISCA with 95% CI
|
||||
#> `Grupo sindrómico` Patógeno Amikacina Gentamicina Tobramicina
|
||||
|
||||
@@ -17,7 +17,7 @@ my_data_with_all_these_columns %&gt;%
|
||||
|
||||
<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">
|
||||
@@ -296,15 +296,15 @@ my_data_with_all_these_columns %&gt;%
|
||||
<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="fu">carbapenems</span><span class="op">(</span><span class="op">)</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></span> <span style="color: #0000BB;"> (`MNC`) are not included since `only_treatable = TRUE`.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></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">#></span> <span style="color: #0000BB;"> • your_data %>% select(carbapenems())</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> • your_data %>% select(column_a, column_b, carbapenems())</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> • your_data %>% filter(any(carbapenems() == "R"))</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> • your_data[, carbapenems()]</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> • your_data[, c("column_a", "column_b", carbapenems())]</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></span> meropenem/nacubactam (`MNC`) are not included since `only_treatable = TRUE`.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> This <span style="color: #0000BB;"><ab></span> vector was retrieved using `carbapenems()`, which should normally</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> be used inside a <span style="color: #0000BB;">dplyr</span> verb or <span style="color: #0000BB;"><data.frame></span> call, e.g.:</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> • your_data <span style="color: #D7AF00;">%>%</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">#></span> • your_data <span style="color: #D7AF00;">%>%</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">#></span> • your_data <span style="color: #D7AF00;">%>%</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">#></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">#></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">#></span> Class 'ab'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] BIA DOR ETP IMR IPM MEM MEV PAN RIA RIT RZM TAN TBP</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
@@ -404,7 +404,7 @@ my_data_with_all_these_columns %&gt;%
|
||||
<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="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">#></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">#></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">#></span> <span style="color: #949494;"># A tibble: 2,000 × 2</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> IPM MEM </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span></span>
|
||||
@@ -422,8 +422,8 @@ my_data_with_all_these_columns %&gt;%
|
||||
<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="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">#></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">#></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">#></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">#></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">#></span> <span style="color: #949494;"># A tibble: 2,000 × 5</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> mo GEN TOB AMK KAN </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span></span>
|
||||
@@ -441,15 +441,14 @@ my_data_with_all_these_columns %&gt;%
|
||||
<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="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">#></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">#></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">#></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">#></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">#></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">#></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">#></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">#></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">#></span> <span style="color: #0000BB;"> (rifampicin)</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></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">#></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">#></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">#></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">#></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">#></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">#></span> (chloramphenicol), '<span style="font-weight: bold;">COL</span>' (colistin), and '<span style="font-weight: bold;">RIF</span>' (rifampicin)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2,000 × 23</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> OXA FLC AMX AMC AMP CXM KAN TMP NIT FOS LNZ CIP MFX </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span></span>
|
||||
@@ -469,7 +468,7 @@ my_data_with_all_these_columns %&gt;%
|
||||
<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="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">#></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">#></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">#></span> <span style="color: #949494;"># A tibble: 55 × 46</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span></span>
|
||||
@@ -491,7 +490,7 @@ my_data_with_all_these_columns %&gt;%
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, …</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">#></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">#></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">#></span> <span style="color: #949494;"># A tibble: 55 × 46</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span></span>
|
||||
@@ -515,8 +514,8 @@ my_data_with_all_these_columns %&gt;%
|
||||
<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="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">#></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">#></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">#></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">#></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">#></span> <span style="color: #949494;"># A tibble: 962 × 46</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span></span>
|
||||
@@ -538,8 +537,8 @@ my_data_with_all_these_columns %&gt;%
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, …</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">#></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">#></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">#></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">#></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">#></span> <span style="color: #949494;"># A tibble: 756 × 46</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span></span>
|
||||
@@ -563,9 +562,9 @@ my_data_with_all_these_columns %&gt;%
|
||||
<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="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">#></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">#></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">#></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">#></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">#></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">#></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">#></span> <span style="color: #949494;"># A tibble: 26 × 46</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span></span>
|
||||
@@ -589,11 +588,11 @@ my_data_with_all_these_columns %&gt;%
|
||||
<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="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">#></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">#></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">#></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">#></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">#></span> <span style="color: #0000BB;"> (piperacillin/tazobactam)</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></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">#></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">#></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">#></span> (piperacillin/tazobactam)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 55 × 7</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> PEN OXA FLC AMX AMC AMP TZP </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span></span>
|
||||
@@ -615,19 +614,18 @@ my_data_with_all_these_columns %&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"># 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">&</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">#></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">#></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">#></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">#></span> <span style="color: #0000BB;"> (piperacillin/tazobactam)</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></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">#></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">#></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">#></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">#></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">#></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">#></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">#></span> <span style="color: #0000BB;"> (rifampicin)</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></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">#></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">#></span> (piperacillin/tazobactam)</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></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">#></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">#></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">#></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">#></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">#></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">#></span> (chloramphenicol), '<span style="font-weight: bold;">COL</span>' (colistin), and '<span style="font-weight: bold;">RIF</span>' (rifampicin)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2,000 × 5</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> OXA FLC AMX AMC AMP </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span></span>
|
||||
@@ -647,11 +645,11 @@ my_data_with_all_these_columns %&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"># 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">></span> <span class="fl">1</span> <span class="op">&</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">#></span> <span style="color: #0000BB;">ℹ For `amr_selector(oral_ddd > 1 & 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">#></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">#></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">#></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">#></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">#></span> <span style="color: #00BBBB;">ℹ</span> For `amr_selector(oral_ddd > 1 & oral_units == "g")` using columns '<span style="font-weight: bold;">OXA</span>'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></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">#></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">#></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">#></span> <span style="color: #949494;"># A tibble: 2,000 × 13</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> OXA FLC AMX AMC AMP KAN FOS LNZ VAN ERY CLI MTR CHL </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span></span>
|
||||
@@ -691,17 +689,17 @@ my_data_with_all_these_columns %&gt;%
|
||||
<span class="r-msg co"><span class="r-pr">#></span> The following objects are masked from ‘package:AMR’:</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> %like%, like</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></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">#></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">#></span> using data.table? Then add the argument `with = FALSE`, see our examples at</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> `?amr_selector`.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></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">#></span> `amr_selector()` (`?AMR::amr_selector()`).</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'amr_selector'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></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="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="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></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">#></span> IPM MEM</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <sir> <sir></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1: <NA> <NA></span>
|
||||
@@ -720,8 +718,8 @@ my_data_with_all_these_columns %&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="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-msg co"><span class="r-pr">#></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">#></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">#></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">#></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">#></span> mo GEN TOB AMK KAN</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <mo> <sir> <sir> <sir> <sir></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1: B_ESCHR_COLI <NA> <NA> <NA> <NA></span>
|
||||
@@ -738,9 +736,9 @@ my_data_with_all_these_columns %&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="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-msg co"><span class="r-pr">#></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">#></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">#></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">#></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">#></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">#></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">#></span> IPM MEM GEN TOB AMK KAN</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <sir> <sir> <sir> <sir> <sir> <sir></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1: <NA> <NA> <NA> <NA> <NA> <NA></span>
|
||||
@@ -759,7 +757,7 @@ my_data_with_all_these_columns %&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="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-msg co"><span class="r-pr">#></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">#></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">#></span> date patient age gender ward mo PEN OXA FLC</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <Date> <char> <num> <char> <char> <mo> <sir> <sir> <sir></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1: 2002-01-19 738003 71 M Clinical B_ESCHR_COLI R <NA> <NA></span>
|
||||
@@ -828,11 +826,11 @@ my_data_with_all_these_columns %&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="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-msg co"><span class="r-pr">#></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">#></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">#></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">#></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">#></span> <span style="color: #0000BB;"> (piperacillin/tazobactam)</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></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">#></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">#></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">#></span> (piperacillin/tazobactam)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> PEN OXA FLC AMX AMC AMP TZP</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <sir> <sir> <sir> <sir> <sir> <sir> <sir></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1: R <NA> <NA> <NA> I <NA> <NA></span>
|
||||
|
||||
@@ -669,10 +669,10 @@ example_isolates
|
||||
|
||||
# you can use the selectors separately to retrieve all possible antimicrobials:
|
||||
carbapenems()
|
||||
#> ℹ in `carbapenems()`: Imipenem/EDTA (`IPE`) and meropenem/nacubactam
|
||||
#> (`MNC`) are not included since `only_treatable = TRUE`.
