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2
404.html
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@@ -31,7 +31,7 @@
<a class="navbar-brand me-2" href="https://amr-for-r.org/index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
CLAUDE.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
LICENSE-text.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

68
articles/AMR.html
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@@ -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="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<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 20 March 2026.</p>
generated on 22 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">2026-03-20</td>
<td align="center">2026-03-22</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">2026-03-20</td>
<td align="center">2026-03-22</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">2026-03-20</td>
<td align="center">2026-03-22</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@@ -224,16 +224,16 @@ short, but still human readable. More importantly, <code><a href="../reference/a
supports all kinds of input:</p>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span>
<span><span class="co">#&gt; Class 'mo'</span></span>
<span><span class="co">#&gt; Class <span style="color: #0000BB;">&lt;mo&gt;</span></span></span>
<span><span class="co">#&gt; [1] B_KLBSL_PNMN</span></span>
<span><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"K. pneumoniae"</span><span class="op">)</span></span>
<span><span class="co">#&gt; Class 'mo'</span></span>
<span><span class="co">#&gt; Class <span style="color: #0000BB;">&lt;mo&gt;</span></span></span>
<span><span class="co">#&gt; [1] B_KLBSL_PNMN</span></span>
<span><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"KLEPNE"</span><span class="op">)</span></span>
<span><span class="co">#&gt; Class 'mo'</span></span>
<span><span class="co">#&gt; Class <span style="color: #0000BB;">&lt;mo&gt;</span></span></span>
<span><span class="co">#&gt; [1] B_KLBSL_PNMN</span></span>
<span><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"KLPN"</span><span class="op">)</span></span>
<span><span class="co">#&gt; Class 'mo'</span></span>
<span><span class="co">#&gt; Class <span style="color: #0000BB;">&lt;mo&gt;</span></span></span>
<span><span class="co">#&gt; [1] B_KLBSL_PNMN</span></span></code></pre></div>
<p>The first character in above codes denote their taxonomic kingdom,
such as Bacteria (B), Fungi (F), and Protozoa (P).</p>
@@ -266,16 +266,14 @@ user input can be used:</p>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Retrieved values from the `microorganisms.codes` data set for "ESCCOL",</span></span>
<span><span class="co">#&gt; "KLEPNE", "STAAUR", and "STRPNE".</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Microorganism translation was uncertain for four microorganisms. Run</span></span>
<span><span class="co">#&gt; `mo_uncertainties()` (`?AMR::mo_uncertainties()`) to review these</span></span>
<span><span class="co">#&gt; uncertainties, or use `add_custom_microorganisms()`</span></span>
<span><span class="co">#&gt; (`?AMR::add_custom_microorganisms()`) to add custom entries.</span></span></code></pre></div>
<span><span class="co">#&gt; `?mo_uncertainties()` to review these uncertainties, or use</span></span>
<span><span class="co">#&gt; `?add_custom_microorganisms()` to add custom entries.</span></span></code></pre></div>
<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">#&gt; Matching scores are based on the resemblance between the input and the full</span></span>
<span><span class="co">#&gt; taxonomic name, and the pathogenicity in humans. See `mo_matching_score()`</span></span>
<span><span class="co">#&gt; (`?AMR::mo_matching_score()`).</span></span>
<span><span class="co">#&gt; taxonomic name, and the pathogenicity in humans. See `?mo_matching_score()`.</span></span>
<span><span class="co">#&gt; Colour keys: <span style="color: #080808; background-color: #FF5F5F;"> 0.000-0.549 </span><span style="color: #080808; background-color: #FFD787;"> 0.550-0.649 </span><span style="color: #080808; background-color: #FFFF87;"> 0.650-0.749 </span><span style="color: #080808; background-color: #5FD7AF;"> 0.750-1.000 </span></span></span>
<span><span class="co">#&gt; <span style="color: #B2B2B2;">-------------------------------------------------------------------------------</span></span></span>
<span><span class="co">#&gt; <span style="color: #0000BB;">"E. coli"</span> -&gt; <span style="font-weight: bold; font-style: italic;">Escherichia coli</span> (B_ESCHR_COLI, <span style="color: #080808; background-color: #FFFF87;">0.688</span>)</span></span>
@@ -307,10 +305,9 @@ taxonomic codes. Let’s check this:</p>
<span><span class="co">#&gt; <span style="font-style: italic;">pseudintermedius</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.532</span>), <span style="font-style: italic;">Serratia proteamaculans proteamaculans</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.526</span>),</span></span>
<span><span class="co">#&gt; <span style="font-style: italic;">Streptococcus gallolyticus pasteurianus</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.526</span>), <span style="font-style: italic;">Salmonella</span> Portanigra<span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.524</span>),</span></span>
<span><span class="co">#&gt; and <span style="font-style: italic;">Streptococcus periodonticum</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.519</span>)</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Only the first 10 other matches of each record are shown. Run</span></span>
<span><span class="co">#&gt; `print(mo_uncertainties(), n = ...)` (`?AMR::mo_uncertainties()`) to view</span></span>
<span><span class="co">#&gt; more entries, or save `mo_uncertainties()` (`?AMR::mo_uncertainties()`) to an</span></span>
<span><span class="co">#&gt; object.</span></span></code></pre></div>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Only the first 10 other matches of each record are shown. Run ``</span></span>
<span><span class="co">#&gt; ?`print(mo_uncertainties(), n = ...)` `` to view more entries, or save</span></span>
<span><span class="co">#&gt; `?mo_uncertainties()` to an object.</span></span></code></pre></div>
<p>That’s all good.</p>
</div>
<div class="section level3">
@@ -522,7 +519,8 @@ 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">%&gt;%</a></span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">date</span>, <span class="fu"><a href="../reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using column '<span style="font-weight: bold;">GEN</span>' (gentamicin)</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `?aminoglycosides()` using column <span style="color: #00BB00; font-weight: bold;">GEN</span></span></span>
<span><span class="co">#&gt; (gentamicin)</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,724 × 2</span></span></span>
<span><span class="co">#&gt; date GEN </span></span>
<span><span class="co">#&gt; <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span></span>
@@ -540,7 +538,7 @@ 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">%&gt;%</a></span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">bacteria</span>, <span class="fu"><a href="../reference/antimicrobial_selectors.html">betalactams</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `betalactams()` using columns '<span style="font-weight: bold;">AMX</span>' (amoxicillin) and '<span style="font-weight: bold;">AMC</span>'</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `?betalactams()` using columns <span style="color: #00BB00; font-weight: bold;">AMX</span> (amoxicillin) and <span style="color: #00BB00; font-weight: bold;">AMC</span></span></span>
<span><span class="co">#&gt; (amoxicillin/clavulanic acid)</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,724 × 3</span></span></span>
<span><span class="co">#&gt; bacteria AMX AMC </span></span>
@@ -577,7 +575,8 @@ 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">%&gt;%</a></span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu"><a href="../reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using column '<span style="font-weight: bold;">GEN</span>' (gentamicin)</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `?aminoglycosides()` using column <span style="color: #00BB00; font-weight: bold;">GEN</span></span></span>
<span><span class="co">#&gt; (gentamicin)</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 981 × 9</span></span></span>
<span><span class="co">#&gt; patient_id hospital date bacteria AMX AMC CIP GEN first</span></span>
<span><span class="co">#&gt; <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span></span></span>
@@ -595,7 +594,7 @@ 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">%&gt;%</a></span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu"><a href="../reference/antimicrobial_selectors.html">betalactams</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `betalactams()` using columns '<span style="font-weight: bold;">AMX</span>' (amoxicillin) and '<span style="font-weight: bold;">AMC</span>'</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `?betalactams()` using columns <span style="color: #00BB00; font-weight: bold;">AMX</span> (amoxicillin) and <span style="color: #00BB00; font-weight: bold;">AMC</span></span></span>
<span><span class="co">#&gt; (amoxicillin/clavulanic acid)</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 462 × 9</span></span></span>
<span><span class="co">#&gt; patient_id hospital date bacteria AMX AMC CIP GEN first</span></span>
@@ -614,7 +613,7 @@ 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">#&gt; <span style="color: #00BBBB;">ℹ</span> For `betalactams()` using columns '<span style="font-weight: bold;">AMX</span>' (amoxicillin) and '<span style="font-weight: bold;">AMC</span>'</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `?betalactams()` using columns <span style="color: #00BB00; font-weight: bold;">AMX</span> (amoxicillin) and <span style="color: #00BB00; font-weight: bold;">AMC</span></span></span>
<span><span class="co">#&gt; (amoxicillin/clavulanic acid)</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 462 × 9</span></span></span>
<span><span class="co">#&gt; patient_id hospital date bacteria AMX AMC CIP GEN first</span></span>
@@ -696,9 +695,9 @@ 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">#&gt; <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns '<span style="font-weight: bold;">GEN</span>' (gentamicin), '<span style="font-weight: bold;">TOB</span>' (tobramycin),</span></span>
<span><span class="co">#&gt; '<span style="font-weight: bold;">AMK</span>' (amikacin), and '<span style="font-weight: bold;">KAN</span>' (kanamycin)</span></span>
<span><span class="co">#&gt; <span style="color: #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>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `?aminoglycosides()` using columns <span style="color: #00BB00; font-weight: bold;">GEN</span> (gentamicin), <span style="color: #00BB00; font-weight: bold;">TOB</span> (tobramycin),</span></span>
<span><span class="co">#&gt; <span style="color: #00BB00; font-weight: bold;">AMK</span> (amikacin), and <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin)</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `?carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span></span></code></pre></div>
<table class="table">
<colgroup>
<col width="12%">
@@ -827,8 +826,8 @@ language to be Spanish using the <code>language</code> argument:</p>
<span> antibiotics <span class="op">=</span> <span class="fu"><a href="../reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> 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">#&gt; <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns '<span style="font-weight: bold;">GEN</span>' (gentamicin), '<span style="font-weight: bold;">TOB</span>' (tobramycin),</span></span>
<span><span class="co">#&gt; '<span style="font-weight: bold;">AMK</span>' (amikacin), and '<span style="font-weight: bold;">KAN</span>' (kanamycin)</span></span></code></pre></div>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `?aminoglycosides()` using columns <span style="color: #00BB00; font-weight: bold;">GEN</span> (gentamicin), <span style="color: #00BB00; font-weight: bold;">TOB</span> (tobramycin),</span></span>
<span><span class="co">#&gt; <span style="color: #00BB00; font-weight: bold;">AMK</span> (amikacin), and <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin)</span></span></code></pre></div>
<table class="table">
<colgroup>
<col width="15%">
@@ -953,9 +952,9 @@ argument must be used. This can be any column in the data, or e.g. an
<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
<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">#&gt; <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns '<span style="font-weight: bold;">GEN</span>' (gentamicin), '<span style="font-weight: bold;">TOB</span>' (tobramycin),</span></span>
<span><span class="co">#&gt; '<span style="font-weight: bold;">AMK</span>' (amikacin), and '<span style="font-weight: bold;">KAN</span>' (kanamycin)</span></span>
<span><span class="co">#&gt; <span style="color: #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>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `?aminoglycosides()` using columns <span style="color: #00BB00; font-weight: bold;">GEN</span> (gentamicin), <span style="color: #00BB00; font-weight: bold;">TOB</span> (tobramycin),</span></span>
<span><span class="co">#&gt; <span style="color: #00BB00; font-weight: bold;">AMK</span> (amikacin), and <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin)</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `?carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span></span></code></pre></div>
<table class="table">
<colgroup>
<col width="10%">
@@ -1282,10 +1281,9 @@ 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">%&gt;%</a></span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> `resistance()` (`?AMR::resistance()`) assumes the EUCAST guideline and thus</span></span>
<span><span class="co">#&gt; considers the 'I' category susceptible. Set the `guideline` argument or the</span></span>
<span><span class="co">#&gt; `AMR_guideline` option to either "CLSI" or "EUCAST", see AMR-options</span></span>
<span><span class="co">#&gt; (`?AMR::AMR-options`).</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> `?resistance()` assumes the EUCAST guideline and thus considers the 'I'</span></span>
<span><span class="co">#&gt; category susceptible. Set the `guideline` argument or the `AMR_guideline`</span></span>
<span><span class="co">#&gt; option to either "CLSI" or "EUCAST", see AMR-options.</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> This message will be shown once per session.</span></span>
<span><span class="co">#&gt; [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

