Built site for AMR@3.0.1.9045: 8ff5d44

2026-05-31 18:21:44 +02:00 · 2026-04-21 20:03:58 +00:00
parent f2e56dbc61
commit 86b5ebf61f
105 changed files with 520 additions and 389 deletions
--- a/articles/AMR.html
+++ b/articles/AMR.html
@@ -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>
--- a/articles/AMR.md
+++ b/articles/AMR.md
@@ -3,7 +3,7 @@
 **Note:** values on this page will change with every website update
 since they are based on randomly created values and the page was written
 in [R Markdown](https://rmarkdown.rstudio.com/). However, the
-methodology remains unchanged. This page was generated on 05 April 2026.
+methodology remains unchanged. This page was generated on 21 April 2026.

 ## Introduction

@@ -51,9 +51,9 @@ structure of your data generally look like this:

 |    date    | patient_id |        mo        | AMX | CIP |
 |:----------:|:----------:|:----------------:|:---:|:---:|
-| 2026-04-05 |    abcd    | Escherichia coli |  S  |  S  |
-| 2026-04-05 |    abcd    | Escherichia coli |  S  |  R  |
-| 2026-04-05 |    efgh    | Escherichia coli |  R  |  S  |
+| 2026-04-21 |    abcd    | Escherichia coli |  S  |  S  |
+| 2026-04-21 |    abcd    | Escherichia coli |  S  |  R  |
+| 2026-04-21 |    efgh    | Escherichia coli |  R  |  S  |

 ### Needed R packages

@@ -623,7 +623,8 @@ antibiotic class selectors:

 ``` r
 antibiogram(example_isolates,
-            antibiotics = c(aminoglycosides(), carbapenems()))
+  antibiotics = c(aminoglycosides(), carbapenems())
+)
 #> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK
 #>   (amikacin), and KAN (kanamycin)
 #> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
@@ -659,10 +660,11 @@ language to be Spanish using the `language` argument:

 ``` r
 antibiogram(example_isolates,
-            mo_transform = "gramstain",
-            antibiotics = aminoglycosides(),
-            ab_transform = "name",
-            language = "es")
+  mo_transform = "gramstain",
+  antibiotics = aminoglycosides(),
+  ab_transform = "name",
+  language = "es"
+)
 #> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK
 #>   (amikacin), and KAN (kanamycin)
 ```
@@ -679,8 +681,9 @@ plus `+` character like this:

 ``` r
 combined_ab <- antibiogram(example_isolates,
-                           antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"),
-                           ab_transform = NULL)
+  antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"),
+  ab_transform = NULL
+)
 combined_ab
 ```

@@ -705,8 +708,9 @@ on certain columns:

 ``` r
 antibiogram(example_isolates,
-            antibiotics = c(aminoglycosides(), carbapenems()),
-            syndromic_group = "ward")
+  antibiotics = c(aminoglycosides(), carbapenems()),
+  syndromic_group = "ward"
+)
 #> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK
 #>   (amikacin), and KAN (kanamycin)
 #> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
@@ -742,8 +746,10 @@ antimicrobial susceptibility patterns.

 ``` r
 example_isolates %>%
-  wisca(antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"),
-        minimum = 10) # Recommended threshold: ≥30
+  wisca(
+    antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"),
+    minimum = 10
+  ) # Recommended threshold: ≥30
 ```

 | Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin |
@@ -771,8 +777,10 @@ first:
 ``` r
 example_isolates %>%
  top_n_microorganisms(n = 10) %>%
-  group_by(age_group = age_groups(age, c(25, 50, 75)),
-           gender) %>%
+  group_by(
+    age_group = age_groups(age, c(25, 50, 75)),
+    gender
+  ) %>%
  wisca(antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"))
 ```