|
||||
#> ℹ This 'ab' vector was retrieved using `carbapenems()`, which should
|
||||
#> normally be used inside a `dplyr` verb or `data.frame` call, e.g.:
|
||||
#> ℹ in `carbapenems()` (`?AMR::carbapenems()`): Imipenem/EDTA (`IPE`) and
|
||||
#> meropenem/nacubactam (`MNC`) are not included since `only_treatable = TRUE`.
|
||||
#> ℹ This <ab> vector was retrieved using `carbapenems()`, which should normally
|
||||
#> be used inside a dplyr verb or <data.frame> call, e.g.:
|
||||
#> • your_data %>% select(carbapenems())
|
||||
#> • your_data %>% select(column_a, column_b, carbapenems())
|
||||
#> • your_data %>% filter(any(carbapenems() == "R"))
|
||||
@@ -795,8 +795,8 @@ example_isolates[, carbapenems()]
|
||||
|
||||
# select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB'
|
||||
example_isolates[, c("mo", aminoglycosides())]
|
||||
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'
|
||||
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
|
||||
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB' (tobramycin),
|
||||
#> 'AMK' (amikacin), and 'KAN' (kanamycin)
|
||||
#> # A tibble: 2,000 × 5
|
||||
#> mo GEN TOB AMK KAN
|
||||
#> <mo> <sir> <sir> <sir> <sir>
|
||||
@@ -818,11 +818,10 @@ example_isolates[, administrable_per_os()]
|
||||
#> (flucloxacillin), 'AMX' (amoxicillin), 'AMC' (amoxicillin/clavulanic acid),
|
||||
#> 'AMP' (ampicillin), 'CXM' (cefuroxime), 'KAN' (kanamycin), 'TMP'
|
||||
#> (trimethoprim), 'NIT' (nitrofurantoin), 'FOS' (fosfomycin), 'LNZ'
|
||||
#> (linezolid), 'CIP' (ciprofloxacin), 'MFX' (moxifloxacin), 'VAN'
|
||||
#> (vancomycin), 'TCY' (tetracycline), 'DOX' (doxycycline), 'ERY'
|
||||
#> (erythromycin), 'CLI' (clindamycin), 'AZM' (azithromycin), 'MTR'
|
||||
#> (metronidazole), 'CHL' (chloramphenicol), 'COL' (colistin), and 'RIF'
|
||||
#> (rifampicin)
|
||||
#> (linezolid), 'CIP' (ciprofloxacin), 'MFX' (moxifloxacin), 'VAN' (vancomycin),
|
||||
#> 'TCY' (tetracycline), 'DOX' (doxycycline), 'ERY' (erythromycin), 'CLI'
|
||||
#> (clindamycin), 'AZM' (azithromycin), 'MTR' (metronidazole), 'CHL'
|
||||
#> (chloramphenicol), 'COL' (colistin), and 'RIF' (rifampicin)
|
||||
#> # A tibble: 2,000 × 23
|
||||
#> 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>
|
||||
@@ -937,8 +936,8 @@ example_isolates[all(carbapenems()), ]
|
||||
# filter with multiple antimicrobial selectors using c()
|
||||
example_isolates[all(c(carbapenems(), aminoglycosides()) == "R"), ]
|
||||
#> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
|
||||
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'
|
||||
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
|
||||
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB' (tobramycin),
|
||||
#> 'AMK' (amikacin), and 'KAN' (kanamycin)
|
||||
#> # A tibble: 26 × 46
|
||||
#> date patient age gender ward mo PEN OXA FLC AMX
|
||||
#> <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),
|
||||
#> 'AMP' (ampicillin), 'CXM' (cefuroxime), 'KAN' (kanamycin), 'TMP'
|
||||
#> (trimethoprim), 'NIT' (nitrofurantoin), 'FOS' (fosfomycin), 'LNZ'
|
||||
#> (linezolid), 'CIP' (ciprofloxacin), 'MFX' (moxifloxacin), 'VAN'
|
||||
#> (vancomycin), 'TCY' (tetracycline), 'DOX' (doxycycline), 'ERY'
|
||||
#> (erythromycin), 'CLI' (clindamycin), 'AZM' (azithromycin), 'MTR'
|
||||
#> (metronidazole), 'CHL' (chloramphenicol), 'COL' (colistin), and 'RIF'
|
||||
#> (rifampicin)
|
||||
#> (linezolid), 'CIP' (ciprofloxacin), 'MFX' (moxifloxacin), 'VAN' (vancomycin),
|
||||
#> 'TCY' (tetracycline), 'DOX' (doxycycline), 'ERY' (erythromycin), 'CLI'
|
||||
#> (clindamycin), 'AZM' (azithromycin), 'MTR' (metronidazole), 'CHL'
|
||||
#> (chloramphenicol), 'COL' (colistin), and 'RIF' (rifampicin)
|
||||
#> # A tibble: 2,000 × 5
|
||||
#> OXA FLC AMX AMC AMP
|
||||
#> <sir> <sir> <sir> <sir> <sir>
|
||||
@@ -1067,7 +1065,7 @@ if (require("data.table")) {
|
||||
#> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
|
||||
#> 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
|
||||
#> `?amr_selector`.
|
||||
#> `amr_selector()` (`?AMR::amr_selector()`).