66
articles/AMR.md
View File

@@ -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 20 March 2026.
methodology remains unchanged. This page was generated on 22 March 2026.
## Introduction
@@ -51,9 +51,9 @@ structure of your data generally look like this:
| date | patient_id | mo | AMX | CIP |
|:----------:|:----------:|:----------------:|:---:|:---:|
| 2026-03-20 | abcd | Escherichia coli | S | S |
| 2026-03-20 | abcd | Escherichia coli | S | R |
| 2026-03-20 | efgh | Escherichia coli | R | S |
| 2026-03-22 | abcd | Escherichia coli | S | S |
| 2026-03-22 | abcd | Escherichia coli | S | R |
| 2026-03-22 | efgh | Escherichia coli | R | S |
### Needed R packages
@@ -120,16 +120,16 @@ of input:
``` r
as.mo("Klebsiella pneumoniae")
#> Class 'mo'
#> Class <mo>
#> [1] B_KLBSL_PNMN
as.mo("K. pneumoniae")
#> Class 'mo'
#> Class <mo>
#> [1] B_KLBSL_PNMN
as.mo("KLEPNE")
#> Class 'mo'
#> Class <mo>
#> [1] B_KLBSL_PNMN
as.mo("KLPN")
#> Class 'mo'
#> Class <mo>
#> [1] B_KLBSL_PNMN
```
@@ -169,9 +169,8 @@ 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()` (`?AMR::mo_uncertainties()`) to review these
#> uncertainties, or use `add_custom_microorganisms()`
#> (`?AMR::add_custom_microorganisms()`) to add custom entries.
#> `?mo_uncertainties()` to review these uncertainties, or use
#> `?add_custom_microorganisms()` to add custom entries.
```
Apparently, there was some uncertainty about the translation to
@@ -180,8 +179,7 @@ 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()`
#> (`?AMR::mo_matching_score()`).
#> taxonomic name, and the pathogenicity in humans. See `?mo_matching_score()`.
#> Colour keys: 0.000-0.549 0.550-0.649 0.650-0.749 0.750-1.000
#> -------------------------------------------------------------------------------
#> "E. coli" -> Escherichia coli (B_ESCHR_COLI, 0.688)
@@ -213,10 +211,9 @@ mo_uncertainties()
#> 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.
#> ℹ 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.
```
That’s all good.
@@ -450,7 +447,8 @@ in:
``` r
our_data_1st %>%
select(date, aminoglycosides())
#> ℹ For `aminoglycosides()` using column 'GEN' (gentamicin)
#> ℹ For `?aminoglycosides()` using column GEN
#> (gentamicin)
#> # A tibble: 2,724 × 2
#> date GEN
#> <date> <sir>
@@ -468,7 +466,7 @@ our_data_1st %>%
our_data_1st %>%
select(bacteria, betalactams())
#> ℹ For `betalactams()` using columns 'AMX' (amoxicillin) and 'AMC'
#> ℹ For `?betalactams()` using columns AMX (amoxicillin) and AMC
#> (amoxicillin/clavulanic acid)
#> # A tibble: 2,724 × 3
#> bacteria AMX AMC
@@ -505,7 +503,8 @@ our_data_1st %>%
# filtering using AB selectors is also possible:
our_data_1st %>%
filter(any(aminoglycosides() == "R"))
#> ℹ For `aminoglycosides()` using column 'GEN' (gentamicin)
#> ℹ For `?aminoglycosides()` using column GEN
#> (gentamicin)
#> # A tibble: 981 × 9
#> patient_id hospital date bacteria AMX AMC CIP GEN first
#> <chr> <chr> <date> <mo> <sir> <sir> <sir> <sir> <lgl>
@@ -523,7 +522,7 @@ our_data_1st %>%
our_data_1st %>%
filter(all(betalactams() == "R"))
#> ℹ For `betalactams()` using columns 'AMX' (amoxicillin) and 'AMC'
#> ℹ For `?betalactams()` using columns AMX (amoxicillin) and AMC
#> (amoxicillin/clavulanic acid)
#> # A tibble: 462 × 9
#> patient_id hospital date bacteria AMX AMC CIP GEN first
@@ -542,7 +541,7 @@ our_data_1st %>%
# even works in base R (since R 3.0):
our_data_1st[all(betalactams() == "R"), ]
#> ℹ For `betalactams()` using columns 'AMX' (amoxicillin) and 'AMC'
#> ℹ For `?betalactams()` using columns AMX (amoxicillin) and AMC
#> (amoxicillin/clavulanic acid)
#> # A tibble: 462 × 9
#> patient_id hospital date bacteria AMX AMC CIP GEN first
@@ -625,9 +624,9 @@ 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 `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> ℹ For `?aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin),
#> AMK (amikacin), and KAN (kanamycin)
#> ℹ For `?carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
```
| Pathogen | Amikacin | Gentamicin | Imipenem | Kanamycin | Meropenem | Tobramycin |
@@ -664,8 +663,8 @@ 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 |
@@ -708,9 +707,9 @@ 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 `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> ℹ For `?aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin),
#> AMK (amikacin), and KAN (kanamycin)
#> ℹ For `?carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
```
| Syndromic Group | Pathogen | Amikacin | Gentamicin | Imipenem | Kanamycin | Meropenem | Tobramycin |
@@ -841,10 +840,9 @@ These functions can be used on their own:
``` r
our_data_1st %>% resistance(AMX)
#> 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 `?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 This message will be shown once per session.
#> [1] 0.4203377
```

2
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@@ -30,7 +30,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

39
articles/AMR_with_tidymodels.html
View File

@@ -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="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<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 +179,13 @@ package.</p>
<span> mo <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">as.factor</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <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">#&gt; <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns '<span style="font-weight: bold;">GEN</span>' (gentamicin), '<span style="font-weight: bold;">TOB</span>' (tobramycin),</span></span>
<span><span class="co">#&gt; '<span style="font-weight: bold;">AMK</span>' (amikacin), and '<span style="font-weight: bold;">KAN</span>' (kanamycin)</span></span>
<span><span class="co">#&gt; <span style="color: #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">#&gt; (oxacillin), '<span style="font-weight: bold;">FLC</span>' (flucloxacillin), '<span style="font-weight: bold;">AMX</span>' (amoxicillin), '<span style="font-weight: bold;">AMC</span>'</span></span>
<span><span class="co">#&gt; (amoxicillin/clavulanic acid), '<span style="font-weight: bold;">AMP</span>' (ampicillin), '<span style="font-weight: bold;">TZP</span>'</span></span>
<span><span class="co">#&gt; (piperacillin/tazobactam), '<span style="font-weight: bold;">CZO</span>' (cefazolin), '<span style="font-weight: bold;">FEP</span>' (cefepime), '<span style="font-weight: bold;">CXM</span>'</span></span>
<span><span class="co">#&gt; (cefuroxime), '<span style="font-weight: bold;">FOX</span>' (cefoxitin), '<span style="font-weight: bold;">CTX</span>' (cefotaxime), '<span style="font-weight: bold;">CAZ</span>' (ceftazidime),</span></span>
<span><span class="co">#&gt; '<span style="font-weight: bold;">CRO</span>' (ceftriaxone), '<span style="font-weight: bold;">IPM</span>' (imipenem), and '<span style="font-weight: bold;">MEM</span>' (meropenem)</span></span></code></pre></div>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `?aminoglycosides()` using columns <span style="color: #00BB00; font-weight: bold;">GEN</span> (gentamicin), <span style="color: #00BB00; font-weight: bold;">TOB</span> (tobramycin),</span></span>
<span><span class="co">#&gt; <span style="color: #00BB00; font-weight: bold;">AMK</span> (amikacin), and <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin)</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `?betalactams()` using columns <span style="color: #00BB00; font-weight: bold;">PEN</span> (benzylpenicillin), <span style="color: #00BB00; font-weight: bold;">OXA</span> (oxacillin),</span></span>
<span><span class="co">#&gt; <span style="color: #00BB00; font-weight: bold;">FLC</span> (flucloxacillin), <span style="color: #00BB00; font-weight: bold;">AMX</span> (amoxicillin), <span style="color: #00BB00; font-weight: bold;">AMC</span> (amoxicillin/clavulanic acid),</span></span>
<span><span class="co">#&gt; <span style="color: #00BB00; font-weight: bold;">AMP</span> (ampicillin), <span style="color: #00BB00; font-weight: bold;">TZP</span> (piperacillin/tazobactam), <span style="color: #00BB00; font-weight: bold;">CZO</span> (cefazolin), <span style="color: #00BB00; font-weight: bold;">FEP</span></span></span>
<span><span class="co">#&gt; (cefepime), <span style="color: #00BB00; font-weight: bold;">CXM</span> (cefuroxime), <span style="color: #00BB00; font-weight: bold;">FOX</span> (cefoxitin), <span style="color: #00BB00; font-weight: bold;">CTX</span> (cefotaxime), <span style="color: #00BB00; font-weight: bold;">CAZ</span></span></span>
<span><span class="co">#&gt; (ceftazidime), <span style="color: #00BB00; font-weight: bold;">CRO</span> (ceftriaxone), <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem), and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span></span></code></pre></div>
<p><strong>Explanation:</strong></p>
<ul>
<li>
@@ -227,14 +226,13 @@ 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">#&gt; <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns '<span style="font-weight: bold;">GEN</span>' (gentamicin), '<span style="font-weight: bold;">TOB</span>' (tobramycin),</span></span>
<span><span class="co">#&gt; '<span style="font-weight: bold;">AMK</span>' (amikacin), and '<span style="font-weight: bold;">KAN</span>' (kanamycin)</span></span>
<span><span class="co">#&gt; <span style="color: #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">#&gt; (oxacillin), '<span style="font-weight: bold;">FLC</span>' (flucloxacillin), '<span style="font-weight: bold;">AMX</span>' (amoxicillin), '<span style="font-weight: bold;">AMC</span>'</span></span>
<span><span class="co">#&gt; (amoxicillin/clavulanic acid), '<span style="font-weight: bold;">AMP</span>' (ampicillin), '<span style="font-weight: bold;">TZP</span>'</span></span>
<span><span class="co">#&gt; (piperacillin/tazobactam), '<span style="font-weight: bold;">CZO</span>' (cefazolin), '<span style="font-weight: bold;">FEP</span>' (cefepime), '<span style="font-weight: bold;">CXM</span>'</span></span>
<span><span class="co">#&gt; (cefuroxime), '<span style="font-weight: bold;">FOX</span>' (cefoxitin), '<span style="font-weight: bold;">CTX</span>' (cefotaxime), '<span style="font-weight: bold;">CAZ</span>' (ceftazidime),</span></span>
<span><span class="co">#&gt; '<span style="font-weight: bold;">CRO</span>' (ceftriaxone), '<span style="font-weight: bold;">IPM</span>' (imipenem), and '<span style="font-weight: bold;">MEM</span>' (meropenem)</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `?aminoglycosides()` using columns <span style="color: #00BB00; font-weight: bold;">GEN</span> (gentamicin), <span style="color: #00BB00; font-weight: bold;">TOB</span> (tobramycin),</span></span>
<span><span class="co">#&gt; <span style="color: #00BB00; font-weight: bold;">AMK</span> (amikacin), and <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin)</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `?betalactams()` using columns <span style="color: #00BB00; font-weight: bold;">PEN</span> (benzylpenicillin), <span style="color: #00BB00; font-weight: bold;">OXA</span> (oxacillin),</span></span>
<span><span class="co">#&gt; <span style="color: #00BB00; font-weight: bold;">FLC</span> (flucloxacillin), <span style="color: #00BB00; font-weight: bold;">AMX</span> (amoxicillin), <span style="color: #00BB00; font-weight: bold;">AMC</span> (amoxicillin/clavulanic acid),</span></span>
<span><span class="co">#&gt; <span style="color: #00BB00; font-weight: bold;">AMP</span> (ampicillin), <span style="color: #00BB00; font-weight: bold;">TZP</span> (piperacillin/tazobactam), <span style="color: #00BB00; font-weight: bold;">CZO</span> (cefazolin), <span style="color: #00BB00; font-weight: bold;">FEP</span></span></span>
<span><span class="co">#&gt; (cefepime), <span style="color: #00BB00; font-weight: bold;">CXM</span> (cefuroxime), <span style="color: #00BB00; font-weight: bold;">FOX</span> (cefoxitin), <span style="color: #00BB00; font-weight: bold;">CTX</span> (cefotaxime), <span style="color: #00BB00; font-weight: bold;">CAZ</span></span></span>
<span><span class="co">#&gt; (ceftazidime), <span style="color: #00BB00; font-weight: bold;">CRO</span> (ceftriaxone), <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem), and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span></span>
<span><span class="co">#&gt; </span></span>
<span><span class="co">#&gt; </span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">Recipe</span> <span style="color: #00BBBB;">──────────────────────────────────────────────────────────────────────</span></span></span>
@@ -749,10 +747,9 @@ into a structured time-series format.</p>
<span> .groups <span class="op">=</span> <span class="st">"drop"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na</a></span><span class="op">(</span><span class="va">res_AMX</span><span class="op">)</span> <span class="op">&amp;</span> <span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na</a></span><span class="op">(</span><span class="va">res_AMC</span><span class="op">)</span> <span class="op">&amp;</span> <span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na</a></span><span class="op">(</span><span class="va">res_CIP</span><span class="op">)</span><span class="op">)</span> <span class="co"># Drop missing values</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Using column '<span style="font-weight: bold;">mo</span>' as input for `col_mo`.</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> `resistance()` (`?AMR::resistance()`) assumes the EUCAST guideline and thus</span></span>
<span><span class="co">#&gt; considers the 'I' category susceptible. Set the `guideline` argument or the</span></span>
<span><span class="co">#&gt; `AMR_guideline` option to either "CLSI" or "EUCAST", see AMR-options</span></span>
<span><span class="co">#&gt; (`?AMR::AMR-options`).</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> `?resistance()` assumes the EUCAST guideline and thus considers the 'I'</span></span>
<span><span class="co">#&gt; category susceptible. Set the `guideline` argument or the `AMR_guideline`</span></span>
<span><span class="co">#&gt; option to either "CLSI" or "EUCAST", see AMR-options.</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> This message will be shown once per session.</span></span>
<span></span>
<span><span class="va">data_time</span></span>

37
articles/AMR_with_tidymodels.md
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@@ -94,14 +94,13 @@ 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 `betalactams()` using columns 'PEN' (benzylpenicillin), 'OXA'
#> (oxacillin), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC'
#> (amoxicillin/clavulanic acid), 'AMP' (ampicillin), 'TZP'
#> (piperacillin/tazobactam), 'CZO' (cefazolin), 'FEP' (cefepime), 'CXM'
#> (cefuroxime), 'FOX' (cefoxitin), 'CTX' (cefotaxime), 'CAZ' (ceftazidime),
#> 'CRO' (ceftriaxone), 'IPM' (imipenem), and 'MEM' (meropenem)
#> 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 (piperacillin/tazobactam), CZO (cefazolin), FEP
#> (cefepime), CXM (cefuroxime), FOX (cefoxitin), CTX (cefotaxime), CAZ
#> (ceftazidime), CRO (ceftriaxone), IPM (imipenem), and MEM (meropenem)
```
**Explanation:**
@@ -144,14 +143,13 @@ 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 `betalactams()` using columns 'PEN' (benzylpenicillin), 'OXA'
#> (oxacillin), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC'
#> (amoxicillin/clavulanic acid), 'AMP' (ampicillin), 'TZP'
#> (piperacillin/tazobactam), 'CZO' (cefazolin), 'FEP' (cefepime), 'CXM'
#> (cefuroxime), 'FOX' (cefoxitin), 'CTX' (cefotaxime), 'CAZ' (ceftazidime),
#> 'CRO' (ceftriaxone), 'IPM' (imipenem), and 'MEM' (meropenem)
#> 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 (piperacillin/tazobactam), CZO (cefazolin), FEP
#> (cefepime), CXM (cefuroxime), FOX (cefoxitin), CTX (cefotaxime), CAZ
#> (ceftazidime), CRO (ceftriaxone), IPM (imipenem), and MEM (meropenem)
#>
#>
#> ── Recipe ──────────────────────────────────────────────────────────────────────
@@ -647,10 +645,9 @@ 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()` (`?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 `?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 This message will be shown once per session.
data_time

2
articles/EUCAST.html
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@@ -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="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<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
articles/PCA.html
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@@ -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="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<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 +163,9 @@ per taxonomic order and genus:</p>
<span> <span class="va">order</span>, <span class="va">genus</span>, <span class="va">AMC</span>, <span class="va">CXM</span>, <span class="va">CTX</span>,</span>
<span> <span class="va">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">#&gt; <span style="color: #00BBBB;">ℹ</span> `resistance()` (`?AMR::resistance()`) assumes the EUCAST guideline and thus</span></span>
<span><span class="co">#&gt; considers the 'I' category susceptible. Set the `guideline` argument or the</span></span>
<span><span class="co">#&gt; `AMR_guideline` option to either "CLSI" or "EUCAST", see AMR-options</span></span>
<span><span class="co">#&gt; (`?AMR::AMR-options`).</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> `?resistance()` assumes the EUCAST guideline and thus considers the 'I'</span></span>
<span><span class="co">#&gt; category susceptible. Set the `guideline` argument or the `AMR_guideline`</span></span>
<span><span class="co">#&gt; option to either "CLSI" or "EUCAST", see AMR-options.</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> This message will be shown once per session.</span></span>
<span></span>
<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>

7
articles/PCA.md
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@@ -78,10 +78,9 @@ resistance_data <- example_isolates %>%
order, genus, AMC, CXM, CTX,
CAZ, GEN, TOB, TMP, SXT
) # and select only relevant columns
#> 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 `?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 This message will be shown once per session.
head(resistance_data)

9
articles/WHONET.html
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@@ -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="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<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 +255,9 @@ 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">%&gt;%</a></span> <span class="fu"><a href="https://msberends.github.io/cleaner/reference/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">AMC_ND2</span><span class="op">)</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> `susceptibility()` (`?AMR::susceptibility()`) assumes the EUCAST guideline</span></span>
<span><span class="co">#&gt; and thus considers the 'I' category susceptible. Set the `guideline` argument</span></span>
<span><span class="co">#&gt; or the `AMR_guideline` option to either "CLSI" or "EUCAST", see AMR-options</span></span>
<span><span class="co">#&gt; (`?AMR::AMR-options`).</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> `?susceptibility()` assumes the EUCAST guideline and thus considers the 'I'</span></span>
<span><span class="co">#&gt; category susceptible. Set the `guideline` argument or the `AMR_guideline`</span></span>
<span><span class="co">#&gt; option to either "CLSI" or "EUCAST", see AMR-options.</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> This message will be shown once per session.</span></span></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: factor &gt; ordered &gt; sir (numeric)<br>

