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2
404.html
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@@ -31,7 +31,7 @@
<a class="navbar-brand me-2" href="https://amr-for-r.org/index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="https://amr-for-r.org/index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
CLAUDE.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
LICENSE-text.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

46
articles/AMR.html
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@@ -30,7 +30,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -91,7 +91,7 @@
website update since they are based on randomly created values and the website update since they are based on randomly created values and the
page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
Markdown</a>. However, the methodology remains unchanged. This page was Markdown</a>. However, the methodology remains unchanged. This page was
generated on 05 April 2026.</p> generated on 21 April 2026.</p>
<div class="section level2"> <div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a> <h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2> </h2>
@@ -147,21 +147,21 @@ make the structure of your data generally look like this:</p>
</tr></thead> </tr></thead>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="center">2026-04-05</td> <td align="center">2026-04-21</td>
<td align="center">abcd</td> <td align="center">abcd</td>
<td align="center">Escherichia coli</td> <td align="center">Escherichia coli</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">2026-04-05</td> <td align="center">2026-04-21</td>
<td align="center">abcd</td> <td align="center">abcd</td>
<td align="center">Escherichia coli</td> <td align="center">Escherichia coli</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">R</td> <td align="center">R</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">2026-04-05</td> <td align="center">2026-04-21</td>
<td align="center">efgh</td> <td align="center">efgh</td>
<td align="center">Escherichia coli</td> <td align="center">Escherichia coli</td>
<td align="center">R</td> <td align="center">R</td>
@@ -694,7 +694,8 @@ should be used. The <code>antibiotics</code> argument in the
previously mentioned antibiotic class selectors:</p> previously mentioned antibiotic class selectors:</p>
<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span> <code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
<span> antibiotics <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="../reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="../reference/antimicrobial_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span> <span> antibiotics <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="../reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="../reference/antimicrobial_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="op">)</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns <span style="color: #00BB00; font-weight: bold;">GEN</span> (gentamicin), <span style="color: #00BB00; font-weight: bold;">TOB</span> (tobramycin), <span style="color: #00BB00; font-weight: bold;">AMK</span></span></span> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns <span style="color: #00BB00; font-weight: bold;">GEN</span> (gentamicin), <span style="color: #00BB00; font-weight: bold;">TOB</span> (tobramycin), <span style="color: #00BB00; font-weight: bold;">AMK</span></span></span>
<span><span class="co">#&gt; (amikacin), and <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin)</span></span> <span><span class="co">#&gt; (amikacin), and <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin)</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span></span></code></pre></div> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span></span></code></pre></div>
@@ -825,7 +826,8 @@ language to be Spanish using the <code>language</code> argument:</p>
<span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span>,</span> <span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span>,</span>
<span> antibiotics <span class="op">=</span> <span class="fu"><a href="../reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>,</span> <span> antibiotics <span class="op">=</span> <span class="fu"><a href="../reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> ab_transform <span class="op">=</span> <span class="st">"name"</span>,</span> <span> ab_transform <span class="op">=</span> <span class="st">"name"</span>,</span>
<span> language <span class="op">=</span> <span class="st">"es"</span><span class="op">)</span></span> <span> language <span class="op">=</span> <span class="st">"es"</span></span>
<span><span class="op">)</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns <span style="color: #00BB00; font-weight: bold;">GEN</span> (gentamicin), <span style="color: #00BB00; font-weight: bold;">TOB</span> (tobramycin), <span style="color: #00BB00; font-weight: bold;">AMK</span></span></span> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns <span style="color: #00BB00; font-weight: bold;">GEN</span> (gentamicin), <span style="color: #00BB00; font-weight: bold;">TOB</span> (tobramycin), <span style="color: #00BB00; font-weight: bold;">AMK</span></span></span>
<span><span class="co">#&gt; (amikacin), and <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin)</span></span></code></pre></div> <span><span class="co">#&gt; (amikacin), and <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin)</span></span></code></pre></div>
<table class="table"> <table class="table">
@@ -869,7 +871,8 @@ a plus <code>+</code> character like this:</p>
<div class="sourceCode" id="cb18"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb18"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">combined_ab</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span> <code class="sourceCode R"><span><span class="va">combined_ab</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
<span> antibiotics <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"TZP"</span>, <span class="st">"TZP+TOB"</span>, <span class="st">"TZP+GEN"</span><span class="op">)</span>,</span> <span> antibiotics <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"TZP"</span>, <span class="st">"TZP+TOB"</span>, <span class="st">"TZP+GEN"</span><span class="op">)</span>,</span>
<span> ab_transform <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></span> <span> ab_transform <span class="op">=</span> <span class="cn">NULL</span></span>
<span><span class="op">)</span></span>
<span><span class="va">combined_ab</span></span></code></pre></div> <span><span class="va">combined_ab</span></span></code></pre></div>
<table class="table"> <table class="table">
<colgroup> <colgroup>
@@ -951,7 +954,8 @@ argument must be used. This can be any column in the data, or e.g. an
<div class="sourceCode" id="cb19"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb19"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span> <code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
<span> antibiotics <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="../reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="../reference/antimicrobial_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>,</span> <span> antibiotics <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="../reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="../reference/antimicrobial_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>,</span>
<span> syndromic_group <span class="op">=</span> <span class="st">"ward"</span><span class="op">)</span></span> <span> syndromic_group <span class="op">=</span> <span class="st">"ward"</span></span>
<span><span class="op">)</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns <span style="color: #00BB00; font-weight: bold;">GEN</span> (gentamicin), <span style="color: #00BB00; font-weight: bold;">TOB</span> (tobramycin), <span style="color: #00BB00; font-weight: bold;">AMK</span></span></span> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns <span style="color: #00BB00; font-weight: bold;">GEN</span> (gentamicin), <span style="color: #00BB00; font-weight: bold;">TOB</span> (tobramycin), <span style="color: #00BB00; font-weight: bold;">AMK</span></span></span>
<span><span class="co">#&gt; (amikacin), and <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin)</span></span> <span><span class="co">#&gt; (amikacin), and <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin)</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span></span></code></pre></div> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span></span></code></pre></div>
@@ -1131,8 +1135,10 @@ provides syndrome-based susceptibility estimates, weighted by pathogen
incidence and antimicrobial susceptibility patterns.</p> incidence and antimicrobial susceptibility patterns.</p>
<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb20"><pre class="downlit sourceCode r">
<code class="sourceCode R"><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> <code class="sourceCode R"><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="fu"><a href="../reference/antibiogram.html">wisca</a></span><span class="op">(</span>antibiotics <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"TZP"</span>, <span class="st">"TZP+TOB"</span>, <span class="st">"TZP+GEN"</span><span class="op">)</span>,</span> <span> <span class="fu"><a href="../reference/antibiogram.html">wisca</a></span><span class="op">(</span></span>
<span> minimum <span class="op">=</span> <span class="fl">10</span><span class="op">)</span> <span class="co"># Recommended threshold: ≥30</span></span></code></pre></div> <span> antibiotics <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"TZP"</span>, <span class="st">"TZP+TOB"</span>, <span class="st">"TZP+GEN"</span><span class="op">)</span>,</span>
<span> minimum <span class="op">=</span> <span class="fl">10</span></span>
<span> <span class="op">)</span> <span class="co"># Recommended threshold: ≥30</span></span></code></pre></div>
<table style="width:100%;" class="table"> <table style="width:100%;" class="table">
<colgroup> <colgroup>
<col width="24%"> <col width="24%">
@@ -1166,8 +1172,10 @@ function on a grouped <code>tibble</code>, i.e., using
<div class="sourceCode" id="cb21"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb21"><pre class="downlit sourceCode r">
<code class="sourceCode R"><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> <code class="sourceCode R"><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="fu"><a href="../reference/top_n_microorganisms.html">top_n_microorganisms</a></span><span class="op">(</span>n <span class="op">=</span> <span class="fl">10</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="../reference/top_n_microorganisms.html">top_n_microorganisms</a></span><span class="op">(</span>n <span class="op">=</span> <span class="fl">10</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/group_by.html" class="external-link">group_by</a></span><span class="op">(</span>age_group <span class="op">=</span> <span class="fu"><a href="../reference/age_groups.html">age_groups</a></span><span class="op">(</span><span class="va">age</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">25</span>, <span class="fl">50</span>, <span class="fl">75</span><span class="op">)</span><span class="op">)</span>,</span> <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>
<span> <span class="va">gender</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> age_group <span class="op">=</span> <span class="fu"><a href="../reference/age_groups.html">age_groups</a></span><span class="op">(</span><span class="va">age</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">25</span>, <span class="fl">50</span>, <span class="fl">75</span><span class="op">)</span><span class="op">)</span>,</span>
<span> <span class="va">gender</span></span>
<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="../reference/antibiogram.html">wisca</a></span><span class="op">(</span>antibiotics <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"TZP"</span>, <span class="st">"TZP+TOB"</span>, <span class="st">"TZP+GEN"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> <span> <span class="fu"><a href="../reference/antibiogram.html">wisca</a></span><span class="op">(</span>antibiotics <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"TZP"</span>, <span class="st">"TZP+TOB"</span>, <span class="st">"TZP+GEN"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
<table class="table"> <table class="table">
<colgroup> <colgroup>
@@ -1341,15 +1349,19 @@ categories.</p>
<code class="sourceCode R"><span><span class="co"># add a group</span></span> <code class="sourceCode R"><span><span class="co"># add a group</span></span>
<span><span class="va">my_data</span><span class="op">$</span><span class="va">group</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"A"</span>, <span class="st">"B"</span>, <span class="st">"C"</span>, <span class="st">"D"</span><span class="op">)</span>, each <span class="op">=</span> <span class="fl">25</span><span class="op">)</span></span> <span><span class="va">my_data</span><span class="op">$</span><span class="va">group</span> <span class="op">&lt;-</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="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"A"</span>, <span class="st">"B"</span>, <span class="st">"C"</span>, <span class="st">"D"</span><span class="op">)</span>, each <span class="op">=</span> <span class="fl">25</span><span class="op">)</span></span>
<span></span> <span></span>
<span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot</a></span><span class="op">(</span><span class="va">my_data</span>,</span> <span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot</a></span><span class="op">(</span></span>
<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span>x <span class="op">=</span> <span class="va">group</span>, y <span class="op">=</span> <span class="va">MIC</span>, colour <span class="op">=</span> <span class="va">SIR</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span> <span> <span class="va">my_data</span>,</span>
<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span>x <span class="op">=</span> <span class="va">group</span>, y <span class="op">=</span> <span class="va">MIC</span>, colour <span class="op">=</span> <span class="va">SIR</span><span class="op">)</span></span>
<span><span class="op">)</span> <span class="op">+</span></span>
<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_jitter.html" class="external-link">geom_jitter</a></span><span class="op">(</span>width <span class="op">=</span> <span class="fl">0.2</span>, size <span class="op">=</span> <span class="fl">2</span><span class="op">)</span> <span class="op">+</span></span> <span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_jitter.html" class="external-link">geom_jitter</a></span><span class="op">(</span>width <span class="op">=</span> <span class="fl">0.2</span>, size <span class="op">=</span> <span class="fl">2</span><span class="op">)</span> <span class="op">+</span></span>
<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_boxplot.html" class="external-link">geom_boxplot</a></span><span class="op">(</span>fill <span class="op">=</span> <span class="cn">NA</span>, colour <span class="op">=</span> <span class="st">"grey40"</span><span class="op">)</span> <span class="op">+</span></span> <span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_boxplot.html" class="external-link">geom_boxplot</a></span><span class="op">(</span>fill <span class="op">=</span> <span class="cn">NA</span>, colour <span class="op">=</span> <span class="st">"grey40"</span><span class="op">)</span> <span class="op">+</span></span>
<span> <span class="fu"><a href="../reference/plot.html">scale_y_mic</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span> <span> <span class="fu"><a href="../reference/plot.html">scale_y_mic</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span>
<span> <span class="fu"><a href="../reference/plot.html">scale_colour_sir</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span> <span> <span class="fu"><a href="../reference/plot.html">scale_colour_sir</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span>
<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">labs</a></span><span class="op">(</span>title <span class="op">=</span> <span class="st">"MIC Distribution and SIR Interpretation"</span>,</span> <span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">labs</a></span><span class="op">(</span></span>
<span> title <span class="op">=</span> <span class="st">"MIC Distribution and SIR Interpretation"</span>,</span>
<span> x <span class="op">=</span> <span class="st">"Sample Groups"</span>,</span> <span> x <span class="op">=</span> <span class="st">"Sample Groups"</span>,</span>
<span> y <span class="op">=</span> <span class="st">"MIC (mg/L)"</span><span class="op">)</span></span></code></pre></div> <span> y <span class="op">=</span> <span class="st">"MIC (mg/L)"</span></span>
<span> <span class="op">)</span></span></code></pre></div>
<p><img src="AMR_files/figure-html/mic_plot-1.png" class="r-plt" alt="" width="720"></p> <p><img src="AMR_files/figure-html/mic_plot-1.png" class="r-plt" alt="" width="720"></p>
<p>This plot provides an intuitive way to assess susceptibility patterns <p>This plot provides an intuitive way to assess susceptibility patterns
across different groups while incorporating clinical breakpoints.</p> across different groups while incorporating clinical breakpoints.</p>

44
articles/AMR.md
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@@ -3,7 +3,7 @@
**Note:** values on this page will change with every website update **Note:** values on this page will change with every website update
since they are based on randomly created values and the page was written since they are based on randomly created values and the page was written
in [R Markdown](https://rmarkdown.rstudio.com/). However, the in [R Markdown](https://rmarkdown.rstudio.com/). However, the
methodology remains unchanged. This page was generated on 05 April 2026. methodology remains unchanged. This page was generated on 21 April 2026.
## Introduction ## Introduction
@@ -51,9 +51,9 @@ structure of your data generally look like this:
| date | patient_id | mo | AMX | CIP | | date | patient_id | mo | AMX | CIP |
|:----------:|:----------:|:----------------:|:---:|:---:| |:----------:|:----------:|:----------------:|:---:|:---:|
| 2026-04-05 | abcd | Escherichia coli | S | S | | 2026-04-21 | abcd | Escherichia coli | S | S |
| 2026-04-05 | abcd | Escherichia coli | S | R | | 2026-04-21 | abcd | Escherichia coli | S | R |
| 2026-04-05 | efgh | Escherichia coli | R | S | | 2026-04-21 | efgh | Escherichia coli | R | S |
### Needed R packages ### Needed R packages
@@ -623,7 +623,8 @@ antibiotic class selectors:
``` r ``` r
antibiogram(example_isolates, antibiogram(example_isolates,
antibiotics = c(aminoglycosides(), carbapenems())) antibiotics = c(aminoglycosides(), carbapenems())
)
#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK #> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK
#> (amikacin), and KAN (kanamycin) #> (amikacin), and KAN (kanamycin)
#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem) #> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
@@ -662,7 +663,8 @@ antibiogram(example_isolates,
mo_transform = "gramstain", mo_transform = "gramstain",
antibiotics = aminoglycosides(), antibiotics = aminoglycosides(),
ab_transform = "name", ab_transform = "name",
language = "es") language = "es"
)
#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK #> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK
#> (amikacin), and KAN (kanamycin) #> (amikacin), and KAN (kanamycin)
``` ```
@@ -680,7 +682,8 @@ plus `+` character like this:
``` r ``` r
combined_ab <- antibiogram(example_isolates, combined_ab <- antibiogram(example_isolates,
antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"), antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"),
ab_transform = NULL) ab_transform = NULL
)
combined_ab combined_ab
``` ```
@@ -706,7 +709,8 @@ on certain columns:
``` r ``` r
antibiogram(example_isolates, antibiogram(example_isolates,
antibiotics = c(aminoglycosides(), carbapenems()), antibiotics = c(aminoglycosides(), carbapenems()),
syndromic_group = "ward") syndromic_group = "ward"
)
#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK #> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK
#> (amikacin), and KAN (kanamycin) #> (amikacin), and KAN (kanamycin)
#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem) #> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
@@ -742,8 +746,10 @@ antimicrobial susceptibility patterns.
``` r ``` r
example_isolates %>% example_isolates %>%
wisca(antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"), wisca(
minimum = 10) # Recommended threshold: ≥30 antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"),
minimum = 10
) # Recommended threshold: ≥30
``` ```
| Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin | | Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin |
@@ -771,8 +777,10 @@ first:
``` r ``` r
example_isolates %>% example_isolates %>%
top_n_microorganisms(n = 10) %>% top_n_microorganisms(n = 10) %>%
group_by(age_group = age_groups(age, c(25, 50, 75)), group_by(
gender) %>% age_group = age_groups(age, c(25, 50, 75)),
gender
) %>%
wisca(antibiotics = c("TZP", "TZP+TOB", "TZP+GEN")) wisca(antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"))
``` ```
@@ -911,15 +919,19 @@ colour-code SIR categories.
# add a group # add a group
my_data$group <- rep(c("A", "B", "C", "D"), each = 25) my_data$group <- rep(c("A", "B", "C", "D"), each = 25)
ggplot(my_data, ggplot(
aes(x = group, y = MIC, colour = SIR)) + my_data,
aes(x = group, y = MIC, colour = SIR)
) +
geom_jitter(width = 0.2, size = 2) + geom_jitter(width = 0.2, size = 2) +
geom_boxplot(fill = NA, colour = "grey40") + geom_boxplot(fill = NA, colour = "grey40") +
scale_y_mic() + scale_y_mic() +
scale_colour_sir() + scale_colour_sir() +
labs(title = "MIC Distribution and SIR Interpretation", labs(
title = "MIC Distribution and SIR Interpretation",
x = "Sample Groups", x = "Sample Groups",
y = "MIC (mg/L)") y = "MIC (mg/L)"
)
``` ```
![](AMR_files/figure-html/mic_plot-1.png) ![](AMR_files/figure-html/mic_plot-1.png)

