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@@ -30,7 +30,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</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">
@@ -91,7 +91,7 @@
website update since they are based on randomly created values and the
page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
Markdown</a>. However, the methodology remains unchanged. This page was
generated on 05 April 2026.</p>
generated on 21 April 2026.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@@ -147,21 +147,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2026-04-05</td>
<td align="center">2026-04-21</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="center">2026-04-05</td>
<td align="center">2026-04-21</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<tr class="odd">
<td align="center">2026-04-05</td>
<td align="center">2026-04-21</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</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>
<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
<span> antibiotics <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="../reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="../reference/antimicrobial_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span>
<span> 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; (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>
@@ -822,10 +823,11 @@ Ukrainian, Urdu, or Vietnamese. In this next example, we force the
language to be Spanish using the <code>language</code> argument:</p>
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
<span> 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> 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> 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> ab_transform <span class="op">=</span> <span class="st">"name"</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; (amikacin), and <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin)</span></span></code></pre></div>
<table class="table">
@@ -868,8 +870,9 @@ language to be Spanish using the <code>language</code> argument:</p>
a plus <code>+</code> character like this:</p>
<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>
<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> 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>
<span><span class="op">)</span></span>
<span><span class="va">combined_ab</span></span></code></pre></div>
<table class="table">
<colgroup>
@@ -950,8 +953,9 @@ argument must be used. This can be any column in the data, or e.g. an
<code><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse()</a></code> with calculations based on certain columns:</p>
<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>
<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> 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>
<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; (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>
@@ -1131,8 +1135,10 @@ provides syndrome-based susceptibility estimates, weighted by pathogen
incidence and antimicrobial susceptibility patterns.</p>
<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>
<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> 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> <span class="fu"><a href="../reference/antibiogram.html">wisca</a></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> 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">
<colgroup>
<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">
<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="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="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> <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> 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>
<table class="table">
<colgroup>
@@ -1339,17 +1347,21 @@ the y-axis and <code><a href="../reference/plot.html">scale_colour_sir()</a></co
categories.</p>
<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
<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 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/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="fu"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot</a></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_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_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> 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> <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> 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>This plot provides an intuitive way to assess susceptibility patterns
across different groups while incorporating clinical breakpoints.</p>