7
articles/WHONET.md
View File

@@ -101,10 +101,9 @@ Longest: 40
# our transformed antibiotic columns
# amoxicillin/clavulanic acid (J01CR02) as an example
data %>% freq(AMC_ND2)
#> 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 `?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 This message will be shown once per session.
```

2
articles/WISCA.html
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@@ -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="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

4
articles/datasets.html
View File

@@ -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="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<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">20 March 2026</h4>
<h4 data-toc-skip class="date">22 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>

2
articles/index.html
View File

@@ -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="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
authors.html
View File

@@ -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="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
index.html
View File

@@ -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="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

10
news/index.html
View File

@@ -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="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<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="3.0.1.9036" id="amr-3019036">AMR 3.0.1.9036<a class="anchor" aria-label="anchor" href="#amr-3019036"></a></h2>
<h2 class="pkg-version" data-toc-text="3.0.1.9037" id="amr-3019037">AMR 3.0.1.9037<a class="anchor" aria-label="anchor" href="#amr-3019037"></a></h2>
<div class="section level4">
<h4 id="new-3-0-1-9036">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9036"></a></h4>
<h4 id="new-3-0-1-9037">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9037"></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>&lt;mic&gt;</code> columns with log2, and <code><a href="../reference/amr-tidymodels.html">step_sir_numeric()</a></code> to convert <code>&lt;sir&gt;</code> columns to numeric</li>
@@ -83,7 +83,7 @@
<li>Function <code><a href="../reference/amr_course.html">amr_course()</a></code>, which allows for automated download and unpacking of a GitHub repository for e.g. webinar use</li>
</ul></div>
<div class="section level4">
<h4 id="fixes-3-0-1-9036">Fixes<a class="anchor" aria-label="anchor" href="#fixes-3-0-1-9036"></a></h4>
<h4 id="fixes-3-0-1-9037">Fixes<a class="anchor" aria-label="anchor" href="#fixes-3-0-1-9037"></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>
@@ -96,7 +96,7 @@
<li>Fixed SIR and MIC coercion of combined values, e.g. <code>as.sir("&lt;= 0.002; S")</code> or <code>as.mic("S; 0.002")</code> (<a href="https://github.com/msberends/AMR/issues/252" class="external-link">#252</a>)</li>
</ul></div>
<div class="section level4">
<h4 id="updates-3-0-1-9036">Updates<a class="anchor" aria-label="anchor" href="#updates-3-0-1-9036"></a></h4>
<h4 id="updates-3-0-1-9037">Updates<a class="anchor" aria-label="anchor" href="#updates-3-0-1-9037"></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>

2
news/index.md
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@@ -1,6 +1,6 @@
# Changelog
## AMR 3.0.1.9036
## AMR 3.0.1.9037
#### New

2
pkgdown.yml
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@@ -10,7 +10,7 @@ articles:
PCA: PCA.html
WHONET: WHONET.html
WISCA: WISCA.html
last_built: 2026-03-20T16:06Z
last_built: 2026-03-22T19:50Z
urls:
reference: https://amr-for-r.org/reference
article: https://amr-for-r.org/articles

2
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/AMR-options.html
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@@ -9,7 +9,7 @@ options(AMR_guideline = "CLSI")'><meta property="og:image" content="https://amr-
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/AMR.html
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@@ -21,7 +21,7 @@ The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

4
reference/WHOCC.html
View File

@@ -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="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -67,7 +67,7 @@
<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.ab.html">as.ab</a></span><span class="op">(</span><span class="st">"meropenem"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'ab'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;ab&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] MEM</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">"J01DH02"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Meropenem"</span>

2
reference/WHOCC.md
View File

@@ -29,7 +29,7 @@ unlike any other info from this package.** See
``` r
as.ab("meropenem")
#> Class 'ab'
#> Class <ab>
#> [1] MEM
ab_name("J01DH02")
#> [1] "Meropenem"

2
reference/WHONET.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

6
reference/ab_from_text.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -124,13 +124,13 @@
<span class="r-in"><span><span class="co"># straight from a true health care record:</span></span></span>
<span class="r-in"><span><span class="fu">ab_from_text</span><span class="op">(</span><span class="st">"28/03/2020 regular amoxicilliin 500mg po tid"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [[1]]</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'ab'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;ab&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] AMX</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">ab_from_text</span><span class="op">(</span><span class="st">"500 mg amoxi po and 400mg cipro iv"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [[1]]</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'ab'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;ab&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] AMX CIP</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-in"><span><span class="fu">ab_from_text</span><span class="op">(</span><span class="st">"500 mg amoxi po and 400mg cipro iv"</span>, type <span class="op">=</span> <span class="st">"dose"</span><span class="op">)</span></span></span>

4
reference/ab_from_text.md
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@@ -123,13 +123,13 @@ With using `collapse`, this function will return a
# straight from a true health care record:
ab_from_text("28/03/2020 regular amoxicilliin 500mg po tid")
#> [[1]]
#> Class 'ab'
#> Class <ab>
#> [1] AMX
#>
ab_from_text("500 mg amoxi po and 400mg cipro iv")
#> [[1]]
#> Class 'ab'
#> Class <ab>
#> [1] AMX CIP
#>
ab_from_text("500 mg amoxi po and 400mg cipro iv", type = "dose")

2
reference/ab_property.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

8
reference/add_custom_antimicrobials.html
View File

@@ -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="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -97,7 +97,7 @@
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \donttest{</span></span></span>
<span class="r-in"><span><span class="co"># returns a wildly guessed result:</span></span></span>
<span class="r-in"><span><span class="fu"><a href="as.ab.html">as.ab</a></span><span class="op">(</span><span class="st">"testab"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'ab'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;ab&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] THA</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># now add a custom entry - it will be considered by as.ab() and</span></span></span>
@@ -115,7 +115,7 @@
<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>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'ab'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;ab&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] TESTAB</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">"testab"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Test Antibiotic"</span>
@@ -197,7 +197,7 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> random_column coflu ampicillin</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 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">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `betalactams()` using columns '<span style="font-weight: bold;">coflu</span>' (co-fluampicil) and '<span style="font-weight: bold;">ampicillin</span>'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?betalactams()` using columns <span style="color: #00BB00; font-weight: bold;">coflu</span> (co-fluampicil) and <span style="color: #00BB00; font-weight: bold;">ampicillin</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> coflu ampicillin</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 S R</span>
<span class="r-in"><span><span class="co"># }</span></span></span>

6
reference/add_custom_antimicrobials.md
View File

@@ -85,7 +85,7 @@ to add custom microorganisms.
# \donttest{
# returns a wildly guessed result:
as.ab("testab")
#> Class 'ab'
#> Class <ab>
#> [1] THA
# now add a custom entry - it will be considered by as.ab() and
@@ -103,7 +103,7 @@ add_custom_antimicrobials(
# "testab" is now a new antibiotic:
as.ab("testab")
#> Class 'ab'
#> Class <ab>
#> [1] TESTAB
ab_name("testab")
#> [1] "Test Antibiotic"
@@ -185,7 +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
# }

4
reference/add_custom_microorganisms.html
View File

@@ -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="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -118,7 +118,7 @@
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># its code:</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">"Enterobacter asburiae/cloacae"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mo'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;mo&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] CUSTOM1_ENTRB_ASB/</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># all internal algorithms will work as well:</span></span></span>

2
reference/add_custom_microorganisms.md
View File

@@ -107,7 +107,7 @@ mo_name("Enterobacter asburiae/cloacae")
# its code:
as.mo("Enterobacter asburiae/cloacae")
#> Class 'mo'
#> Class <mo>
#> [1] CUSTOM1_ENTRB_ASB/
# all internal algorithms will work as well:

22
reference/age.html
View File

@@ -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="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<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">#&gt;</span> birth_date age age_exact age_at_y2k</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1999-06-30 26 26.72055 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1968-01-29 58 58.13699 31</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1965-12-05 60 60.28767 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1980-03-01 46 46.05205 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1949-11-01 76 76.38082 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1947-02-14 79 79.09315 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1940-02-19 86 86.07945 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1988-01-10 38 38.18904 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1997-08-27 28 28.56164 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1978-01-26 48 48.14521 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1999-06-30 26 26.72603 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1968-01-29 58 58.14247 31</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1965-12-05 60 60.29315 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1980-03-01 46 46.05753 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1949-11-01 76 76.38630 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1947-02-14 79 79.09863 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1940-02-19 86 86.08493 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1988-01-10 38 38.19452 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1997-08-27 28 28.56712 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1978-01-26 48 48.15068 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>