2
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@@ -30,7 +30,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

84
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@@ -30,7 +30,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -170,13 +170,19 @@ package.</p>
<span> <span class="co"># select AB results dynamically</span></span> <span> <span class="co"># select AB results dynamically</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">mo</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">betalactams</a></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="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">mo</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">betalactams</a></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"># replace NAs with NI (not-interpretable)</span></span> <span> <span class="co"># replace NAs with NI (not-interpretable)</span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.sir</span><span class="op">)</span>,</span> <span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span></span>
<span> <span class="op">~</span><span class="fu">replace_na</span><span class="op">(</span><span class="va">.x</span>, <span class="st">"NI"</span><span class="op">)</span><span class="op">)</span>,</span> <span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span></span>
<span> <span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.sir</span><span class="op">)</span>,</span>
<span> <span class="op">~</span> <span class="fu">replace_na</span><span class="op">(</span><span class="va">.x</span>, <span class="st">"NI"</span><span class="op">)</span></span>
<span> <span class="op">)</span>,</span>
<span> <span class="co"># make factors of SIR columns</span></span> <span> <span class="co"># make factors of SIR columns</span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.sir</span><span class="op">)</span>,</span> <span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span></span>
<span> <span class="va">as.integer</span><span class="op">)</span>,</span> <span> <span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.sir</span><span class="op">)</span>,</span>
<span> <span class="va">as.integer</span></span>
<span> <span class="op">)</span>,</span>
<span> <span class="co"># get Gramstain of microorganisms</span></span> <span> <span class="co"># get Gramstain of microorganisms</span></span>
<span> mo <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">as.factor</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span> <span> 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>
<span> <span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="co"># drop NAs - the ones without a Gramstain (fungi, etc.)</span></span> <span> <span class="co"># drop NAs - the ones without a Gramstain (fungi, etc.)</span></span>
<span> <span class="fu">drop_na</span><span class="op">(</span><span class="op">)</span></span> <span> <span class="fu">drop_na</span><span class="op">(</span><span class="op">)</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns <span style="color: #00BB00; font-weight: bold;">GEN</span> (gentamicin), <span style="color: #00BB00; font-weight: bold;">TOB</span> (tobramycin), <span style="color: #00BB00; font-weight: bold;">AMK</span></span></span> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns <span style="color: #00BB00; font-weight: bold;">GEN</span> (gentamicin), <span style="color: #00BB00; font-weight: bold;">TOB</span> (tobramycin), <span style="color: #00BB00; font-weight: bold;">AMK</span></span></span>
@@ -665,27 +671,38 @@ status.</p>
<span></span> <span></span>
<span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot</a></span><span class="op">(</span><span class="va">predictions</span>, <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span>x <span class="op">=</span> <span class="va">esbl</span>, fill <span class="op">=</span> <span class="va">.pred_class</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span> <span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot</a></span><span class="op">(</span><span class="va">predictions</span>, <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span>x <span class="op">=</span> <span class="va">esbl</span>, fill <span class="op">=</span> <span class="va">.pred_class</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span>
<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_bar.html" class="external-link">geom_bar</a></span><span class="op">(</span>position <span class="op">=</span> <span class="st">"stack"</span><span class="op">)</span> <span class="op">+</span></span> <span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_bar.html" class="external-link">geom_bar</a></span><span class="op">(</span>position <span class="op">=</span> <span class="st">"stack"</span><span class="op">)</span> <span class="op">+</span></span>
<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">labs</a></span><span class="op">(</span>title <span class="op">=</span> <span class="st">"Predicted vs Actual ESBL Status"</span>,</span> <span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">labs</a></span><span class="op">(</span></span>
<span> title <span class="op">=</span> <span class="st">"Predicted vs Actual ESBL Status"</span>,</span>
<span> x <span class="op">=</span> <span class="st">"Actual ESBL"</span>,</span> <span> x <span class="op">=</span> <span class="st">"Actual ESBL"</span>,</span>
<span> y <span class="op">=</span> <span class="st">"Count"</span><span class="op">)</span> <span class="op">+</span></span> <span> y <span class="op">=</span> <span class="st">"Count"</span></span>
<span> <span class="op">)</span> <span class="op">+</span></span>
<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggtheme.html" class="external-link">theme_minimal</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div> <span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggtheme.html" class="external-link">theme_minimal</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<p><img src="AMR_with_tidymodels_files/figure-html/unnamed-chunk-14-1.png" class="r-plt" alt="" width="720"></p> <p><img src="AMR_with_tidymodels_files/figure-html/unnamed-chunk-14-1.png" class="r-plt" alt="" width="720"></p>
<p>And plot the certainties too - how certain were the actual <p>And plot the certainties too - how certain were the actual
predictions?</p> predictions?</p>
<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">predictions</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span> <code class="sourceCode R"><span><span class="va">predictions</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>certainty <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="va">.pred_class</span> <span class="op">==</span> <span class="st">"FALSE"</span>,</span> <span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span></span>
<span> certainty <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="va">.pred_class</span> <span class="op">==</span> <span class="st">"FALSE"</span>,</span>
<span> <span class="va">.pred_FALSE</span>,</span> <span> <span class="va">.pred_FALSE</span>,</span>
<span> <span class="va">.pred_TRUE</span><span class="op">)</span>,</span> <span> <span class="va">.pred_TRUE</span></span>
<span> correct <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="va">esbl</span> <span class="op">==</span> <span class="va">.pred_class</span>, <span class="st">"Right"</span>, <span class="st">"Wrong"</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="op">)</span>,</span>
<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot</a></span><span class="op">(</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span>x <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq_len</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/nrow.html" class="external-link">nrow</a></span><span class="op">(</span><span class="va">predictions</span><span class="op">)</span><span class="op">)</span>,</span> <span> correct <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="va">esbl</span> <span class="op">==</span> <span class="va">.pred_class</span>, <span class="st">"Right"</span>, <span class="st">"Wrong"</span><span class="op">)</span></span>
<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://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot</a></span><span class="op">(</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span></span>
<span> x <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq_len</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/nrow.html" class="external-link">nrow</a></span><span class="op">(</span><span class="va">predictions</span><span class="op">)</span><span class="op">)</span>,</span>
<span> y <span class="op">=</span> <span class="va">certainty</span>,</span> <span> y <span class="op">=</span> <span class="va">certainty</span>,</span>
<span> colour <span class="op">=</span> <span class="va">correct</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span> <span> colour <span class="op">=</span> <span class="va">correct</span></span>
<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/scale_manual.html" class="external-link">scale_colour_manual</a></span><span class="op">(</span>values <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>Right <span class="op">=</span> <span class="st">"green3"</span>, Wrong <span class="op">=</span> <span class="st">"red2"</span><span class="op">)</span>,</span> <span> <span class="op">)</span><span class="op">)</span> <span class="op">+</span></span>
<span> name <span class="op">=</span> <span class="st">"Correct?"</span><span class="op">)</span> <span class="op">+</span></span> <span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/scale_manual.html" class="external-link">scale_colour_manual</a></span><span class="op">(</span></span>
<span> values <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>Right <span class="op">=</span> <span class="st">"green3"</span>, Wrong <span class="op">=</span> <span class="st">"red2"</span><span class="op">)</span>,</span>
<span> name <span class="op">=</span> <span class="st">"Correct?"</span></span>
<span> <span class="op">)</span> <span class="op">+</span></span>
<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_point.html" class="external-link">geom_point</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span> <span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_point.html" class="external-link">geom_point</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span>
<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/scale_continuous.html" class="external-link">scale_y_continuous</a></span><span class="op">(</span>labels <span class="op">=</span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="va">x</span> <span class="op">*</span> <span class="fl">100</span>, <span class="st">"%"</span><span class="op">)</span>,</span> <span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/scale_continuous.html" class="external-link">scale_y_continuous</a></span><span class="op">(</span></span>
<span> limits <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">0.5</span>, <span class="fl">1</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span> <span> labels <span class="op">=</span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="va">x</span> <span class="op">*</span> <span class="fl">100</span>, <span class="st">"%"</span><span class="op">)</span>,</span>
<span> limits <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">0.5</span>, <span class="fl">1</span><span class="op">)</span></span>
<span> <span class="op">)</span> <span class="op">+</span></span>
<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggtheme.html" class="external-link">theme_minimal</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div> <span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggtheme.html" class="external-link">theme_minimal</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<p><img src="AMR_with_tidymodels_files/figure-html/unnamed-chunk-15-1.png" class="r-plt" alt="" width="720"></p> <p><img src="AMR_with_tidymodels_files/figure-html/unnamed-chunk-15-1.png" class="r-plt" alt="" width="720"></p>
</div> </div>
@@ -738,13 +755,18 @@ into a structured time-series format.</p>
<span><span class="co"># Transform dataset</span></span> <span><span class="co"># Transform dataset</span></span>
<span><span class="va">data_time</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span> <span><span class="va">data_time</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="../reference/top_n_microorganisms.html">top_n_microorganisms</a></span><span class="op">(</span>n <span class="op">=</span> <span class="fl">10</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="co"># Filter on the top #10 species</span></span> <span> <span class="fu"><a href="../reference/top_n_microorganisms.html">top_n_microorganisms</a></span><span class="op">(</span>n <span class="op">=</span> <span class="fl">10</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="co"># Filter on the top #10 species</span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>year <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/format.html" class="external-link">format</a></span><span class="op">(</span><span class="va">date</span>, <span class="st">"%Y"</span><span class="op">)</span><span class="op">)</span>, <span class="co"># Extract year from date</span></span> <span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span></span>
<span> gramstain <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"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="co"># Get taxonomic names</span></span> <span> year <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/format.html" class="external-link">format</a></span><span class="op">(</span><span class="va">date</span>, <span class="st">"%Y"</span><span class="op">)</span><span class="op">)</span>, <span class="co"># Extract year from date</span></span>
<span> gramstain <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>
<span> <span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="co"># Get taxonomic names</span></span>
<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">year</span>, <span class="va">gramstain</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/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">year</span>, <span class="va">gramstain</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/summarise.html" class="external-link">summarise</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</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="va">AMX</span>, <span class="va">AMC</span>, <span class="va">CIP</span><span class="op">)</span>, </span> <span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</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="va">AMX</span>, <span class="va">AMC</span>, <span class="va">CIP</span><span class="op">)</span>,</span>
<span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">x</span>, minimum <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>,</span> <span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">x</span>, minimum <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>,</span>
<span> .names <span class="op">=</span> <span class="st">"res_{.col}"</span><span class="op">)</span>, </span> <span> .names <span class="op">=</span> <span class="st">"res_{.col}"</span></span>
<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="op">)</span>,</span>
<span> .groups <span class="op">=</span> <span class="st">"drop"</span></span>
<span> <span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na</a></span><span class="op">(</span><span class="va">res_AMX</span><span class="op">)</span> <span class="op">&amp;</span> <span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na</a></span><span class="op">(</span><span class="va">res_AMC</span><span class="op">)</span> <span class="op">&amp;</span> <span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na</a></span><span class="op">(</span><span class="va">res_CIP</span><span class="op">)</span><span class="op">)</span> <span class="co"># Drop missing values</span></span> <span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na</a></span><span class="op">(</span><span class="va">res_AMX</span><span class="op">)</span> <span class="op">&amp;</span> <span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na</a></span><span class="op">(</span><span class="va">res_AMC</span><span class="op">)</span> <span class="op">&amp;</span> <span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na</a></span><span class="op">(</span><span class="va">res_CIP</span><span class="op">)</span><span class="op">)</span> <span class="co"># Drop missing values</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Using column <span style="color: #00BB00; font-weight: bold;">mo</span> as input for `col_mo`.</span></span> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Using column <span style="color: #00BB00; font-weight: bold;">mo</span> as input for `col_mo`.</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> `resistance()` assumes the EUCAST guideline and thus considers the 'I'</span></span> <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> `resistance()` assumes the EUCAST guideline and thus considers the 'I'</span></span>
@@ -929,9 +951,11 @@ sets.</li>
<span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot</a></span><span class="op">(</span><span class="va">predictions_time</span>, <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span>x <span class="op">=</span> <span class="va">year</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span> <span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot</a></span><span class="op">(</span><span class="va">predictions_time</span>, <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span>x <span class="op">=</span> <span class="va">year</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span>
<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_point.html" class="external-link">geom_point</a></span><span class="op">(</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span>y <span class="op">=</span> <span class="va">res_AMX</span>, color <span class="op">=</span> <span class="st">"Actual"</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span> <span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_point.html" class="external-link">geom_point</a></span><span class="op">(</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span>y <span class="op">=</span> <span class="va">res_AMX</span>, color <span class="op">=</span> <span class="st">"Actual"</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span>
<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_path.html" class="external-link">geom_line</a></span><span class="op">(</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span>y <span class="op">=</span> <span class="va">.pred</span>, color <span class="op">=</span> <span class="st">"Predicted"</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span> <span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_path.html" class="external-link">geom_line</a></span><span class="op">(</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span>y <span class="op">=</span> <span class="va">.pred</span>, color <span class="op">=</span> <span class="st">"Predicted"</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span>
<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">labs</a></span><span class="op">(</span>title <span class="op">=</span> <span class="st">"Predicted vs Actual AMX Resistance Over Time"</span>,</span> <span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">labs</a></span><span class="op">(</span></span>
<span> title <span class="op">=</span> <span class="st">"Predicted vs Actual AMX Resistance Over Time"</span>,</span>
<span> x <span class="op">=</span> <span class="st">"Year"</span>,</span> <span> x <span class="op">=</span> <span class="st">"Year"</span>,</span>
<span> y <span class="op">=</span> <span class="st">"Resistance Proportion"</span><span class="op">)</span> <span class="op">+</span></span> <span> y <span class="op">=</span> <span class="st">"Resistance Proportion"</span></span>
<span> <span class="op">)</span> <span class="op">+</span></span>
<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggtheme.html" class="external-link">theme_minimal</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div> <span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggtheme.html" class="external-link">theme_minimal</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<p><img src="AMR_with_tidymodels_files/figure-html/unnamed-chunk-21-1.png" class="r-plt" alt="" width="720"></p> <p><img src="AMR_with_tidymodels_files/figure-html/unnamed-chunk-21-1.png" class="r-plt" alt="" width="720"></p>
<p>Additionally, we can visualise resistance trends in <p>Additionally, we can visualise resistance trends in
@@ -939,13 +963,17 @@ sets.</li>
<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb23"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot</a></span><span class="op">(</span><span class="va">data_time</span>, <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span>x <span class="op">=</span> <span class="va">year</span>, y <span class="op">=</span> <span class="va">res_AMX</span>, color <span class="op">=</span> <span class="va">gramstain</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span> <code class="sourceCode R"><span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot</a></span><span class="op">(</span><span class="va">data_time</span>, <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span>x <span class="op">=</span> <span class="va">year</span>, y <span class="op">=</span> <span class="va">res_AMX</span>, color <span class="op">=</span> <span class="va">gramstain</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span>
<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_path.html" class="external-link">geom_line</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span> <span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_path.html" class="external-link">geom_line</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span>
<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">labs</a></span><span class="op">(</span>title <span class="op">=</span> <span class="st">"AMX Resistance Trends"</span>,</span> <span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">labs</a></span><span class="op">(</span></span>
<span> title <span class="op">=</span> <span class="st">"AMX Resistance Trends"</span>,</span>
<span> x <span class="op">=</span> <span class="st">"Year"</span>,</span> <span> x <span class="op">=</span> <span class="st">"Year"</span>,</span>
<span> y <span class="op">=</span> <span class="st">"Resistance Proportion"</span><span class="op">)</span> <span class="op">+</span></span> <span> y <span class="op">=</span> <span class="st">"Resistance Proportion"</span></span>
<span> <span class="op">)</span> <span class="op">+</span></span>
<span> <span class="co"># add a linear model directly in ggplot2:</span></span> <span> <span class="co"># add a linear model directly in ggplot2:</span></span>
<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_smooth.html" class="external-link">geom_smooth</a></span><span class="op">(</span>method <span class="op">=</span> <span class="st">"lm"</span>,</span> <span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_smooth.html" class="external-link">geom_smooth</a></span><span class="op">(</span></span>
<span> method <span class="op">=</span> <span class="st">"lm"</span>,</span>
<span> formula <span class="op">=</span> <span class="va">y</span> <span class="op">~</span> <span class="va">x</span>,</span> <span> formula <span class="op">=</span> <span class="va">y</span> <span class="op">~</span> <span class="va">x</span>,</span>
<span> alpha <span class="op">=</span> <span class="fl">0.25</span><span class="op">)</span> <span class="op">+</span></span> <span> alpha <span class="op">=</span> <span class="fl">0.25</span></span>
<span> <span class="op">)</span> <span class="op">+</span></span>
<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggtheme.html" class="external-link">theme_minimal</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div> <span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggtheme.html" class="external-link">theme_minimal</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<p><img src="AMR_with_tidymodels_files/figure-html/unnamed-chunk-22-1.png" class="r-plt" alt="" width="720"></p> <p><img src="AMR_with_tidymodels_files/figure-html/unnamed-chunk-22-1.png" class="r-plt" alt="" width="720"></p>
</div> </div>