|
||||
#> Class 'amr_selector'
|
||||
#> [1] IPM MEM
|
||||
if (require("data.table")) {
|
||||
@@ -1093,8 +1091,8 @@ if (require("data.table")) {
|
||||
if (require("data.table")) {
|
||||
dt[, c("mo", aminoglycosides())]
|
||||
}
|
||||
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'
|
||||
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
|
||||
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB' (tobramycin),
|
||||
#> 'AMK' (amikacin), and 'KAN' (kanamycin)
|
||||
#> mo GEN TOB AMK KAN
|
||||
#> <mo> <sir> <sir> <sir> <sir>
|
||||
#> 1: B_ESCHR_COLI <NA> <NA> <NA> <NA>
|
||||
@@ -1112,8 +1110,8 @@ if (require("data.table")) {
|
||||
dt[, c(carbapenems(), aminoglycosides())]
|
||||
}
|
||||
#> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
|
||||
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'
|
||||
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
|
||||
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB' (tobramycin),
|
||||
#> 'AMK' (amikacin), and 'KAN' (kanamycin)
|
||||
#> IPM MEM GEN TOB AMK KAN
|
||||
#> <sir> <sir> <sir> <sir> <sir> <sir>
|
||||
#> 1: <NA> <NA> <NA> <NA> <NA> <NA>
|
||||
|
||||
@@ -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>
|
||||
|
||||
<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">
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
@@ -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-out co"><span class="r-pr">#></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-msg co"><span class="r-pr">#></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">#></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">#></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">#></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">#></span> [1] TRUE</span>
|
||||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||||
</code></pre></div>
|
||||
|
||||
@@ -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>
|
||||
|
||||
<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">
|
||||
@@ -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">#></span> <span style="color: #949494;"># A tibble: 4 × 18</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> datetime index method ab_given mo_given host_given input_given</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><dttm></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></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">#></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">#></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">#></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">#></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">#></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">#></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">#></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">#></span> <span style="color: #949494;"># ℹ 11 more variables: ab <ab>, mo <mo>, host <chr>, input <chr>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># outcome <sir>, notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># breakpoint_S_R <chr>, site <chr></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"># 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-msg co"><span class="r-pr">#></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">#></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">#></span> <span style="color: #0000BB;"> session.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></span> `ab_reset_session()` (`?AMR::ab_reset_session()`) to reset this. This note</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> will be shown once per session.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></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">#></span> <span style="color: #080808; background-color: #5FD7AF;"> DONE</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></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">#></span> <span style="color: #080808; background-color: #5FD7AF;">DONE</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></span> <span style="color: #00BB00;"> of the breakpoint interpretations.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></span> retrieve a logbook with all details of the breakpoint interpretations.</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> microorganism amoxicillin cipro tobra genta ERY</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 Escherichia coli S I S S R</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">%>%</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="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></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">#></span> <span class="warning">Warning: </span>There was 1 warning in `mutate()`.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> In argument: `across(...)`.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> Caused by warning:</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></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">#></span> CLSI interpretation guideline.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></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">#></span> interpretation guideline.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>There was 1 warning in `mutate()`.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> In argument: `cipro = (function (x, ...) ...`.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> Caused by warning:</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></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">#></span> CLSI interpretation guideline.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></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">#></span> interpretation guideline.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>There was 1 warning in `mutate()`.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> In argument: `across(...)`.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> Caused by warning:</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></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">#></span> CLSI interpretation guideline.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></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">#></span> interpretation guideline.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>There was 1 warning in `mutate()`.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> In argument: `mics = (function (x, ...) ...`.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> Caused by warning:</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></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">#></span> CLSI interpretation guideline.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></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">#></span> interpretation guideline.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>There was 1 warning in `mutate()`.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> In argument: `across(...)`.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> Caused by warning:</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></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">#></span> CLSI interpretation guideline.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></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">#></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">#></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">#></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">#></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">#></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">#></span> interpretation guideline.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></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">#></span> <span style="font-weight: bold;">2025</span>...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></span> <span style="font-weight: bold;">2025</span>...</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>There was 1 warning in `mutate()`.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> In argument: `cipro = (function (x, ...) ...`.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> Caused by warning:</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></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">#></span> CLSI interpretation guideline.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></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">#></span> interpretation guideline.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>There was 1 warning in `mutate()`.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> In argument: `across(...)`.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> Caused by warning:</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></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">#></span> CLSI interpretation guideline.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></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">#></span> interpretation guideline.</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> microorganism amoxicillin cipro tobra genta ERY</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 Escherichia coli 8 <NA> S S R</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></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">#></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">#></span> interpretations: "A", "B", and "C"</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></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">#></span> antimicrobial interpretations: "A", "B", and "C"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'sir'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] S SDD I R NI <NA> <NA> <NA></span>
|
||||
<span class="r-in"><span><span class="fu">as.sir</span><span class="op">(</span><span class="st">"<= 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">#></span> [1] S</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-msg co"><span class="r-pr">#></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">#></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">#></span> "I", and 3 as "R"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'sir'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></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-msg co"><span class="r-pr">#></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">#></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">#></span> "I", and 3 as "S"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'sir'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] R I S</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
|
||||
@@ -660,10 +660,10 @@ sir_interpretation_history()
|
||||
#> # A tibble: 4 × 18
|
||||
#> datetime index method ab_given mo_given host_given input_given
|
||||
#> <dttm> <int> <chr> <chr> <chr> <chr> <chr>
|
||||
#> 1 2026-03-18 09:41:20 1 MIC amoxicillin Escherich… human 8
|
||||
#> 2 2026-03-18 09:41:20 1 MIC cipro Escherich… human 0.256
|
||||
#> 3 2026-03-18 09:41:21 1 DISK tobra Escherich… human 16
|
||||
#> 4 2026-03-18 09:41:21 1 DISK genta Escherich… human 18
|
||||
#> 1 2026-03-20 16:07:38 1 MIC amoxicillin Escherich… human 8
|
||||
#> 2 2026-03-20 16:07:38 1 MIC cipro Escherich… human 0.256
|
||||
#> 3 2026-03-20 16:07:39 1 DISK tobra Escherich… human 16
|
||||
#> 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>,
|
||||
#> # outcome <sir>, notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,
|
||||
#> # breakpoint_S_R <chr>, site <chr>
|
||||
@@ -671,17 +671,16 @@ sir_interpretation_history()
|
||||
# \donttest{
|
||||
# using parallel computing, which is available in base R:
|
||||
as.sir(df_wide, parallel = TRUE, info = TRUE)
|
||||
#> ℹ Returning previously coerced values for various antimicrobials. Run
|
||||
#> `ab_reset_session()` to reset this. This note will be shown once per
|
||||
#> session.
|
||||
#> ℹ Returning a previously coerced value for an antimicrobial. Run
|
||||
#> `ab_reset_session()` (`?AMR::ab_reset_session()`) to reset this. This note
|
||||
#> will be shown once per session.
|
||||
#>
|
||||
#> Running in parallel mode using 3 out of 4 cores, on columns 'amoxicillin',
|
||||
#> 'cipro', 'tobra', 'genta', and 'ERY'...
|
||||
#> DONE
|
||||
#> DONE
|
||||
#>
|
||||
#>
|
||||
#> ℹ Run `sir_interpretation_history()` to retrieve a logbook with all details
|
||||
#> of the breakpoint interpretations.
|
||||
#> ℹ Run `sir_interpretation_history()` (`?AMR::sir_interpretation_history()`) to
|
||||
#> retrieve a logbook with all details of the breakpoint interpretations.
|
||||
#> microorganism amoxicillin cipro tobra genta ERY
|
||||
#> 1 Escherichia coli S I S S R
|
||||
|
||||
@@ -797,44 +796,43 @@ if (require("dplyr")) {
|
||||
#> Warning: There was 1 warning in `mutate()`.
|
||||
#> ℹ In argument: `across(...)`.
|
||||
#> Caused by warning:
|
||||
#> ! Some MICs were converted to the nearest higher log2 level, following the
|
||||
#> CLSI interpretation guideline.
|
||||
#> ! Some MICs were converted to the nearest higher log2 level, following the CLSI
|
||||
#> interpretation guideline.
|
||||
#> Warning: There was 1 warning in `mutate()`.
|
||||
#> ℹ In argument: `cipro = (function (x, ...) ...`.
|
||||
#> Caused by warning:
|
||||
#> ! Some MICs were converted to the nearest higher log2 level, following the
|
||||
#> CLSI interpretation guideline.
|
||||
#> ! Some MICs were converted to the nearest higher log2 level, following the CLSI
|
||||
#> interpretation guideline.
|
||||
#> Warning: There was 1 warning in `mutate()`.
|
||||
#> ℹ In argument: `across(...)`.
|
||||
#> Caused by warning:
|
||||
#> ! Some MICs were converted to the nearest higher log2 level, following the
|
||||
#> CLSI interpretation guideline.
|
||||
#> ! Some MICs were converted to the nearest higher log2 level, following the CLSI
|
||||
#> interpretation guideline.
|
||||
#> Warning: There was 1 warning in `mutate()`.
|
||||
#> ℹ In argument: `mics = (function (x, ...) ...`.
|
||||
#> Caused by warning:
|
||||
#> ! Some MICs were converted to the nearest higher log2 level, following the
|
||||
#> CLSI interpretation guideline.
|
||||
#> ! Some MICs were converted to the nearest higher log2 level, following the CLSI
|
||||
#> interpretation guideline.
|
||||
#> Warning: There was 1 warning in `mutate()`.
|
||||
#> ℹ In argument: `across(...)`.
|
||||
#> Caused by warning:
|
||||
#> ! Some MICs were converted to the nearest higher log2 level, following the
|
||||
#> CLSI interpretation guideline.
|
||||
#> Interpreting MIC values: 'antibiotic' (TESTAB, test Antibiotic), CLSI
|
||||
#> ! Some MICs were converted to the nearest higher log2 level, following the CLSI
|
||||
#> interpretation guideline.
|
||||
#> Interpreting MIC values: 'antibiotic' (TESTAB, test Antibiotic), CLSI 2025...