20
reference/age.md
View File

@@ -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 26.72055 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
#> 1 1999-06-30 26 26.72603 0
#> 2 1968-01-29 58 58.14247 31
#> 3 1965-12-05 60 60.29315 34
#> 4 1980-03-01 46 46.05753 19
#> 5 1949-11-01 76 76.38630 50
#> 6 1947-02-14 79 79.09863 52
#> 7 1940-02-19 86 86.08493 59
#> 8 1988-01-10 38 38.19452 11
#> 9 1997-08-27 28 28.56712 2
#> 10 1978-01-26 48 48.15068 21
```

2
reference/age_groups.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/amr-tidymodels.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/amr_course.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<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
reference/antibiogram.html
View File

@@ -9,7 +9,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<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">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns '<span style="font-weight: bold;">GEN</span>' (gentamicin), '<span style="font-weight: bold;">TOB</span>' (tobramycin),</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> '<span style="font-weight: bold;">AMK</span>' (amikacin), and '<span style="font-weight: bold;">KAN</span>' (kanamycin)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns '<span style="font-weight: bold;">IPM</span>' (imipenem) and '<span style="font-weight: bold;">MEM</span>' (meropenem)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?aminoglycosides()` using columns <span style="color: #00BB00; font-weight: bold;">GEN</span> (gentamicin), <span style="color: #00BB00; font-weight: bold;">TOB</span> (tobramycin),</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00; font-weight: bold;">AMK</span> (amikacin), and <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram: 10 × 7</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Type: Non-WISCA with 95% CI</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Pathogen Amikacin Gentamicin Imipenem Kanamycin Meropenem Tobramycin</span>
@@ -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">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns '<span style="font-weight: bold;">GEN</span>' (gentamicin), '<span style="font-weight: bold;">TOB</span>' (tobramycin),</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> '<span style="font-weight: bold;">AMK</span>' (amikacin), and '<span style="font-weight: bold;">KAN</span>' (kanamycin)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?aminoglycosides()` using columns <span style="color: #00BB00; font-weight: bold;">GEN</span> (gentamicin), <span style="color: #00BB00; font-weight: bold;">TOB</span> (tobramycin),</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00; font-weight: bold;">AMK</span> (amikacin), and <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram: 2 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Type: Non-WISCA with 95% CI</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Pathogen J01GB01 J01GB03 J01GB04 J01GB06 </span>
@@ -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">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns '<span style="font-weight: bold;">IPM</span>' (imipenem) and '<span style="font-weight: bold;">MEM</span>' (meropenem)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram: 5 × 3</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Type: Non-WISCA with 95% CI</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Pathogen Imipenem Meropenem </span>
@@ -487,7 +487,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
<span class="r-in"><span> antimicrobials <span class="op">=</span> <span class="fu"><a href="antimicrobial_selectors.html">ureidopenicillins</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">""</span>, <span class="st">"GEN"</span>, <span class="st">"tobra"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> 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">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `ureidopenicillins()` using column '<span style="font-weight: bold;">TZP</span>' (piperacillin/tazobactam)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?ureidopenicillins()` using column <span style="color: #00BB00; font-weight: bold;">TZP</span> (piperacillin/tazobactam)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram: 2 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Type: Non-WISCA with 95% CI</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Pathogen Piperacillin/tazobac…¹ Piperacillin/tazobac…² Piperacillin/tazobac…³</span>
@@ -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">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns '<span style="font-weight: bold;">GEN</span>' (gentamicin), '<span style="font-weight: bold;">TOB</span>' (tobramycin),</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> '<span style="font-weight: bold;">AMK</span>' (amikacin), and '<span style="font-weight: bold;">KAN</span>' (kanamycin)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns '<span style="font-weight: bold;">IPM</span>' (imipenem) and '<span style="font-weight: bold;">MEM</span>' (meropenem)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?aminoglycosides()` using columns <span style="color: #00BB00; font-weight: bold;">GEN</span> (gentamicin), <span style="color: #00BB00; font-weight: bold;">TOB</span> (tobramycin),</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00; font-weight: bold;">AMK</span> (amikacin), and <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram: 14 × 8</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Type: Non-WISCA with 95% CI</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> `Syndromic Group` Pathogen Amikacin Gentamicin Imipenem Kanamycin Meropenem</span>
@@ -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">&lt;-</span> <span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu"><a href="mo_property.html">mo_genus</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"Escherichia"</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Using column '<span style="font-weight: bold;">mo</span>' as input for `mo_genus()` (`?AMR::mo_genus()`)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Using column '<span style="font-weight: bold;">mo</span>' as input for `?mo_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">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns '<span style="font-weight: bold;">GEN</span>' (gentamicin), '<span style="font-weight: bold;">TOB</span>' (tobramycin),</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> '<span style="font-weight: bold;">AMK</span>' (amikacin), and '<span style="font-weight: bold;">KAN</span>' (kanamycin)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?aminoglycosides()` using columns <span style="color: #00BB00; font-weight: bold;">GEN</span> (gentamicin), <span style="color: #00BB00; font-weight: bold;">TOB</span> (tobramycin),</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00; font-weight: bold;">AMK</span> (amikacin), and <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram: 2 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Type: Non-WISCA with 95% CI</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> `Grupo sindrómico` Patógeno Amikacina Gentamicina Tobramicina</span>
@@ -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">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `ureidopenicillins()` using column '<span style="font-weight: bold;">TZP</span>' (piperacillin/tazobactam)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?ureidopenicillins()` using column <span style="color: #00BB00; font-weight: bold;">TZP</span> (piperacillin/tazobactam)</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span 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>

28
reference/antibiogram.md
View File

@@ -598,9 +598,9 @@ 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 `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> 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
#> Pathogen Amikacin Gentamicin Imipenem Kanamycin Meropenem Tobramycin
@@ -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
@@ -639,7 +639,7 @@ antibiogram(example_isolates,
ab_transform = "name",
mo_transform = "name"
)
#> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> ℹ For `?carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> # An Antibiogram: 5 × 3
#> # Type: Non-WISCA with 95% CI
#> Pathogen Imipenem Meropenem
@@ -677,7 +677,7 @@ antibiogram(example_isolates,
antimicrobials = ureidopenicillins() + c("", "GEN", "tobra"),
mo_transform = "gramstain"
)
#> ℹ For `ureidopenicillins()` using column 'TZP' (piperacillin/tazobactam)
#> ℹ For `?ureidopenicillins()` using column TZP (piperacillin/tazobactam)
#> # An Antibiogram: 2 × 4
#> # Type: Non-WISCA with 95% CI
#> Pathogen Piperacillin/tazobac…¹ Piperacillin/tazobac…² Piperacillin/tazobac…³
@@ -714,9 +714,9 @@ 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 `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> 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
#> `Syndromic Group` Pathogen Amikacin Gentamicin Imipenem Kanamycin Meropenem
@@ -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()` (`?AMR::mo_genus()`)
#> ℹ Using column 'mo' as input for `?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
@@ -793,7 +793,7 @@ ureido <- antibiogram(example_isolates,
syndromic_group = "ward",
wisca = TRUE
)
#> ℹ For `ureidopenicillins()` using column 'TZP' (piperacillin/tazobactam)
#> ℹ For `?ureidopenicillins()` using column TZP (piperacillin/tazobactam)
# in an Rmd file, you would just need to return `ureido` in a chunk,
# but to be explicit here:

113
reference/antimicrobial_selectors.html
View File

@@ -17,7 +17,7 @@ my_data_with_all_these_columns %&amp;gt;%
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -296,8 +296,8 @@ my_data_with_all_these_columns %&amp;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">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> in `carbapenems()` (`?AMR::carbapenems()`): Imipenem/EDTA (`IPE`) and</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> meropenem/nacubactam (`MNC`) are not included since `only_treatable = TRUE`.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> in `?carbapenems()`: Imipenem/EDTA (<span style="color: #00BB00;">IPE</span>) and meropenem/nacubactam (<span style="color: #00BB00;">MNC</span>) are</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> not included since `only_treatable = TRUE`.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> This <span style="color: #0000BB;">&lt;ab&gt;</span> vector was retrieved using `carbapenems()`, which should normally</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> be used inside a <span style="color: #0000BB;">dplyr</span> verb or <span style="color: #0000BB;">&lt;data.frame&gt;</span> call, e.g.:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • your_data <span style="color: #D7AF00;">%&gt;%</span> <span style="font-weight: bold;">select</span><span style="color: #D7AF00;">(</span><span style="font-weight: bold;">carbapenems</span><span style="color: #BBBB00;">()</span><span style="color: #D7AF00;">)</span></span>
@@ -305,7 +305,7 @@ my_data_with_all_these_columns %&amp;gt;%
<span class="r-msg co"><span class="r-pr">#&gt;</span> • your_data <span style="color: #D7AF00;">%&gt;%</span> <span style="font-weight: bold;">filter</span><span style="color: #D7AF00;">(</span><span style="font-weight: bold;">any</span><span style="color: #BBBB00;">(</span><span style="font-weight: bold;">carbapenems</span><span style="color: #0000BB;">()</span> <span style="color: #D7AF00;">==</span> <span style="color: #00AFAF;">"R"</span><span style="color: #BBBB00;">)</span><span style="color: #D7AF00;">)</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • your_data<span style="color: #D7AF00;">[</span>, <span style="font-weight: bold;">carbapenems</span><span style="color: #BBBB00;">()</span><span style="color: #D7AF00;">]</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • your_data<span style="color: #D7AF00;">[</span>, <span style="font-weight: bold;">c</span><span style="color: #BBBB00;">(</span><span style="color: #00AFAF;">"column_a"</span>, <span style="color: #00AFAF;">"column_b"</span>, <span style="font-weight: bold;">carbapenems</span><span style="color: #0000BB;">()</span><span style="color: #BBBB00;">)</span><span style="color: #D7AF00;">]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'ab'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;ab&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] BIA DOR ETP IMR IPM MEM MEV PAN RIA RIT RZM TAN TBP</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span></span></span>
@@ -404,7 +404,7 @@ my_data_with_all_these_columns %&amp;gt;%
<span class="r-in"><span></span></span>
<span class="r-in"><span><span 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">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns '<span style="font-weight: bold;">IPM</span>' (imipenem) and '<span style="font-weight: bold;">MEM</span>' (meropenem)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2,000 × 2</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> IPM MEM </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
@@ -422,8 +422,8 @@ my_data_with_all_these_columns %&amp;gt;%
<span class="r-in"><span></span></span>
<span class="r-in"><span><span 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">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns '<span style="font-weight: bold;">GEN</span>' (gentamicin), '<span style="font-weight: bold;">TOB</span>' (tobramycin),</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> '<span style="font-weight: bold;">AMK</span>' (amikacin), and '<span style="font-weight: bold;">KAN</span>' (kanamycin)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?aminoglycosides()` using columns <span style="color: #00BB00; font-weight: bold;">GEN</span> (gentamicin), <span style="color: #00BB00; font-weight: bold;">TOB</span> (tobramycin),</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00; font-weight: bold;">AMK</span> (amikacin), and <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2,000 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo GEN TOB AMK KAN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
@@ -441,14 +441,13 @@ my_data_with_all_these_columns %&amp;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">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `administrable_per_os()` using columns '<span style="font-weight: bold;">OXA</span>' (oxacillin), '<span style="font-weight: bold;">FLC</span>'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (flucloxacillin), '<span style="font-weight: bold;">AMX</span>' (amoxicillin), '<span style="font-weight: bold;">AMC</span>' (amoxicillin/clavulanic acid),</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> '<span style="font-weight: bold;">AMP</span>' (ampicillin), '<span style="font-weight: bold;">CXM</span>' (cefuroxime), '<span style="font-weight: bold;">KAN</span>' (kanamycin), '<span style="font-weight: bold;">TMP</span>'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (trimethoprim), '<span style="font-weight: bold;">NIT</span>' (nitrofurantoin), '<span style="font-weight: bold;">FOS</span>' (fosfomycin), '<span style="font-weight: bold;">LNZ</span>'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (linezolid), '<span style="font-weight: bold;">CIP</span>' (ciprofloxacin), '<span style="font-weight: bold;">MFX</span>' (moxifloxacin), '<span style="font-weight: bold;">VAN</span>' (vancomycin),</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> '<span style="font-weight: bold;">TCY</span>' (tetracycline), '<span style="font-weight: bold;">DOX</span>' (doxycycline), '<span style="font-weight: bold;">ERY</span>' (erythromycin), '<span style="font-weight: bold;">CLI</span>'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (clindamycin), '<span style="font-weight: bold;">AZM</span>' (azithromycin), '<span style="font-weight: bold;">MTR</span>' (metronidazole), '<span style="font-weight: bold;">CHL</span>'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (chloramphenicol), '<span style="font-weight: bold;">COL</span>' (colistin), and '<span style="font-weight: bold;">RIF</span>' (rifampicin)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?administrable_per_os()` using columns <span style="color: #00BB00; font-weight: bold;">OXA</span> (oxacillin), <span style="color: #00BB00; font-weight: bold;">FLC</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (flucloxacillin), <span style="color: #00BB00; font-weight: bold;">AMX</span> (amoxicillin), <span style="color: #00BB00; font-weight: bold;">AMC</span> (amoxicillin/clavulanic acid), <span style="color: #00BB00; font-weight: bold;">AMP</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (ampicillin), <span style="color: #00BB00; font-weight: bold;">CXM</span> (cefuroxime), <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin), <span style="color: #00BB00; font-weight: bold;">TMP</span> (trimethoprim), <span style="color: #00BB00; font-weight: bold;">NIT</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (nitrofurantoin), <span style="color: #00BB00; font-weight: bold;">FOS</span> (fosfomycin), <span style="color: #00BB00; font-weight: bold;">LNZ</span> (linezolid), <span style="color: #00BB00; font-weight: bold;">CIP</span> (ciprofloxacin), <span style="color: #00BB00; font-weight: bold;">MFX</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (moxifloxacin), <span style="color: #00BB00; font-weight: bold;">VAN</span> (vancomycin), <span style="color: #00BB00; font-weight: bold;">TCY</span> (tetracycline), <span style="color: #00BB00; font-weight: bold;">DOX</span> (doxycycline), <span style="color: #00BB00; font-weight: bold;">ERY</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (erythromycin), <span style="color: #00BB00; font-weight: bold;">CLI</span> (clindamycin), <span style="color: #00BB00; font-weight: bold;">AZM</span> (azithromycin), <span style="color: #00BB00; font-weight: bold;">MTR</span> (metronidazole),</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00; font-weight: bold;">CHL</span> (chloramphenicol), <span style="color: #00BB00; font-weight: bold;">COL</span> (colistin), and <span style="color: #00BB00; font-weight: bold;">RIF</span> (rifampicin)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2,000 × 23</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> OXA FLC AMX AMC AMP CXM KAN TMP NIT FOS LNZ CIP MFX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
@@ -468,7 +467,7 @@ my_data_with_all_these_columns %&amp;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">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns '<span style="font-weight: bold;">IPM</span>' (imipenem) and '<span style="font-weight: bold;">MEM</span>' (meropenem)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 55 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
@@ -490,7 +489,7 @@ my_data_with_all_these_columns %&amp;gt;%
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># TCY &lt;sir&gt;, TGC &lt;sir&gt;, DOX &lt;sir&gt;, ERY &lt;sir&gt;, CLI &lt;sir&gt;, AZM &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># IPM &lt;sir&gt;, MEM &lt;sir&gt;, MTR &lt;sir&gt;, CHL &lt;sir&gt;, COL &lt;sir&gt;, MUP &lt;sir&gt;, …</span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">example_isolates</span>, <span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns '<span style="font-weight: bold;">IPM</span>' (imipenem) and '<span style="font-weight: bold;">MEM</span>' (meropenem)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 55 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
@@ -514,7 +513,7 @@ my_data_with_all_these_columns %&amp;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">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns '<span style="font-weight: bold;">IPM</span>' (imipenem) and '<span style="font-weight: bold;">MEM</span>' (meropenem)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Filtering any of columns '<span style="font-weight: bold;">IPM</span>' and '<span style="font-weight: bold;">MEM</span>' to contain value "S", "I" or "R"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 962 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
@@ -537,7 +536,7 @@ my_data_with_all_these_columns %&amp;gt;%
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># TCY &lt;sir&gt;, TGC &lt;sir&gt;, DOX &lt;sir&gt;, ERY &lt;sir&gt;, CLI &lt;sir&gt;, AZM &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># IPM &lt;sir&gt;, MEM &lt;sir&gt;, MTR &lt;sir&gt;, CHL &lt;sir&gt;, COL &lt;sir&gt;, MUP &lt;sir&gt;, …</span></span>
<span class="r-in"><span><span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns '<span style="font-weight: bold;">IPM</span>' (imipenem) and '<span style="font-weight: bold;">MEM</span>' (meropenem)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Filtering all of columns '<span style="font-weight: bold;">IPM</span>' and '<span style="font-weight: bold;">MEM</span>' to contain value "S", "I" or "R"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 756 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
@@ -562,9 +561,9 @@ my_data_with_all_these_columns %&amp;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">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns '<span style="font-weight: bold;">IPM</span>' (imipenem) and '<span style="font-weight: bold;">MEM</span>' (meropenem)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns '<span style="font-weight: bold;">GEN</span>' (gentamicin), '<span style="font-weight: bold;">TOB</span>' (tobramycin),</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> '<span style="font-weight: bold;">AMK</span>' (amikacin), and '<span style="font-weight: bold;">KAN</span>' (kanamycin)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?aminoglycosides()` using columns <span style="color: #00BB00; font-weight: bold;">GEN</span> (gentamicin), <span style="color: #00BB00; font-weight: bold;">TOB</span> (tobramycin),</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00; font-weight: bold;">AMK</span> (amikacin), and <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 26 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
@@ -588,11 +587,10 @@ my_data_with_all_these_columns %&amp;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">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns '<span style="font-weight: bold;">IPM</span>' (imipenem) and '<span style="font-weight: bold;">MEM</span>' (meropenem)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `penicillins()` using columns '<span style="font-weight: bold;">PEN</span>' (benzylpenicillin), '<span style="font-weight: bold;">OXA</span>'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (oxacillin), '<span style="font-weight: bold;">FLC</span>' (flucloxacillin), '<span style="font-weight: bold;">AMX</span>' (amoxicillin), '<span style="font-weight: bold;">AMC</span>'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (amoxicillin/clavulanic acid), '<span style="font-weight: bold;">AMP</span>' (ampicillin), and '<span style="font-weight: bold;">TZP</span>'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (piperacillin/tazobactam)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?penicillins()` using columns <span style="color: #00BB00; font-weight: bold;">PEN</span> (benzylpenicillin), <span style="color: #00BB00; font-weight: bold;">OXA</span> (oxacillin),</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00; font-weight: bold;">FLC</span> (flucloxacillin), <span style="color: #00BB00; font-weight: bold;">AMX</span> (amoxicillin), <span style="color: #00BB00; font-weight: bold;">AMC</span> (amoxicillin/clavulanic acid),</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00; font-weight: bold;">AMP</span> (ampicillin), and <span style="color: #00BB00; font-weight: bold;">TZP</span> (piperacillin/tazobactam)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 55 × 7</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> PEN OXA FLC AMX AMC AMP TZP </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
@@ -614,18 +612,16 @@ my_data_with_all_these_columns %&amp;gt;%
<span class="r-in"><span><span class="co"># drugs are both omitted since benzylpenicillin is not administrable per os</span></span></span>
<span class="r-in"><span><span class="co"># and erythromycin is not a penicillin:</span></span></span>
<span class="r-in"><span><span class="va">example_isolates</span><span class="op">[</span>, <span class="fu">penicillins</span><span class="op">(</span><span class="op">)</span> <span class="op">&amp;</span> <span class="fu">administrable_per_os</span><span class="op">(</span><span class="op">)</span><span class="op">]</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `penicillins()` using columns '<span style="font-weight: bold;">PEN</span>' (benzylpenicillin), '<span style="font-weight: bold;">OXA</span>'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (oxacillin), '<span style="font-weight: bold;">FLC</span>' (flucloxacillin), '<span style="font-weight: bold;">AMX</span>' (amoxicillin), '<span style="font-weight: bold;">AMC</span>'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (amoxicillin/clavulanic acid), '<span style="font-weight: bold;">AMP</span>' (ampicillin), and '<span style="font-weight: bold;">TZP</span>'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (piperacillin/tazobactam)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `administrable_per_os()` using columns '<span style="font-weight: bold;">OXA</span>' (oxacillin), '<span style="font-weight: bold;">FLC</span>'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (flucloxacillin), '<span style="font-weight: bold;">AMX</span>' (amoxicillin), '<span style="font-weight: bold;">AMC</span>' (amoxicillin/clavulanic acid),</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> '<span style="font-weight: bold;">AMP</span>' (ampicillin), '<span style="font-weight: bold;">CXM</span>' (cefuroxime), '<span style="font-weight: bold;">KAN</span>' (kanamycin), '<span style="font-weight: bold;">TMP</span>'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (trimethoprim), '<span style="font-weight: bold;">NIT</span>' (nitrofurantoin), '<span style="font-weight: bold;">FOS</span>' (fosfomycin), '<span style="font-weight: bold;">LNZ</span>'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (linezolid), '<span style="font-weight: bold;">CIP</span>' (ciprofloxacin), '<span style="font-weight: bold;">MFX</span>' (moxifloxacin), '<span style="font-weight: bold;">VAN</span>' (vancomycin),</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> '<span style="font-weight: bold;">TCY</span>' (tetracycline), '<span style="font-weight: bold;">DOX</span>' (doxycycline), '<span style="font-weight: bold;">ERY</span>' (erythromycin), '<span style="font-weight: bold;">CLI</span>'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (clindamycin), '<span style="font-weight: bold;">AZM</span>' (azithromycin), '<span style="font-weight: bold;">MTR</span>' (metronidazole), '<span style="font-weight: bold;">CHL</span>'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (chloramphenicol), '<span style="font-weight: bold;">COL</span>' (colistin), and '<span style="font-weight: bold;">RIF</span>' (rifampicin)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?penicillins()` using columns <span style="color: #00BB00; font-weight: bold;">PEN</span> (benzylpenicillin), <span style="color: #00BB00; font-weight: bold;">OXA</span> (oxacillin),</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00; font-weight: bold;">FLC</span> (flucloxacillin), <span style="color: #00BB00; font-weight: bold;">AMX</span> (amoxicillin), <span style="color: #00BB00; font-weight: bold;">AMC</span> (amoxicillin/clavulanic acid),</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00; font-weight: bold;">AMP</span> (ampicillin), and <span style="color: #00BB00; font-weight: bold;">TZP</span> (piperacillin/tazobactam)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?administrable_per_os()` using columns <span style="color: #00BB00; font-weight: bold;">OXA</span> (oxacillin), <span style="color: #00BB00; font-weight: bold;">FLC</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (flucloxacillin), <span style="color: #00BB00; font-weight: bold;">AMX</span> (amoxicillin), <span style="color: #00BB00; font-weight: bold;">AMC</span> (amoxicillin/clavulanic acid), <span style="color: #00BB00; font-weight: bold;">AMP</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (ampicillin), <span style="color: #00BB00; font-weight: bold;">CXM</span> (cefuroxime), <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin), <span style="color: #00BB00; font-weight: bold;">TMP</span> (trimethoprim), <span style="color: #00BB00; font-weight: bold;">NIT</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (nitrofurantoin), <span style="color: #00BB00; font-weight: bold;">FOS</span> (fosfomycin), <span style="color: #00BB00; font-weight: bold;">LNZ</span> (linezolid), <span style="color: #00BB00; font-weight: bold;">CIP</span> (ciprofloxacin), <span style="color: #00BB00; font-weight: bold;">MFX</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (moxifloxacin), <span style="color: #00BB00; font-weight: bold;">VAN</span> (vancomycin), <span style="color: #00BB00; font-weight: bold;">TCY</span> (tetracycline), <span style="color: #00BB00; font-weight: bold;">DOX</span> (doxycycline), <span style="color: #00BB00; font-weight: bold;">ERY</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (erythromycin), <span style="color: #00BB00; font-weight: bold;">CLI</span> (clindamycin), <span style="color: #00BB00; font-weight: bold;">AZM</span> (azithromycin), <span style="color: #00BB00; font-weight: bold;">MTR</span> (metronidazole),</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00; font-weight: bold;">CHL</span> (chloramphenicol), <span style="color: #00BB00; font-weight: bold;">COL</span> (colistin), and <span style="color: #00BB00; font-weight: bold;">RIF</span> (rifampicin)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2,000 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> OXA FLC AMX AMC AMP </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
@@ -645,11 +641,11 @@ my_data_with_all_these_columns %&amp;gt;%
<span class="r-in"><span><span class="co"># very flexible. For instance, to select antimicrobials with an oral DDD</span></span></span>
<span class="r-in"><span><span class="co"># of at least 1 gram:</span></span></span>
<span class="r-in"><span><span class="va">example_isolates</span><span class="op">[</span>, <span class="fu">amr_selector</span><span class="op">(</span><span class="va">oral_ddd</span> <span class="op">&gt;</span> <span class="fl">1</span> <span class="op">&amp;</span> <span class="va">oral_units</span> <span class="op">==</span> <span class="st">"g"</span><span class="op">)</span><span class="op">]</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `amr_selector(oral_ddd &gt; 1 &amp; oral_units == "g")` using columns '<span style="font-weight: bold;">OXA</span>'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (oxacillin), '<span style="font-weight: bold;">FLC</span>' (flucloxacillin), '<span style="font-weight: bold;">AMX</span>' (amoxicillin), '<span style="font-weight: bold;">AMC</span>'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (amoxicillin/clavulanic acid), '<span style="font-weight: bold;">AMP</span>' (ampicillin), '<span style="font-weight: bold;">KAN</span>' (kanamycin), '<span style="font-weight: bold;">FOS</span>'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (fosfomycin), '<span style="font-weight: bold;">LNZ</span>' (linezolid), '<span style="font-weight: bold;">VAN</span>' (vancomycin), '<span style="font-weight: bold;">ERY</span>' (erythromycin),</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> '<span style="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-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?amr_selector(oral_ddd &gt; 1 &amp; oral_units == "g")` using columns <span style="color: #00BB00; font-weight: bold;">OXA</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (oxacillin), <span style="color: #00BB00; font-weight: bold;">FLC</span> (flucloxacillin), <span style="color: #00BB00; font-weight: bold;">AMX</span> (amoxicillin), <span style="color: #00BB00; font-weight: bold;">AMC</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (amoxicillin/clavulanic acid), <span style="color: #00BB00; font-weight: bold;">AMP</span> (ampicillin), <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin), <span style="color: #00BB00; font-weight: bold;">FOS</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (fosfomycin), <span style="color: #00BB00; font-weight: bold;">LNZ</span> (linezolid), <span style="color: #00BB00; font-weight: bold;">VAN</span> (vancomycin), <span style="color: #00BB00; font-weight: bold;">ERY</span> (erythromycin), <span style="color: #00BB00; font-weight: bold;">CLI</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (clindamycin), <span style="color: #00BB00; font-weight: bold;">MTR</span> (metronidazole), and <span style="color: #00BB00; font-weight: bold;">CHL</span> (chloramphenicol)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2,000 × 13</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> OXA FLC AMX AMC AMP KAN FOS LNZ VAN ERY CLI MTR CHL </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
@@ -689,17 +685,17 @@ my_data_with_all_these_columns %&amp;gt;%
<span class="r-msg co"><span class="r-pr">#&gt;</span> The following objects are masked from ‘package:AMR’:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> %like%, like</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns '<span style="font-weight: bold;">IPM</span>' (imipenem) and '<span style="font-weight: bold;">MEM</span>' (meropenem)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>It should never be needed to print an antimicrobial selector class. Are you</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> using <span style="color: #0000BB;">data.table</span>? Then add the argument `with = FALSE`, see our examples at</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> `amr_selector()` (`?AMR::amr_selector()`).</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'amr_selector'</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> `?amr_selector()`.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;amr_selector&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [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">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns '<span style="font-weight: bold;">IPM</span>' (imipenem) and '<span style="font-weight: bold;">MEM</span>' (meropenem)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> IPM MEM</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> &lt;sir&gt; &lt;sir&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1: &lt;NA&gt; &lt;NA&gt;</span>
@@ -718,8 +714,8 @@ my_data_with_all_these_columns %&amp;gt;%
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://r-datatable.com" class="external-link">"data.table"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="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">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns '<span style="font-weight: bold;">GEN</span>' (gentamicin), '<span style="font-weight: bold;">TOB</span>' (tobramycin),</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> '<span style="font-weight: bold;">AMK</span>' (amikacin), and '<span style="font-weight: bold;">KAN</span>' (kanamycin)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?aminoglycosides()` using columns <span style="color: #00BB00; font-weight: bold;">GEN</span> (gentamicin), <span style="color: #00BB00; font-weight: bold;">TOB</span> (tobramycin),</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00; font-weight: bold;">AMK</span> (amikacin), and <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo GEN TOB AMK KAN</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> &lt;mo&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1: B_ESCHR_COLI &lt;NA&gt; &lt;NA&gt; &lt;NA&gt; &lt;NA&gt;</span>
@@ -736,9 +732,9 @@ my_data_with_all_these_columns %&amp;gt;%
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://r-datatable.com" class="external-link">"data.table"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="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">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns '<span style="font-weight: bold;">IPM</span>' (imipenem) and '<span style="font-weight: bold;">MEM</span>' (meropenem)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns '<span style="font-weight: bold;">GEN</span>' (gentamicin), '<span style="font-weight: bold;">TOB</span>' (tobramycin),</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> '<span style="font-weight: bold;">AMK</span>' (amikacin), and '<span style="font-weight: bold;">KAN</span>' (kanamycin)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?aminoglycosides()` using columns <span style="color: #00BB00; font-weight: bold;">GEN</span> (gentamicin), <span style="color: #00BB00; font-weight: bold;">TOB</span> (tobramycin),</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00; font-weight: bold;">AMK</span> (amikacin), and <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> IPM MEM GEN TOB AMK KAN</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> &lt;sir&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1: &lt;NA&gt; &lt;NA&gt; &lt;NA&gt; &lt;NA&gt; &lt;NA&gt; &lt;NA&gt;</span>
@@ -757,7 +753,7 @@ my_data_with_all_these_columns %&amp;gt;%
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://r-datatable.com" class="external-link">"data.table"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="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">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns '<span style="font-weight: bold;">IPM</span>' (imipenem) and '<span style="font-weight: bold;">MEM</span>' (meropenem)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> &lt;Date&gt; &lt;char&gt; &lt;num&gt; &lt;char&gt; &lt;char&gt; &lt;mo&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1: 2002-01-19 738003 71 M Clinical B_ESCHR_COLI R &lt;NA&gt; &lt;NA&gt;</span>
@@ -826,11 +822,10 @@ my_data_with_all_these_columns %&amp;gt;%
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://r-datatable.com" class="external-link">"data.table"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="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">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns '<span style="font-weight: bold;">IPM</span>' (imipenem) and '<span style="font-weight: bold;">MEM</span>' (meropenem)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `penicillins()` using columns '<span style="font-weight: bold;">PEN</span>' (benzylpenicillin), '<span style="font-weight: bold;">OXA</span>'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (oxacillin), '<span style="font-weight: bold;">FLC</span>' (flucloxacillin), '<span style="font-weight: bold;">AMX</span>' (amoxicillin), '<span style="font-weight: bold;">AMC</span>'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (amoxicillin/clavulanic acid), '<span style="font-weight: bold;">AMP</span>' (ampicillin), and '<span style="font-weight: bold;">TZP</span>'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (piperacillin/tazobactam)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?penicillins()` using columns <span style="color: #00BB00; font-weight: bold;">PEN</span> (benzylpenicillin), <span style="color: #00BB00; font-weight: bold;">OXA</span> (oxacillin),</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00; font-weight: bold;">FLC</span> (flucloxacillin), <span style="color: #00BB00; font-weight: bold;">AMX</span> (amoxicillin), <span style="color: #00BB00; font-weight: bold;">AMC</span> (amoxicillin/clavulanic acid),</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00; font-weight: bold;">AMP</span> (ampicillin), and <span style="color: #00BB00; font-weight: bold;">TZP</span> (piperacillin/tazobactam)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> PEN OXA FLC AMX AMC AMP TZP</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> &lt;sir&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1: R &lt;NA&gt; &lt;NA&gt; &lt;NA&gt; I &lt;NA&gt; &lt;NA&gt;</span>

111
reference/antimicrobial_selectors.md
View File

@@ -669,8 +669,8 @@ example_isolates
# you can use the selectors separately to retrieve all possible antimicrobials:
carbapenems()
#> ℹ in `carbapenems()` (`?AMR::carbapenems()`): Imipenem/EDTA (`IPE`) and
#> meropenem/nacubactam (`MNC`) are not included since `only_treatable = TRUE`.
#> 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.:
#> • your_data %>% select(carbapenems())
@@ -678,7 +678,7 @@ carbapenems()
#> • your_data %>% filter(any(carbapenems() == "R"))
#> • your_data[, carbapenems()]
#> • your_data[, c("column_a", "column_b", carbapenems())]
#> Class 'ab'
#> Class <ab>
#> [1] BIA DOR ETP IMR IPM MEM MEV PAN RIA RIT RZM TAN TBP
@@ -777,7 +777,7 @@ identical(x, y) && identical(y, z)
# select columns 'IPM' (imipenem) and 'MEM' (meropenem)
example_isolates[, carbapenems()]
#> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> ℹ For `?carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> # A tibble: 2,000 × 2
#> IPM MEM
#> <sir> <sir>
@@ -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>
@@ -814,14 +814,13 @@ example_isolates[, c("mo", aminoglycosides())]
# select only antimicrobials with DDDs for oral treatment
example_isolates[, administrable_per_os()]
#> ℹ For `administrable_per_os()` using columns 'OXA' (oxacillin), 'FLC'
#> (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)
#> ℹ For `?administrable_per_os()` using columns OXA (oxacillin), FLC
#> (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)
#> # 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>
@@ -841,7 +840,7 @@ example_isolates[, administrable_per_os()]
# filter using any() or all()
example_isolates[any(carbapenems() == "R"), ]
#> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> ℹ For `?carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> # A tibble: 55 × 46
#> date patient age gender ward mo PEN OXA FLC AMX
#> <date> <chr> <dbl> <chr> <chr> <mo> <sir> <sir> <sir> <sir>
@@ -863,7 +862,7 @@ example_isolates[any(carbapenems() == "R"), ]
#> # TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>,
#> # IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, …
subset(example_isolates, any(carbapenems() == "R"))
#> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> ℹ For `?carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> # A tibble: 55 × 46
#> date patient age gender ward mo PEN OXA FLC AMX
#> <date> <chr> <dbl> <chr> <chr> <mo> <sir> <sir> <sir> <sir>
@@ -887,7 +886,7 @@ subset(example_isolates, any(carbapenems() == "R"))
# filter on any or all results in the carbapenem columns (i.e., IPM, MEM):
example_isolates[any(carbapenems()), ]
#> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> ℹ For `?carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> ℹ Filtering any of columns 'IPM' and 'MEM' to contain value "S", "I" or "R"
#> # A tibble: 962 × 46
#> date patient age gender ward mo PEN OXA FLC AMX
@@ -910,7 +909,7 @@ example_isolates[any(carbapenems()), ]
#> # TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>,
#> # IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, …
example_isolates[all(carbapenems()), ]
#> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> ℹ For `?carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> ℹ Filtering all of columns 'IPM' and 'MEM' to contain value "S", "I" or "R"
#> # A tibble: 756 × 46
#> date patient age gender ward mo PEN OXA FLC AMX
@@ -935,9 +934,9 @@ 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 `?carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> 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>
@@ -961,11 +960,10 @@ example_isolates[all(c(carbapenems(), aminoglycosides()) == "R"), ]
# filter + select in one go: get penicillins in carbapenem-resistant strains
example_isolates[any(carbapenems() == "R"), penicillins()]
#> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> ℹ For `penicillins()` using columns 'PEN' (benzylpenicillin), 'OXA'
#> (oxacillin), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC'
#> (amoxicillin/clavulanic acid), 'AMP' (ampicillin), and 'TZP'
#> (piperacillin/tazobactam)
#> ℹ For `?carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> ℹ For `?penicillins()` using columns PEN (benzylpenicillin), OXA (oxacillin),
#> FLC (flucloxacillin), AMX (amoxicillin), AMC (amoxicillin/clavulanic acid),
#> AMP (ampicillin), and TZP (piperacillin/tazobactam)
#> # A tibble: 55 × 7
#> PEN OXA FLC AMX AMC AMP TZP
#> <sir> <sir> <sir> <sir> <sir> <sir> <sir>
@@ -987,18 +985,16 @@ example_isolates[any(carbapenems() == "R"), penicillins()]
# drugs are both omitted since benzylpenicillin is not administrable per os
# and erythromycin is not a penicillin:
example_isolates[, penicillins() & administrable_per_os()]
#> ℹ For `penicillins()` using columns 'PEN' (benzylpenicillin), 'OXA'
#> (oxacillin), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC'
#> (amoxicillin/clavulanic acid), 'AMP' (ampicillin), and 'TZP'
#> (piperacillin/tazobactam)
#> ℹ For `administrable_per_os()` using columns 'OXA' (oxacillin), 'FLC'
#> (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)
#> ℹ For `?penicillins()` using columns PEN (benzylpenicillin), OXA (oxacillin),
#> FLC (flucloxacillin), AMX (amoxicillin), AMC (amoxicillin/clavulanic acid),
#> AMP (ampicillin), and TZP (piperacillin/tazobactam)
#> ℹ For `?administrable_per_os()` using columns OXA (oxacillin), FLC
#> (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)
#> # A tibble: 2,000 × 5
#> OXA FLC AMX AMC AMP
#> <sir> <sir> <sir> <sir> <sir>
@@ -1018,11 +1014,11 @@ example_isolates[, penicillins() & administrable_per_os()]
# very flexible. For instance, to select antimicrobials with an oral DDD
# of at least 1 gram:
example_isolates[, amr_selector(oral_ddd > 1 & oral_units == "g")]
#> ℹ For `amr_selector(oral_ddd > 1 & oral_units == "g")` using columns 'OXA'
#> (oxacillin), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC'
#> (amoxicillin/clavulanic acid), 'AMP' (ampicillin), 'KAN' (kanamycin), 'FOS'
#> (fosfomycin), 'LNZ' (linezolid), 'VAN' (vancomycin), 'ERY' (erythromycin),
#> 'CLI' (clindamycin), 'MTR' (metronidazole), and 'CHL' (chloramphenicol)
#> ℹ For `?amr_selector(oral_ddd > 1 & oral_units == "g")` using columns OXA
#> (oxacillin), FLC (flucloxacillin), AMX (amoxicillin), AMC
#> (amoxicillin/clavulanic acid), AMP (ampicillin), KAN (kanamycin), FOS
#> (fosfomycin), LNZ (linezolid), VAN (vancomycin), ERY (erythromycin), CLI
#> (clindamycin), MTR (metronidazole), and CHL (chloramphenicol)
#> # A tibble: 2,000 × 13
#> OXA FLC AMX AMC AMP KAN FOS LNZ VAN ERY CLI MTR CHL
#> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir>
@@ -1062,17 +1058,17 @@ if (require("data.table")) {
#> The following objects are masked from ‘package:AMR’:
#>
#> %like%, like
#> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> ℹ For `?carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> Warning: It should never be needed to print an antimicrobial selector class. Are you
#> using data.table? Then add the argument `with = FALSE`, see our examples at
#> `amr_selector()` (`?AMR::amr_selector()`).
#> Class 'amr_selector'
#> `?amr_selector()`.
#> Class <amr_selector>
#> [1] IPM MEM
if (require("data.table")) {
# so `with = FALSE` is required
dt[, carbapenems(), with = FALSE]
}
#> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> ℹ For `?carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> IPM MEM
#> <sir> <sir>
#> 1: <NA> <NA>
@@ -1091,8 +1087,8 @@ 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>
@@ -1109,9 +1105,9 @@ if (require("data.table")) {
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 `?carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> 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>
@@ -1130,7 +1126,7 @@ if (require("data.table")) {
if (require("data.table")) {
dt[any(carbapenems() == "S"), ]
}
#> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> ℹ For `?carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> date patient age gender ward mo PEN OXA FLC
#> <Date> <char> <num> <char> <char> <mo> <sir> <sir> <sir>
#> 1: 2002-01-19 738003 71 M Clinical B_ESCHR_COLI R <NA> <NA>
@@ -1199,11 +1195,10 @@ if (require("data.table")) {
if (require("data.table")) {
dt[any(carbapenems() == "S"), penicillins(), with = FALSE]
}
#> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> ℹ For `penicillins()` using columns 'PEN' (benzylpenicillin), 'OXA'
#> (oxacillin), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC'
#> (amoxicillin/clavulanic acid), 'AMP' (ampicillin), and 'TZP'
#> (piperacillin/tazobactam)
#> ℹ For `?carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> ℹ For `?penicillins()` using columns PEN (benzylpenicillin), OXA (oxacillin),
#> FLC (flucloxacillin), AMX (amoxicillin), AMC (amoxicillin/clavulanic acid),
#> AMP (ampicillin), and TZP (piperacillin/tazobactam)
#> PEN OXA FLC AMX AMC AMP TZP
#> <sir> <sir> <sir> <sir> <sir> <sir> <sir>
#> 1: R <NA> <NA> <NA> I <NA> <NA>

2
reference/antimicrobials.html
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@@ -9,7 +9,7 @@ The antibiotics data set has been renamed to antimicrobials. The old name will b
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

18
reference/as.ab.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -141,28 +141,28 @@
<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="co"># these examples all return "ERY", the ID of erythromycin:</span></span></span>
<span class="r-in"><span><span class="fu">as.ab</span><span class="op">(</span><span class="st">"J01FA01"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'ab'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;ab&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] ERY</span>
<span class="r-in"><span><span class="fu">as.ab</span><span class="op">(</span><span class="st">"J 01 FA 01"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'ab'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;ab&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] ERY</span>
<span class="r-in"><span><span class="fu">as.ab</span><span class="op">(</span><span class="st">"Erythromycin"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'ab'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;ab&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] ERY</span>
<span class="r-in"><span><span class="fu">as.ab</span><span class="op">(</span><span class="st">"eryt"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'ab'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;ab&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] ERY</span>
<span class="r-in"><span><span class="fu">as.ab</span><span class="op">(</span><span class="st">"ERYT"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'ab'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;ab&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] ERY</span>
<span class="r-in"><span><span class="fu">as.ab</span><span class="op">(</span><span class="st">"ERY"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'ab'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;ab&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] ERY</span>
<span class="r-in"><span><span class="fu">as.ab</span><span class="op">(</span><span class="st">"eritromicine"</span><span class="op">)</span> <span class="co"># spelled wrong, yet works</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'ab'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;ab&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] ERY</span>
<span class="r-in"><span><span class="fu">as.ab</span><span class="op">(</span><span class="st">"Erythrocin"</span><span class="op">)</span> <span class="co"># trade name</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'ab'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;ab&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] ERY</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># spelling from different languages and dyslexia are no problem</span></span></span>

16
reference/as.ab.md
View File

@@ -156,28 +156,28 @@ repository](https://github.com/msberends/AMR/tree/main/data-raw/datasets).
``` r
# these examples all return "ERY", the ID of erythromycin:
as.ab("J01FA01")
#> Class 'ab'
#> Class <ab>
#> [1] ERY
as.ab("J 01 FA 01")
#> Class 'ab'
#> Class <ab>
#> [1] ERY
as.ab("Erythromycin")
#> Class 'ab'
#> Class <ab>
#> [1] ERY
as.ab("eryt")
#> Class 'ab'
#> Class <ab>
#> [1] ERY
as.ab("ERYT")
#> Class 'ab'
#> Class <ab>
#> [1] ERY
as.ab("ERY")
#> Class 'ab'
#> Class <ab>
#> [1] ERY
as.ab("eritromicine") # spelled wrong, yet works
#> Class 'ab'
#> Class <ab>
#> [1] ERY
as.ab("Erythrocin") # trade name
#> Class 'ab'
#> Class <ab>
#> [1] ERY
# spelling from different languages and dyslexia are no problem

