Built site for AMR@3.0.1.9088: bbdd3a9

2026-09-12 16:18:54 +02:00 · 2026-09-03 12:36:14 +00:00
parent 8fbf4f8f0b
commit 9a21a80414
96 changed files with 272 additions and 272 deletions
--- a/404.html
+++ b/404.html
@@ -31,7 +31,7 @@
    <a class="navbar-brand me-2" href="https://amr-for-r.org/index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/CLAUDE.html
+++ b/CLAUDE.html
@@ -7,7 +7,7 @@
    <a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/LICENSE-text.html
+++ b/LICENSE-text.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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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.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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -91,7 +91,7 @@
 website update since they are based on randomly created values and the
 page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
 Markdown</a>. However, the methodology remains unchanged. This page was
-generated on 20 August 2026.</p>
+generated on 03 September 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">2026-08-20</td>
+<td align="center">2026-09-03</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">2026-08-20</td>
+<td align="center">2026-09-03</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">2026-08-20</td>
+<td align="center">2026-09-03</td>
 <td align="center">efgh</td>
 <td align="center">Escherichia coli</td>
 <td align="center">R</td>
--- 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 20 August
+methodology remains unchanged. This page was generated on 03 September
 2026.
 ## Introduction
@@ -52,9 +52,9 @@ structure of your data generally look like this:
 |    date    | patient_id |        mo        | AMX | CIP |
 |:----------:|:----------:|:----------------:|:---:|:---:|
-| 2026-08-20 |    abcd    | Escherichia coli |  S  |  S  |
+| 2026-09-03 |    abcd    | Escherichia coli |  S  |  S  |
-| 2026-08-20 |    abcd    | Escherichia coli |  S  |  R  |
+| 2026-09-03 |    abcd    | Escherichia coli |  S  |  R  |
-| 2026-08-20 |    efgh    | Escherichia coli |  R  |  S  |
+| 2026-09-03 |    efgh    | Escherichia coli |  R  |  S  |
 ### Needed R packages
--- 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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -80,7 +80,7 @@
  <main id="main" class="col-md-9"><div class="page-header">
      <img src="../logo.svg" class="logo" alt=""><h1>Download data sets for download / own use</h1>
-            <h4 data-toc-skip class="date">20 August 2026</h4>
+            <h4 data-toc-skip class="date">03 September 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>
@@ -893,11 +893,11 @@ DTA file</a> (82 kB)</li>
 <code>intrinsic_resistant</code>: Intrinsic Bacterial
 Resistance<a class="anchor" aria-label="anchor" href="#intrinsic_resistant-intrinsic-bacterial-resistance"></a>
 </h2>
-<p>A data set with 294 079 rows and 2 columns, containing the following
+<p>A data set with 294 079 rows and 3 columns, containing the following
-column names:<br><em>mo</em> and <em>ab</em>.</p>
+column names:<br><em>mo</em>, <em>ab</em>, and <em>version</em>.</p>
 <p>This data set is in R available as <code>intrinsic_resistant</code>,
 after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 22 June 2026 23:38:13 UTC. Find more info
+<p>It was last updated on 3 September 2026 10:14:25 UTC. Find more info
 about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/intrinsic_resistant.html">data set
 here</a>.</p>
 <p><strong>Direct download links:</strong></p>
--- a/articles/datasets.md
+++ b/articles/datasets.md
@@ -249,15 +249,15 @@ here](https://amr-for-r.org/reference/microorganisms.groups.html).
 ## `intrinsic_resistant`: Intrinsic Bacterial Resistance
-A data set with 294 079 rows and 2 columns, containing the following
+A data set with 294 079 rows and 3 columns, containing the following
 column names:  
-*mo* and *ab*.
+*mo*, *ab*, and *version*.
 This data set is in R available as `intrinsic_resistant`, after you load
 the `AMR` package.
-It was last updated on 22 June 2026 23:38:13 UTC. Find more info about
+It was last updated on 3 September 2026 10:14:25 UTC. Find more info
-the contents, (scientific) source, and structure of this [data set
+about the contents, (scientific) source, and structure of this [data set
 here](https://amr-for-r.org/reference/intrinsic_resistant.html).