|
||||
#> Interpreting disk diffusion zones: 'antibiotic' (TESTAB, test Antibiotic), CLSI
|
||||
#> 2025...
|
||||
#> Interpreting disk diffusion zones: 'antibiotic' (TESTAB, test Antibiotic), CLSI
|
||||
#> 2025...
|
||||
#> 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()`.
|
||||
#> ℹ In argument: `cipro = (function (x, ...) ...`.
|
||||
#> Caused by warning:
|
||||
#> ! Some MICs were converted to the nearest higher log2 level, following the
|
||||
#> CLSI interpretation guideline.
|
||||
#> ! Some MICs were converted to the nearest higher log2 level, following the CLSI
|
||||
#> interpretation guideline.
|
||||
#> Warning: There was 1 warning in `mutate()`.
|
||||
#> ℹ In argument: `across(...)`.
|
||||
#> Caused by warning:
|
||||
#> ! Some MICs were converted to the nearest higher log2 level, following the
|
||||
#> CLSI interpretation guideline.
|
||||
#> ! Some MICs were converted to the nearest higher log2 level, following the CLSI
|
||||
#> interpretation guideline.
|
||||
#> microorganism amoxicillin cipro tobra genta ERY
|
||||
#> 1 Escherichia coli 8 <NA> S S R
|
||||
|
||||
@@ -865,8 +863,8 @@ as.sir(
|
||||
# For CLEANING existing SIR values -------------------------------------
|
||||
|
||||
as.sir(c("S", "SDD", "I", "R", "NI", "A", "B", "C"))
|
||||
#> Warning: in `as.sir()`: 3 results truncated (38%) that were invalid antimicrobial
|
||||
#> interpretations: "A", "B", and "C"
|
||||
#> Warning: in `as.sir()` (`?AMR::as.sir()`): 3 results truncated (38%) that were invalid
|
||||
#> antimicrobial interpretations: "A", "B", and "C"
|
||||
#> Class 'sir'
|
||||
#> [1] S SDD I R NI <NA> <NA> <NA>
|
||||
as.sir("<= 0.002; S") # will return "S"
|
||||
@@ -874,11 +872,13 @@ as.sir("<= 0.002; S") # will return "S"
|
||||
#> [1] S
|
||||
|
||||
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'
|
||||
#> [1] S I R
|
||||
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'
|
||||
#> [1] R I S
|
||||
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
@@ -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="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Loading required namespace: rvest</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></span> <span style="color: #0000BB;"> check</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> https://atcddd.fhi.no/atcvet/atcvet_index/?code=QG51AA03&showdescription=no.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></span> <span style="color: #0000BB;"> check</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01CA04&showdescription=no.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></span> found for ATC QG51AA03. Please check</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB; font-style: italic;"><https://atcddd.fhi.no/atcvet/atcvet_index/?code=QG51AA03&showdescription=no</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB; font-style: italic;">this WHOCC webpage></span>.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></span> found for ATC QJ01CA04. Please check</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB; font-style: italic;"><https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01CA04&showdescription=no</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB; font-style: italic;">this WHOCC webpage></span>.</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "ANTIINFECTIVES FOR SYSTEMIC USE" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [2] "ANTIBACTERIALS FOR SYSTEMIC USE" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [3] "BETA-LACTAM ANTIBACTERIALS, PENICILLINS"</span>
|
||||
|
||||
@@ -117,12 +117,14 @@ if (requireNamespace("curl") && requireNamespace("rvest") && requireNamespace("x
|
||||
atc_online_property("J01CA04", property = "groups") # search hierarchical groups of amoxicillin
|
||||
}
|
||||
#> Loading required namespace: rvest
|
||||
#> ℹ in `atc_online_property()`: no properties found for ATC QG51AA03. Please
|
||||
#> check
|
||||
#> https://atcddd.fhi.no/atcvet/atcvet_index/?code=QG51AA03&showdescription=no.
|
||||
#> ℹ in `atc_online_property()`: no properties found for ATC QJ01CA04. Please
|
||||
#> check
|
||||
#> https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01CA04&showdescription=no.
|
||||
#> ℹ in `atc_online_property()` (`?AMR::atc_online_property()`): no properties
|
||||
#> found for ATC QG51AA03. Please check
|
||||
#> <https://atcddd.fhi.no/atcvet/atcvet_index/?code=QG51AA03&showdescription=no
|
||||
#> this WHOCC webpage>.
|
||||
#> ℹ in `atc_online_property()` (`?AMR::atc_online_property()`): no properties
|
||||
#> 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"
|
||||
#> [2] "ANTIBACTERIALS FOR SYSTEMIC USE"
|
||||
#> [3] "BETA-LACTAM ANTIBACTERIALS, PENICILLINS"
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
@@ -82,10 +82,11 @@
|
||||
<div class="section level2">
|
||||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="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">#></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">#></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">#></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">#></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">#></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">#></span> considers the 'I' category susceptible. Set the `guideline` argument or the</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> `AMR_guideline` option to either "CLSI" or "EUCAST", see AMR-options</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (`?AMR::AMR-options`).</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></span> count available visual_availabilty resistant visual_resistance</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date 2000 100.0% |####################| </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> patient 2000 100.0% |####################| </span>
|
||||
|
||||
@@ -41,9 +41,10 @@ calculated with
|
||||
|
||||
``` r
|
||||
availability(example_isolates)
|
||||
#> ℹ `resistance()` assumes the EUCAST guideline and thus considers the 'I'
|
||||
#> category susceptible. Set the `guideline` argument or the `AMR_guideline`
|
||||
#> option to either "CLSI" or "EUCAST", see `?AMR-options`.
|
||||
#> ℹ `resistance()` (`?AMR::resistance()`) assumes the EUCAST guideline and thus
|
||||
#> considers the 'I' category susceptible. Set the `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.
|
||||
#> count available visual_availabilty resistant visual_resistance
|
||||
#> date 2000 100.0% |####################|
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
@@ -172,7 +172,7 @@
|
||||
<span class="r-out co"><span class="r-pr">#></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">#></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">#></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">#></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">#></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-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 39 × 12</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></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">#></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">#></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">#></span> <span style="color: #949494;"># ℹ 70 more rows</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></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 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>
|
||||
@@ -233,7 +233,7 @@
|
||||
<span class="r-out co"><span class="r-pr">#></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">#></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">#></span> <span style="color: #949494;"># ℹ 70 more rows</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></span> Use 'format()' on this result to get a publishable/printable format.</span>
|
||||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
|
||||
@@ -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>
|
||||
|
||||
<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">
|
||||
|
||||
@@ -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>
|
||||
|
||||
<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">
|
||||
@@ -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 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-msg co"><span class="r-pr">#></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">#></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">#></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">#></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">#></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">#></span> and thus considers the 'I' category susceptible. Set the `guideline` argument</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> or the `AMR_guideline` option to either "CLSI" or "EUCAST", see AMR-options</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (`?AMR::AMR-options`).</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></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">$</span><span class="va">AMX</span><span class="op">)</span> <span class="co"># counts "S" and "I"</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ `count_susceptible()` assumes the EUCAST guideline and thus considers the</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> 'I' category susceptible. Set the `guideline` argument or the</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> `AMR_guideline` option to either "CLSI" or "EUCAST", see `?AMR-options`.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ This message will be shown once per session.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> `count_susceptible()` (`?AMR::count_susceptible()`) assumes the EUCAST</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> guideline and thus considers the 'I' category susceptible. Set the</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> `guideline` argument or the `AMR_guideline` option to either "CLSI" or</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> "EUCAST", see AMR-options (`?AMR::AMR-options`).</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> This message will be shown once per session.</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 546</span>
|
||||
<span class="r-in"><span><span class="fu">count_all</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span> <span class="co"># counts "S", "I" and "R"</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></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">$</span><span class="va">AMX</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 546</span>
|
||||
<span class="r-in"><span><span class="fu"><a href="proportion.html">susceptibility</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</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-msg co"><span class="r-pr">#></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">#></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">#></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">#></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">#></span> <span style="color: #00BBBB;">ℹ</span> `susceptibility()` (`?AMR::susceptibility()`) assumes the EUCAST guideline</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> and thus considers the 'I' category susceptible. Set the `guideline` argument</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> or the `AMR_guideline` option to either "CLSI" or "EUCAST", see AMR-options</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (`?AMR::AMR-options`).</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></span> [1] 546</span>
|
||||
<span class="r-in"><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">%>%</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="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></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">#></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">#></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">#></span> <span style="color: #949494;"># A tibble: 12 × 4</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> ward antibiotic interpretation value</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><ord></span> <span style="color: #949494; font-style: italic;"><int></span></span>
|
||||
|
||||
@@ -188,15 +188,17 @@ calculate microbial resistance and susceptibility.