22
reference/as.av.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -130,35 +130,35 @@
<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="co"># these examples all return "ACI", the ID of aciclovir:</span></span></span>
<span class="r-in"><span><span class="fu">as.av</span><span class="op">(</span><span class="st">"J05AB01"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'av'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;av&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] ACI</span>
<span class="r-in"><span><span class="fu">as.av</span><span class="op">(</span><span class="st">"J 05 AB 01"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'av'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;av&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] ACI</span>
<span class="r-in"><span><span class="fu">as.av</span><span class="op">(</span><span class="st">"Aciclovir"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'av'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;av&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] ACI</span>
<span class="r-in"><span><span class="fu">as.av</span><span class="op">(</span><span class="st">"aciclo"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'av'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;av&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] ACI</span>
<span class="r-in"><span><span class="fu">as.av</span><span class="op">(</span><span class="st">" aciclo 123"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'av'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;av&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] ACI</span>
<span class="r-in"><span><span class="fu">as.av</span><span class="op">(</span><span class="st">"ACICL"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'av'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;av&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] ACI</span>
<span class="r-in"><span><span class="fu">as.av</span><span class="op">(</span><span class="st">"ACI"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'av'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;av&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] ACI</span>
<span class="r-in"><span><span class="fu">as.av</span><span class="op">(</span><span class="st">"Virorax"</span><span class="op">)</span> <span class="co"># trade name</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'av'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;av&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] ACI</span>
<span class="r-in"><span><span class="fu">as.av</span><span class="op">(</span><span class="st">"Zovirax"</span><span class="op">)</span> <span class="co"># trade name</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'av'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;av&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] ACI</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">as.av</span><span class="op">(</span><span class="st">"acyklofir"</span><span class="op">)</span> <span class="co"># severe spelling error, yet works</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'av'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;av&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] ACI</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># use av_* functions to get a specific properties (see ?av_property);</span></span></span>