@@ -909,17 +917,21 @@ colour-code SIR categories.

 ``` r
 # 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,
-       aes(x = group, y = MIC, colour = SIR)) +
+ggplot(
+  my_data,
+  aes(x = group, y = MIC, colour = SIR)
+) +
  geom_jitter(width = 0.2, size = 2) +
  geom_boxplot(fill = NA, colour = "grey40") +
  scale_y_mic() +
  scale_colour_sir() +
-  labs(title = "MIC Distribution and SIR Interpretation",
-       x = "Sample Groups",
-       y = "MIC (mg/L)")
+  labs(
+    title = "MIC Distribution and SIR Interpretation",
+    x = "Sample Groups",
+    y = "MIC (mg/L)"
+  )
 ```

 ![](AMR_files/figure-html/mic_plot-1.png)
--- a/articles/AMR_for_Python.html
+++ b/articles/AMR_for_Python.html
@@ -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">
--- a/articles/AMR_with_tidymodels.html
+++ b/articles/AMR_with_tidymodels.html
@@ -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">
@@ -138,8 +138,8 @@ train, and evaluate the model.</li>
 package.</p>
 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="co"># Load required libraries</span></span>
-<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://amr-for-r.org">AMR</a></span><span class="op">)</span>          <span class="co"># For AMR data analysis</span></span>
-<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://tidymodels.tidymodels.org" class="external-link">tidymodels</a></span><span class="op">)</span>   <span class="co"># For machine learning workflows, and data manipulation (dplyr, tidyr, ...)</span></span></code></pre></div>
+<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://amr-for-r.org">AMR</a></span><span class="op">)</span> <span class="co"># For AMR data analysis</span></span>
+<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://tidymodels.tidymodels.org" class="external-link">tidymodels</a></span><span class="op">)</span> <span class="co"># For machine learning workflows, and data manipulation (dplyr, tidyr, ...)</span></span></code></pre></div>
 <p>Prepare the data:</p>
 <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="co"># Your data could look like this:</span></span>
@@ -170,13 +170,19 @@ package.</p>
 <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="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="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="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="va">as.integer</span><span class="op">)</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>  <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="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="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="va">as.integer</span></span>
+<span>    <span class="op">)</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>
+<span>  <span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
 <span>  <span class="co"># drop NAs - the ones without a Gramstain (fungi, etc.)</span></span>
 <span>  <span class="fu">drop_na</span><span class="op">(</span><span class="op">)</span></span>
 <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns <span style="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>
@@ -334,7 +340,7 @@ performance.</p>
 <span><span class="fu"><a href="https://rdrr.io/r/base/Random.html" class="external-link">set.seed</a></span><span class="op">(</span><span class="fl">123</span><span class="op">)</span> <span class="co"># For reproducibility</span></span>
 <span><span class="va">data_split</span> <span class="op">&lt;-</span> <span class="fu">initial_split</span><span class="op">(</span><span class="va">data</span>, prop <span class="op">=</span> <span class="fl">0.8</span><span class="op">)</span> <span class="co"># 80% training, 20% testing</span></span>
 <span><span class="va">training_data</span> <span class="op">&lt;-</span> <span class="fu">training</span><span class="op">(</span><span class="va">data_split</span><span class="op">)</span> <span class="co"># Training set</span></span>
-<span><span class="va">testing_data</span> <span class="op">&lt;-</span> <span class="fu">testing</span><span class="op">(</span><span class="va">data_split</span><span class="op">)</span>   <span class="co"># Testing set</span></span>
+<span><span class="va">testing_data</span> <span class="op">&lt;-</span> <span class="fu">testing</span><span class="op">(</span><span class="va">data_split</span><span class="op">)</span> <span class="co"># Testing set</span></span>
 <span></span>
 <span><span class="co"># Fit the workflow to the training data</span></span>
 <span><span class="va">fitted_workflow</span> <span class="op">&lt;-</span> <span class="va">resistance_workflow</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
@@ -354,7 +360,7 @@ called since they are stored in the recipe.</p>
 <div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="co"># Make predictions on the testing set</span></span>
 <span><span class="va">predictions</span> <span class="op">&lt;-</span> <span class="va">fitted_workflow</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://rdrr.io/r/stats/predict.html" class="external-link">predict</a></span><span class="op">(</span><span class="va">testing_data</span><span class="op">)</span>                <span class="co"># Generate predictions</span></span>
+<span>  <span class="fu"><a href="https://rdrr.io/r/stats/predict.html" class="external-link">predict</a></span><span class="op">(</span><span class="va">testing_data</span><span class="op">)</span> <span class="co"># Generate predictions</span></span>
 <span><span class="va">probabilities</span> <span class="op">&lt;-</span> <span class="va">fitted_workflow</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://rdrr.io/r/stats/predict.html" class="external-link">predict</a></span><span class="op">(</span><span class="va">testing_data</span>, type <span class="op">=</span> <span class="st">"prob"</span><span class="op">)</span> <span class="co"># Generate probabilities</span></span>
 <span></span>
@@ -529,8 +535,8 @@ predictors can easily and agnostically selected using the new
 <span></span>
 <span><span class="co"># Define the recipe</span></span>
 <span><span class="va">mic_recipe</span> <span class="op">&lt;-</span> <span class="fu">recipe</span><span class="op">(</span><span class="va">esbl</span> <span class="op">~</span> <span class="va">.</span>, data <span class="op">=</span> <span class="va">training_data</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">remove_role</span><span class="op">(</span><span class="va">genus</span>, old_role <span class="op">=</span> <span class="st">"predictor"</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"># Remove non-informative variable</span></span>
-<span>  <span class="fu"><a href="../reference/amr-tidymodels.html">step_mic_log2</a></span><span class="op">(</span><span class="fu"><a href="../reference/amr-tidymodels.html">all_mic_predictors</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>             <span class="co"># Log2 transform all MIC predictors</span></span>