|
||||
|
||||
# base R ------------------------------------------------------------
|
||||
count_resistant(example_isolates$AMX) # counts "R"
|
||||
#> ℹ `count_resistant()` assumes the EUCAST guideline and thus considers the
|
||||
#> 'I' category susceptible. Set the `guideline` argument or the
|
||||
#> `AMR_guideline` option to either "CLSI" or "EUCAST", see `?AMR-options`.
|
||||
#> ℹ `count_resistant()` (`?AMR::count_resistant()`) assumes the EUCAST guideline
|
||||
#> and thus considers the 'I' category susceptible. Set the `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.
|
||||
#> [1] 804
|
||||
count_susceptible(example_isolates$AMX) # counts "S" and "I"
|
||||
#> ℹ `count_susceptible()` assumes the EUCAST guideline and thus considers the
|
||||
#> 'I' category susceptible. Set the `guideline` argument or the
|
||||
#> `AMR_guideline` option to either "CLSI" or "EUCAST", see `?AMR-options`.
|
||||
#> ℹ `count_susceptible()` (`?AMR::count_susceptible()`) assumes the EUCAST
|
||||
#> guideline and thus considers the 'I' category susceptible. Set the
|
||||
#> `guideline` argument or the `AMR_guideline` option to either "CLSI" or
|
||||
#> "EUCAST", see AMR-options (`?AMR::AMR-options`).
|
||||
#> ℹ This message will be shown once per session.
|
||||
#> [1] 546
|
||||
count_all(example_isolates$AMX) # counts "S", "I" and "R"
|
||||
@@ -227,9 +229,10 @@ n_sir(example_isolates$AMX)
|
||||
count_susceptible(example_isolates$AMX)
|
||||
#> [1] 546
|
||||
susceptibility(example_isolates$AMX) * n_sir(example_isolates$AMX)
|
||||
#> ℹ `susceptibility()` assumes the EUCAST guideline and thus considers the
|
||||
#> 'I' category susceptible. Set the `guideline` argument or the
|
||||
#> `AMR_guideline` option to either "CLSI" or "EUCAST", see `?AMR-options`.
|
||||
#> ℹ `susceptibility()` (`?AMR::susceptibility()`) assumes the EUCAST guideline
|
||||
#> and thus considers the 'I' category susceptible. Set the `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.
|
||||
#> [1] 546
|
||||
|
||||
@@ -276,8 +279,8 @@ if (require("dplyr")) {
|
||||
group_by(ward) %>%
|
||||
count_df(translate = FALSE)
|
||||
}
|
||||
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'
|
||||
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
|
||||
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB' (tobramycin),
|
||||
#> 'AMK' (amikacin), and 'KAN' (kanamycin)
|
||||
#> # A tibble: 12 × 4
|
||||
#> ward antibiotic interpretation value
|
||||
#> <chr> <chr> <ord> <int>
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
@@ -244,11 +244,7 @@
|
||||
<span class="r-out co"><span class="r-pr">#></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">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></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">#></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">#></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">#></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">#></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">#></span> (TAN), <span style="color: #0000BB;">tebipenem</span> (TBP)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></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>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
|
||||
|
||||
@@ -546,9 +546,5 @@ x2
|
||||
#> amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), ampicillin (AMP)
|
||||
#>
|
||||
#> 3. If TZP is R then set to R :
|
||||
#> 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)
|
||||
#> 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)
|
||||
```
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
@@ -192,9 +192,9 @@
|
||||
<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-out co"><span class="r-pr">#></span> A set of custom MDRO rules:</span>
|
||||
<span class="r-out co"><span class="r-pr">#></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">#></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">#></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">#></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">#></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">#></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">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Unmatched rows will return <span style="color: #BB0000;">NA</span>.</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Results will be of class 'factor', with ordered levels: Negative < Elderly Type A < 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="va">my_guideline</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> A set of custom MDRO rules:</span>
|
||||
<span class="r-out co"><span class="r-pr">#></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">#></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">#></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">#></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">#></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">#></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">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Unmatched rows will return <span style="color: #BB0000;">NA</span>.</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Results will be of class 'factor', with ordered levels: Negative < Custom MDRO 1 < Custom MDRO 2</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="va">out</span> <span class="op"><-</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">#></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">#></span> <span style="color: #0000BB;"> (cefoxitin)</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></span> <span style="color: #0000BB;"> `any()` to prevent this note.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></span> (cefoxitin)</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></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-out co"><span class="r-pr">#></span> out</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Negative Custom MDRO 1 Custom MDRO 2 </span>
|
||||
|
||||
@@ -473,9 +473,9 @@ x <- custom_mdro_guideline(
|
||||
)
|
||||
x
|
||||
#> A set of custom MDRO rules:
|
||||
#> 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
|
||||
#> 3. Otherwise: Negative
|
||||
#> 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
|
||||
#> 3. Otherwise: Negative
|
||||
#>
|
||||
#> Unmatched rows will return NA.
|
||||
#> 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
|
||||
#> A set of custom MDRO rules:
|
||||
#> 1. If AMX is R then: Custom MDRO 1
|
||||
#> 2. If all of cephalosporins_2nd() is R then: Custom MDRO 2
|
||||
#> 3. Otherwise: Negative
|
||||
#> 1. If AMX is R then: Custom MDRO 1
|
||||
#> 2. If all of cephalosporins_2nd() is R then: Custom MDRO 2
|
||||
#> 3. Otherwise: Negative
|
||||
#>
|
||||
#> Unmatched rows will return NA.
|
||||
#> 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)
|
||||
#> ℹ For `cephalosporins_2nd()` using columns 'CXM' (cefuroxime) and 'FOX'
|
||||
#> (cefoxitin)
|
||||
#> ℹ Assuming a filter on all 2 cephalosporins_2nd. Wrap around `all()` or
|
||||
#> `any()` to prevent this note.
|
||||
#> ℹ Assuming a filter on all 2 cephalosporins_2nd. Wrap around `all()` or `any()`
|
||||
#> to prevent this note.
|
||||
table(out)
|
||||
#> out
|
||||
#> Negative Custom MDRO 1 Custom MDRO 2
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
|
||||
@@ -9,7 +9,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
@@ -210,14 +210,13 @@
|
||||
<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 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">#></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">#></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">#></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">#></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">#></span> <span style="color: #BB0000;"> of 2</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></span> <span style="color: #BBBBBB;">=> 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">#></span> <span style="color: #BBBBBB;"> microbial ID was available)</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></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">#></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">#></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">#></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">#></span> => 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">#></span> microbial ID was available)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 1,387 × 46</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></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"># 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">&</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">#></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">#></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">#></span> (`?AMR::mo_is_gram_negative()`)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 441 × 46</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></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">%>%</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="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></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">#></span> <span style="color: #BB0000;"> of 2</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></span> <span style="color: #BBBBBB;">=> 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">#></span> <span style="color: #BBBBBB;"> microbial ID was available)</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></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">#></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">#></span> => 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">#></span> microbial ID was available)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 1,387 × 46</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></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">%>%</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="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></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">#></span> <span style="color: #BB0000;"> of 2</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #BB0000;">Group: ward = "Clinical"</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></span> <span style="color: #BBBBBB;">=> 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">#></span> <span style="color: #BBBBBB;"> microbial ID was available)</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #BB0000;">Group: ward = "ICU"</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></span> <span style="color: #BBBBBB;">=> 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">#></span> <span style="color: #BBBBBB;"> microbial ID was available)</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #BB0000;">Group: ward = "Outpatient"</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></span> <span style="color: #BBBBBB;">=> 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">#></span> <span style="color: #BBBBBB;"> microbial ID was available)</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></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">#></span> Group: ward = "Clinical"</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></span> => 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">#></span> ID was available)</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Group: ward = "ICU"</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></span> => 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">#></span> ID was available)</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Group: ward = "Outpatient"</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></span> => 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">#></span> ID was available)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2,000 × 5</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: ward [3]</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> ward date patient mo first</span>
|
||||
|
||||
@@ -332,11 +332,10 @@ example_isolates[first_isolate(info = TRUE), ]
|
||||
#> ℹ Determining first isolates using an episode length of 365 days
|
||||
#> ℹ Using column 'date' as input for `col_date`.