20
reference/as.av.md
View File

@@ -137,35 +137,35 @@ repository](https://github.com/msberends/AMR/tree/main/data-raw/datasets).
``` r
# these examples all return "ACI", the ID of aciclovir:
as.av("J05AB01")
#> Class 'av'
#> Class <av>
#> [1] ACI
as.av("J 05 AB 01")
#> Class 'av'
#> Class <av>
#> [1] ACI
as.av("Aciclovir")
#> Class 'av'
#> Class <av>
#> [1] ACI
as.av("aciclo")
#> Class 'av'
#> Class <av>
#> [1] ACI
as.av(" aciclo 123")
#> Class 'av'
#> Class <av>
#> [1] ACI
as.av("ACICL")
#> Class 'av'
#> Class <av>
#> [1] ACI
as.av("ACI")
#> Class 'av'
#> Class <av>
#> [1] ACI
as.av("Virorax") # trade name
#> Class 'av'
#> Class <av>
#> [1] ACI
as.av("Zovirax") # trade name
#> Class 'av'
#> Class <av>
#> [1] ACI
as.av("acyklofir") # severe spelling error, yet works
#> Class 'av'
#> Class <av>
#> [1] ACI
# use av_* functions to get a specific properties (see ?av_property);

4
reference/as.disk.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -128,7 +128,7 @@
<span class="r-in"><span> ab <span class="op">=</span> <span class="st">"ampicillin"</span>, <span class="co"># and `ab` with as.ab()</span></span></span>
<span class="r-in"><span> guideline <span class="op">=</span> <span class="st">"EUCAST"</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] R</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># interpret whole data set, pretend to be all from urinary tract infections:</span></span></span>

2
reference/as.disk.md
View File

@@ -86,7 +86,7 @@ as.sir(
ab = "ampicillin", # and `ab` with as.ab()
guideline = "EUCAST"
)
#> Class 'sir'
#> Class <sir>
#> [1] R
# interpret whole data set, pretend to be all from urinary tract infections:

18
reference/as.mic.html
View File

@@ -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="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -115,7 +115,7 @@
<p>This class for MIC values is a quite a special data type: formally it is an ordered <a href="https://rdrr.io/pkg/data.table/man/fctr.html" class="external-link">factor</a> with valid MIC values as <a href="https://rdrr.io/pkg/data.table/man/fctr.html" class="external-link">factor</a> levels (to make sure only valid MIC values are retained), but for any mathematical operation it acts as decimal numbers:</p>
<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a>x <span class="ot">&lt;-</span> <span class="fu">random_mic</span>(<span class="dv">10</span>)</span>
<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a>x</span>
<span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a><span class="co">#&gt; Class 'mic'</span></span>
<span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a><span class="co">#&gt; Class &lt;mic&gt;</span></span>
<span id="cb1-4"><a href="#cb1-4" tabindex="-1"></a><span class="co">#&gt; [1] 16 1 8 8 64 &gt;=128 0.0625 32 32 16</span></span>
<span id="cb1-5"><a href="#cb1-5" tabindex="-1"></a></span>
<span id="cb1-6"><a href="#cb1-6" tabindex="-1"></a><span class="fu">is.factor</span>(x)</span>
@@ -128,7 +128,7 @@
<span id="cb1-13"><a href="#cb1-13" tabindex="-1"></a><span class="co">#&gt; [1] 26</span></span></code></pre><p></p></div>
<p>This makes it possible to maintain operators that often come with MIC values, such "&gt;=" and "&lt;=", even when filtering using <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> values in data analysis, e.g.:</p>
<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a>x[x <span class="sc">&gt;</span> <span class="dv">4</span>]</span>
<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a><span class="co">#&gt; Class 'mic'</span></span>
<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a><span class="co">#&gt; Class &lt;mic&gt;</span></span>
<span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a><span class="co">#&gt; [1] 16 8 8 64 &gt;=128 32 32 16</span></span>
<span id="cb1-4"><a href="#cb1-4" tabindex="-1"></a></span>
<span id="cb1-5"><a href="#cb1-5" tabindex="-1"></a>df <span class="ot">&lt;-</span> <span class="fu">data.frame</span>(x, <span class="at">hospital =</span> <span class="st">"A"</span>)</span>
@@ -158,14 +158,14 @@
<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">mic_data</span> <span class="op">&lt;-</span> <span class="fu">as.mic</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">"&gt;=32"</span>, <span class="st">"1.0"</span>, <span class="st">"1"</span>, <span class="st">"1.00"</span>, <span class="fl">8</span>, <span class="st">"&lt;=0.128"</span>, <span class="st">"8"</span>, <span class="st">"16"</span>, <span class="st">"16"</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">mic_data</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;mic&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] &gt;=32 1 1 1 8 &lt;=0.128 8 16 16 </span>
<span class="r-in"><span><span class="fu">is.mic</span><span class="op">(</span><span class="va">mic_data</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># this can also coerce combined MIC/SIR values:</span></span></span>
<span class="r-in"><span><span class="fu">as.mic</span><span class="op">(</span><span class="st">"&lt;=0.002; S"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;mic&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] &lt;=0.002</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># mathematical processing treats MICs as, and returns, numeric values</span></span></span>
@@ -179,14 +179,14 @@
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># rescale MICs using rescale_mic()</span></span></span>
<span class="r-in"><span><span class="fu">rescale_mic</span><span class="op">(</span><span class="va">mic_data</span>, mic_range <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">4</span>, <span class="fl">16</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;mic&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] &gt;=16 &lt;=4 &lt;=4 &lt;=4 8 &lt;=4 8 &gt;=16 &gt;=16</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># round up to nearest log2 level, e.g. for CLSI breakpoint interpretation:</span></span></span>
<span class="r-in"><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="op">:</span><span class="fl">8</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1 2 3 4 5 6 7 8</span>
<span class="r-in"><span><span class="fu">as.mic</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="op">:</span><span class="fl">8</span><span class="op">)</span>, round_to_next_log2 <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;mic&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1 2 4 4 8 8 8 8</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># interpret MIC values</span></span></span>
@@ -196,7 +196,7 @@
<span class="r-in"><span> ab <span class="op">=</span> <span class="st">"AMX"</span>,</span></span>
<span class="r-in"><span> guideline <span class="op">=</span> <span class="st">"EUCAST"</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] R</span>
<span class="r-in"><span><span class="fu"><a href="as.sir.html">as.sir</a></span><span class="op">(</span></span></span>
<span class="r-in"><span> x <span class="op">=</span> <span class="fu">as.mic</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">0.01</span>, <span class="fl">2</span>, <span class="fl">4</span>, <span class="fl">8</span><span class="op">)</span><span class="op">)</span>,</span></span>
@@ -204,7 +204,7 @@
<span class="r-in"><span> ab <span class="op">=</span> <span class="st">"AMX"</span>,</span></span>
<span class="r-in"><span> guideline <span class="op">=</span> <span class="st">"EUCAST"</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] S R R R</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># plot MIC values, see ?plot</span></span></span>

16
reference/as.mic.md
View File

@@ -96,7 +96,7 @@ operation it acts as decimal numbers:
x <- random_mic(10)
x
#> Class 'mic'
#> Class <mic>
#> [1] 16 1 8 8 64 >=128 0.0625 32 32 16
is.factor(x)
@@ -114,7 +114,7 @@ values, such "\>=" and "\<=", even when filtering using
e.g.:
x[x > 4]
#> Class 'mic'
#> Class <mic>
#> [1] 16 8 8 64 >=128 32 32 16
df <- data.frame(x, hospital = "A")
@@ -187,14 +187,14 @@ MIC values. They return 'normal'
``` r
mic_data <- as.mic(c(">=32", "1.0", "1", "1.00", 8, "<=0.128", "8", "16", "16"))
mic_data
#> Class 'mic'
#> Class <mic>
#> [1] >=32 1 1 1 8 <=0.128 8 16 16
is.mic(mic_data)
#> [1] TRUE
# this can also coerce combined MIC/SIR values:
as.mic("<=0.002; S")
#> Class 'mic'
#> Class <mic>
#> [1] <=0.002
# mathematical processing treats MICs as, and returns, numeric values
@@ -208,14 +208,14 @@ all(mic_data < 512)
# rescale MICs using rescale_mic()
rescale_mic(mic_data, mic_range = c(4, 16))
#> Class 'mic'
#> Class <mic>
#> [1] >=16 <=4 <=4 <=4 8 <=4 8 >=16 >=16
# round up to nearest log2 level, e.g. for CLSI breakpoint interpretation:
c(1:8)
#> [1] 1 2 3 4 5 6 7 8
as.mic(c(1:8), round_to_next_log2 = TRUE)
#> Class 'mic'
#> Class <mic>
#> [1] 1 2 4 4 8 8 8 8
# interpret MIC values
@@ -225,7 +225,7 @@ as.sir(
ab = "AMX",
guideline = "EUCAST"
)
#> Class 'sir'
#> Class <sir>
#> [1] R
as.sir(
x = as.mic(c(0.01, 2, 4, 8)),
@@ -233,7 +233,7 @@ as.sir(
ab = "AMX",
guideline = "EUCAST"
)
#> Class 'sir'
#> Class <sir>
#> [1] S R R R
# plot MIC values, see ?plot

16
reference/as.mo.html
View File

@@ -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="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -278,7 +278,7 @@
<span class="r-in"><span> <span class="st">"VRSA"</span>, <span class="co"># Vancomycin Resistant S. aureus</span></span></span>
<span class="r-in"><span> <span class="fl">115329001</span> <span class="co"># SNOMED CT code</span></span></span>
<span class="r-in"><span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mo'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;mo&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] B_STPHY_AURS B_STPHY_AURS B_STPHY_AURS B_STPHY_AURS B_STPHY_AURS</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [6] B_STPHY_AURS B_STPHY_AURS B_STPHY_AURS B_STPHY_AURS B_STPHY_AURS</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] B_STPHY_AURS B_STPHY_AURS</span>
@@ -290,7 +290,7 @@
<span class="r-in"><span> <span class="st">"Ureaplasmium urealytica"</span>,</span></span>
<span class="r-in"><span> <span class="st">"Ureaplazma urealitycium"</span></span></span>
<span class="r-in"><span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mo'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;mo&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] B_URPLS_URLY B_URPLS_URLY B_URPLS_URLY B_URPLS_URLY</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># input will get cleaned up with the input given in the `cleaning_regex` argument,</span></span></span>
@@ -299,21 +299,21 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> ([^A-Za-z- \(\)\[\]{}]+|([({]|\[).+([})]|\])|(^| )( ?[a-z-]+[-](resistant|susceptible) ?|e?spp([^a-z]+|$)|e?ssp([^a-z]+|$)|serogr.?up[a-z]*|e?ss([^a-z]+|$)|e?sp([^a-z]+|$)|var([^a-z]+|$)|serovar[a-z]*|sube?species|biovar[a-z]*|e?species|Ig[ADEGM]|e?subsp|biotype|titer|dummy)) </span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"Streptococcus group A"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mo'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;mo&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] B_STRPT_GRPA</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"S. epidermidis"</span><span class="op">)</span> <span class="co"># will remain species: B_STPHY_EPDR</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mo'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;mo&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] B_STPHY_EPDR</span>
<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"S. epidermidis"</span>, Becker <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="co"># will not remain species: B_STPHY_CONS</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mo'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;mo&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] B_STPHY_CONS</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"S. pyogenes"</span><span class="op">)</span> <span class="co"># will remain species: B_STRPT_PYGN</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mo'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;mo&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] B_STRPT_PYGN</span>
<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"S. pyogenes"</span>, Lancefield <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="co"># will not remain species: B_STRPT_GRPA</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mo'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;mo&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] B_STRPT_GRPA</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># All mo_* functions use as.mo() internally too (see ?mo_property):</span></span></span>