+<span>  <span class="fu">remove_role</span><span class="op">(</span><span class="va">genus</span>, old_role <span class="op">=</span> <span class="st">"predictor"</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"># Remove non-informative variable</span></span>
+<span>  <span class="fu"><a href="../reference/amr-tidymodels.html">step_mic_log2</a></span><span class="op">(</span><span class="fu"><a href="../reference/amr-tidymodels.html">all_mic_predictors</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="co"># Log2 transform all MIC predictors</span></span>
 <span></span>
 <span><span class="fu">prep</span><span class="op">(</span><span class="va">mic_recipe</span><span class="op">)</span></span>
 <span><span class="co">#&gt; </span></span>
@@ -665,27 +671,38 @@ status.</p>
 <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/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>       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>  <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>    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>
 <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
 predictions?</p>
 <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>
-<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="va">.pred_FALSE</span>,</span>
-<span>                            <span class="va">.pred_TRUE</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 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>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>             colour <span class="op">=</span> <span class="va">correct</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_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>                      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://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_TRUE</span></span>
+<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>    colour <span class="op">=</span> <span class="va">correct</span></span>
+<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_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/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>                     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>  <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>    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>
 <p><img src="AMR_with_tidymodels_files/figure-html/unnamed-chunk-15-1.png" class="r-plt" alt="" width="720"></p>
 </div>
@@ -738,13 +755,18 @@ into a structured time-series format.</p>
 <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="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>         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>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</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/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="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>            .groups <span class="op">=</span> <span class="st">"drop"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/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>      .names <span class="op">=</span> <span class="st">"res_{.col}"</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="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>
@@ -792,9 +814,9 @@ preprocessing step, a model specification, and the fitting process.</p>
 <div class="sourceCode" id="cb18"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="co"># Define the recipe</span></span>
 <span><span class="va">resistance_recipe_time</span> <span class="op">&lt;-</span> <span class="fu">recipe</span><span class="op">(</span><span class="va">res_AMX</span> <span class="op">~</span> <span class="va">year</span> <span class="op">+</span> <span class="va">gramstain</span>, data <span class="op">=</span> <span class="va">data_time</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">step_dummy</span><span class="op">(</span><span class="va">gramstain</span>, one_hot <span class="op">=</span> <span class="cn">TRUE</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"># Convert categorical to numerical</span></span>
-<span>  <span class="fu">step_normalize</span><span class="op">(</span><span class="va">year</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"># Normalise year for better model performance</span></span>
-<span>  <span class="fu">step_nzv</span><span class="op">(</span><span class="fu">all_predictors</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>  <span class="co"># Remove near-zero variance predictors</span></span>
+<span>  <span class="fu">step_dummy</span><span class="op">(</span><span class="va">gramstain</span>, one_hot <span class="op">=</span> <span class="cn">TRUE</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"># Convert categorical to numerical</span></span>
+<span>  <span class="fu">step_normalize</span><span class="op">(</span><span class="va">year</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"># Normalise year for better model performance</span></span>
+<span>  <span class="fu">step_nzv</span><span class="op">(</span><span class="fu">all_predictors</span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="co"># Remove near-zero variance predictors</span></span>
 <span></span>
 <span><span class="va">resistance_recipe_time</span></span>
 <span><span class="co">#&gt; </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/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/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>       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>  <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>    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>
 <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
@@ -939,13 +963,17 @@ sets.</li>
 <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>
 <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>       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>  <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>    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="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>              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>  <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>    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>
 <p><img src="AMR_with_tidymodels_files/figure-html/unnamed-chunk-22-1.png" class="r-plt" alt="" width="720"></p>
 </div>
--- a/articles/AMR_with_tidymodels.md
+++ b/articles/AMR_with_tidymodels.md
@@ -50,8 +50,8 @@ We begin by loading the required libraries and preparing the

 ``` r
 # Load required libraries
-library(AMR)          # For AMR data analysis
-library(tidymodels)   # For machine learning workflows, and data manipulation (dplyr, tidyr, ...)
+library(AMR) # For AMR data analysis
+library(tidymodels) # For machine learning workflows, and data manipulation (dplyr, tidyr, ...)
 ```