|
||||
#> ℹ Using column 'patient' as input for `col_patient_id`.
|
||||
#> ℹ Basing inclusion on all antimicrobial results, using a points threshold
|
||||
#> of 2
|
||||
#> ℹ Basing inclusion on all antimicrobial results, using a points threshold of 2
|
||||
#> ℹ Excluding 16 isolates with a microbial ID 'UNKNOWN' (in column 'mo')
|
||||
#> => Found 1,387 'phenotype-based' first isolates (69.4% of total where a
|
||||
#> microbial ID was available)
|
||||
#> microbial ID was available)
|
||||
#> # A tibble: 1,387 × 46
|
||||
#> date patient age gender ward mo PEN OXA FLC AMX
|
||||
#> <date> <chr> <dbl> <chr> <chr> <mo> <sir> <sir> <sir> <sir>
|
||||
@@ -361,6 +360,7 @@ example_isolates[first_isolate(info = TRUE), ]
|
||||
# get all first Gram-negatives
|
||||
example_isolates[which(first_isolate(info = FALSE) & mo_is_gram_negative()), ]
|
||||
#> ℹ Using column 'mo' as input for `mo_is_gram_negative()`
|
||||
#> (`?AMR::mo_is_gram_negative()`)
|
||||
#> # A tibble: 441 × 46
|
||||
#> date patient age gender ward mo PEN OXA FLC AMX
|
||||
#> <date> <chr> <dbl> <chr> <chr> <mo> <sir> <sir> <sir> <sir>
|
||||
@@ -388,11 +388,10 @@ if (require("dplyr")) {
|
||||
filter(first_isolate(info = TRUE))
|
||||
}
|
||||
#> ℹ Determining first isolates using an episode length of 365 days
|
||||
#> ℹ Basing inclusion on all antimicrobial results, using a points threshold
|
||||
#> of 2
|
||||
#> ℹ Basing inclusion on all antimicrobial results, using a points threshold of 2
|
||||
#> ℹ Excluding 16 isolates with a microbial ID 'UNKNOWN' (in column 'mo')
|
||||
#> => Found 1,387 'phenotype-based' first isolates (69.4% of total where a
|
||||
#> microbial ID was available)
|
||||
#> microbial ID was available)
|
||||
#> # A tibble: 1,387 × 46
|
||||
#> date patient age gender ward mo PEN OXA FLC AMX
|
||||
#> <date> <chr> <dbl> <chr> <chr> <mo> <sir> <sir> <sir> <sir>
|
||||
@@ -446,23 +445,19 @@ if (require("dplyr")) {
|
||||
select(ward, date, patient, mo, first)
|
||||
}
|
||||
#> ℹ Determining first isolates using an episode length of 365 days
|
||||
#> ℹ Basing inclusion on all antimicrobial results, using a points threshold
|
||||
#> of 2
|
||||
#>
|
||||
#> ℹ Basing inclusion on all antimicrobial results, using a points threshold of 2
|
||||
#> Group: ward = "Clinical"
|
||||
#> ℹ Excluding 9 isolates with a microbial ID 'UNKNOWN' (in column 'mo')
|
||||
#> => Found 865 'phenotype-based' first isolates (70.1% of total where a
|
||||
#> microbial ID was available)
|
||||
#>
|
||||
#> => Found 865 'phenotype-based' first isolates (70.1% of total where a microbial
|
||||
#> ID was available)
|
||||
#> Group: ward = "ICU"
|
||||
#> ℹ Excluding 6 isolates with a microbial ID 'UNKNOWN' (in column 'mo')
|
||||
#> => Found 452 'phenotype-based' first isolates (70.0% of total where a
|
||||
#> microbial ID was available)
|
||||
#>
|
||||
#> => Found 452 'phenotype-based' first isolates (70.0% of total where a microbial
|
||||
#> ID was available)
|
||||
#> Group: ward = "Outpatient"
|
||||
#> ℹ Excluding 1 isolates with a microbial ID 'UNKNOWN' (in column 'mo')
|
||||
#> => Found 99 'phenotype-based' first isolates (82.5% of total where a
|
||||
#> microbial ID was available)
|
||||
#> => Found 99 'phenotype-based' first isolates (82.5% of total where a microbial
|
||||
#> ID was available)
|
||||
#> # A tibble: 2,000 × 5
|
||||
#> # Groups: ward [3]
|
||||
#> ward date patient mo first
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
@@ -226,8 +226,8 @@
|
||||
<span class="r-wrn co"><span class="r-pr">#></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">#></span> "Lactobacillales", genus = "Enterococcus" (`minimum` = 30).</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></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">#></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">#></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">#></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">#></span> and "<span style="font-weight: bold;">TOB</span>". Total observations available: 7.</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Groups (n=4, named as 'order'):</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Caryophanales" "Enterobacterales" "Lactobacillales" "Pseudomonadales" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
|
||||
@@ -217,8 +217,8 @@ if (require("dplyr")) {
|
||||
#> ! Introducing NA: only 14 results available for PEN in group: order =
|
||||
#> "Lactobacillales", genus = "Enterococcus" (`minimum` = 30).
|
||||
#> ℹ Run `dplyr::last_dplyr_warnings()` to see the 72 remaining warnings.
|
||||
#> ℹ Columns selected for PCA: "AMC", "CAZ", "CTX", "CXM", "GEN", "SXT",
|
||||
#> "TMP", and "TOB". Total observations available: 7.
|
||||
#> ℹ Columns selected for PCA: "AMC", "CAZ", "CTX", "CXM", "GEN", "SXT", "TMP",
|
||||
#> and "TOB". Total observations available: 7.
|
||||
#> Groups (n=4, named as 'order'):
|
||||
#> [1] "Caryophanales" "Enterobacterales" "Lactobacillales" "Pseudomonadales"
|
||||
#>
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
@@ -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> <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">#></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">#></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">#></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-in"><span><span class="co"># }</span></span></span>
|
||||
</code></pre></div>
|
||||
|
||||
@@ -296,6 +296,7 @@ if (require("ggplot2") && require("dplyr")) {
|
||||
)
|
||||
}
|
||||
#> ℹ Using column 'mo' as input for `mo_is_gram_negative()`
|
||||
#> (`?AMR::mo_is_gram_negative()`)
|
||||
|
||||
# }
|
||||
```
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
@@ -101,12 +101,12 @@
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "tetr"</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-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">Auto-guessing columns suitable for analysis</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">...</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00; font-weight: bold;"> OK.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></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">#></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">#></span> Auto-guessing columns suitable for analysis</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></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">#></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">#></span> [1] "tetr"</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># WHONET codes</span></span></span>
|
||||
|
||||
@@ -63,7 +63,7 @@ guess_ab_col(df, "J01AA07") # ATC code of tetracycline
|
||||
guess_ab_col(df, "J01AA07", verbose = TRUE)
|
||||
#> Auto-guessing columns suitable for analysis
|
||||
#> ...
|
||||
#> OK.
|
||||
#> OK.
|
||||
#> ℹ Using column 'amox' as input for AMX (amoxicillin).
|
||||
#> ℹ Using column 'tetr' as input for TCY (tetracycline).
|
||||
#> ℹ Using column 'tetr' as input for J01AA07 (tetracycline).