82
articles/AMR_with_tidymodels.md
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@@ -85,13 +85,19 @@ data <- example_isolates %>%
# select AB results dynamically # select AB results dynamically
select(mo, aminoglycosides(), betalactams()) %>% select(mo, aminoglycosides(), betalactams()) %>%
# replace NAs with NI (not-interpretable) # replace NAs with NI (not-interpretable)
mutate(across(where(is.sir), mutate(
~replace_na(.x, "NI")), across(
where(is.sir),
~ replace_na(.x, "NI")
),
# make factors of SIR columns # make factors of SIR columns
across(where(is.sir), across(
as.integer), where(is.sir),
as.integer
),
# get Gramstain of microorganisms # get Gramstain of microorganisms
mo = as.factor(mo_gramstain(mo))) %>% mo = as.factor(mo_gramstain(mo))
) %>%
# drop NAs - the ones without a Gramstain (fungi, etc.) # drop NAs - the ones without a Gramstain (fungi, etc.)
drop_na() drop_na()
#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK #> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK
@@ -564,9 +570,11 @@ library(ggplot2)
ggplot(predictions, aes(x = esbl, fill = .pred_class)) + ggplot(predictions, aes(x = esbl, fill = .pred_class)) +
geom_bar(position = "stack") + geom_bar(position = "stack") +
labs(title = "Predicted vs Actual ESBL Status", labs(
title = "Predicted vs Actual ESBL Status",
x = "Actual ESBL", x = "Actual ESBL",
y = "Count") + y = "Count"
) +
theme_minimal() theme_minimal()
``` ```
@@ -576,18 +584,27 @@ And plot the certainties too - how certain were the actual predictions?
``` r ``` r
predictions %>% predictions %>%
mutate(certainty = ifelse(.pred_class == "FALSE", mutate(
certainty = ifelse(.pred_class == "FALSE",
.pred_FALSE, .pred_FALSE,
.pred_TRUE), .pred_TRUE
correct = ifelse(esbl == .pred_class, "Right", "Wrong")) %>% ),
ggplot(aes(x = seq_len(nrow(predictions)), correct = ifelse(esbl == .pred_class, "Right", "Wrong")
) %>%
ggplot(aes(
x = seq_len(nrow(predictions)),
y = certainty, y = certainty,
colour = correct)) + colour = correct
scale_colour_manual(values = c(Right = "green3", Wrong = "red2"), )) +
name = "Correct?") + scale_colour_manual(
values = c(Right = "green3", Wrong = "red2"),
name = "Correct?"
) +
geom_point() + geom_point() +
scale_y_continuous(labels = function(x) paste0(x * 100, "%"), scale_y_continuous(
limits = c(0.5, 1)) + labels = function(x) paste0(x * 100, "%"),
limits = c(0.5, 1)
) +
theme_minimal() theme_minimal()
``` ```
@@ -636,13 +653,18 @@ library(tidymodels)
# Transform dataset # Transform dataset
data_time <- example_isolates %>% data_time <- example_isolates %>%
top_n_microorganisms(n = 10) %>% # Filter on the top #10 species top_n_microorganisms(n = 10) %>% # Filter on the top #10 species
mutate(year = as.integer(format(date, "%Y")), # Extract year from date mutate(
gramstain = mo_gramstain(mo)) %>% # Get taxonomic names year = as.integer(format(date, "%Y")), # Extract year from date
gramstain = mo_gramstain(mo)
) %>% # Get taxonomic names
group_by(year, gramstain) %>% group_by(year, gramstain) %>%
summarise(across(c(AMX, AMC, CIP), summarise(
across(c(AMX, AMC, CIP),
function(x) resistance(x, minimum = 0), function(x) resistance(x, minimum = 0),
.names = "res_{.col}"), .names = "res_{.col}"
.groups = "drop") %>% ),
.groups = "drop"
) %>%
filter(!is.na(res_AMX) & !is.na(res_AMC) & !is.na(res_CIP)) # Drop missing values filter(!is.na(res_AMX) & !is.na(res_AMC) & !is.na(res_CIP)) # Drop missing values
#> ℹ Using column mo as input for `col_mo`. #> ℹ Using column mo as input for `col_mo`.
#> ℹ `resistance()` assumes the EUCAST guideline and thus considers the 'I' #> ℹ `resistance()` assumes the EUCAST guideline and thus considers the 'I'
@@ -813,9 +835,11 @@ library(ggplot2)
ggplot(predictions_time, aes(x = year)) + ggplot(predictions_time, aes(x = year)) +
geom_point(aes(y = res_AMX, color = "Actual")) + geom_point(aes(y = res_AMX, color = "Actual")) +
geom_line(aes(y = .pred, color = "Predicted")) + geom_line(aes(y = .pred, color = "Predicted")) +
labs(title = "Predicted vs Actual AMX Resistance Over Time", labs(
title = "Predicted vs Actual AMX Resistance Over Time",
x = "Year", x = "Year",
y = "Resistance Proportion") + y = "Resistance Proportion"
) +
theme_minimal() theme_minimal()
``` ```
@@ -827,13 +851,17 @@ directly add linear models there:
``` r ``` r
ggplot(data_time, aes(x = year, y = res_AMX, color = gramstain)) + ggplot(data_time, aes(x = year, y = res_AMX, color = gramstain)) +
geom_line() + geom_line() +
labs(title = "AMX Resistance Trends", labs(
title = "AMX Resistance Trends",
x = "Year", x = "Year",
y = "Resistance Proportion") + y = "Resistance Proportion"
) +
# add a linear model directly in ggplot2: # add a linear model directly in ggplot2:
geom_smooth(method = "lm", geom_smooth(
method = "lm",
formula = y ~ x, formula = y ~ x,
alpha = 0.25) + alpha = 0.25
) +
theme_minimal() theme_minimal()
``` ```

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> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
articles/PCA.html
View File

@@ -30,7 +30,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
articles/WHONET.html
View File

@@ -30,7 +30,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

14
articles/WISCA.html
View File

@@ -30,7 +30,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -279,7 +279,8 @@ I (intermediate [CLSI], or susceptible, increased exposure
</h3> </h3>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">wisca</a></span><span class="op">(</span><span class="va">data</span>,</span> <code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">wisca</a></span><span class="op">(</span><span class="va">data</span>,</span>
<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="st">"AMC"</span>, <span class="st">"CIP"</span>, <span class="st">"GEN"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> <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="st">"AMC"</span>, <span class="st">"CIP"</span>, <span class="st">"GEN"</span><span class="op">)</span></span>
<span><span class="op">)</span></span></code></pre></div>
<table class="table"> <table class="table">
<thead><tr class="header"> <thead><tr class="header">
<th align="left">Amoxicillin/clavulanic acid</th> <th align="left">Amoxicillin/clavulanic acid</th>
@@ -298,7 +299,8 @@ I (intermediate [CLSI], or susceptible, increased exposure
</h3> </h3>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">wisca</a></span><span class="op">(</span><span class="va">data</span>,</span> <code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">wisca</a></span><span class="op">(</span><span class="va">data</span>,</span>
<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="st">"AMC"</span>, <span class="st">"AMC + CIP"</span>, <span class="st">"AMC + GEN"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> <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="st">"AMC"</span>, <span class="st">"AMC + CIP"</span>, <span class="st">"AMC + GEN"</span><span class="op">)</span></span>
<span><span class="op">)</span></span></code></pre></div>
<table class="table"> <table class="table">
<colgroup> <colgroup>
<col width="24%"> <col width="24%">
@@ -323,7 +325,8 @@ I (intermediate [CLSI], or susceptible, increased exposure
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">wisca</a></span><span class="op">(</span><span class="va">data</span>,</span> <code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">wisca</a></span><span class="op">(</span><span class="va">data</span>,</span>
<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="st">"AMC"</span>, <span class="st">"AMC + CIP"</span>, <span class="st">"AMC + GEN"</span><span class="op">)</span>,</span> <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="st">"AMC"</span>, <span class="st">"AMC + CIP"</span>, <span class="st">"AMC + GEN"</span><span class="op">)</span>,</span>
<span> syndromic_group <span class="op">=</span> <span class="st">"syndrome"</span><span class="op">)</span></span></code></pre></div> <span> syndromic_group <span class="op">=</span> <span class="st">"syndrome"</span></span>
<span><span class="op">)</span></span></code></pre></div>
<table class="table"> <table class="table">
<colgroup> <colgroup>
<col width="12%"> <col width="12%">
@@ -358,7 +361,8 @@ all be used for the <code><a href="../reference/antibiogram.html">wisca()</a></c
<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">wisca</a></span><span class="op">(</span><span class="va">data</span>,</span> <code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">wisca</a></span><span class="op">(</span><span class="va">data</span>,</span>
<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="st">"AMC"</span>, <span class="st">"AMC + CIP"</span>, <span class="st">"AMC + GEN"</span><span class="op">)</span>,</span> <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="st">"AMC"</span>, <span class="st">"AMC + CIP"</span>, <span class="st">"AMC + GEN"</span><span class="op">)</span>,</span>
<span> syndromic_group <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/grep.html" class="external-link">gsub</a></span><span class="op">(</span><span class="st">"UTI"</span>, <span class="st">"UCI"</span>, <span class="va">data</span><span class="op">$</span><span class="va">syndrome</span><span class="op">)</span>,</span> <span> syndromic_group <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/grep.html" class="external-link">gsub</a></span><span class="op">(</span><span class="st">"UTI"</span>, <span class="st">"UCI"</span>, <span class="va">data</span><span class="op">$</span><span class="va">syndrome</span><span class="op">)</span>,</span>
<span> language <span class="op">=</span> <span class="st">"Spanish"</span><span class="op">)</span></span></code></pre></div> <span> language <span class="op">=</span> <span class="st">"Spanish"</span></span>
<span><span class="op">)</span></span></code></pre></div>
<table class="table"> <table class="table">
<colgroup> <colgroup>
<col width="12%"> <col width="12%">