 Prepare the data:
@@ -85,13 +85,19 @@ data <- example_isolates %>%
  # select AB results dynamically
  select(mo, aminoglycosides(), betalactams()) %>%
  # replace NAs with NI (not-interpretable)
-   mutate(across(where(is.sir),
-                 ~replace_na(.x, "NI")),
-          # make factors of SIR columns
-          across(where(is.sir),
-                 as.integer),
-          # get Gramstain of microorganisms
-          mo = as.factor(mo_gramstain(mo))) %>%
+  mutate(
+    across(
+      where(is.sir),
+      ~ replace_na(.x, "NI")
+    ),
+    # make factors of SIR columns
+    across(
+      where(is.sir),
+      as.integer
+    ),
+    # get Gramstain of microorganisms
+    mo = as.factor(mo_gramstain(mo))
+  ) %>%
  # drop NAs - the ones without a Gramstain (fungi, etc.)
  drop_na()
 #> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK
@@ -246,7 +252,7 @@ performance.
 set.seed(123) # For reproducibility
 data_split <- initial_split(data, prop = 0.8) # 80% training, 20% testing
 training_data <- training(data_split) # Training set
-testing_data <- testing(data_split)   # Testing set
+testing_data <- testing(data_split) # Testing set

 # Fit the workflow to the training data
 fitted_workflow <- resistance_workflow %>%
@@ -267,7 +273,7 @@ Next, we evaluate the model on the testing data.
 ``` r
 # Make predictions on the testing set
 predictions <- fitted_workflow %>%
-  predict(testing_data)                # Generate predictions
+  predict(testing_data) # Generate predictions
 probabilities <- fitted_workflow %>%
  predict(testing_data, type = "prob") # Generate probabilities

@@ -439,8 +445,8 @@ testing_data <- testing(split)

 # Define the recipe
 mic_recipe <- recipe(esbl ~ ., data = training_data) %>%
-  remove_role(genus, old_role = "predictor") %>%  # Remove non-informative variable
-  step_mic_log2(all_mic_predictors())             # Log2 transform all MIC predictors
+  remove_role(genus, old_role = "predictor") %>% # Remove non-informative variable
+  step_mic_log2(all_mic_predictors()) # Log2 transform all MIC predictors

 prep(mic_recipe)
 #> 
@@ -564,9 +570,11 @@ library(ggplot2)

 ggplot(predictions, aes(x = esbl, fill = .pred_class)) +
  geom_bar(position = "stack") +
-  labs(title = "Predicted vs Actual ESBL Status",
-       x = "Actual ESBL",
-       y = "Count") +
+  labs(
+    title = "Predicted vs Actual ESBL Status",
+    x = "Actual ESBL",
+    y = "Count"
+  ) +
  theme_minimal()
 ```

@@ -576,18 +584,27 @@ And plot the certainties too - how certain were the actual predictions?

 ``` r
 predictions %>%
-  mutate(certainty = ifelse(.pred_class == "FALSE",
-                            .pred_FALSE,
-                            .pred_TRUE),
-         correct = ifelse(esbl == .pred_class, "Right", "Wrong")) %>%
-  ggplot(aes(x = seq_len(nrow(predictions)),
-             y = certainty,
-             colour = correct)) +