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
|
||||
@@ -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>
|
||||
|
||||
<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">
|
||||
@@ -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 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"><-</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">#></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">#></span> class 'sir'. Transform them on beforehand, with e.g.:</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> - x %>% as.sir(CXM:AMX)</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> - x %>% mutate_if(is_sir_eligible, as.sir)</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> - x %>% mutate(across(where(is_sir_eligible), as.sir))</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></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">#></span> antimicrobial results are of class <span style="color: #0000BB;"><sir></span>. Transform them on beforehand, e.g.: -</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> x <span style="color: #D7AF00;">%>%</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;">%>%</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;">%>%</span></span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></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-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-out co"><span class="r-pr">#></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"># containing all details about the transformations:</span></span></span>
|
||||
<span class="r-in"><span><span class="va">c</span> <span class="op"><-</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">#></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">#></span> class 'sir'. Transform them on beforehand, with e.g.:</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> - x %>% as.sir(CXM:AMX)</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> - x %>% mutate_if(is_sir_eligible, as.sir)</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> - x %>% mutate(across(where(is_sir_eligible), as.sir))</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></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">#></span> antimicrobial results are of class <span style="color: #0000BB;"><sir></span>. Transform them on beforehand, e.g.: -</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> x <span style="color: #D7AF00;">%>%</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;">%>%</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;">%>%</span></span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></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-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">#></span> row col mo_fullname old new rule rule_group</span>
|
||||
<span class="r-out co"><span class="r-pr">#></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></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">#></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">#></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">#></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">#></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">#></span> <span style="color: #949494;"># A tibble: 3 × 5</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> ab name standard_dosage high_dosage eucast_version</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><ab></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span></span>
|
||||
|
||||
@@ -306,11 +306,10 @@ head(a)
|
||||
|
||||
# apply EUCAST rules: some results wil be changed
|
||||
b <- eucast_rules(a, overwrite = TRUE)
|
||||
#> Warning: in `eucast_rules()`: not all columns with antimicrobial results are of
|
||||
#> class 'sir'. Transform them on beforehand, with e.g.:
|
||||
#> - x %>% as.sir(CXM:AMX)
|
||||
#> - x %>% mutate_if(is_sir_eligible, as.sir)
|
||||
#> - x %>% mutate(across(where(is_sir_eligible), as.sir))
|
||||
#> Warning: in `eucast_rules()` (`?AMR::eucast_rules()`): not all columns with
|
||||
#> antimicrobial results are of class <sir>. Transform them on beforehand, e.g.: -
|
||||
#> x %>% as.sir(CXM:AMX) - x %>% mutate_if(is_sir_eligible, as.sir) - x %>%
|
||||
#> mutate(across(where(is_sir_eligible), as.sir))
|
||||
|
||||
head(b)
|
||||
#> 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
|
||||
# containing all details about the transformations:
|
||||
c <- eucast_rules(a, overwrite = TRUE, verbose = TRUE)
|
||||
#> Warning: in `eucast_rules()`: not all columns with antimicrobial results are of
|
||||
#> class 'sir'. Transform them on beforehand, with e.g.:
|
||||
#> - x %>% as.sir(CXM:AMX)
|
||||
#> - x %>% mutate_if(is_sir_eligible, as.sir)
|
||||
#> - x %>% mutate(across(where(is_sir_eligible), as.sir))
|
||||
#> Warning: in `eucast_rules()` (`?AMR::eucast_rules()`): not all columns with
|
||||
#> antimicrobial results are of class <sir>. Transform them on beforehand, e.g.: -
|
||||
#> x %>% as.sir(CXM:AMX) - x %>% mutate_if(is_sir_eligible, as.sir) - x %>%
|
||||
#> mutate(across(where(is_sir_eligible), as.sir))
|
||||
head(c)
|
||||
#> row col mo_fullname old new rule rule_group
|
||||
#> 1 1 AMX Staphylococcus aureus - S Breakpoints
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
@@ -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">%>%</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="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #BBBBBB;">Joining, by = "mo"</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Joining, by = "mo"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "date" "patient" "age" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [4] "gender" "ward" "mo" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] "PEN" "OXA" "FLC" </span>
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
@@ -133,7 +133,7 @@
|
||||
<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="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">#></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">#></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">#></span> <span style="color: #949494;"># A tibble: 106 × 46</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></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">%>%</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="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></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">#></span> <span style="color: #949494;"># A tibble: 106 × 46</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span></span>
|
||||
|
||||
@@ -114,7 +114,7 @@ a %like% b[1]
|
||||
# \donttest{
|
||||
# get isolates whose name start with 'Entero' (case-insensitive)
|
||||
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
|
||||
#> date patient age gender ward mo PEN OXA FLC AMX
|
||||
#> <date> <chr> <dbl> <chr> <chr> <mo> <sir> <sir> <sir> <sir>
|
||||
@@ -140,7 +140,7 @@ if (require("dplyr")) {
|
||||
example_isolates %>%
|
||||
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
|
||||
#> date patient age gender ward mo PEN OXA FLC AMX
|
||||
#> <date> <chr> <dbl> <chr> <chr> <mo> <sir> <sir> <sir> <sir>
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
@@ -210,8 +210,9 @@ Ordered <a href="https://rdrr.io/pkg/data.table/man/fctr.html" class="external-l
|
||||
<div class="section level2">
|
||||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">out</span> <span class="op"><-</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">#></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">#></span> antimicrobial classes was below 50% (set with `pct_required_classes`)</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></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">#></span> percentage of antimicrobial classes was below 50% (set with</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></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-out co"><span class="r-pr">#></span> Ord.factor w/ 4 levels "Negative"<"Multi-drug-resistant (MDR)"<..: 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>
|
||||
@@ -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">#></span> <span class="warning">Warning: </span>There was 1 warning in `mutate()`.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> In argument: `MDRO = mdro()`.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> Caused by warning:</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></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">#></span> antimicrobial classes was below 50% (set with `pct_required_classes`)</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></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">#></span> percentage of antimicrobial classes was below 50% (set with</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> `pct_required_classes`)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 3 × 2</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> MDRO n</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><ord></span> <span style="color: #949494; font-style: italic;"><int></span></span>
|
||||
|
||||
@@ -297,8 +297,9 @@ susceptible isolates.
|
||||
|
||||
``` r
|
||||
out <- mdro(example_isolates)
|
||||
#> Warning: in `mdro()`: NA introduced for isolates where the available percentage of
|
||||
#> antimicrobial classes was below 50% (set with `pct_required_classes`)
|
||||
#> Warning: in `mdro()` (`?AMR::mdro()`): NA introduced for isolates where the available
|
||||
#> percentage of antimicrobial classes was below 50% (set with
|
||||
#> `pct_required_classes`)
|
||||
str(out)
|
||||
#> Ord.factor w/ 4 levels "Negative"<"Multi-drug-resistant (MDR)"<..: NA NA 1 1 1 1 NA NA 1 1 ...
|
||||
table(out)
|
||||
@@ -324,8 +325,9 @@ if (require("dplyr")) {
|
||||
#> Warning: There was 1 warning in `mutate()`.
|
||||
#> ℹ In argument: `MDRO = mdro()`.