12
articles/WISCA.md
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@@ -165,7 +165,8 @@ data$syndrome <- ifelse(data$mo %like% "coli", "UTI", "No UTI")
``` r ``` r
wisca(data, wisca(data,
antimicrobials = c("AMC", "CIP", "GEN")) antimicrobials = c("AMC", "CIP", "GEN")
)
``` ```
| Amoxicillin/clavulanic acid | Ciprofloxacin | Gentamicin | | Amoxicillin/clavulanic acid | Ciprofloxacin | Gentamicin |
@@ -176,7 +177,8 @@ wisca(data,
``` r ``` r
wisca(data, wisca(data,
antimicrobials = c("AMC", "AMC + CIP", "AMC + GEN")) antimicrobials = c("AMC", "AMC + CIP", "AMC + GEN")
)
``` ```
| Amoxicillin/clavulanic acid | Amoxicillin/clavulanic acid + Ciprofloxacin | Amoxicillin/clavulanic acid + Gentamicin | | Amoxicillin/clavulanic acid | Amoxicillin/clavulanic acid + Ciprofloxacin | Amoxicillin/clavulanic acid + Gentamicin |
@@ -188,7 +190,8 @@ wisca(data,
``` r ``` r
wisca(data, wisca(data,
antimicrobials = c("AMC", "AMC + CIP", "AMC + GEN"), antimicrobials = c("AMC", "AMC + CIP", "AMC + GEN"),
syndromic_group = "syndrome") syndromic_group = "syndrome"
)
``` ```
| Syndromic Group | Amoxicillin/clavulanic acid | Amoxicillin/clavulanic acid + Ciprofloxacin | Amoxicillin/clavulanic acid + Gentamicin | | Syndromic Group | Amoxicillin/clavulanic acid | Amoxicillin/clavulanic acid + Ciprofloxacin | Amoxicillin/clavulanic acid + Gentamicin |
@@ -204,7 +207,8 @@ function too:
wisca(data, wisca(data,
antimicrobials = c("AMC", "AMC + CIP", "AMC + GEN"), antimicrobials = c("AMC", "AMC + CIP", "AMC + GEN"),
syndromic_group = gsub("UTI", "UCI", data$syndrome), syndromic_group = gsub("UTI", "UCI", data$syndrome),
language = "Spanish") language = "Spanish"
)
``` ```
| Grupo sindrómico | Amoxicilina/ácido clavulánico | Amoxicilina/ácido clavulánico + Ciprofloxacina | Amoxicilina/ácido clavulánico + Gentamicina | | Grupo sindrómico | Amoxicilina/ácido clavulánico | Amoxicilina/ácido clavulánico + Ciprofloxacina | Amoxicilina/ácido clavulánico + Gentamicina |

4
articles/datasets.html
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@@ -30,7 +30,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -80,7 +80,7 @@
<main id="main" class="col-md-9"><div class="page-header"> <main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Download data sets for download / own use</h1> <img src="../logo.svg" class="logo" alt=""><h1>Download data sets for download / own use</h1>
<h4 data-toc-skip class="date">05 April 2026</h4> <h4 data-toc-skip class="date">21 April 2026</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small> <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<div class="d-none name"><code>datasets.Rmd</code></div> <div class="d-none name"><code>datasets.Rmd</code></div>

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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
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<a class="navbar-brand me-2" href="index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
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<a class="navbar-brand me-2" href="index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
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@@ -49,9 +49,9 @@
</div> </div>
<div class="section level2"> <div class="section level2">
<h2 class="pkg-version" data-toc-text="3.0.1.9044" id="amr-3019044">AMR 3.0.1.9044<a class="anchor" aria-label="anchor" href="#amr-3019044"></a></h2> <h2 class="pkg-version" data-toc-text="3.0.1.9045" id="amr-3019045">AMR 3.0.1.9045<a class="anchor" aria-label="anchor" href="#amr-3019045"></a></h2>
<div class="section level4"> <div class="section level4">
<h4 id="new-3-0-1-9044">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9044"></a></h4> <h4 id="new-3-0-1-9045">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9045"></a></h4>
<ul><li>Support for clinical breakpoints of 2026 of both CLSI and EUCAST, by adding all of their over 5,700 new clinical breakpoints to the <code>clinical_breakpoints</code> data set for usage in <code><a href="../reference/as.sir.html">as.sir()</a></code>. EUCAST 2026 is now the new default guideline for all MIC and disk diffusion interpretations.</li> <ul><li>Support for clinical breakpoints of 2026 of both CLSI and EUCAST, by adding all of their over 5,700 new clinical breakpoints to the <code>clinical_breakpoints</code> data set for usage in <code><a href="../reference/as.sir.html">as.sir()</a></code>. EUCAST 2026 is now the new default guideline for all MIC and disk diffusion interpretations.</li>
<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> <li>Integration with the <strong>tidymodels</strong> framework to allow seamless use of SIR, MIC and disk data in modelling pipelines via <code>recipes</code>
<ul><li> <ul><li>
@@ -80,11 +80,13 @@
<li>Function <code><a href="../reference/interpretive_rules.html">interpretive_rules()</a></code>, which allows future implementation of CLSI interpretive rules (<a href="https://github.com/msberends/AMR/issues/235" class="external-link">#235</a>) <li>Function <code><a href="../reference/interpretive_rules.html">interpretive_rules()</a></code>, which allows future implementation of CLSI interpretive rules (<a href="https://github.com/msberends/AMR/issues/235" class="external-link">#235</a>)
<ul><li> <ul><li>
<code><a href="../reference/interpretive_rules.html">eucast_rules()</a></code> has become a wrapper around that function</li> <code><a href="../reference/interpretive_rules.html">eucast_rules()</a></code> has become a wrapper around that function</li>
<li>Gained argument <code>add_if_missing</code> (default: <code>TRUE</code>). When set to <code>FALSE</code>, rules are only applied to cells that already contain an SIR value; <code>NA</code> cells are left untouched. This is useful with <code>overwrite = TRUE</code> to update reported results without imputing values for drugs that were not tested (<a href="https://github.com/msberends/AMR/issues/259" class="external-link">#259</a>)</li>
</ul></li> </ul></li>
<li>Function <code><a href="../reference/amr_course.html">amr_course()</a></code>, which allows for automated download and unpacking of a GitHub repository for e.g. webinar use</li> <li>Function <code><a href="../reference/amr_course.html">amr_course()</a></code>, which allows for automated download and unpacking of a GitHub repository for e.g. webinar use</li>
<li>Two new <code>NA</code> objects, <code>NA_ab_</code> and <code>NA_mo_</code>, analogous to base R’s <code>NA_character_</code> and <code>NA_integer_</code>, for use in pipelines that require typed missing values</li>
</ul></div> </ul></div>
<div class="section level4"> <div class="section level4">
<h4 id="fixes-3-0-1-9044">Fixes<a class="anchor" aria-label="anchor" href="#fixes-3-0-1-9044"></a></h4> <h4 id="fixes-3-0-1-9045">Fixes<a class="anchor" aria-label="anchor" href="#fixes-3-0-1-9045"></a></h4>
<ul><li>Fixed a bug in <code><a href="../reference/as.sir.html">as.sir()</a></code> where values that were purely numeric (e.g., <code>"1"</code>) and matched the broad SIR-matching regex would be incorrectly stripped of all content by the Unicode letter filter</li> <ul><li>Fixed a bug in <code><a href="../reference/as.sir.html">as.sir()</a></code> where values that were purely numeric (e.g., <code>"1"</code>) and matched the broad SIR-matching regex would be incorrectly stripped of all content by the Unicode letter filter</li>
<li>Fixed a bug in <code><a href="../reference/as.mic.html">as.mic()</a></code> where MIC values in scientific notation (e.g., <code>"1e-3"</code>) were incorrectly handled because the letter <code>e</code> was removed along with other Unicode letters; scientific notation <code>e</code> is now preserved</li> <li>Fixed a bug in <code><a href="../reference/as.mic.html">as.mic()</a></code> where MIC values in scientific notation (e.g., <code>"1e-3"</code>) were incorrectly handled because the letter <code>e</code> was removed along with other Unicode letters; scientific notation <code>e</code> is now preserved</li>
<li>Fixed a bug in <code><a href="../reference/as.ab.html">as.ab()</a></code> where certain AB codes containing “PH” or “TH” (such as <code>ETH</code>, <code>MTH</code>, <code>PHE</code>, <code>PHN</code>, <code>STH</code>, <code>THA</code>, <code>THI1</code>) would incorrectly return <code>NA</code> when combined in a vector with any untranslatable value (<a href="https://github.com/msberends/AMR/issues/245" class="external-link">#245</a>)</li> <li>Fixed a bug in <code><a href="../reference/as.ab.html">as.ab()</a></code> where certain AB codes containing “PH” or “TH” (such as <code>ETH</code>, <code>MTH</code>, <code>PHE</code>, <code>PHN</code>, <code>STH</code>, <code>THA</code>, <code>THI1</code>) would incorrectly return <code>NA</code> when combined in a vector with any untranslatable value (<a href="https://github.com/msberends/AMR/issues/245" class="external-link">#245</a>)</li>
@@ -99,7 +101,7 @@
<li>Fixed SIR and MIC coercion of combined values, e.g. <code>as.sir("&lt;= 0.002; S")</code> or <code>as.mic("S; 0.002")</code> (<a href="https://github.com/msberends/AMR/issues/252" class="external-link">#252</a>)</li> <li>Fixed SIR and MIC coercion of combined values, e.g. <code>as.sir("&lt;= 0.002; S")</code> or <code>as.mic("S; 0.002")</code> (<a href="https://github.com/msberends/AMR/issues/252" class="external-link">#252</a>)</li>
</ul></div> </ul></div>
<div class="section level4"> <div class="section level4">
<h4 id="updates-3-0-1-9044">Updates<a class="anchor" aria-label="anchor" href="#updates-3-0-1-9044"></a></h4> <h4 id="updates-3-0-1-9045">Updates<a class="anchor" aria-label="anchor" href="#updates-3-0-1-9045"></a></h4>
<ul><li>Extensive <code>cli</code> integration for better message handling and clickable links in messages and warnings (<a href="https://github.com/msberends/AMR/issues/191" class="external-link">#191</a>, <a href="https://github.com/msberends/AMR/issues/265" class="external-link">#265</a>)</li> <ul><li>Extensive <code>cli</code> integration for better message handling and clickable links in messages and warnings (<a href="https://github.com/msberends/AMR/issues/191" class="external-link">#191</a>, <a href="https://github.com/msberends/AMR/issues/265" class="external-link">#265</a>)</li>
<li> <li>
<code><a href="../reference/mdro.html">mdro()</a></code> now infers resistance for a <em>missing</em> base drug column from an <em>available</em> corresponding drug+inhibitor combination showing resistance (e.g., piperacillin is absent but required, while piperacillin/tazobactam available and resistant). Can be set with the new argument <code>infer_from_combinations</code>, which defaults to <code>TRUE</code> (<a href="https://github.com/msberends/AMR/issues/209" class="external-link">#209</a>). Note that this can yield a higher MDRO detection (which is a good thing as it has become more reliable).</li> <code><a href="../reference/mdro.html">mdro()</a></code> now infers resistance for a <em>missing</em> base drug column from an <em>available</em> corresponding drug+inhibitor combination showing resistance (e.g., piperacillin is absent but required, while piperacillin/tazobactam available and resistant). Can be set with the new argument <code>infer_from_combinations</code>, which defaults to <code>TRUE</code> (<a href="https://github.com/msberends/AMR/issues/209" class="external-link">#209</a>). Note that this can yield a higher MDRO detection (which is a good thing as it has become more reliable).</li>

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@@ -1,6 +1,6 @@
# Changelog # Changelog
## AMR 3.0.1.9044 ## AMR 3.0.1.9045
#### New #### New
@@ -47,10 +47,19 @@
([\#235](https://github.com/msberends/AMR/issues/235)) ([\#235](https://github.com/msberends/AMR/issues/235))
- [`eucast_rules()`](https://amr-for-r.org/reference/interpretive_rules.md) - [`eucast_rules()`](https://amr-for-r.org/reference/interpretive_rules.md)
has become a wrapper around that function has become a wrapper around that function
- Gained argument `add_if_missing` (default: `TRUE`). When set to
`FALSE`, rules are only applied to cells that already contain an SIR
value; `NA` cells are left untouched. This is useful with
`overwrite = TRUE` to update reported results without imputing
values for drugs that were not tested
([\#259](https://github.com/msberends/AMR/issues/259))
- Function - Function
[`amr_course()`](https://amr-for-r.org/reference/amr_course.md), which [`amr_course()`](https://amr-for-r.org/reference/amr_course.md), which
allows for automated download and unpacking of a GitHub repository for allows for automated download and unpacking of a GitHub repository for
e.g. webinar use e.g. webinar use
- Two new `NA` objects, `NA_ab_` and `NA_mo_`, analogous to base R’s
`NA_character_` and `NA_integer_`, for use in pipelines that require
typed missing values
#### Fixes #### Fixes

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@@ -10,7 +10,7 @@ articles:
PCA: PCA.html PCA: PCA.html
WHONET: WHONET.html WHONET: WHONET.html
WISCA: WISCA.html WISCA: WISCA.html
last_built: 2026-04-05T15:31Z last_built: 2026-04-21T19:58Z
urls: urls:
reference: https://amr-for-r.org/reference reference: https://amr-for-r.org/reference
article: https://amr-for-r.org/articles article: https://amr-for-r.org/articles

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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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@@ -9,7 +9,7 @@ options(AMR_guideline = "CLSI")'><meta property="og:image" content="https://amr-
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -62,7 +62,7 @@ options(AMR_guideline = "CLSI")'><meta property="og:image" content="https://amr-
<ul><li><p><code>AMR_antibiogram_formatting_type</code> <br> A <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> (1-22) to use in <code><a href="antibiogram.html">antibiogram()</a></code>, to indicate which formatting type to use.</p></li> <ul><li><p><code>AMR_antibiogram_formatting_type</code> <br> A <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> (1-22) to use in <code><a href="antibiogram.html">antibiogram()</a></code>, to indicate which formatting type to use.</p></li>
<li><p><code>AMR_breakpoint_type</code> <br> A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> to use in <code><a href="as.sir.html">as.sir()</a></code>, to indicate which breakpoint type to use. This must be either .val ECOFF, .val animal, or .val human.</p></li> <li><p><code>AMR_breakpoint_type</code> <br> A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> to use in <code><a href="as.sir.html">as.sir()</a></code>, to indicate which breakpoint type to use. This must be either <code>"ECOFF"</code>, <code>"animal"</code>, or <code>"human"</code>.</p></li>
<li><p><code>AMR_capped_mic_handling</code> <br> A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> to use in <code><a href="as.sir.html">as.sir()</a></code>, to indicate how capped MIC values (<code>&lt;</code>, <code>&lt;=</code>, <code>&gt;</code>, <code>&gt;=</code>) should be interpreted. Must be one of <code>"none"</code>, <code>"conservative"</code>, <code>"standard"</code>, or <code>"lenient"</code> - the default is <code>"conservative"</code>.</p></li> <li><p><code>AMR_capped_mic_handling</code> <br> A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> to use in <code><a href="as.sir.html">as.sir()</a></code>, to indicate how capped MIC values (<code>&lt;</code>, <code>&lt;=</code>, <code>&gt;</code>, <code>&gt;=</code>) should be interpreted. Must be one of <code>"none"</code>, <code>"conservative"</code>, <code>"standard"</code>, or <code>"lenient"</code> - the default is <code>"conservative"</code>.</p></li>
<li><p><code>AMR_cleaning_regex</code> <br> A <a href="https://rdrr.io/r/base/regex.html" class="external-link">regular expression</a> (case-insensitive) to use in <code><a href="as.mo.html">as.mo()</a></code> and all <code><a href="mo_property.html">mo_*</a></code> functions, to clean the user input. The default is the outcome of <code><a href="as.mo.html">mo_cleaning_regex()</a></code>, which removes texts between brackets and texts such as "species" and "serovar".</p></li> <li><p><code>AMR_cleaning_regex</code> <br> A <a href="https://rdrr.io/r/base/regex.html" class="external-link">regular expression</a> (case-insensitive) to use in <code><a href="as.mo.html">as.mo()</a></code> and all <code><a href="mo_property.html">mo_*</a></code> functions, to clean the user input. The default is the outcome of <code><a href="as.mo.html">mo_cleaning_regex()</a></code>, which removes texts between brackets and texts such as "species" and "serovar".</p></li>
<li><p><code>AMR_custom_ab</code> <br> A file location to an RDS file, to use custom antimicrobial drugs with this package. This is explained in <code><a href="add_custom_antimicrobials.html">add_custom_antimicrobials()</a></code>.</p></li> <li><p><code>AMR_custom_ab</code> <br> A file location to an RDS file, to use custom antimicrobial drugs with this package. This is explained in <code><a href="add_custom_antimicrobials.html">add_custom_antimicrobials()</a></code>.</p></li>

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@@ -16,8 +16,8 @@ the `AMR` package. Set them using the
- `AMR_breakpoint_type` - `AMR_breakpoint_type`
A [character](https://rdrr.io/r/base/character.html) to use in A [character](https://rdrr.io/r/base/character.html) to use in
[`as.sir()`](https://amr-for-r.org/reference/as.sir.md), to indicate [`as.sir()`](https://amr-for-r.org/reference/as.sir.md), to indicate
which breakpoint type to use. This must be either .val ECOFF, .val which breakpoint type to use. This must be either `"ECOFF"`,
animal, or .val human. `"animal"`, or `"human"`.
- `AMR_capped_mic_handling` - `AMR_capped_mic_handling`
A [character](https://rdrr.io/r/base/character.html) to use in A [character](https://rdrr.io/r/base/character.html) to use in

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@@ -21,7 +21,7 @@ The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -124,7 +124,7 @@
<dt id="arg-property">property<a class="anchor" aria-label="anchor" href="#arg-property"></a></dt> <dt id="arg-property">property<a class="anchor" aria-label="anchor" href="#arg-property"></a></dt>
<dd><p>One of the column names of one of the <a href="antimicrobials.html">antimicrobials</a> data set: <code>vector_or(colnames(antimicrobials), sort = FALSE)</code>.</p></dd> <dd><p>One of the column names of one of the <a href="antimicrobials.html">antimicrobials</a> data set: <code>"ab"</code>, <code>"cid"</code>, <code>"name"</code>, <code>"group"</code>, <code>"atc"</code>, <code>"atc_group1"</code>, <code>"atc_group2"</code>, <code>"abbreviations"</code>, <code>"synonyms"</code>, <code>"oral_ddd"</code>, <code>"oral_units"</code>, <code>"iv_ddd"</code>, <code>"iv_units"</code>, or <code>"loinc"</code>.</p></dd>
<dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a></dt> <dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a></dt>

4
reference/ab_property.md
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@@ -101,7 +101,9 @@ set_ab_names(data, ..., property = "name", language = get_AMR_locale(),
One of the column names of one of the One of the column names of one of the
[antimicrobials](https://amr-for-r.org/reference/antimicrobials.md) [antimicrobials](https://amr-for-r.org/reference/antimicrobials.md)
data set: `vector_or(colnames(antimicrobials), sort = FALSE)`. data set: `"ab"`, `"cid"`, `"name"`, `"group"`, `"atc"`,
`"atc_group1"`, `"atc_group2"`, `"abbreviations"`, `"synonyms"`,
`"oral_ddd"`, `"oral_units"`, `"iv_ddd"`, `"iv_units"`, or `"loinc"`.
- data: - data:

2
reference/add_custom_antimicrobials.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/add_custom_microorganisms.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

22
reference/age.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -112,16 +112,16 @@
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">df</span></span></span> <span class="r-in"><span><span class="va">df</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> birth_date age age_exact age_at_y2k</span> <span class="r-out co"><span class="r-pr">#&gt;</span> birth_date age age_exact age_at_y2k</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1999-06-30 26 26.76438 0</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 1 1999-06-30 26 26.80822 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1968-01-29 58 58.18082 31</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 2 1968-01-29 58 58.22466 31</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1965-12-05 60 60.33151 34</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 3 1965-12-05 60 60.37534 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1980-03-01 46 46.09589 19</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 4 1980-03-01 46 46.13973 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1949-11-01 76 76.42466 50</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 5 1949-11-01 76 76.46849 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1947-02-14 79 79.13699 52</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 6 1947-02-14 79 79.18082 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1940-02-19 86 86.12329 59</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 7 1940-02-19 86 86.16712 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1988-01-10 38 38.23288 11</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 8 1988-01-10 38 38.27671 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1997-08-27 28 28.60548 2</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 9 1997-08-27 28 28.64932 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1978-01-26 48 48.18904 21</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 10 1978-01-26 48 48.23288 21</span>
</code></pre></div> </code></pre></div>
</div> </div>
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>

20
reference/age.md
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@@ -81,14 +81,14 @@ df$age_at_y2k <- age(df$birth_date, "2000-01-01")
df df
#> birth_date age age_exact age_at_y2k #> birth_date age age_exact age_at_y2k
#> 1 1999-06-30 26 26.76438 0 #> 1 1999-06-30 26 26.80822 0
#> 2 1968-01-29 58 58.18082 31 #> 2 1968-01-29 58 58.22466 31
#> 3 1965-12-05 60 60.33151 34 #> 3 1965-12-05 60 60.37534 34
#> 4 1980-03-01 46 46.09589 19 #> 4 1980-03-01 46 46.13973 19
#> 5 1949-11-01 76 76.42466 50 #> 5 1949-11-01 76 76.46849 50
#> 6 1947-02-14 79 79.13699 52 #> 6 1947-02-14 79 79.18082 52
#> 7 1940-02-19 86 86.12329 59 #> 7 1940-02-19 86 86.16712 59
#> 8 1988-01-10 38 38.23288 11 #> 8 1988-01-10 38 38.27671 11
#> 9 1997-08-27 28 28.60548 2 #> 9 1997-08-27 28 28.64932 2
#> 10 1978-01-26 48 48.18904 21 #> 10 1978-01-26 48 48.23288 21
``` ```