-  scale_colour_manual(values = c(Right = "green3", Wrong = "red2"),
-                      name = "Correct?") +
+  mutate(
+    certainty = ifelse(.pred_class == "FALSE",
+      .pred_FALSE,
+      .pred_TRUE
+    ),
+    correct = ifelse(esbl == .pred_class, "Right", "Wrong")
+  ) %>%
+  ggplot(aes(
+    x = seq_len(nrow(predictions)),
+    y = certainty,
+    colour = correct
+  )) +
+  scale_colour_manual(
+    values = c(Right = "green3", Wrong = "red2"),
+    name = "Correct?"
+  ) +
  geom_point() +
-  scale_y_continuous(labels = function(x) paste0(x * 100, "%"),
-                     limits = c(0.5, 1)) +
+  scale_y_continuous(
+    labels = function(x) paste0(x * 100, "%"),
+    limits = c(0.5, 1)
+  ) +
  theme_minimal()
 ```

@@ -636,13 +653,18 @@ library(tidymodels)
 # Transform dataset
 data_time <- example_isolates %>%
  top_n_microorganisms(n = 10) %>% # Filter on the top #10 species
-  mutate(year = as.integer(format(date, "%Y")),  # Extract year from date
-         gramstain = mo_gramstain(mo)) %>% # Get taxonomic names
+  mutate(
+    year = as.integer(format(date, "%Y")), # Extract year from date
+    gramstain = mo_gramstain(mo)
+  ) %>% # Get taxonomic names
  group_by(year, gramstain) %>%
-  summarise(across(c(AMX, AMC, CIP), 
-                   function(x) resistance(x, minimum = 0),
-                   .names = "res_{.col}"), 
-            .groups = "drop") %>% 
+  summarise(
+    across(c(AMX, AMC, CIP),
+      function(x) resistance(x, minimum = 0),
+      .names = "res_{.col}"
+    ),
+    .groups = "drop"
+  ) %>%
  filter(!is.na(res_AMX) & !is.na(res_AMC) & !is.na(res_CIP)) # Drop missing values
 #> ℹ Using column mo as input for `col_mo`.
 #> ℹ `resistance()` assumes the EUCAST guideline and thus considers the 'I'
@@ -686,9 +708,9 @@ step, a model specification, and the fitting process.
 ``` r
 # Define the recipe
 resistance_recipe_time <- recipe(res_AMX ~ year + gramstain, data = data_time) %>%
-  step_dummy(gramstain, one_hot = TRUE) %>%  # Convert categorical to numerical
-  step_normalize(year) %>%  # Normalise year for better model performance
-  step_nzv(all_predictors())  # Remove near-zero variance predictors
+  step_dummy(gramstain, one_hot = TRUE) %>% # Convert categorical to numerical
+  step_normalize(year) %>% # Normalise year for better model performance
+  step_nzv(all_predictors()) # Remove near-zero variance predictors

 resistance_recipe_time
 #> 
@@ -813,9 +835,11 @@ library(ggplot2)
 ggplot(predictions_time, aes(x = year)) +
  geom_point(aes(y = res_AMX, color = "Actual")) +
  geom_line(aes(y = .pred, color = "Predicted")) +
-  labs(title = "Predicted vs Actual AMX Resistance Over Time",
-       x = "Year",
-       y = "Resistance Proportion") +
+  labs(
+    title = "Predicted vs Actual AMX Resistance Over Time",
+    x = "Year",
+    y = "Resistance Proportion"
+  ) +
  theme_minimal()
 ```