|
||||
#> Caused by warning:
|
||||
#> ! in `mdro()`: NA introduced for isolates where the available percentage of
|
||||
#> antimicrobial classes was below 50% (set with `pct_required_classes`)
|
||||
#> ! in `mdro()` (`?AMR::mdro()`): NA introduced for isolates where the available
|
||||
#> percentage of antimicrobial classes was below 50% (set with
|
||||
#> `pct_required_classes`)
|
||||
#> # A tibble: 3 × 2
|
||||
#> MDRO n
|
||||
#> <ord> <int>
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
@@ -156,12 +156,12 @@
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I R 28 16 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></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-msg co"><span class="r-pr">#></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">#></span> <span style="color: #0000BB;"> and "tobr"</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></span> "tobr"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.52677313 0.16501937 0.34372779 -0.05155946 -0.97765805 0.26901032</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.30452889 -0.58337098 0.36899264 -0.36546366</span>
|
||||
<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op"><-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu"><a href="as.mic.html">is.mic</a></span><span class="op">(</span><span class="va">y</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ Calculating mean AMR distance based on columns "gent" and "tobr"</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> Calculating mean AMR distance based on columns "gent" and "tobr"</span>
|
||||
<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr amr_distance</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H I 31 <=8 <=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">%>%</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="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></span> <span style="color: #0000BB;"> and "tobr"</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></span> "tobr"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr amr_distance check_id_C</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 C S 27 16 32 0.34372779 0.00000000</span>
|
||||
<span class="r-out co"><span class="r-pr">#></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">%>%</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="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></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">#></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">#></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">#></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">#></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">#></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">#></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">#></span> <span style="color: #949494;"># A tibble: 63 × 5</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: mo [4]</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> mo TCY IPM MEM dist</span>
|
||||
|
||||
@@ -131,8 +131,8 @@ y
|
||||
#> 9 I R 28 16 2
|
||||
#> 10 J S 22 16 4
|
||||
mean_amr_distance(y)
|
||||
#> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",
|
||||
#> and "tobr"
|
||||
#> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent", and
|
||||
#> "tobr"
|
||||
#> [1] 0.52677313 0.16501937 0.34372779 -0.05155946 -0.97765805 0.26901032
|
||||
#> [7] 0.30452889 -0.58337098 0.36899264 -0.36546366
|
||||
y$amr_distance <- mean_amr_distance(y, is.mic(y))
|
||||
@@ -158,8 +158,8 @@ if (require("dplyr")) {
|
||||
) %>%
|
||||
arrange(check_id_C)
|
||||
}
|
||||
#> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",
|
||||
#> and "tobr"
|
||||
#> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent", and
|
||||
#> "tobr"
|
||||
#> id amox cipr gent tobr amr_distance check_id_C
|
||||
#> 1 C S 27 16 32 0.34372779 0.00000000
|
||||
#> 2 I R 28 16 2 0.36899264 0.02526485
|
||||
@@ -180,8 +180,8 @@ if (require("dplyr")) {
|
||||
mutate(dist = mean_amr_distance(.)) %>%
|
||||
arrange(mo, dist)
|
||||
}
|
||||
#> ℹ Using column 'mo' as input for `mo_genus()`
|
||||
#> ℹ Using column 'mo' as input for `mo_species()`
|
||||
#> ℹ Using column 'mo' as input for `mo_genus()` (`?AMR::mo_genus()`)
|
||||
#> ℹ Using column 'mo' as input for `mo_species()` (`?AMR::mo_species()`)
|
||||
#> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
|
||||
#> ℹ Calculating mean AMR distance based on columns "TCY", "IPM", and "MEM"
|
||||
#> # A tibble: 63 × 5
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
|
||||
@@ -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>
|
||||
|
||||
<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">
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
@@ -113,28 +113,28 @@
|
||||
<div class="section level2">
|
||||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="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">#></span> <span style="color: #0000BB;">ℹ Reset 17 previously matched input values.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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 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">#></span> Class 'mo'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></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-out co"><span class="r-pr">#></span> <span style="color: #0000BB;">Matching scores are based on the resemblance between the input and the full</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #0000BB;">taxonomic name, and the pathogenicity in humans. See `?mo_matching_score`.</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></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">#></span> Matching scores are based on the resemblance between the input and the full</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> taxonomic name, and the pathogenicity in humans. See `mo_matching_score()`</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (`?AMR::mo_matching_score()`).</span>
|
||||
<span class="r-out co"><span class="r-pr">#></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">#></span> <span style="color: #B2B2B2;">-------------------------------------------------------------------------------</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">"E. coli"</span> -> <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">#></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">#></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">#></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">#></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">#></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">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #B2B2B2;">--------------------------------------------------------------------------------</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> "E. coli" -> <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-out co"><span class="r-pr">#></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-out co"><span class="r-pr">#></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-out co"><span class="r-pr">#></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">#></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">#></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">#></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">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></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">#></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">#></span> <span style="color: #0000BB;">`mo_uncertainties()` to an object.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> Only the first 10 other matches of each record are shown. Run</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> `print(mo_uncertainties(), n = ...)` (`?AMR::mo_uncertainties()`) to view</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> more entries, or save `mo_uncertainties()` (`?AMR::mo_uncertainties()`) to an</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> object.</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> x <span class="op">=</span> <span class="st">"E. coli"</span>,</span></span>
|
||||
|
||||
@@ -190,21 +190,21 @@ as.mo("E. coli")
|
||||
#> [1] B_ESCHR_COLI
|
||||
mo_uncertainties()
|
||||
#> 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
|
||||
#>
|
||||
#> --------------------------------------------------------------------------------
|
||||
#> -------------------------------------------------------------------------------
|
||||
#> "E. coli" -> Escherichia coli (B_ESCHR_COLI, 0.688)
|
||||
#> Also matched: Enterococcus crotali (0.650), Escherichia coli coli
|
||||
#> (0.643), Escherichia coli expressing (0.611), Enterobacter cowanii
|
||||
#> (0.600), Enterococcus columbae (0.595), Enterococcus camelliae (0.591),
|
||||
#> Enterococcus casseliflavus (0.577), Enterobacter cloacae cloacae
|
||||
#> (0.571), Enterobacter cloacae complex (0.571), and Enterobacter cloacae
|
||||
#> dissolvens (0.565)
|
||||
#> Also matched: Enterococcus crotali (0.650), Escherichia coli coli (0.643),
|
||||
#> Escherichia coli expressing (0.611), Enterobacter cowanii (0.600), Enterococcus
|
||||
#> columbae (0.595), Enterococcus camelliae (0.591), Enterococcus casseliflavus
|
||||
#> (0.577), Enterobacter cloacae cloacae (0.571), Enterobacter cloacae complex
|
||||
#> (0.571), and Enterobacter cloacae dissolvens (0.565)
|
||||
#>
|
||||
#> Only the first 10 other matches of each record are shown. Run
|
||||
#> `print(mo_uncertainties(), n = ...)` to view more entries, or save
|
||||
#> `mo_uncertainties()` to an object.
|
||||
#> ℹ Only the first 10 other matches of each record are shown. Run
|
||||
#> `print(mo_uncertainties(), n = ...)` (`?AMR::mo_uncertainties()`) to view
|
||||
#> more entries, or save `mo_uncertainties()` (`?AMR::mo_uncertainties()`) to an
|
||||
#> object.
|
||||
|
||||
mo_matching_score(
|
||||
x = "E. coli",
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
|
||||
@@ -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-out co"><span class="r-pr">#></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-wrn co"><span class="r-pr">#></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">#></span> keep_synonyms = FALSE)` to clean the input to currently accepted taxonomic</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> names, or set the R option `AMR_keep_synonyms` to `FALSE`. This warning</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> will be shown once per session.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></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">#></span> `keep_synonyms = FALSE` to clean the input to currently accepted taxonomic</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></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">#></span> shown once per session.</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "268707"</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">%>%</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="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></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">#></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">#></span> (`?AMR::mo_is_gram_positive()`)</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></span> <span style="color: #949494;"># A tibble: 18 × 2</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> `mo_genus()` n</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><int></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">%>%</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="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></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">#></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">#></span> (`?AMR::mo_is_intrinsic_resistant()`)</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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">#></span> <span style="color: #949494;"># A tibble: 19 × 2</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> `mo_genus()` n</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><int></span></span>
|
||||
|
||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user