14
reference/as.mo.md
View File

@@ -559,7 +559,7 @@ as.mo(c(
"VRSA", # Vancomycin Resistant S. aureus
115329001 # SNOMED CT code
))
#> Class 'mo'
#> Class <mo>
#> [1] B_STPHY_AURS B_STPHY_AURS B_STPHY_AURS B_STPHY_AURS B_STPHY_AURS
#> [6] B_STPHY_AURS B_STPHY_AURS B_STPHY_AURS B_STPHY_AURS B_STPHY_AURS
#> [11] B_STPHY_AURS B_STPHY_AURS
@@ -571,7 +571,7 @@ as.mo(c(
"Ureaplasmium urealytica",
"Ureaplazma urealitycium"
))
#> Class 'mo'
#> Class <mo>
#> [1] B_URPLS_URLY B_URPLS_URLY B_URPLS_URLY B_URPLS_URLY
# input will get cleaned up with the input given in the `cleaning_regex` argument,
@@ -580,21 +580,21 @@ cat(mo_cleaning_regex(), "\n")
#> ([^A-Za-z- \(\)\[\]{}]+|([({]|\[).+([})]|\])|(^| )( ?[a-z-]+[-](resistant|susceptible) ?|e?spp([^a-z]+|$)|e?ssp([^a-z]+|$)|serogr.?up[a-z]*|e?ss([^a-z]+|$)|e?sp([^a-z]+|$)|var([^a-z]+|$)|serovar[a-z]*|sube?species|biovar[a-z]*|e?species|Ig[ADEGM]|e?subsp|biotype|titer|dummy))
as.mo("Streptococcus group A")
#> Class 'mo'
#> Class <mo>
#> [1] B_STRPT_GRPA
as.mo("S. epidermidis") # will remain species: B_STPHY_EPDR
#> Class 'mo'
#> Class <mo>
#> [1] B_STPHY_EPDR
as.mo("S. epidermidis", Becker = TRUE) # will not remain species: B_STPHY_CONS
#> Class 'mo'
#> Class <mo>
#> [1] B_STPHY_CONS
as.mo("S. pyogenes") # will remain species: B_STRPT_PYGN
#> Class 'mo'
#> Class <mo>
#> [1] B_STRPT_PYGN
as.mo("S. pyogenes", Lancefield = TRUE) # will not remain species: B_STRPT_GRPA
#> Class 'mo'
#> Class <mo>
#> [1] B_STRPT_GRPA
# All mo_* functions use as.mo() internally too (see ?mo_property):

42
reference/as.sir.html
View File

@@ -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="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -424,10 +424,10 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4 × 18</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index method ab_given mo_given host_given input_given</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2026-03-20 <span style="color: #949494;">16:07:38</span> 1 MIC amoxicillin Escherich… human 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2026-03-20 <span style="color: #949494;">16:07:38</span> 1 MIC cipro Escherich… human 0.256 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2026-03-20 <span style="color: #949494;">16:07:39</span> 1 DISK tobra Escherich… human 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2026-03-20 <span style="color: #949494;">16:07:39</span> 1 DISK genta Escherich… human 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2026-03-22 <span style="color: #949494;">19:51:52</span> 1 MIC amoxicillin Escherich… human 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2026-03-22 <span style="color: #949494;">19:51:52</span> 1 MIC cipro Escherich… human 0.256 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2026-03-22 <span style="color: #949494;">19:51:52</span> 1 DISK tobra Escherich… human 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2026-03-22 <span style="color: #949494;">19:51:53</span> 1 DISK genta Escherich… human 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 11 more variables: ab &lt;ab&gt;, mo &lt;mo&gt;, host &lt;chr&gt;, input &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># outcome &lt;sir&gt;, notes &lt;chr&gt;, guideline &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># breakpoint_S_R &lt;chr&gt;, site &lt;chr&gt;</span></span>
@@ -436,15 +436,15 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<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">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Returning a previously coerced value for an antimicrobial. Run</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> `ab_reset_session()` (`?AMR::ab_reset_session()`) to reset this. This note</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> will be shown once per session.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> `?ab_reset_session()` to reset this. This note will be shown once per</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> session.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Running in parallel mode using 3 out of 4 cores, on columns '<span style="font-weight: bold;">amoxicillin</span>',</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> '<span style="font-weight: bold;">cipro</span>', '<span style="font-weight: bold;">tobra</span>', '<span style="font-weight: bold;">genta</span>', and '<span style="font-weight: bold;">ERY</span>'...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #5FD7AF;">DONE</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Run `sir_interpretation_history()` (`?AMR::sir_interpretation_history()`) to</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> retrieve a logbook with all details of the breakpoint interpretations.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Run `?sir_interpretation_history()` to retrieve a logbook with all details of</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> the breakpoint interpretations.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> microorganism amoxicillin cipro tobra genta ERY</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 Escherichia coli S I S S R</span>
<span class="r-in"><span></span></span>
@@ -556,7 +556,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<span class="r-in"><span> <span class="va">df_wide</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="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">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `aminopenicillins()` using column '<span style="font-weight: bold;">amoxicillin</span>'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?aminopenicillins()` using column <span style="color: #00BB00; font-weight: bold;">amoxicillin</span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>There was 1 warning in `mutate()`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In argument: `across(...)`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> Caused by warning:</span>
@@ -611,7 +611,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<span class="r-in"><span> ab <span class="op">=</span> <span class="st">"AMP"</span>,</span></span>
<span class="r-in"><span> guideline <span class="op">=</span> <span class="st">"EUCAST"</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] R</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">as.sir</span><span class="op">(</span></span></span>
@@ -620,30 +620,28 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<span class="r-in"><span> ab <span class="op">=</span> <span class="st">"ampicillin"</span>, <span class="co"># and `ab` with as.ab()</span></span></span>
<span class="r-in"><span> guideline <span class="op">=</span> <span class="st">"EUCAST"</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] R</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># For CLEANING existing SIR values -------------------------------------</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">as.sir</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"S"</span>, <span class="st">"SDD"</span>, <span class="st">"I"</span>, <span class="st">"R"</span>, <span class="st">"NI"</span>, <span class="st">"A"</span>, <span class="st">"B"</span>, <span class="st">"C"</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in `as.sir()` (`?AMR::as.sir()`): 3 results truncated (38%) that were invalid</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> antimicrobial interpretations: "A", "B", and "C"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in `?as.sir()`: 3 results truncated (38%) that were invalid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> interpretations: "A", "B", and "C"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] S SDD I R NI &lt;NA&gt; &lt;NA&gt; &lt;NA&gt;</span>
<span class="r-in"><span><span class="fu">as.sir</span><span class="op">(</span><span class="st">"&lt;= 0.002; S"</span><span class="op">)</span> <span class="co"># will return "S"</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] S</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">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> in `as.sir()` (`?AMR::as.sir()`): Interpreting input value 1 as "S", 2 as</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "I", and 3 as "R"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> `?as.sir()`: Interpreting input value 1 as "S", 2 as "I", and 3 as "R"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [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">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> in `as.sir()` (`?AMR::as.sir()`): Interpreting input value 1 as "R", 2 as</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "I", and 3 as "S"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> `?as.sir()`: Interpreting input value 1 as "R", 2 as "I", and 3 as "S"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] R I S</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">sir_data</span> <span class="op">&lt;-</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="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"S"</span>, <span class="fl">474</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"I"</span>, <span class="fl">36</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"R"</span>, <span class="fl">370</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>

40
reference/as.sir.md
View File

@@ -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 2026-03-20 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
#> 1 2026-03-22 19:51:52 1 MIC amoxicillin Escherich… human 8
#> 2 2026-03-22 19:51:52 1 MIC cipro Escherich… human 0.256
#> 3 2026-03-22 19:51:52 1 DISK tobra Escherich… human 16
#> 4 2026-03-22 19:51:53 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>
@@ -672,15 +672,15 @@ sir_interpretation_history()
# using parallel computing, which is available in base R:
as.sir(df_wide, parallel = TRUE, info = TRUE)
#> 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.
#> `?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
#>
#> ℹ Run `sir_interpretation_history()` (`?AMR::sir_interpretation_history()`) to
#> retrieve a logbook with all details of the breakpoint interpretations.
#> ℹ Run `?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
@@ -792,7 +792,7 @@ if (require("dplyr")) {
df_wide %>%
mutate_at(vars(cipro:genta), as.sir, mo = "E. coli", uti = TRUE)
}
#> ℹ For `aminopenicillins()` using column 'amoxicillin'
#> ℹ For `?aminopenicillins()` using column amoxicillin
#> Warning: There was 1 warning in `mutate()`.
#> ℹ In argument: `across(...)`.
#> Caused by warning:
@@ -847,7 +847,7 @@ as.sir(
ab = "AMP",
guideline = "EUCAST"
)
#> Class 'sir'
#> Class <sir>
#> [1] R
as.sir(
@@ -856,30 +856,28 @@ as.sir(
ab = "ampicillin", # and `ab` with as.ab()
guideline = "EUCAST"
)
#> Class 'sir'
#> Class <sir>
#> [1] R
# For CLEANING existing SIR values -------------------------------------
as.sir(c("S", "SDD", "I", "R", "NI", "A", "B", "C"))
#> Warning: in `as.sir()` (`?AMR::as.sir()`): 3 results truncated (38%) that were invalid
#> antimicrobial interpretations: "A", "B", and "C"
#> Class 'sir'
#> Warning: in `?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"
#> Class 'sir'
#> Class <sir>
#> [1] S
as.sir(c(1, 2, 3))
#> ℹ in `as.sir()` (`?AMR::as.sir()`): Interpreting input value 1 as "S", 2 as
#> "I", and 3 as "R"
#> Class 'sir'
#> ℹ `?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()` (`?AMR::as.sir()`): Interpreting input value 1 as "R", 2 as
#> "I", and 3 as "S"
#> Class 'sir'
#> ℹ `?as.sir()`: Interpreting input value 1 as "R", 2 as "I", and 3 as "S"
#> Class <sir>
#> [1] R I S
sir_data <- as.sir(c(rep("S", 474), rep("I", 36), rep("R", 370)))

8
reference/atc_online.html
View File

@@ -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="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<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 +135,10 @@
<span class="r-in"><span> <span class="fu">atc_online_property</span><span class="op">(</span><span class="st">"J01CA04"</span>, property <span class="op">=</span> <span class="st">"groups"</span><span class="op">)</span> <span class="co"># search hierarchical groups of amoxicillin</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Loading required namespace: rvest</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> in `atc_online_property()` (`?AMR::atc_online_property()`): no properties</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> found for ATC QG51AA03. Please check</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> `?atc_online_property()`: no properties found for ATC QG51AA03. Please check</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB; font-style: italic;">&lt;https://atcddd.fhi.no/atcvet/atcvet_index/?code=QG51AA03&amp;showdescription=no</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB; font-style: italic;">this WHOCC webpage&gt;</span>.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> in `atc_online_property()` (`?AMR::atc_online_property()`): no properties</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> found for ATC QJ01CA04. Please check</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> `?atc_online_property()`: no properties found for ATC QJ01CA04. Please check</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB; font-style: italic;">&lt;https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01CA04&amp;showdescription=no</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB; font-style: italic;">this WHOCC webpage&gt;</span>.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "ANTIINFECTIVES FOR SYSTEMIC USE" </span>

6
reference/atc_online.md
View File

@@ -117,12 +117,10 @@ 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()` (`?AMR::atc_online_property()`): no properties
#> found for ATC QG51AA03. Please check
#> ℹ `?atc_online_property()`: no properties found for ATC QG51AA03. Please check
#> <https://atcddd.fhi.no/atcvet/atcvet_index/?code=QG51AA03&showdescription=no
#> this WHOCC webpage>.
#> ℹ in `atc_online_property()` (`?AMR::atc_online_property()`): no properties
#> found for ATC QJ01CA04. Please check
#> ℹ `?atc_online_property()`: no properties found for ATC QJ01CA04. Please check
#> <https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01CA04&showdescription=no
#> this WHOCC webpage>.
#> [1] "ANTIINFECTIVES FOR SYSTEMIC USE"

4
reference/av_from_text.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -122,7 +122,7 @@
<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">av_from_text</span><span class="op">(</span><span class="st">"28/03/2020 valaciclovir po tid"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [[1]]</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'av'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;av&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] VALA</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-in"><span><span class="fu">av_from_text</span><span class="op">(</span><span class="st">"28/03/2020 valaciclovir po tid"</span>, type <span class="op">=</span> <span class="st">"admin"</span><span class="op">)</span></span></span>

2
reference/av_from_text.md
View File

@@ -120,7 +120,7 @@ With using `collapse`, this function will return a
``` r
av_from_text("28/03/2020 valaciclovir po tid")
#> [[1]]
#> Class 'av'
#> Class <av>
#> [1] VALA
#>
av_from_text("28/03/2020 valaciclovir po tid", type = "admin")

2
reference/av_property.html
View File

@@ -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="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

9
reference/availability.html
View File

@@ -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="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<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 +82,9 @@
<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">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> `resistance()` (`?AMR::resistance()`) assumes the EUCAST guideline and thus</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> considers the 'I' category susceptible. Set the `guideline` argument or the</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> `AMR_guideline` option to either "CLSI" or "EUCAST", see AMR-options</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (`?AMR::AMR-options`).</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> `?resistance()` assumes the EUCAST guideline and thus considers the 'I'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> category susceptible. Set the `guideline` argument or the `AMR_guideline`</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> option to either "CLSI" or "EUCAST", see AMR-options.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> This message will be shown once per session.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> count available visual_availabilty resistant visual_resistance</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date 2000 100.0% |####################| </span>

7
reference/availability.md
View File

@@ -41,10 +41,9 @@ calculated with
``` r
availability(example_isolates)
#> 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 `?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 This message will be shown once per session.
#> count available visual_availabilty resistant visual_resistance
#> date 2000 100.0% |####################|

2
reference/bug_drug_combinations.html
View File

@@ -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="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/clinical_breakpoints.html
View File

@@ -21,7 +21,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

27
reference/count.html
View File

@@ -9,7 +9,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -174,17 +174,15 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<span class="r-in"><span></span></span>
<span class="r-in"><span><span 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">$</span><span class="va">AMX</span><span class="op">)</span> <span class="co"># counts "R"</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> `count_resistant()` (`?AMR::count_resistant()`) assumes the EUCAST guideline</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> and thus considers the 'I' category susceptible. Set the `guideline` argument</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> or the `AMR_guideline` option to either "CLSI" or "EUCAST", see AMR-options</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (`?AMR::AMR-options`).</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> `?count_resistant()` assumes the EUCAST guideline and thus considers the 'I'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> category susceptible. Set the `guideline` argument or the `AMR_guideline`</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> option to either "CLSI" or "EUCAST", see AMR-options.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> This message will be shown once per session.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 804</span>
<span class="r-in"><span><span class="fu">count_susceptible</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span> <span class="co"># counts "S" and "I"</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> `count_susceptible()` (`?AMR::count_susceptible()`) assumes the EUCAST</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> guideline and thus considers the 'I' category susceptible. Set the</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> `guideline` argument or the `AMR_guideline` option to either "CLSI" or</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "EUCAST", see AMR-options (`?AMR::AMR-options`).</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> `?count_susceptible()` assumes the EUCAST guideline and thus considers the</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'I' category susceptible. Set the `guideline` argument or the `AMR_guideline`</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> option to either "CLSI" or "EUCAST", see AMR-options.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> This message will be shown once per session.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 546</span>
<span class="r-in"><span><span class="fu">count_all</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span> <span class="co"># counts "S", "I" and "R"</span></span></span>
@@ -215,10 +213,9 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<span class="r-in"><span><span class="fu">count_susceptible</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 546</span>
<span class="r-in"><span><span class="fu"><a href="proportion.html">susceptibility</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span> <span class="op">*</span> <span class="fu">n_sir</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> `susceptibility()` (`?AMR::susceptibility()`) assumes the EUCAST guideline</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> and thus considers the 'I' category susceptible. Set the `guideline` argument</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> or the `AMR_guideline` option to either "CLSI" or "EUCAST", see AMR-options</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (`?AMR::AMR-options`).</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> `?susceptibility()` assumes the EUCAST guideline and thus considers the 'I'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> category susceptible. Set the `guideline` argument or the `AMR_guideline`</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> option to either "CLSI" or "EUCAST", see AMR-options.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> This message will be shown once per session.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 546</span>
<span class="r-in"><span></span></span>
@@ -265,8 +262,8 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">ward</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="fu">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">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns '<span style="font-weight: bold;">GEN</span>' (gentamicin), '<span style="font-weight: bold;">TOB</span>' (tobramycin),</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> '<span style="font-weight: bold;">AMK</span>' (amikacin), and '<span style="font-weight: bold;">KAN</span>' (kanamycin)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?aminoglycosides()` using columns <span style="color: #00BB00; font-weight: bold;">GEN</span> (gentamicin), <span style="color: #00BB00; font-weight: bold;">TOB</span> (tobramycin),</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00; font-weight: bold;">AMK</span> (amikacin), and <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 12 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward antibiotic interpretation value</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ord&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span>