@@ -827,13 +851,17 @@ directly add linear models there:
 ``` r
 ggplot(data_time, aes(x = year, y = res_AMX, color = gramstain)) +
  geom_line() +
-  labs(title = "AMX Resistance Trends",
-       x = "Year",
-       y = "Resistance Proportion") +
+  labs(
+    title = "AMX Resistance Trends",
+    x = "Year",
+    y = "Resistance Proportion"
+  ) +
  # add a linear model directly in ggplot2:
-  geom_smooth(method = "lm",
-              formula = y ~ x,
-              alpha = 0.25) +
+  geom_smooth(
+    method = "lm",
+    formula = y ~ x,
+    alpha = 0.25
+  ) +
  theme_minimal()
 ```

--- a/articles/EUCAST.html
+++ b/articles/EUCAST.html
@@ -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">
@@ -177,7 +177,7 @@ reading</em>, and is basically a form of imputation:</p>
 <span>  CAZ <span class="op">=</span> <span class="st">"-"</span>, <span class="co"># Ceftazidime</span></span>
 <span>  CXM <span class="op">=</span> <span class="st">"-"</span>, <span class="co"># Cefuroxime</span></span>
 <span>  PEN <span class="op">=</span> <span class="st">"S"</span>, <span class="co"># Benzylenicillin</span></span>
-<span>  FOX <span class="op">=</span> <span class="st">"S"</span>  <span class="co"># Cefoxitin</span></span>
+<span>  FOX <span class="op">=</span> <span class="st">"S"</span> <span class="co"># Cefoxitin</span></span>
 <span><span class="op">)</span></span></code></pre></div>
 <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">data</span></span></code></pre></div>
--- a/articles/EUCAST.md
+++ b/articles/EUCAST.md
@@ -97,7 +97,7 @@ data <- tibble::tibble(
  CAZ = "-", # Ceftazidime
  CXM = "-", # Cefuroxime
  PEN = "S", # Benzylenicillin
-  FOX = "S"  # Cefoxitin
+  FOX = "S" # Cefoxitin
 )
 ```

--- a/articles/PCA.html
+++ b/articles/PCA.html
@@ -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">
--- a/articles/WHONET.html
+++ b/articles/WHONET.html
@@ -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">
--- a/articles/WISCA.html
+++ b/articles/WISCA.html
@@ -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">
@@ -279,7 +279,8 @@ I (intermediate [CLSI], or susceptible, increased exposure
 </h3>
 <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>
-<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">
 <thead><tr class="header">
 <th align="left">Amoxicillin/clavulanic acid</th>
@@ -298,7 +299,8 @@ I (intermediate [CLSI], or susceptible, increased exposure
 </h3>
 <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>
-<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">
 <colgroup>
 <col width="24%">
@@ -322,8 +324,9 @@ I (intermediate [CLSI], or susceptible, increased exposure
 </h3>
 <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>
-<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>  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>
+<span><span class="op">)</span></span></code></pre></div>
 <table class="table">
 <colgroup>
 <col width="12%">
@@ -356,9 +359,10 @@ I (intermediate [CLSI], or susceptible, increased exposure
 all be used for the <code><a href="../reference/antibiogram.html">wisca()</a></code> function too:</p>
 <div class="sourceCode" id="cb6"><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>
-<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">$</span><span class="va">syndrome</span><span class="op">)</span>,</span>
-<span>      language <span class="op">=</span> <span class="st">"Spanish"</span><span class="op">)</span></span></code></pre></div>
+<span>  antimicrobials <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"AMC"</span>, <span class="st">"AMC + CIP"</span>, <span class="st">"AMC + GEN"</span><span class="op">)</span>,</span>
+<span>  syndromic_group <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/grep.html" class="external-link">gsub</a></span><span class="op">(</span><span class="st">"UTI"</span>, <span class="st">"UCI"</span>, <span class="va">data</span><span class="op">$</span><span class="va">syndrome</span><span class="op">)</span>,</span>
+<span>  language <span class="op">=</span> <span class="st">"Spanish"</span></span>
+<span><span class="op">)</span></span></code></pre></div>
 <table class="table">
 <colgroup>
 <col width="12%">
--- a/articles/WISCA.md
+++ b/articles/WISCA.md
@@ -165,7 +165,8 @@ data$syndrome <- ifelse(data$mo %like% "coli", "UTI", "No UTI")