 **Direct download links:**
--- 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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/authors.html
+++ b/authors.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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/index.html
+++ b/index.html
@@ -33,7 +33,7 @@
    <a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -113,7 +113,7 @@
 </h2>
 <p>The <code>AMR</code> package is a peer-reviewed, <a href="#copyright">free and open-source</a> R package with <a href="https://en.wikipedia.org/wiki/Dependency_hell" class="external-link">zero dependencies</a> to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods.</p>
 <p><strong>Our aim has always been to provide a standard</strong> for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. We are a team of <a href="./authors.html">many different researchers</a> from around the globe to make this a successful and durable project! The <code>AMR</code> package was already cited <a href="https://scholar.google.com/citations?view_op=view_citation&amp;hl=en&amp;citation_for_view=sAoHvIgAAAAJ:0EnyYjriUFMC" class="external-link">over 100 times</a> in scientific research.</p>
-<p>After installing this package, R knows <a href="./reference/microorganisms.html"><strong>~97 000 distinct microbial species</strong></a> (updated mei 2026) and all <a href="./reference/antimicrobials.html"><strong>~620 antimicrobial and antiviral drugs</strong></a> by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI 2011-2026 and EUCAST 2011-2026 are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a> and the <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p>
+<p>After installing this package, R knows <a href="./reference/microorganisms.html"><strong>~97 000 distinct microbial species</strong></a> (updated May 2026) and all <a href="./reference/antimicrobials.html"><strong>~620 antimicrobial and antiviral drugs</strong></a> by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI 2011-2026 and EUCAST 2011-2026 are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a> and the <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p>
 <div class="section level3">
 <h3 id="used-in-over-175-countries-available-in-28-languages">Used in over 175 countries, available in 28 languages<a class="anchor" aria-label="anchor" href="#used-in-over-175-countries-available-in-28-languages"></a>
 </h3>
@@ -146,13 +146,11 @@
 <span><span class="co">#&gt; ℹ Using column mo as input for `mo_fullname()`</span></span>
 <span><span class="co">#&gt; ℹ Using column mo as input for `mo_is_gram_negative()`</span></span>
 <span><span class="co">#&gt; ℹ Using column mo as input for `mo_is_intrinsic_resistant()`</span></span>
-<span><span class="co">#&gt; ℹ Determining intrinsic resistance based on 'EUCAST Expected</span></span>
+<span><span class="co">#&gt; ℹ Determining intrinsic resistance based on 'EUCAST Expected Resistant Phenotypes' v1.2 (2023).</span></span>
-<span><span class="co">#&gt;   Resistant Phenotypes' v1.2 (2023). This note will be shown</span></span>
+<span><span class="co">#&gt;   This note will be shown once per session.</span></span>
-<span><span class="co">#&gt;   once per session.</span></span>
+<span><span class="co">#&gt; ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK (amikacin), and KAN</span></span>
-<span><span class="co">#&gt; ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB</span></span>
+<span><span class="co">#&gt;   (kanamycin)</span></span>
-<span><span class="co">#&gt;   (tobramycin), AMK (amikacin), and KAN (kanamycin)</span></span>
+<span><span class="co">#&gt; ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)</span></span>
 <span><span class="co">#&gt; ℹ For `carbapenems()` using columns IPM (imipenem) and MEM</span></span>
 <span><span class="co">#&gt;   (meropenem)</span></span>
 <span><span class="co">#&gt; # A tibble: 35 × 7</span></span>
 <span><span class="co">#&gt;    bacteria                     GEN   TOB   AMK   KAN   IPM   MEM  </span></span>
 <span><span class="co">#&gt;    &lt;chr&gt;                        &lt;sir&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt;</span></span>
@@ -181,9 +179,9 @@
 <span><span class="co">#&gt; Warning: invalid microorganism code, NA generated</span></span></code></pre></div>
 <table class="table">
 <colgroup>
-<col width="24%">
+<col width="33%">
-<col width="37%">
+<col width="33%">
-<col width="37%">
+<col width="33%">
 </colgroup>
 <thead><tr>
 <th align="left">Piperacillin/tazobactam</th>
@@ -191,9 +189,9 @@
 <th align="left">Piperacillin/tazobactam + Tobramycin</th>
 </tr></thead>
 <tbody><tr>
-<td align="left">70% (64.8-75.1%)</td>
+<td align="left">70.2% (64.6-75.4%)</td>
 <td align="left">93.6% (92.1-95%)</td>
-<td align="left">89.9% (86.9-92.3%)</td>
+<td align="left">89.9% (87-92.5%)</td>
 </tr></tbody>
 </table>
 <p>WISCA supports stratification by any clinical variable, so you can generate syndrome-specific or ward-specific coverage estimates:</p>
@@ -205,10 +203,10 @@