2
reference/age_groups.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

12
reference/amr-tidymodels.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -188,12 +188,12 @@ may affect the computations for subsequent operations.</p></dd>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Loading required package: tidymodels</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> Loading required package: tidymodels</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ── <span style="font-weight: bold;">Attaching packages</span> ────────────────────────────────────── tidymodels 1.4.1 ──</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> ── <span style="font-weight: bold;">Attaching packages</span> ────────────────────────────────────── tidymodels 1.4.1 ──</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">broom </span> 1.0.12 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">rsample </span> 1.3.2 </span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">broom </span> 1.0.12 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">rsample </span> 1.3.2 </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">dials </span> 1.4.2 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">tailor </span> 0.1.0 </span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">dials </span> 1.4.3 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">tailor </span> 0.1.0 </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">infer </span> 1.1.0 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">tidyr </span> 1.3.2 </span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">infer </span> 1.1.0 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">tidyr </span> 1.3.2 </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">modeldata </span> 1.5.1 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">tune </span> 2.0.1 </span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">modeldata </span> 1.5.1 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">tune </span> 2.1.0 </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">parsnip </span> 1.4.1 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">workflows </span> 1.3.0 </span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">parsnip </span> 1.5.0 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">workflows </span> 1.3.0 </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">purrr </span> 1.2.1 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">workflowsets</span> 1.1.1 </span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">purrr </span> 1.2.2 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">workflowsets</span> 1.1.1 </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">recipes </span> 1.3.2 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">yardstick </span> 1.3.2 </span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">recipes </span> 1.3.2 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">yardstick </span> 1.4.0 </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ── <span style="font-weight: bold;">Conflicts</span> ───────────────────────────────────────── tidymodels_conflicts() ──</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> ── <span style="font-weight: bold;">Conflicts</span> ───────────────────────────────────────── tidymodels_conflicts() ──</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #BB0000;">✖</span> <span style="color: #0000BB;">purrr</span>::<span style="color: #00BB00;">discard()</span> masks <span style="color: #0000BB;">scales</span>::discard()</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #BB0000;">✖</span> <span style="color: #0000BB;">purrr</span>::<span style="color: #00BB00;">discard()</span> masks <span style="color: #0000BB;">scales</span>::discard()</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #BB0000;">✖</span> <span style="color: #0000BB;">dplyr</span>::<span style="color: #00BB00;">filter()</span> masks <span style="color: #0000BB;">stats</span>::filter()</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #BB0000;">✖</span> <span style="color: #0000BB;">dplyr</span>::<span style="color: #00BB00;">filter()</span> masks <span style="color: #0000BB;">stats</span>::filter()</span>

10
reference/amr-tidymodels.md
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@@ -167,12 +167,12 @@ if (require("tidymodels")) {
#> Loading required package: tidymodels #> Loading required package: tidymodels
#> ── Attaching packages ────────────────────────────────────── tidymodels 1.4.1 ── #> ── Attaching packages ────────────────────────────────────── tidymodels 1.4.1 ──
#> ✔ broom 1.0.12 ✔ rsample 1.3.2 #> ✔ broom 1.0.12 ✔ rsample 1.3.2
#> ✔ dials 1.4.2 ✔ tailor 0.1.0 #> ✔ dials 1.4.3 ✔ tailor 0.1.0
#> ✔ infer 1.1.0 ✔ tidyr 1.3.2 #> ✔ infer 1.1.0 ✔ tidyr 1.3.2
#> ✔ modeldata 1.5.1 ✔ tune 2.0.1 #> ✔ modeldata 1.5.1 ✔ tune 2.1.0
#> ✔ parsnip 1.4.1 ✔ workflows 1.3.0 #> ✔ parsnip 1.5.0 ✔ workflows 1.3.0
#> ✔ purrr 1.2.1 ✔ workflowsets 1.1.1 #> ✔ purrr 1.2.2 ✔ workflowsets 1.1.1
#> ✔ recipes 1.3.2 ✔ yardstick 1.3.2 #> ✔ recipes 1.3.2 ✔ yardstick 1.4.0
#> ── Conflicts ───────────────────────────────────────── tidymodels_conflicts() ── #> ── Conflicts ───────────────────────────────────────── tidymodels_conflicts() ──
#> ✖ purrr::discard() masks scales::discard() #> ✖ purrr::discard() masks scales::discard()
#> ✖ dplyr::filter() masks stats::filter() #> ✖ dplyr::filter() masks stats::filter()

2
reference/amr_course.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

6
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@@ -9,7 +9,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -123,11 +123,11 @@ Adhering to previously described approaches (see Source) and especially the Baye
<dt id="arg-mo-transform">mo_transform<a class="anchor" aria-label="anchor" href="#arg-mo-transform"></a></dt> <dt id="arg-mo-transform">mo_transform<a class="anchor" aria-label="anchor" href="#arg-mo-transform"></a></dt>
<dd><p>A character to transform microorganism input - must be <code>"name"</code>, <code>"shortname"</code> (default), <code>"gramstain"</code>, or one of the column names of the <a href="microorganisms.html">microorganisms</a> data set: .val mo, .val fullname, .val status, .val kingdom, .val phylum, .val class, .val order, .val family, .val genus, .val species, .val subspecies, .val rank, .val ref, .val oxygen_tolerance, .val source, .val lpsn, .val lpsn_parent, .val lpsn_renamed_to, .val mycobank, .val mycobank_parent, .val mycobank_renamed_to, .val gbif, .val gbif_parent, .val gbif_renamed_to, .val prevalence, or .val snomed. Can also be <code>NULL</code> to not transform the input or <code>NA</code> to consider all microorganisms 'unknown'.</p></dd> <dd><p>A character to transform microorganism input - must be <code>"name"</code>, <code>"shortname"</code> (default), <code>"gramstain"</code>, or one of the column names of the <a href="microorganisms.html">microorganisms</a> data set: <code>"mo"</code>, <code>"fullname"</code>, <code>"status"</code>, <code>"kingdom"</code>, <code>"phylum"</code>, <code>"class"</code>, <code>"order"</code>, <code>"family"</code>, <code>"genus"</code>, <code>"species"</code>, <code>"subspecies"</code>, <code>"rank"</code>, <code>"ref"</code>, <code>"oxygen_tolerance"</code>, <code>"source"</code>, <code>"lpsn"</code>, <code>"lpsn_parent"</code>, <code>"lpsn_renamed_to"</code>, <code>"mycobank"</code>, <code>"mycobank_parent"</code>, <code>"mycobank_renamed_to"</code>, <code>"gbif"</code>, <code>"gbif_parent"</code>, <code>"gbif_renamed_to"</code>, <code>"prevalence"</code>, or <code>"snomed"</code>. Can also be <code>NULL</code> to not transform the input or <code>NA</code> to consider all microorganisms 'unknown'.</p></dd>
<dt id="arg-ab-transform">ab_transform<a class="anchor" aria-label="anchor" href="#arg-ab-transform"></a></dt> <dt id="arg-ab-transform">ab_transform<a class="anchor" aria-label="anchor" href="#arg-ab-transform"></a></dt>
<dd><p>A character to transform antimicrobial input - must be one of the column names of the <a href="antimicrobials.html">antimicrobials</a> data set (defaults to <code>"name"</code>): .val ab, .val cid, .val name, .val group, .val atc, .val atc_group1, .val atc_group2, .val abbreviations, .val synonyms, .val oral_ddd, .val oral_units, .val iv_ddd, .val iv_units, or .val loinc. Can also be <code>NULL</code> to not transform the input.</p></dd> <dd><p>A character to transform antimicrobial input - must be one of the column names of the <a href="antimicrobials.html">antimicrobials</a> data set (defaults to <code>"name"</code>): <code>"ab"</code>, <code>"cid"</code>, <code>"name"</code>, <code>"group"</code>, <code>"atc"</code>, <code>"atc_group1"</code>, <code>"atc_group2"</code>, <code>"abbreviations"</code>, <code>"synonyms"</code>, <code>"oral_ddd"</code>, <code>"oral_units"</code>, <code>"iv_ddd"</code>, <code>"iv_units"</code>, or <code>"loinc"</code>. Can also be <code>NULL</code> to not transform the input.</p></dd>
<dt id="arg-syndromic-group">syndromic_group<a class="anchor" aria-label="anchor" href="#arg-syndromic-group"></a></dt> <dt id="arg-syndromic-group">syndromic_group<a class="anchor" aria-label="anchor" href="#arg-syndromic-group"></a></dt>

25
reference/antibiogram.md
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@@ -132,25 +132,24 @@ knit_print(x, italicise = TRUE,
`"shortname"` (default), `"gramstain"`, or one of the column names of `"shortname"` (default), `"gramstain"`, or one of the column names of
the the
[microorganisms](https://amr-for-r.org/reference/microorganisms.md) [microorganisms](https://amr-for-r.org/reference/microorganisms.md)
data set: .val mo, .val fullname, .val status, .val kingdom, .val data set: `"mo"`, `"fullname"`, `"status"`, `"kingdom"`, `"phylum"`,
phylum, .val class, .val order, .val family, .val genus, .val species, `"class"`, `"order"`, `"family"`, `"genus"`, `"species"`,
.val subspecies, .val rank, .val ref, .val oxygen_tolerance, .val `"subspecies"`, `"rank"`, `"ref"`, `"oxygen_tolerance"`, `"source"`,
source, .val lpsn, .val lpsn_parent, .val lpsn_renamed_to, .val `"lpsn"`, `"lpsn_parent"`, `"lpsn_renamed_to"`, `"mycobank"`,
mycobank, .val mycobank_parent, .val mycobank_renamed_to, .val gbif, `"mycobank_parent"`, `"mycobank_renamed_to"`, `"gbif"`,
.val gbif_parent, .val gbif_renamed_to, .val prevalence, or .val `"gbif_parent"`, `"gbif_renamed_to"`, `"prevalence"`, or `"snomed"`.
snomed. Can also be `NULL` to not transform the input or `NA` to Can also be `NULL` to not transform the input or `NA` to consider all
consider all microorganisms 'unknown'. microorganisms 'unknown'.
- ab_transform: - ab_transform:
A character to transform antimicrobial input - must be one of the A character to transform antimicrobial input - must be one of the
column names of the column names of the
[antimicrobials](https://amr-for-r.org/reference/antimicrobials.md) [antimicrobials](https://amr-for-r.org/reference/antimicrobials.md)
data set (defaults to `"name"`): .val ab, .val cid, .val name, .val data set (defaults to `"name"`): `"ab"`, `"cid"`, `"name"`, `"group"`,
group, .val atc, .val atc_group1, .val atc_group2, .val abbreviations, `"atc"`, `"atc_group1"`, `"atc_group2"`, `"abbreviations"`,
.val synonyms, .val oral_ddd, .val oral_units, .val iv_ddd, .val `"synonyms"`, `"oral_ddd"`, `"oral_units"`, `"iv_ddd"`, `"iv_units"`,
iv_units, or .val loinc. Can also be `NULL` to not transform the or `"loinc"`. Can also be `NULL` to not transform the input.
input.
- syndromic_group: - syndromic_group:

4
reference/antimicrobial_selectors.html
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@@ -17,7 +17,7 @@ my_data_with_all_these_columns %&amp;gt;%
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -200,7 +200,7 @@ my_data_with_all_these_columns %&amp;gt;%
<dt id="arg-version-expected-phenotypes">version_expected_phenotypes<a class="anchor" aria-label="anchor" href="#arg-version-expected-phenotypes"></a></dt> <dt id="arg-version-expected-phenotypes">version_expected_phenotypes<a class="anchor" aria-label="anchor" href="#arg-version-expected-phenotypes"></a></dt>
<dd><p>The version number to use for the EUCAST Expected Phenotypes. Can be .val 1.2.</p></dd> <dd><p>The version number to use for the EUCAST Expected Phenotypes. Can be <code>"1.2"</code>.</p></dd>
</dl></div> </dl></div>
<div class="section level2"> <div class="section level2">

2
reference/antimicrobial_selectors.md
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@@ -170,7 +170,7 @@ not_intrinsic_resistant(only_sir_columns = FALSE, col_mo = NULL,
- version_expected_phenotypes: - version_expected_phenotypes:
The version number to use for the EUCAST Expected Phenotypes. Can be The version number to use for the EUCAST Expected Phenotypes. Can be
.val 1.2. `"1.2"`.
## Value ## Value

2
reference/antimicrobials.html
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@@ -9,7 +9,7 @@ The antibiotics data set has been renamed to antimicrobials. The old name will b
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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2
reference/as.ab.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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2
reference/as.av.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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2
reference/as.disk.html
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@@ -7,7 +7,7 @@
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2
reference/as.mic.html
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@@ -7,7 +7,7 @@
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2
reference/as.mo.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
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12
reference/as.sir.html
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@@ -9,7 +9,7 @@ Breakpoints are currently implemented from EUCAST 2011-2026 and CLSI 2011-2026,
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
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@@ -203,7 +203,7 @@ Breakpoints are currently implemented from EUCAST 2011-2026 and CLSI 2011-2026,
<dt id="arg-breakpoint-type">breakpoint_type<a class="anchor" aria-label="anchor" href="#arg-breakpoint-type"></a></dt> <dt id="arg-breakpoint-type">breakpoint_type<a class="anchor" aria-label="anchor" href="#arg-breakpoint-type"></a></dt>
<dd><p>The type of breakpoints to use, either .val ECOFF, .val animal, or .val human. ECOFF stands for Epidemiological Cut-Off values. The default is <code>"human"</code>, which can also be set with the package option <code><a href="AMR-options.html">AMR_breakpoint_type</a></code>. If <code>host</code> is set to values of veterinary species, this will automatically be set to <code>"animal"</code>.</p></dd> <dd><p>The type of breakpoints to use, either <code>"ECOFF"</code>, <code>"animal"</code>, or <code>"human"</code>. ECOFF stands for Epidemiological Cut-Off values. The default is <code>"human"</code>, which can also be set with the package option <code><a href="AMR-options.html">AMR_breakpoint_type</a></code>. If <code>host</code> is set to values of veterinary species, this will automatically be set to <code>"animal"</code>.</p></dd>
<dt id="arg-host">host<a class="anchor" aria-label="anchor" href="#arg-host"></a></dt> <dt id="arg-host">host<a class="anchor" aria-label="anchor" href="#arg-host"></a></dt>
@@ -424,10 +424,10 @@ Breakpoints are currently implemented from EUCAST 2011-2026 and CLSI 2011-2026,
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4 × 18</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4 × 18</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index method ab_given mo_given host_given input_given</span> <span class="r-out co"><span class="r-pr">#&gt;</span> datetime index method ab_given mo_given host_given input_given</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2026-04-05 <span style="color: #949494;">15:32:33</span> 1 MIC amoxicillin Escherich… human 8 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2026-04-21 <span style="color: #949494;">19:59:41</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> 2026-04-05 <span style="color: #949494;">15:32:33</span> 1 MIC cipro Escherich… human 0.256 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2026-04-21 <span style="color: #949494;">19:59:42</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> 2026-04-05 <span style="color: #949494;">15:32:33</span> 1 DISK tobra Escherich… human 16 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2026-04-21 <span style="color: #949494;">19:59:42</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> 2026-04-05 <span style="color: #949494;">15:32:33</span> 1 DISK genta Escherich… human 18 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2026-04-21 <span style="color: #949494;">19:59:42</span> 1 DISK genta Escherich… human 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 11 more variables: ab &lt;ab&gt;, mo &lt;mo&gt;, host &lt;chr&gt;, input &lt;chr&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 11 more variables: ab &lt;ab&gt;, mo &lt;mo&gt;, host &lt;chr&gt;, input &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># outcome &lt;sir&gt;, notes &lt;chr&gt;, guideline &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># outcome &lt;sir&gt;, notes &lt;chr&gt;, guideline &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># breakpoint_S_R &lt;chr&gt;, site &lt;chr&gt;</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># breakpoint_S_R &lt;chr&gt;, site &lt;chr&gt;</span></span>