 ``` r
 wisca(data,
-      antimicrobials = c("AMC", "CIP", "GEN"))
+  antimicrobials = c("AMC", "CIP", "GEN")
+)
 ```

 | Amoxicillin/clavulanic acid | Ciprofloxacin    | Gentamicin         |
@@ -176,7 +177,8 @@ wisca(data,

 ``` r
 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 |
@@ -187,8 +189,9 @@ wisca(data,

 ``` r
 wisca(data,
-      antimicrobials = c("AMC", "AMC + CIP", "AMC + GEN"),
-      syndromic_group = "syndrome")
+  antimicrobials = c("AMC", "AMC + CIP", "AMC + GEN"),
+  syndromic_group = "syndrome"
+)
 ```

 | Syndromic Group | Amoxicillin/clavulanic acid | Amoxicillin/clavulanic acid + Ciprofloxacin | Amoxicillin/clavulanic acid + Gentamicin |
@@ -202,9 +205,10 @@ function too:

 ``` r
 wisca(data,
-      antimicrobials = c("AMC", "AMC + CIP", "AMC + GEN"),
-      syndromic_group = gsub("UTI", "UCI", data$syndrome),
-      language = "Spanish")
+  antimicrobials = c("AMC", "AMC + CIP", "AMC + GEN"),
+  syndromic_group = gsub("UTI", "UCI", data$syndrome),
+  language = "Spanish"
+)
 ```

 | Grupo sindrómico | Amoxicilina/ácido clavulánico | Amoxicilina/ácido clavulánico + Ciprofloxacina | Amoxicilina/ácido clavulánico + Gentamicina |
--- a/articles/datasets.html
+++ b/articles/datasets.html
@@ -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">
@@ -80,7 +80,7 @@
  <main id="main" class="col-md-9"><div class="page-header">
      <img src="../logo.svg" class="logo" alt=""><h1>Download data sets for download / own use</h1>
            
-            <h4 data-toc-skip class="date">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>
      <div class="d-none name"><code>datasets.Rmd</code></div>
--- a/articles/index.html
+++ b/articles/index.html
@@ -7,7 +7,7 @@

    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</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">