25
reference/count.md
View File

@@ -188,17 +188,15 @@ calculate microbial resistance and susceptibility.
# base R ------------------------------------------------------------
count_resistant(example_isolates$AMX) # counts "R"
#> ℹ `count_resistant()` (`?AMR::count_resistant()`) assumes the EUCAST guideline
#> and thus considers the 'I' category susceptible. Set the `guideline` argument
#> or the `AMR_guideline` option to either "CLSI" or "EUCAST", see AMR-options
#> (`?AMR::AMR-options`).
#> ℹ `?count_resistant()` assumes the EUCAST guideline and thus considers the 'I'
#> category susceptible. Set the `guideline` argument or the `AMR_guideline`
#> option to either "CLSI" or "EUCAST", see AMR-options.
#> ℹ This message will be shown once per session.
#> [1] 804
count_susceptible(example_isolates$AMX) # counts "S" and "I"
#> 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 `?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 This message will be shown once per session.
#> [1] 546
count_all(example_isolates$AMX) # counts "S", "I" and "R"
@@ -229,10 +227,9 @@ n_sir(example_isolates$AMX)
count_susceptible(example_isolates$AMX)
#> [1] 546
susceptibility(example_isolates$AMX) * n_sir(example_isolates$AMX)
#> 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 `?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 This message will be shown once per session.
#> [1] 546
@@ -279,8 +276,8 @@ 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>

2
reference/custom_eucast_rules.html
View File

@@ -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="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

4
reference/custom_mdro_guideline.html
View File

@@ -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="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -245,7 +245,7 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> Results will be of class 'factor', with ordered levels: Negative &lt; Custom MDRO 1 &lt; Custom MDRO 2</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">out</span> <span class="op">&lt;-</span> <span class="fu"><a href="mdro.html">mdro</a></span><span class="op">(</span><span class="va">example_isolates</span>, guideline <span class="op">=</span> <span class="va">my_guideline</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `cephalosporins_2nd()` using columns '<span style="font-weight: bold;">CXM</span>' (cefuroxime) and '<span style="font-weight: bold;">FOX</span>'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?cephalosporins_2nd()` using columns <span style="color: #00BB00; font-weight: bold;">CXM</span> (cefuroxime) and <span style="color: #00BB00; font-weight: bold;">FOX</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (cefoxitin)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Assuming a filter on all 2 cephalosporins_2nd. Wrap around `all()` or `any()`</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> to prevent this note.</span>

2
reference/custom_mdro_guideline.md
View File

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

2
reference/dosage.html
View File

@@ -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="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/esbl_isolates.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/example_isolates.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/example_isolates_unclean.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/export_ncbi_biosample.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

5
reference/first_isolate.html
View File

@@ -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="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -240,8 +240,7 @@
<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">&amp;</span> <span class="fu"><a href="mo_property.html">mo_is_gram_negative</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Using column '<span style="font-weight: bold;">mo</span>' as input for `mo_is_gram_negative()`</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (`?AMR::mo_is_gram_negative()`)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Using column '<span style="font-weight: bold;">mo</span>' as input for `?mo_is_gram_negative()`</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 441 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>

3
reference/first_isolate.md
View File

@@ -359,8 +359,7 @@ example_isolates[first_isolate(info = TRUE), ]
# \donttest{
# 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()`)
#> ℹ Using column 'mo' as input for `?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>

2
reference/g.test.html
View File

@@ -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="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/get_episode.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

4
reference/ggplot_pca.html
View File

@@ -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="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -224,7 +224,7 @@
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In group 5: `order = "Lactobacillales"`, `genus = "Enterococcus"`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> Caused by warning:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> Introducing NA: only 14 results available for PEN in group: order =</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Enterococcus" (`minimum` = 30).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Enterococcus" (whilst `minimum = 30`).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Run `dplyr::last_dplyr_warnings()` to see the 72 remaining warnings.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Columns selected for PCA: "<span style="font-weight: bold;">AMC</span>", "<span style="font-weight: bold;">CAZ</span>", "<span style="font-weight: bold;">CTX</span>", "<span style="font-weight: bold;">CXM</span>", "<span style="font-weight: bold;">GEN</span>", "<span style="font-weight: bold;">SXT</span>", "<span style="font-weight: bold;">TMP</span>",</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> and "<span style="font-weight: bold;">TOB</span>". Total observations available: 7.</span>

2
reference/ggplot_pca.md
View File

@@ -215,7 +215,7 @@ if (require("dplyr")) {
#> ℹ In group 5: `order = "Lactobacillales"`, `genus = "Enterococcus"`.
#> Caused by warning:
#> ! Introducing NA: only 14 results available for PEN in group: order =
#> "Lactobacillales", genus = "Enterococcus" (`minimum` = 30).
#> "Lactobacillales", genus = "Enterococcus" (whilst `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.

5
reference/ggplot_sir.html
View File

@@ -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="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -285,8 +285,7 @@
<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">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Using column '<span style="font-weight: bold;">mo</span>' as input for `mo_is_gram_negative()`</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (`?AMR::mo_is_gram_negative()`)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Using column '<span style="font-weight: bold;">mo</span>' as input for `?mo_is_gram_negative()`</span>
<span class="r-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>

3
reference/ggplot_sir.md
View File

@@ -295,8 +295,7 @@ if (require("ggplot2") && require("dplyr")) {
datalabels = FALSE
)
}
#> ℹ Using column 'mo' as input for `mo_is_gram_negative()`
#> (`?AMR::mo_is_gram_negative()`)
#> ℹ Using column 'mo' as input for `?mo_is_gram_negative()`
# }
```

2
reference/guess_ab_col.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/index.html
View File

@@ -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="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
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14
reference/interpretive_rules.html
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@@ -9,7 +9,7 @@ To improve the interpretation of the antibiogram before CLSI/EUCAST interpretive
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
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@@ -228,9 +228,9 @@ 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">&lt;-</span> <span class="fu">eucast_rules</span><span class="op">(</span><span class="va">a</span>, overwrite <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in `eucast_rules()` (`?AMR::eucast_rules()`): not all columns with</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> antimicrobial results are of class <span style="color: #0000BB;">&lt;sir&gt;</span>. Transform them on beforehand, e.g.: -</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> x <span style="color: #D7AF00;">%&gt;%</span> <span style="font-weight: bold;">as.sir</span><span style="color: #D7AF00;">(</span>CXM<span style="color: #D7AF00;">:</span>AMX<span style="color: #D7AF00;">)</span> - x <span style="color: #D7AF00;">%&gt;%</span> <span style="font-weight: bold;">mutate_if</span><span style="color: #D7AF00;">(</span>is_sir_eligible, as.sir<span style="color: #D7AF00;">)</span> - x <span style="color: #D7AF00;">%&gt;%</span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in `?eucast_rules()`: not all columns with antimicrobial results are of class</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">&lt;sir&gt;</span>. Transform them on beforehand, e.g.: - x <span style="color: #D7AF00;">%&gt;%</span> <span style="font-weight: bold;">as.sir</span><span style="color: #D7AF00;">(</span>CXM<span style="color: #D7AF00;">:</span>AMX<span style="color: #D7AF00;">)</span> - x <span style="color: #D7AF00;">%&gt;%</span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="font-weight: bold;">mutate_if</span><span style="color: #D7AF00;">(</span>is_sir_eligible, as.sir<span style="color: #D7AF00;">)</span> - x <span style="color: #D7AF00;">%&gt;%</span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="font-weight: bold;">mutate</span><span style="color: #D7AF00;">(</span><span style="font-weight: bold;">across</span><span style="color: #BBBB00;">(</span><span style="font-weight: bold;">where</span><span style="color: #0000BB;">(</span>is_sir_eligible<span style="color: #0000BB;">)</span>, as.sir<span style="color: #BBBB00;">)</span><span style="color: #D7AF00;">)</span></span>
<span class="r-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>
@@ -245,9 +245,9 @@ 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">&lt;-</span> <span class="fu">eucast_rules</span><span class="op">(</span><span class="va">a</span>, overwrite <span class="op">=</span> <span class="cn">TRUE</span>, verbose <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in `eucast_rules()` (`?AMR::eucast_rules()`): not all columns with</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> antimicrobial results are of class <span style="color: #0000BB;">&lt;sir&gt;</span>. Transform them on beforehand, e.g.: -</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> x <span style="color: #D7AF00;">%&gt;%</span> <span style="font-weight: bold;">as.sir</span><span style="color: #D7AF00;">(</span>CXM<span style="color: #D7AF00;">:</span>AMX<span style="color: #D7AF00;">)</span> - x <span style="color: #D7AF00;">%&gt;%</span> <span style="font-weight: bold;">mutate_if</span><span style="color: #D7AF00;">(</span>is_sir_eligible, as.sir<span style="color: #D7AF00;">)</span> - x <span style="color: #D7AF00;">%&gt;%</span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in `?eucast_rules()`: not all columns with antimicrobial results are of class</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">&lt;sir&gt;</span>. Transform them on beforehand, e.g.: - x <span style="color: #D7AF00;">%&gt;%</span> <span style="font-weight: bold;">as.sir</span><span style="color: #D7AF00;">(</span>CXM<span style="color: #D7AF00;">:</span>AMX<span style="color: #D7AF00;">)</span> - x <span style="color: #D7AF00;">%&gt;%</span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="font-weight: bold;">mutate_if</span><span style="color: #D7AF00;">(</span>is_sir_eligible, as.sir<span style="color: #D7AF00;">)</span> - x <span style="color: #D7AF00;">%&gt;%</span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="font-weight: bold;">mutate</span><span style="color: #D7AF00;">(</span><span style="font-weight: bold;">across</span><span style="color: #BBBB00;">(</span><span style="font-weight: bold;">where</span><span style="color: #0000BB;">(</span>is_sir_eligible<span style="color: #0000BB;">)</span>, as.sir<span style="color: #BBBB00;">)</span><span style="color: #D7AF00;">)</span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">c</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> row col mo_fullname old new rule rule_group</span>

12
reference/interpretive_rules.md
View File

@@ -306,9 +306,9 @@ head(a)
# apply EUCAST rules: some results wil be changed
b <- eucast_rules(a, overwrite = TRUE)
#> 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 %>%
#> Warning: in `?eucast_rules()`: not all columns with antimicrobial results are of class
#> <sir>. Transform them on beforehand, e.g.: - x %>% as.sir(CXM:AMX) - x %>%
#> mutate_if(is_sir_eligible, as.sir) - x %>%
#> mutate(across(where(is_sir_eligible), as.sir))
head(b)
@@ -323,9 +323,9 @@ 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()` (`?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 %>%
#> Warning: in `?eucast_rules()`: not all columns with antimicrobial results are of class
#> <sir>. Transform them on beforehand, e.g.: - x %>% as.sir(CXM:AMX) - x %>%
#> 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

2
reference/intrinsic_resistant.html
View File

@@ -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="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/italicise_taxonomy.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/join.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/key_antimicrobials.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
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2
reference/kurtosis.html
View File

@@ -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="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

6
reference/like.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<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">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Using column '<span style="font-weight: bold;">mo</span>' as input for `mo_name()` (`?AMR::mo_name()`)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Using column '<span style="font-weight: bold;">mo</span>' as input for `?mo_name()`</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 106 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
@@ -159,7 +159,7 @@
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="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">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Using column '<span style="font-weight: bold;">mo</span>' as input for `mo_name()` (`?AMR::mo_name()`)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Using column '<span style="font-weight: bold;">mo</span>' as input for `?mo_name()`</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 106 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>

4
reference/like.md
View File

@@ -114,7 +114,7 @@ a %like% b[1]
# \donttest{
# 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()` (`?AMR::mo_name()`)
#> ℹ Using column 'mo' as input for `?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()` (`?AMR::mo_name()`)
#> ℹ Using column 'mo' as input for `?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>

12
reference/mdro.html
View File

@@ -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="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -210,9 +210,8 @@ 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">&lt;-</span> <span class="fu">mdro</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span></span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in `mdro()` (`?AMR::mdro()`): NA introduced for isolates where the available</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> percentage of antimicrobial classes was below 50% (set with</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> `pct_required_classes`)</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in `?mdro()`: NA introduced for isolates where the available percentage of</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> antimicrobial classes was below 50% (set with `pct_required_classes`)</span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/str.html" class="external-link">str</a></span><span class="op">(</span><span class="va">out</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Ord.factor w/ 4 levels "Negative"&lt;"Multi-drug-resistant (MDR)"&lt;..: NA NA 1 1 1 1 NA NA 1 1 ...</span>
<span class="r-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>
@@ -238,9 +237,8 @@ Ordered <a href="https://rdrr.io/pkg/data.table/man/fctr.html" class="external-l
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>There was 1 warning in `mutate()`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In argument: `MDRO = mdro()`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> Caused by warning:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> in `mdro()` (`?AMR::mdro()`): NA introduced for isolates where the available</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> percentage of antimicrobial classes was below 50% (set with</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> `pct_required_classes`)</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> in `?mdro()`: NA introduced for isolates where the available percentage of</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> antimicrobial classes was below 50% (set with `pct_required_classes`)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 2</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> MDRO n</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ord&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span>

10
reference/mdro.md
View File

@@ -297,9 +297,8 @@ susceptible isolates.
``` r
out <- mdro(example_isolates)
#> Warning: in `mdro()` (`?AMR::mdro()`): NA introduced for isolates where the available
#> percentage of antimicrobial classes was below 50% (set with
#> `pct_required_classes`)
#> Warning: in `?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)
@@ -325,9 +324,8 @@ if (require("dplyr")) {
#> Warning: There was 1 warning in `mutate()`.
#> ℹ In argument: `MDRO = mdro()`.
#> Caused by warning:
#> ! in `mdro()` (`?AMR::mdro()`): NA introduced for isolates where the available
#> percentage of antimicrobial classes was below 50% (set with
#> `pct_required_classes`)
#> ! in `?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>

14
reference/mean_amr_distance.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -109,7 +109,7 @@
<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">sir</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_sir</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">sir</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] S R S R I I R R R S</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">sir</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.9486833 0.9486833 -0.9486833 0.9486833 -0.9486833 -0.9486833</span>
@@ -117,7 +117,7 @@
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">mic</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">mic</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;mic&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.5 &lt;=0.0001 0.25 0.0005 0.001 0.0002 8 &lt;=0.0001</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [9] &lt;=0.0001 0.004 </span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">mic</span><span class="op">)</span></span></span>
@@ -130,7 +130,7 @@
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">disk</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_disk</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">disk</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;disk&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 20 45 31 26 23 38 44 41 20 49</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">disk</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -1.2414143 1.0239402 -0.2446583 -0.6977292 -0.9695717 0.3896410</span>
@@ -205,9 +205,9 @@
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>dist <span class="op">=</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">.</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">mo</span>, <span class="va">dist</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Using column '<span style="font-weight: bold;">mo</span>' as input for `mo_genus()` (`?AMR::mo_genus()`)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Using column '<span style="font-weight: bold;">mo</span>' as input for `mo_species()` (`?AMR::mo_species()`)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns '<span style="font-weight: bold;">IPM</span>' (imipenem) and '<span style="font-weight: bold;">MEM</span>' (meropenem)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Using column '<span style="font-weight: bold;">mo</span>' as input for `?mo_genus()`</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Using column '<span style="font-weight: bold;">mo</span>' as input for `?mo_species()`</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `?carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Calculating mean AMR distance based on columns "TCY", "IPM", and "MEM"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 63 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: mo [4]</span></span>

12
reference/mean_amr_distance.md
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@@ -84,7 +84,7 @@ suspicious.
``` r
sir <- random_sir(10)
sir
#> Class 'sir'
#> Class <sir>
#> [1] S R S R I I R R R S
mean_amr_distance(sir)
#> [1] -0.9486833 0.9486833 -0.9486833 0.9486833 -0.9486833 -0.9486833
@@ -92,7 +92,7 @@ mean_amr_distance(sir)
mic <- random_mic(10)
mic
#> Class 'mic'
#> Class <mic>
#> [1] 0.5 <=0.0001 0.25 0.0005 0.001 0.0002 8 <=0.0001
#> [9] <=0.0001 0.004
mean_amr_distance(mic)
@@ -105,7 +105,7 @@ mean_amr_distance(mic)
disk <- random_disk(10)
disk
#> Class 'disk'
#> Class <disk>
#> [1] 20 45 31 26 23 38 44 41 20 49
mean_amr_distance(disk)
#> [1] -1.2414143 1.0239402 -0.2446583 -0.6977292 -0.9695717 0.3896410
@@ -180,9 +180,9 @@ if (require("dplyr")) {
mutate(dist = mean_amr_distance(.)) %>%
arrange(mo, dist)
}
#> 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 Using column 'mo' as input for `?mo_genus()`
#> ℹ Using column 'mo' as input for `?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
#> # Groups: mo [4]

2
reference/microorganisms.codes.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/microorganisms.groups.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
<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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