12
reference/as.sir.md
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@@ -280,8 +280,8 @@ disk diffusion diameters:
- breakpoint_type: - breakpoint_type:
The type of breakpoints to use, either .val ECOFF, .val animal, or The type of breakpoints to use, either `"ECOFF"`, `"animal"`, or
.val human. ECOFF stands for Epidemiological Cut-Off values. The `"human"`. ECOFF stands for Epidemiological Cut-Off values. The
default is `"human"`, which can also be set with the package option default is `"human"`, which can also be set with the package option
[`AMR_breakpoint_type`](https://amr-for-r.org/reference/AMR-options.md). [`AMR_breakpoint_type`](https://amr-for-r.org/reference/AMR-options.md).
If `host` is set to values of veterinary species, this will If `host` is set to values of veterinary species, this will
@@ -660,10 +660,10 @@ sir_interpretation_history()
#> # A tibble: 4 × 18 #> # A tibble: 4 × 18
#> datetime index method ab_given mo_given host_given input_given #> datetime index method ab_given mo_given host_given input_given
#> <dttm> <int> <chr> <chr> <chr> <chr> <chr> #> <dttm> <int> <chr> <chr> <chr> <chr> <chr>
#> 1 2026-04-05 15:32:33 1 MIC amoxicillin Escherich… human 8 #> 1 2026-04-21 19:59:41 1 MIC amoxicillin Escherich… human 8
#> 2 2026-04-05 15:32:33 1 MIC cipro Escherich… human 0.256 #> 2 2026-04-21 19:59:42 1 MIC cipro Escherich… human 0.256
#> 3 2026-04-05 15:32:33 1 DISK tobra Escherich… human 16 #> 3 2026-04-21 19:59:42 1 DISK tobra Escherich… human 16
#> 4 2026-04-05 15:32:33 1 DISK genta Escherich… human 18 #> 4 2026-04-21 19:59:42 1 DISK genta Escherich… human 18
#> # ℹ 11 more variables: ab <ab>, mo <mo>, host <chr>, input <chr>, #> # ℹ 11 more variables: ab <ab>, mo <mo>, host <chr>, input <chr>,
#> # outcome <sir>, notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>, #> # outcome <sir>, notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,
#> # breakpoint_S_R <chr>, site <chr> #> # breakpoint_S_R <chr>, site <chr>

2
reference/atc_online.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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2
reference/av_from_text.html
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@@ -7,7 +7,7 @@
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4
reference/av_property.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
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@@ -109,7 +109,7 @@
<dt id="arg-property">property<a class="anchor" aria-label="anchor" href="#arg-property"></a></dt> <dt id="arg-property">property<a class="anchor" aria-label="anchor" href="#arg-property"></a></dt>
<dd><p>One of the column names of one of the <a href="antimicrobials.html">antivirals</a> data set: <code>vector_or(colnames(antivirals), sort = FALSE)</code>.</p></dd> <dd><p>One of the column names of one of the <a href="antimicrobials.html">antivirals</a> data set: <code>"av"</code>, <code>"name"</code>, <code>"atc"</code>, <code>"cid"</code>, <code>"atc_group"</code>, <code>"synonyms"</code>, <code>"oral_ddd"</code>, <code>"oral_units"</code>, <code>"iv_ddd"</code>, <code>"iv_units"</code>, or <code>"loinc"</code>.</p></dd>
</dl></div> </dl></div>
<div class="section level2"> <div class="section level2">

3
reference/av_property.md
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@@ -73,7 +73,8 @@ av_property(x, property = "name", language = get_AMR_locale(), ...)
One of the column names of one of the One of the column names of one of the
[antivirals](https://amr-for-r.org/reference/antimicrobials.md) data [antivirals](https://amr-for-r.org/reference/antimicrobials.md) data
set: `vector_or(colnames(antivirals), sort = FALSE)`. set: `"av"`, `"name"`, `"atc"`, `"cid"`, `"atc_group"`, `"synonyms"`,
`"oral_ddd"`, `"oral_units"`, `"iv_ddd"`, `"iv_units"`, or `"loinc"`.
## Value ## Value

2
reference/availability.html
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@@ -7,7 +7,7 @@
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reference/bug_drug_combinations.html
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@@ -7,7 +7,7 @@
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8
reference/clinical_breakpoints.html
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@@ -21,7 +21,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
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@@ -79,9 +79,9 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
<div class="section level2"> <div class="section level2">
<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2> <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
<p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 45 730 observations and 14 variables:</p><ul><li><p><code>guideline</code><br> Name of the guideline</p></li> <p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 45 730 observations and 14 variables:</p><ul><li><p><code>guideline</code><br> Name of the guideline</p></li>
<li><p><code>type</code><br> Breakpoint type, either .val ECOFF, .val animal, or .val human</p></li> <li><p><code>type</code><br> Breakpoint type, either <code>"ECOFF"</code>, <code>"animal"</code>, or <code>"human"</code></p></li>
<li><p><code>host</code><br> Host of infectious agent. This is mostly useful for veterinary breakpoints and is either .val ECOFF, .val aquatic, .val cats, .val cattle, .val dogs, .val horse, .val human, .val poultry, or .val swine</p></li> <li><p><code>host</code><br> Host of infectious agent. This is mostly useful for veterinary breakpoints and is either <code>"ECOFF"</code>, <code>"aquatic"</code>, <code>"cats"</code>, <code>"cattle"</code>, <code>"dogs"</code>, <code>"horse"</code>, <code>"human"</code>, <code>"poultry"</code>, or <code>"swine"</code></p></li>
<li><p><code>method</code><br> Testing method, either .val DISK or .val MIC</p></li> <li><p><code>method</code><br> Testing method, either <code>"DISK"</code> or <code>"MIC"</code></p></li>
<li><p><code>site</code><br> Body site for which the breakpoint must be applied, e.g. "Oral" or "Respiratory"</p></li> <li><p><code>site</code><br> Body site for which the breakpoint must be applied, e.g. "Oral" or "Respiratory"</p></li>
<li><p><code>mo</code><br> Microbial ID, see <code><a href="as.mo.html">as.mo()</a></code></p></li> <li><p><code>mo</code><br> Microbial ID, see <code><a href="as.mo.html">as.mo()</a></code></p></li>
<li><p><code>rank_index</code><br> Taxonomic rank index of <code>mo</code> from 1 (subspecies/infraspecies) to 5 (unknown microorganism)</p></li> <li><p><code>rank_index</code><br> Taxonomic rank index of <code>mo</code> from 1 (subspecies/infraspecies) to 5 (unknown microorganism)</p></li>

8
reference/clinical_breakpoints.md
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@@ -32,15 +32,15 @@ A [tibble](https://tibble.tidyverse.org/reference/tibble.html) with 45
Name of the guideline Name of the guideline
- `type` - `type`
Breakpoint type, either .val ECOFF, .val animal, or .val human Breakpoint type, either `"ECOFF"`, `"animal"`, or `"human"`
- `host` - `host`
Host of infectious agent. This is mostly useful for veterinary Host of infectious agent. This is mostly useful for veterinary
breakpoints and is either .val ECOFF, .val aquatic, .val cats, .val breakpoints and is either `"ECOFF"`, `"aquatic"`, `"cats"`,
cattle, .val dogs, .val horse, .val human, .val poultry, or .val swine `"cattle"`, `"dogs"`, `"horse"`, `"human"`, `"poultry"`, or `"swine"`
- `method` - `method`
Testing method, either .val DISK or .val MIC Testing method, either `"DISK"` or `"MIC"`
- `site` - `site`
Body site for which the breakpoint must be applied, e.g. "Oral" or Body site for which the breakpoint must be applied, e.g. "Oral" or

2
reference/count.html
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@@ -9,7 +9,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

4
reference/custom_eucast_rules.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -112,7 +112,7 @@
<h3 id="using-taxonomic-properties-in-rules">Using taxonomic properties in rules<a class="anchor" aria-label="anchor" href="#using-taxonomic-properties-in-rules"></a></h3> <h3 id="using-taxonomic-properties-in-rules">Using taxonomic properties in rules<a class="anchor" aria-label="anchor" href="#using-taxonomic-properties-in-rules"></a></h3>
<p>There is one exception in columns used for the rules: all column names of the <a href="microorganisms.html">microorganisms</a> data set can also be used, but do not have to exist in the data set. These column names are: "mo", "fullname", "status", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "oxygen_tolerance", "source", "lpsn", "lpsn_parent", "lpsn_renamed_to", "mycobank", "mycobank_parent", "mycobank_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence", and "snomed". Thus, this next example will work as well, despite the fact that the <code>df</code> data set does not contain a column <code>genus</code>:</p> <p>There is one exception in columns used for the rules: all column names of the <a href="microorganisms.html">microorganisms</a> data set can also be used, but do not have to exist in the data set. These column names are: <code>"mo"</code>, <code>"fullname"</code>, <code>"status"</code>, <code>"kingdom"</code>, <code>"phylum"</code>, <code>"class"</code>, <code>"order"</code>, <code>"family"</code>, <code>"genus"</code>, <code>"species"</code>, <code>"subspecies"</code>, <code>"rank"</code>, <code>"ref"</code>, <code>"oxygen_tolerance"</code>, <code>"source"</code>, <code>"lpsn"</code>, <code>"lpsn_parent"</code>, <code>"lpsn_renamed_to"</code>, <code>"mycobank"</code>, <code>"mycobank_parent"</code>, <code>"mycobank_renamed_to"</code>, <code>"gbif"</code>, <code>"gbif_parent"</code>, <code>"gbif_renamed_to"</code>, <code>"prevalence"</code>, and <code>"snomed"</code>. Thus, this next example will work as well, despite the fact that the <code>df</code> data set does not contain a column <code>genus</code>:</p>
<p></p><div class="sourceCode r"><pre><code><span><span class="va">y</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/custom_eucast_rules.html">custom_eucast_rules</a></span><span class="op">(</span></span> <p></p><div class="sourceCode r"><pre><code><span><span class="va">y</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/custom_eucast_rules.html">custom_eucast_rules</a></span><span class="op">(</span></span>
<span> <span class="va">TZP</span> <span class="op">==</span> <span class="st">"S"</span> <span class="op">&amp;</span> <span class="va">genus</span> <span class="op">==</span> <span class="st">"Klebsiella"</span> <span class="op">~</span> <span class="va">aminopenicillins</span> <span class="op">==</span> <span class="st">"S"</span>,</span> <span> <span class="va">TZP</span> <span class="op">==</span> <span class="st">"S"</span> <span class="op">&amp;</span> <span class="va">genus</span> <span class="op">==</span> <span class="st">"Klebsiella"</span> <span class="op">~</span> <span class="va">aminopenicillins</span> <span class="op">==</span> <span class="st">"S"</span>,</span>
<span> <span class="va">TZP</span> <span class="op">==</span> <span class="st">"R"</span> <span class="op">&amp;</span> <span class="va">genus</span> <span class="op">==</span> <span class="st">"Klebsiella"</span> <span class="op">~</span> <span class="va">aminopenicillins</span> <span class="op">==</span> <span class="st">"R"</span></span> <span> <span class="va">TZP</span> <span class="op">==</span> <span class="st">"R"</span> <span class="op">&amp;</span> <span class="va">genus</span> <span class="op">==</span> <span class="st">"Klebsiella"</span> <span class="op">~</span> <span class="va">aminopenicillins</span> <span class="op">==</span> <span class="st">"R"</span></span>

15
reference/custom_eucast_rules.md
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@@ -85,13 +85,14 @@ There is one exception in columns used for the rules: all column names
of the of the
[microorganisms](https://amr-for-r.org/reference/microorganisms.md) data [microorganisms](https://amr-for-r.org/reference/microorganisms.md) data
set can also be used, but do not have to exist in the data set. These set can also be used, but do not have to exist in the data set. These
column names are: "mo", "fullname", "status", "kingdom", "phylum", column names are: `"mo"`, `"fullname"`, `"status"`, `"kingdom"`,
"class", "order", "family", "genus", "species", "subspecies", "rank", `"phylum"`, `"class"`, `"order"`, `"family"`, `"genus"`, `"species"`,
"ref", "oxygen_tolerance", "source", "lpsn", "lpsn_parent", `"subspecies"`, `"rank"`, `"ref"`, `"oxygen_tolerance"`, `"source"`,
"lpsn_renamed_to", "mycobank", "mycobank_parent", "mycobank_renamed_to", `"lpsn"`, `"lpsn_parent"`, `"lpsn_renamed_to"`, `"mycobank"`,
"gbif", "gbif_parent", "gbif_renamed_to", "prevalence", and "snomed". `"mycobank_parent"`, `"mycobank_renamed_to"`, `"gbif"`, `"gbif_parent"`,
Thus, this next example will work as well, despite the fact that the `"gbif_renamed_to"`, `"prevalence"`, and `"snomed"`. Thus, this next
`df` data set does not contain a column `genus`: example will work as well, despite the fact that the `df` data set does
not contain a column `genus`:
y <- custom_eucast_rules( y <- custom_eucast_rules(
TZP == "S" & genus == "Klebsiella" ~ aminopenicillins == "S", TZP == "S" & genus == "Klebsiella" ~ aminopenicillins == "S",

2
reference/custom_mdro_guideline.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
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6
reference/dosage.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
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@@ -62,10 +62,10 @@
<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2> <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
<p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 759 observations and 9 variables:</p><ul><li><p><code>ab</code><br> Antimicrobial ID as used in this package (such as <code>AMC</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available</p></li> <p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 759 observations and 9 variables:</p><ul><li><p><code>ab</code><br> Antimicrobial ID as used in this package (such as <code>AMC</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available</p></li>
<li><p><code>name</code><br> Official name of the antimicrobial drug as used by WHONET/EARS-Net or the WHO</p></li> <li><p><code>name</code><br> Official name of the antimicrobial drug as used by WHONET/EARS-Net or the WHO</p></li>
<li><p><code>type</code><br> Type of the dosage, either .val high_dosage, .val standard_dosage, or .val uncomplicated_uti</p></li> <li><p><code>type</code><br> Type of the dosage, either <code>"high_dosage"</code>, <code>"standard_dosage"</code>, or <code>"uncomplicated_uti"</code></p></li>
<li><p><code>dose</code><br> Dose, such as "2 g" or "25 mg/kg"</p></li> <li><p><code>dose</code><br> Dose, such as "2 g" or "25 mg/kg"</p></li>
<li><p><code>dose_times</code><br> Number of times a dose must be administered</p></li> <li><p><code>dose_times</code><br> Number of times a dose must be administered</p></li>
<li><p><code>administration</code><br> Route of administration, either .val , .val im, .val iv, .val oral, or NA</p></li> <li><p><code>administration</code><br> Route of administration, either <code>""</code>, <code>"im"</code>, <code>"iv"</code>, <code>"oral"</code>, or NA</p></li>
<li><p><code>notes</code><br> Additional dosage notes</p></li> <li><p><code>notes</code><br> Additional dosage notes</p></li>
<li><p><code>original_txt</code><br> Original text in the PDF file of EUCAST</p></li> <li><p><code>original_txt</code><br> Original text in the PDF file of EUCAST</p></li>
<li><p><code>eucast_version</code><br> Version number of the EUCAST Clinical Breakpoints guideline to which these dosages apply, either 15, 14, 13.1, 12, or 11</p></li> <li><p><code>eucast_version</code><br> Version number of the EUCAST Clinical Breakpoints guideline to which these dosages apply, either 15, 14, 13.1, 12, or 11</p></li>

7
reference/dosage.md
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@@ -25,8 +25,8 @@ observations and 9 variables:
the WHO the WHO
- `type` - `type`
Type of the dosage, either .val high_dosage, .val standard_dosage, or Type of the dosage, either `"high_dosage"`, `"standard_dosage"`, or
.val uncomplicated_uti `"uncomplicated_uti"`
- `dose` - `dose`
Dose, such as "2 g" or "25 mg/kg" Dose, such as "2 g" or "25 mg/kg"
@@ -35,8 +35,7 @@ observations and 9 variables:
Number of times a dose must be administered Number of times a dose must be administered
- `administration` - `administration`
Route of administration, either .val , .val im, .val iv, .val oral, or Route of administration, either `""`, `"im"`, `"iv"`, `"oral"`, or NA
NA
- `notes` - `notes`
Additional dosage notes Additional dosage notes

2
reference/esbl_isolates.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

6
reference/example_isolates.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -63,8 +63,8 @@
<p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 2 000 observations and 46 variables:</p><ul><li><p><code>date</code><br> Date of receipt at the laboratory</p></li> <p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 2 000 observations and 46 variables:</p><ul><li><p><code>date</code><br> Date of receipt at the laboratory</p></li>
<li><p><code>patient</code><br> ID of the patient</p></li> <li><p><code>patient</code><br> ID of the patient</p></li>
<li><p><code>age</code><br> Age of the patient</p></li> <li><p><code>age</code><br> Age of the patient</p></li>
<li><p><code>gender</code><br> Gender of the patient, either .val F or .val M</p></li> <li><p><code>gender</code><br> Gender of the patient, either <code>"F"</code> or <code>"M"</code></p></li>
<li><p><code>ward</code><br> Ward type where the patient was admitted, either .val Clinical, .val ICU, or .val Outpatient</p></li> <li><p><code>ward</code><br> Ward type where the patient was admitted, either <code>"Clinical"</code>, <code>"ICU"</code>, or <code>"Outpatient"</code></p></li>
<li><p><code>mo</code><br> ID of microorganism created with <code><a href="as.mo.html">as.mo()</a></code>, see also the <a href="microorganisms.html">microorganisms</a> data set</p></li> <li><p><code>mo</code><br> ID of microorganism created with <code><a href="as.mo.html">as.mo()</a></code>, see also the <a href="microorganisms.html">microorganisms</a> data set</p></li>
<li><p><code>PEN:RIF</code><br> 40 different antimicrobials with class <code><a href="as.sir.html">sir</a></code> (see <code><a href="as.sir.html">as.sir()</a></code>); these column names occur in the <a href="antimicrobials.html">antimicrobials</a> data set and can be translated with <code><a href="ab_property.html">set_ab_names()</a></code> or <code><a href="ab_property.html">ab_name()</a></code></p></li> <li><p><code>PEN:RIF</code><br> 40 different antimicrobials with class <code><a href="as.sir.html">sir</a></code> (see <code><a href="as.sir.html">as.sir()</a></code>); these column names occur in the <a href="antimicrobials.html">antimicrobials</a> data set and can be translated with <code><a href="ab_property.html">set_ab_names()</a></code> or <code><a href="ab_property.html">ab_name()</a></code></p></li>
</ul></div> </ul></div>

6
reference/example_isolates.md
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@@ -27,11 +27,11 @@ A [tibble](https://tibble.tidyverse.org/reference/tibble.html) with 2
Age of the patient Age of the patient
- `gender` - `gender`
Gender of the patient, either .val F or .val M Gender of the patient, either `"F"` or `"M"`
- `ward` - `ward`
Ward type where the patient was admitted, either .val Clinical, .val Ward type where the patient was admitted, either `"Clinical"`,
ICU, or .val Outpatient `"ICU"`, or `"Outpatient"`
- `mo` - `mo`
ID of microorganism created with ID of microorganism created with

2
reference/example_isolates_unclean.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
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2
reference/export_ncbi_biosample.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/first_isolate.html
View File

@@ -9,7 +9,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/g.test.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/get_episode.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/ggplot_pca.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/ggplot_sir.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/guess_ab_col.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/index.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

36
reference/interpretive_rules.html
View File

@@ -9,7 +9,7 @@ To improve the interpretation of the antibiogram before CLSI/EUCAST interpretive
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -64,7 +64,7 @@ To improve the interpretation of the antibiogram before CLSI/EUCAST interpretive
<span> verbose <span class="op">=</span> <span class="cn">FALSE</span>, version_breakpoints <span class="op">=</span> <span class="fl">16</span>,</span> <span> verbose <span class="op">=</span> <span class="cn">FALSE</span>, version_breakpoints <span class="op">=</span> <span class="fl">16</span>,</span>
<span> version_expected_phenotypes <span class="op">=</span> <span class="fl">1.2</span>, version_expertrules <span class="op">=</span> <span class="fl">3.3</span>,</span> <span> version_expected_phenotypes <span class="op">=</span> <span class="fl">1.2</span>, version_expertrules <span class="op">=</span> <span class="fl">3.3</span>,</span>
<span> ampc_cephalosporin_resistance <span class="op">=</span> <span class="cn">NA</span>, only_sir_columns <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="as.sir.html">is.sir</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>,</span> <span> ampc_cephalosporin_resistance <span class="op">=</span> <span class="cn">NA</span>, only_sir_columns <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="as.sir.html">is.sir</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>,</span>
<span> custom_rules <span class="op">=</span> <span class="cn">NULL</span>, overwrite <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span> <span> custom_rules <span class="op">=</span> <span class="cn">NULL</span>, overwrite <span class="op">=</span> <span class="cn">FALSE</span>, add_if_missing <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span> <span></span>
<span><span class="fu">eucast_rules</span><span class="op">(</span><span class="va">x</span>, col_mo <span class="op">=</span> <span class="cn">NULL</span>, info <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span>,</span> <span><span class="fu">eucast_rules</span><span class="op">(</span><span class="va">x</span>, col_mo <span class="op">=</span> <span class="cn">NULL</span>, info <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> rules <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_interpretive_rules"</span>, default <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">"breakpoints"</span>,</span> <span> rules <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_interpretive_rules"</span>, default <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">"breakpoints"</span>,</span>
@@ -119,15 +119,15 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<dt id="arg-version-breakpoints">version_breakpoints<a class="anchor" aria-label="anchor" href="#arg-version-breakpoints"></a></dt> <dt id="arg-version-breakpoints">version_breakpoints<a class="anchor" aria-label="anchor" href="#arg-version-breakpoints"></a></dt>
<dd><p>The version number to use for the EUCAST Clinical Breakpoints guideline. Can be .val 16.0, .val 15.0, .val 14.0, .val 13.1, .val 12.0, .val 11.0, or .val 10.0.</p></dd> <dd><p>The version number to use for the EUCAST Clinical Breakpoints guideline. Can be <code>"16.0"</code>, <code>"15.0"</code>, <code>"14.0"</code>, <code>"13.1"</code>, <code>"12.0"</code>, <code>"11.0"</code>, or <code>"10.0"</code>.</p></dd>
<dt id="arg-version-expected-phenotypes">version_expected_phenotypes<a class="anchor" aria-label="anchor" href="#arg-version-expected-phenotypes"></a></dt> <dt id="arg-version-expected-phenotypes">version_expected_phenotypes<a class="anchor" aria-label="anchor" href="#arg-version-expected-phenotypes"></a></dt>
<dd><p>The version number to use for the EUCAST Expected Phenotypes. Can be .val 1.2.</p></dd> <dd><p>The version number to use for the EUCAST Expected Phenotypes. Can be <code>"1.2"</code>.</p></dd>
<dt id="arg-version-expertrules">version_expertrules<a class="anchor" aria-label="anchor" href="#arg-version-expertrules"></a></dt> <dt id="arg-version-expertrules">version_expertrules<a class="anchor" aria-label="anchor" href="#arg-version-expertrules"></a></dt>
<dd><p>The version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be .val 3.3, .val 3.2, or .val 3.1.</p></dd> <dd><p>The version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be <code>"3.3"</code>, <code>"3.2"</code>, or <code>"3.1"</code>.</p></dd>
<dt id="arg-ampc-cephalosporin-resistance">ampc_cephalosporin_resistance<a class="anchor" aria-label="anchor" href="#arg-ampc-cephalosporin-resistance"></a></dt> <dt id="arg-ampc-cephalosporin-resistance">ampc_cephalosporin_resistance<a class="anchor" aria-label="anchor" href="#arg-ampc-cephalosporin-resistance"></a></dt>
@@ -146,6 +146,10 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> indicating whether to overwrite existing SIR values (default: <code>FALSE</code>). When <code>FALSE</code>, only non-SIR values are modified (i.e., any value that is not already S, I or R). To ensure compliance with EUCAST guidelines, <strong>this should remain</strong> <code>FALSE</code>, as EUCAST notes often state that an organism "should be tested for susceptibility to individual agents or be reported resistant".</p></dd> <dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> indicating whether to overwrite existing SIR values (default: <code>FALSE</code>). When <code>FALSE</code>, only non-SIR values are modified (i.e., any value that is not already S, I or R). To ensure compliance with EUCAST guidelines, <strong>this should remain</strong> <code>FALSE</code>, as EUCAST notes often state that an organism "should be tested for susceptibility to individual agents or be reported resistant".</p></dd>
<dt id="arg-add-if-missing">add_if_missing<a class="anchor" aria-label="anchor" href="#arg-add-if-missing"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> indicating whether rules should also be applied to missing (<code>NA</code>) values (default: <code>TRUE</code>). When <code>FALSE</code>, rules are only applied to cells that already contain an SIR value; cells with <code>NA</code> are left untouched. This is particularly useful when using <code>overwrite = TRUE</code> with custom rules and you want to update reported results without imputing values for untested drugs.</p></dd>
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt> <dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>Column names of antimicrobials. To automatically detect antimicrobial column names, do not provide any named arguments; <code><a href="guess_ab_col.html">guess_ab_col()</a></code> will then be used for detection. To manually specify a column, provide its name (case-insensitive) as an argument, e.g. <code>AMX = "amoxicillin"</code>. To skip a specific antimicrobial, set it to <code>NULL</code>, e.g. <code>TIC = NULL</code> to exclude ticarcillin. If a manually defined column does not exist in the data, it will be skipped with a warning.</p></dd> <dd><p>Column names of antimicrobials. To automatically detect antimicrobial column names, do not provide any named arguments; <code><a href="guess_ab_col.html">guess_ab_col()</a></code> will then be used for detection. To manually specify a column, provide its name (case-insensitive) as an argument, e.g. <code>AMX = "amoxicillin"</code>. To skip a specific antimicrobial, set it to <code>NULL</code>, e.g. <code>TIC = NULL</code> to exclude ticarcillin. If a manually defined column does not exist in the data, it will be skipped with a warning.</p></dd>
@@ -155,7 +159,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<dt id="arg-administration">administration<a class="anchor" aria-label="anchor" href="#arg-administration"></a></dt> <dt id="arg-administration">administration<a class="anchor" aria-label="anchor" href="#arg-administration"></a></dt>
<dd><p>Route of administration, either .val , .val im, .val iv, .val oral, or NA.</p></dd> <dd><p>Route of administration, either <code>""</code>, <code>"im"</code>, <code>"iv"</code>, <code>"oral"</code>, or NA.</p></dd>
</dl></div> </dl></div>
<div class="section level2"> <div class="section level2">
@@ -229,9 +233,13 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<span class="r-in"><span><span class="co"># apply EUCAST rules: some results wil be changed</span></span></span> <span class="r-in"><span><span class="co"># apply EUCAST rules: some results wil be changed</span></span></span>
<span class="r-in"><span><span class="va">b</span> <span class="op">&lt;-</span> <span class="fu">eucast_rules</span><span class="op">(</span><span class="va">a</span>, overwrite <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="va">b</span> <span class="op">&lt;-</span> <span class="fu">eucast_rules</span><span class="op">(</span><span class="va">a</span>, overwrite <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in `eucast_rules()`: not all columns with antimicrobial results are of class</span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in `eucast_rules()`: not all columns with antimicrobial results are of class</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">&lt;sir&gt;</span>. Transform them on beforehand, e.g.: - x <span style="color: #D7AF00;">%&gt;%</span> <span style="font-weight: bold;">as.sir</span><span style="color: #D7AF00;">(</span>CXM<span style="color: #D7AF00;">:</span>AMX<span style="color: #D7AF00;">)</span> - x <span style="color: #D7AF00;">%&gt;%</span></span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">&lt;sir&gt;</span>. Transform them on beforehand, e.g.:</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>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="font-weight: bold;">mutate</span><span style="color: #D7AF00;">(</span><span style="font-weight: bold;">across</span><span style="color: #BBBB00;">(</span><span style="font-weight: bold;">where</span><span style="color: #0000BB;">(</span>is_sir_eligible<span style="color: #0000BB;">)</span>, as.sir<span style="color: #BBBB00;">)</span><span style="color: #D7AF00;">)</span></span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> • x <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></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> </span>
<span class="r-wrn co"><span class="r-pr">#&gt;</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></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> </span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> • x <span style="color: #D7AF00;">|&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></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">b</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">b</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo VAN AMX COL CAZ CXM PEN FOX</span> <span class="r-out co"><span class="r-pr">#&gt;</span> mo VAN AMX COL CAZ CXM PEN FOX</span>
@@ -246,9 +254,13 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<span class="r-in"><span><span class="co"># containing all details about the transformations:</span></span></span> <span class="r-in"><span><span class="co"># containing all details about the transformations:</span></span></span>
<span class="r-in"><span><span class="va">c</span> <span class="op">&lt;-</span> <span class="fu">eucast_rules</span><span class="op">(</span><span class="va">a</span>, overwrite <span class="op">=</span> <span class="cn">TRUE</span>, verbose <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="va">c</span> <span class="op">&lt;-</span> <span class="fu">eucast_rules</span><span class="op">(</span><span class="va">a</span>, overwrite <span class="op">=</span> <span class="cn">TRUE</span>, verbose <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in `eucast_rules()`: not all columns with antimicrobial results are of class</span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in `eucast_rules()`: not all columns with antimicrobial results are of class</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">&lt;sir&gt;</span>. Transform them on beforehand, e.g.: - x <span style="color: #D7AF00;">%&gt;%</span> <span style="font-weight: bold;">as.sir</span><span style="color: #D7AF00;">(</span>CXM<span style="color: #D7AF00;">:</span>AMX<span style="color: #D7AF00;">)</span> - x <span style="color: #D7AF00;">%&gt;%</span></span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">&lt;sir&gt;</span>. Transform them on beforehand, e.g.:</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>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="font-weight: bold;">mutate</span><span style="color: #D7AF00;">(</span><span style="font-weight: bold;">across</span><span style="color: #BBBB00;">(</span><span style="font-weight: bold;">where</span><span style="color: #0000BB;">(</span>is_sir_eligible<span style="color: #0000BB;">)</span>, as.sir<span style="color: #BBBB00;">)</span><span style="color: #D7AF00;">)</span></span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> • x <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></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> </span>
<span class="r-wrn co"><span class="r-pr">#&gt;</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></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> </span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> • x <span style="color: #D7AF00;">|&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-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">c</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> row col mo_fullname old new rule rule_group</span> <span class="r-out co"><span class="r-pr">#&gt;</span> row col mo_fullname old new rule rule_group</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1 AMX Staphylococcus aureus - S Breakpoints</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 1 1 AMX Staphylococcus aureus - S Breakpoints</span>

43
reference/interpretive_rules.md
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@@ -21,7 +21,7 @@ interpretive_rules(x, col_mo = NULL, info = interactive(),
verbose = FALSE, version_breakpoints = 16, verbose = FALSE, version_breakpoints = 16,
version_expected_phenotypes = 1.2, version_expertrules = 3.3, version_expected_phenotypes = 1.2, version_expertrules = 3.3,
ampc_cephalosporin_resistance = NA, only_sir_columns = any(is.sir(x)), ampc_cephalosporin_resistance = NA, only_sir_columns = any(is.sir(x)),
custom_rules = NULL, overwrite = FALSE, ...) custom_rules = NULL, overwrite = FALSE, add_if_missing = TRUE, ...)
eucast_rules(x, col_mo = NULL, info = interactive(), eucast_rules(x, col_mo = NULL, info = interactive(),
rules = getOption("AMR_interpretive_rules", default = c("breakpoints", rules = getOption("AMR_interpretive_rules", default = c("breakpoints",
@@ -119,18 +119,18 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 15)
- version_breakpoints: - version_breakpoints:
The version number to use for the EUCAST Clinical Breakpoints The version number to use for the EUCAST Clinical Breakpoints
guideline. Can be .val 16.0, .val 15.0, .val 14.0, .val 13.1, .val guideline. Can be `"16.0"`, `"15.0"`, `"14.0"`, `"13.1"`, `"12.0"`,
12.0, .val 11.0, or .val 10.0. `"11.0"`, or `"10.0"`.
- version_expected_phenotypes: - version_expected_phenotypes:
The version number to use for the EUCAST Expected Phenotypes. Can be The version number to use for the EUCAST Expected Phenotypes. Can be
.val 1.2. `"1.2"`.
- version_expertrules: - version_expertrules:
The version number to use for the EUCAST Expert Rules and Intrinsic The version number to use for the EUCAST Expert Rules and Intrinsic
Resistance guideline. Can be .val 3.3, .val 3.2, or .val 3.1. Resistance guideline. Can be `"3.3"`, `"3.2"`, or `"3.1"`.
- ampc_cephalosporin_resistance: - ampc_cephalosporin_resistance:
@@ -178,6 +178,16 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 15)
be tested for susceptibility to individual agents or be reported be tested for susceptibility to individual agents or be reported
resistant". resistant".
- add_if_missing:
A [logical](https://rdrr.io/r/base/logical.html) indicating whether
rules should also be applied to missing (`NA`) values (default:
`TRUE`). When `FALSE`, rules are only applied to cells that already
contain an SIR value; cells with `NA` are left untouched. This is
particularly useful when using `overwrite = TRUE` with custom rules
and you want to update reported results without imputing values for
untested drugs.
- ...: - ...:
Column names of antimicrobials. To automatically detect antimicrobial Column names of antimicrobials. To automatically detect antimicrobial
@@ -197,8 +207,7 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 15)
- administration: - administration:
Route of administration, either .val , .val im, .val iv, .val oral, or Route of administration, either `""`, `"im"`, `"iv"`, `"oral"`, or NA.
NA.
## Value ## Value
@@ -310,9 +319,13 @@ head(a)
# apply EUCAST rules: some results wil be changed # apply EUCAST rules: some results wil be changed
b <- eucast_rules(a, overwrite = TRUE) b <- eucast_rules(a, overwrite = TRUE)
#> Warning: in `eucast_rules()`: not all columns with antimicrobial results are of class #> Warning: in `eucast_rules()`: not all columns with antimicrobial results are of class
#> <sir>. Transform them on beforehand, e.g.: - x %>% as.sir(CXM:AMX) - x %>% #> <sir>. Transform them on beforehand, e.g.:
#> mutate_if(is_sir_eligible, as.sir) - x %>% #>
#> mutate(across(where(is_sir_eligible), as.sir)) #> • x |> as.sir(CXM:AMX)
#>
#> • x |> mutate_if(is_sir_eligible, as.sir)
#>
#> • x |> mutate(across(where(is_sir_eligible), as.sir))
head(b) head(b)
#> mo VAN AMX COL CAZ CXM PEN FOX #> mo VAN AMX COL CAZ CXM PEN FOX
@@ -327,9 +340,13 @@ head(b)
# containing all details about the transformations: # containing all details about the transformations:
c <- eucast_rules(a, overwrite = TRUE, verbose = TRUE) c <- eucast_rules(a, overwrite = TRUE, verbose = TRUE)
#> Warning: in `eucast_rules()`: not all columns with antimicrobial results are of class #> Warning: in `eucast_rules()`: not all columns with antimicrobial results are of class
#> <sir>. Transform them on beforehand, e.g.: - x %>% as.sir(CXM:AMX) - x %>% #> <sir>. Transform them on beforehand, e.g.:
#> mutate_if(is_sir_eligible, as.sir) - x %>% #>
#> mutate(across(where(is_sir_eligible), as.sir)) #> • x |> as.sir(CXM:AMX)
#>
#> • x |> mutate_if(is_sir_eligible, as.sir)
#>
#> • x |> mutate(across(where(is_sir_eligible), as.sir))
head(c) head(c)
#> row col mo_fullname old new rule rule_group #> row col mo_fullname old new rule rule_group
#> 1 1 AMX Staphylococcus aureus - S Breakpoints #> 1 1 AMX Staphylococcus aureus - S Breakpoints

2
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
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2
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/join.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/key_antimicrobials.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/kurtosis.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
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2
reference/like.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
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2
reference/mdro.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/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> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/microorganisms.codes.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/microorganisms.groups.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
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8
reference/microorganisms.html
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@@ -9,7 +9,7 @@ This data set is carefully crafted, yet made 100% reproducible from public and a
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -65,12 +65,12 @@ This data set is carefully crafted, yet made 100% reproducible from public and a
<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2> <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
<p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 78 679 observations and 26 variables:</p><ul><li><p><code>mo</code><br> ID of microorganism as used by this package. <em><strong>This is a unique identifier.</strong></em></p></li> <p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 78 679 observations and 26 variables:</p><ul><li><p><code>mo</code><br> ID of microorganism as used by this package. <em><strong>This is a unique identifier.</strong></em></p></li>
<li><p><code>fullname</code><br> Full name, like <code>"Escherichia coli"</code>. For the taxonomic ranks genus, species and subspecies, this is the 'pasted' text of genus, species, and subspecies. For all taxonomic ranks higher than genus, this is the name of the taxon. <em><strong>This is a unique identifier.</strong></em></p></li> <li><p><code>fullname</code><br> Full name, like <code>"Escherichia coli"</code>. For the taxonomic ranks genus, species and subspecies, this is the 'pasted' text of genus, species, and subspecies. For all taxonomic ranks higher than genus, this is the name of the taxon. <em><strong>This is a unique identifier.</strong></em></p></li>
<li><p><code>status</code> <br> Status of the taxon, either .val accepted, .val not validly published, .val synonym, or .val unknown</p></li> <li><p><code>status</code> <br> Status of the taxon, either <code>"accepted"</code>, <code>"not validly published"</code>, <code>"synonym"</code>, or <code>"unknown"</code></p></li>
<li><p><code>kingdom</code>, <code>phylum</code>, <code>class</code>, <code>order</code>, <code>family</code>, <code>genus</code>, <code>species</code>, <code>subspecies</code><br> Taxonomic rank of the microorganism. Note that for fungi, <em>phylum</em> is equal to their taxonomic <em>division</em>. Also, for fungi, <em>subkingdom</em> and <em>subdivision</em> were left out since they do not occur in the bacterial taxonomy.</p></li> <li><p><code>kingdom</code>, <code>phylum</code>, <code>class</code>, <code>order</code>, <code>family</code>, <code>genus</code>, <code>species</code>, <code>subspecies</code><br> Taxonomic rank of the microorganism. Note that for fungi, <em>phylum</em> is equal to their taxonomic <em>division</em>. Also, for fungi, <em>subkingdom</em> and <em>subdivision</em> were left out since they do not occur in the bacterial taxonomy.</p></li>
<li><p><code>rank</code><br> Text of the taxonomic rank of the microorganism, such as <code>"species"</code> or <code>"genus"</code></p></li> <li><p><code>rank</code><br> Text of the taxonomic rank of the microorganism, such as <code>"species"</code> or <code>"genus"</code></p></li>
<li><p><code>ref</code><br> Author(s) and year of related scientific publication. This contains only the <em>first surname</em> and year of the <em>latest</em> authors, e.g. "Wallis <em>et al.</em> 2006 <em>emend.</em> Smith and Jones 2018" becomes "Smith <em>et al.</em>, 2018". This field is directly retrieved from the source specified in the column <code>source</code>. Moreover, accents were removed to comply with CRAN that only allows ASCII characters.</p></li> <li><p><code>ref</code><br> Author(s) and year of related scientific publication. This contains only the <em>first surname</em> and year of the <em>latest</em> authors, e.g. "Wallis <em>et al.</em> 2006 <em>emend.</em> Smith and Jones 2018" becomes "Smith <em>et al.</em>, 2018". This field is directly retrieved from the source specified in the column <code>source</code>. Moreover, accents were removed to comply with CRAN that only allows ASCII characters.</p></li>
<li><p><code>oxygen_tolerance</code> <br> Oxygen tolerance, either .val aerobe, .val anaerobe, .val anaerobe/microaerophile, .val facultative anaerobe, .val likely facultative anaerobe, .val microaerophile, or NA. These data were retrieved from BacDive (see <em>Source</em>). Items that contain "likely" are missing from BacDive and were extrapolated from other species within the same genus to guess the oxygen tolerance. Currently 68.3% of all ~39 000 bacteria in the data set contain an oxygen tolerance.</p></li> <li><p><code>oxygen_tolerance</code> <br> Oxygen tolerance, either <code>"aerobe"</code>, <code>"anaerobe"</code>, <code>"anaerobe/microaerophile"</code>, <code>"facultative anaerobe"</code>, <code>"likely facultative anaerobe"</code>, <code>"microaerophile"</code>, or NA. These data were retrieved from BacDive (see <em>Source</em>). Items that contain "likely" are missing from BacDive and were extrapolated from other species within the same genus to guess the oxygen tolerance. Currently 68.3% of all ~39 000 bacteria in the data set contain an oxygen tolerance.</p></li>
<li><p><code>source</code><br> Either .val GBIF, .val LPSN, .val Manually added, .val MycoBank, or .val manually added (see <em>Source</em>)</p></li> <li><p><code>source</code><br> Either <code>"GBIF"</code>, <code>"LPSN"</code>, <code>"Manually added"</code>, <code>"MycoBank"</code>, or <code>"manually added"</code> (see <em>Source</em>)</p></li>
<li><p><code>lpsn</code><br> Identifier ('Record number') of List of Prokaryotic names with Standing in Nomenclature (LPSN). This will be the first/highest LPSN identifier to keep one identifier per row. For example, <em>Acetobacter ascendens</em> has LPSN Record number 7864 and 11011. Only the first is available in the <code>microorganisms</code> data set. <em><strong>This is a unique identifier</strong></em>, though available for only ~33 000 records.</p></li> <li><p><code>lpsn</code><br> Identifier ('Record number') of List of Prokaryotic names with Standing in Nomenclature (LPSN). This will be the first/highest LPSN identifier to keep one identifier per row. For example, <em>Acetobacter ascendens</em> has LPSN Record number 7864 and 11011. Only the first is available in the <code>microorganisms</code> data set. <em><strong>This is a unique identifier</strong></em>, though available for only ~33 000 records.</p></li>
<li><p><code>lpsn_parent</code><br> LPSN identifier of the parent taxon</p></li> <li><p><code>lpsn_parent</code><br> LPSN identifier of the parent taxon</p></li>
<li><p><code>lpsn_renamed_to</code><br> LPSN identifier of the currently valid taxon</p></li> <li><p><code>lpsn_renamed_to</code><br> LPSN identifier of the currently valid taxon</p></li>

23
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@@ -36,8 +36,8 @@ A [tibble](https://tibble.tidyverse.org/reference/tibble.html) with 78
name of the taxon. ***This is a unique identifier.*** name of the taxon. ***This is a unique identifier.***
- `status` - `status`
Status of the taxon, either .val accepted, .val not validly published, Status of the taxon, either `"accepted"`, `"not validly published"`,
.val synonym, or .val unknown `"synonym"`, or `"unknown"`
- `kingdom`, `phylum`, `class`, `order`, `family`, `genus`, `species`, - `kingdom`, `phylum`, `class`, `order`, `family`, `genus`, `species`,
`subspecies` `subspecies`
@@ -59,17 +59,18 @@ A [tibble](https://tibble.tidyverse.org/reference/tibble.html) with 78
comply with CRAN that only allows ASCII characters. comply with CRAN that only allows ASCII characters.
- `oxygen_tolerance` - `oxygen_tolerance`
Oxygen tolerance, either .val aerobe, .val anaerobe, .val Oxygen tolerance, either `"aerobe"`, `"anaerobe"`,
anaerobe/microaerophile, .val facultative anaerobe, .val likely `"anaerobe/microaerophile"`, `"facultative anaerobe"`,
facultative anaerobe, .val microaerophile, or NA. These data were `"likely facultative anaerobe"`, `"microaerophile"`, or NA. These data
retrieved from BacDive (see *Source*). Items that contain "likely" are were retrieved from BacDive (see *Source*). Items that contain
missing from BacDive and were extrapolated from other species within "likely" are missing from BacDive and were extrapolated from other
the same genus to guess the oxygen tolerance. Currently 68.3% of all species within the same genus to guess the oxygen tolerance. Currently
~39 000 bacteria in the data set contain an oxygen tolerance. 68.3% of all ~39 000 bacteria in the data set contain an oxygen
tolerance.
- `source` - `source`
Either .val GBIF, .val LPSN, .val Manually added, .val MycoBank, or Either `"GBIF"`, `"LPSN"`, `"Manually added"`, `"MycoBank"`, or
.val manually added (see *Source*) `"manually added"` (see *Source*)
- `lpsn` - `lpsn`
Identifier ('Record number') of List of Prokaryotic names with Identifier ('Record number') of List of Prokaryotic names with

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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
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4
reference/mo_property.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
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@@ -196,7 +196,7 @@
<dt id="arg-property">property<a class="anchor" aria-label="anchor" href="#arg-property"></a></dt> <dt id="arg-property">property<a class="anchor" aria-label="anchor" href="#arg-property"></a></dt>
<dd><p>One of the column names of the <a href="microorganisms.html">microorganisms</a> data set: .val mo, .val fullname, .val status, .val kingdom, .val phylum, .val class, .val order, .val family, .val genus, .val species, .val subspecies, .val rank, .val ref, .val oxygen_tolerance, .val source, .val lpsn, .val lpsn_parent, .val lpsn_renamed_to, .val mycobank, .val mycobank_parent, .val mycobank_renamed_to, .val gbif, .val gbif_parent, .val gbif_renamed_to, .val prevalence, or .val snomed, or must be <code>"shortname"</code>.</p></dd> <dd><p>One of the column names of the <a href="microorganisms.html">microorganisms</a> data set: <code>"mo"</code>, <code>"fullname"</code>, <code>"status"</code>, <code>"kingdom"</code>, <code>"phylum"</code>, <code>"class"</code>, <code>"order"</code>, <code>"family"</code>, <code>"genus"</code>, <code>"species"</code>, <code>"subspecies"</code>, <code>"rank"</code>, <code>"ref"</code>, <code>"oxygen_tolerance"</code>, <code>"source"</code>, <code>"lpsn"</code>, <code>"lpsn_parent"</code>, <code>"lpsn_renamed_to"</code>, <code>"mycobank"</code>, <code>"mycobank_parent"</code>, <code>"mycobank_renamed_to"</code>, <code>"gbif"</code>, <code>"gbif_parent"</code>, <code>"gbif_renamed_to"</code>, <code>"prevalence"</code>, or <code>"snomed"</code>, or must be <code>"shortname"</code>.</p></dd>
</dl></div> </dl></div>
<div class="section level2"> <div class="section level2">

14
reference/mo_property.md
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@@ -174,13 +174,13 @@ mo_property(x, property = "fullname", language = get_AMR_locale(),
One of the column names of the One of the column names of the
[microorganisms](https://amr-for-r.org/reference/microorganisms.md) [microorganisms](https://amr-for-r.org/reference/microorganisms.md)
data set: .val mo, .val fullname, .val status, .val kingdom, .val data set: `"mo"`, `"fullname"`, `"status"`, `"kingdom"`, `"phylum"`,
phylum, .val class, .val order, .val family, .val genus, .val species, `"class"`, `"order"`, `"family"`, `"genus"`, `"species"`,
.val subspecies, .val rank, .val ref, .val oxygen_tolerance, .val `"subspecies"`, `"rank"`, `"ref"`, `"oxygen_tolerance"`, `"source"`,
source, .val lpsn, .val lpsn_parent, .val lpsn_renamed_to, .val `"lpsn"`, `"lpsn_parent"`, `"lpsn_renamed_to"`, `"mycobank"`,
mycobank, .val mycobank_parent, .val mycobank_renamed_to, .val gbif, `"mycobank_parent"`, `"mycobank_renamed_to"`, `"gbif"`,
.val gbif_parent, .val gbif_renamed_to, .val prevalence, or .val `"gbif_parent"`, `"gbif_renamed_to"`, `"prevalence"`, or `"snomed"`,
snomed, or must be `"shortname"`. or must be `"shortname"`.
## Value ## Value

2
reference/mo_source.html
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@@ -9,7 +9,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
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2
reference/pca.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
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4
reference/plot.html
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@@ -9,7 +9,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -209,7 +209,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<dt id="arg-breakpoint-type">breakpoint_type<a class="anchor" aria-label="anchor" href="#arg-breakpoint-type"></a></dt> <dt id="arg-breakpoint-type">breakpoint_type<a class="anchor" aria-label="anchor" href="#arg-breakpoint-type"></a></dt>
<dd><p>The type of breakpoints to use, either .val ECOFF, .val animal, or .val human. ECOFF stands for Epidemiological Cut-Off values. The default is <code>"human"</code>, which can also be set with the package option <code><a href="AMR-options.html">AMR_breakpoint_type</a></code>. If <code>host</code> is set to values of veterinary species, this will automatically be set to <code>"animal"</code>.</p></dd> <dd><p>The type of breakpoints to use, either <code>"ECOFF"</code>, <code>"animal"</code>, or <code>"human"</code>. ECOFF stands for Epidemiological Cut-Off values. The default is <code>"human"</code>, which can also be set with the package option <code><a href="AMR-options.html">AMR_breakpoint_type</a></code>. If <code>host</code> is set to values of veterinary species, this will automatically be set to <code>"animal"</code>.</p></dd>
<dt id="arg-facet">facet<a class="anchor" aria-label="anchor" href="#arg-facet"></a></dt> <dt id="arg-facet">facet<a class="anchor" aria-label="anchor" href="#arg-facet"></a></dt>

4
reference/plot.md
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@@ -199,8 +199,8 @@ labels_sir_count(position = NULL, x = "antibiotic",
- breakpoint_type: - breakpoint_type:
The type of breakpoints to use, either .val ECOFF, .val animal, or The type of breakpoints to use, either `"ECOFF"`, `"animal"`, or
.val human. ECOFF stands for Epidemiological Cut-Off values. The `"human"`. ECOFF stands for Epidemiological Cut-Off values. The
default is `"human"`, which can also be set with the package option default is `"human"`, which can also be set with the package option
[`AMR_breakpoint_type`](https://amr-for-r.org/reference/AMR-options.md). [`AMR_breakpoint_type`](https://amr-for-r.org/reference/AMR-options.md).
If `host` is set to values of veterinary species, this will If `host` is set to values of veterinary species, this will

2
reference/proportion.html
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@@ -9,7 +9,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
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2
reference/random.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/resistance_predict.html
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@@ -9,7 +9,7 @@ NOTE: These functions are deprecated and will be removed in a future version. Us
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</small>
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2
reference/skewness.html
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@@ -9,7 +9,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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