 <span><span class="co">#&gt; Warning: invalid microorganism code, NA generated</span></span></code></pre></div>
 <table class="table">
 <colgroup>
-<col width="14%">
+<col width="25%">
-<col width="21%">
+<col width="25%">
-<col width="32%">
+<col width="25%">
-<col width="32%">
+<col width="25%">
 </colgroup>
 <thead><tr>
 <th align="left">Syndromic Group</th>
@@ -219,21 +217,21 @@
 <tbody>
 <tr>
 <td align="left">Clinical</td>
-<td align="left">74.7% (69-80.3%)</td>
+<td align="left">74.7% (68.9-80.8%)</td>
-<td align="left">93.6% (92-95.2%)</td>
+<td align="left">93.7% (92.1-95.2%)</td>
-<td align="left">90.4% (86.8-93.1%)</td>
+<td align="left">90.5% (87-93.2%)</td>
 </tr>
 <tr>
 <td align="left">ICU</td>
-<td align="left">56.9% (48.7-66%)</td>
+<td align="left">57% (48.2-65.7%)</td>
-<td align="left">86.8% (83.6-90%)</td>
+<td align="left">86.8% (83.4-89.8%)</td>
-<td align="left">82.8% (78.3-87.3%)</td>
+<td align="left">83% (78-87.6%)</td>
 </tr>
 <tr>
 <td align="left">Outpatient</td>
-<td align="left">57.2% (46-68.2%)</td>
+<td align="left">57.2% (46.2-68.9%)</td>
-<td align="left">76.5% (70.3-82.2%)</td>
+<td align="left">76.6% (70.1-82.1%)</td>
-<td align="left">67.7% (57.3-77.2%)</td>
+<td align="left">67.7% (57.6-77.5%)</td>
 </tr>
 </tbody>
 </table>
@@ -242,15 +240,14 @@
 <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>            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="fu"><a href="reference/antimicrobial_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span>, <span class="st">"TZP"</span><span class="op">)</span><span class="op">)</span></span>
-<span><span class="co">#&gt; ℹ For `carbapenems()` using columns IPM (imipenem) and MEM</span></span>
+<span><span class="co">#&gt; ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)</span></span></code></pre></div>
 <span><span class="co">#&gt;   (meropenem)</span></span></code></pre></div>
 <table class="table">
 <colgroup>
-<col width="13%">
+<col width="20%">
-<col width="25%">
+<col width="20%">
-<col width="18%">
+<col width="20%">
-<col width="19%">
+<col width="20%">
-<col width="22%">
+<col width="20%">
 </colgroup>
 <thead><tr>
 <th align="left">Pathogen</th>
@@ -283,10 +280,10 @@
 <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">"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>
-<col width="12%">
+<col width="25%">
-<col width="21%">
+<col width="25%">
-<col width="32%">
+<col width="25%">
-<col width="32%">
+<col width="25%">
 </colgroup>
 <thead><tr>
 <th align="left">Pathogen</th>
@@ -408,16 +405,15 @@
 <span>  <span class="co"># calculate AMR using resistance(), over all aminoglycosides and polymyxins:</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="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">polymyxins</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>,</span>
 <span>            <span class="va">resistance</span><span class="op">)</span><span class="op">)</span></span>
-<span><span class="co">#&gt; ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB</span></span>
+<span><span class="co">#&gt; ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK (amikacin), and KAN</span></span>
-<span><span class="co">#&gt;   (tobramycin), AMK (amikacin), and KAN (kanamycin)</span></span>
+<span><span class="co">#&gt;   (kanamycin)</span></span>
 <span><span class="co">#&gt; ℹ For `polymyxins()` using column COL (colistin)</span></span>
 <span><span class="co">#&gt; Warning: There was 1 warning in `summarise()`.</span></span>
-<span><span class="co">#&gt; ℹ In argument: `across(c(aminoglycosides(), polymyxins()),</span></span>
+<span><span class="co">#&gt; ℹ In argument: `across(c(aminoglycosides(), polymyxins()), resistance)`.</span></span>
 <span><span class="co">#&gt;   resistance)`.</span></span>
 <span><span class="co">#&gt; ℹ In group 3: `ward = "Outpatient"`.</span></span>
 <span><span class="co">#&gt; Caused by warning:</span></span>
-<span><span class="co">#&gt; ! Introducing NA: only 23 results available for KAN in group:</span></span>
+<span><span class="co">#&gt; ! Introducing NA: only 23 results available for KAN in group: ward = "Outpatient" (whilst `minimum =</span></span>
-<span><span class="co">#&gt; ward = "Outpatient" (whilst `minimum = 30`).</span></span>
+<span><span class="co">#&gt; 30`).</span></span>
 <span><span class="va">out</span></span>
 <span><span class="co">#&gt; # A tibble: 3 × 6</span></span>
 <span><span class="co">#&gt;   ward         GEN   TOB   AMK   KAN   COL</span></span>
--- a/index.md
+++ b/index.md
@@ -50,7 +50,7 @@ in scientific research.
 After installing this package, R knows [**~97 000 distinct microbial
 species**](https://amr-for-r.org/reference/microorganisms.md) (updated
-mei 2026) and all [**~620 antimicrobial and antiviral
+May 2026) and all [**~620 antimicrobial and antiviral
 drugs**](https://amr-for-r.org/reference/antimicrobials.md) by name and
 code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED
 CT), and knows all about valid SIR and MIC values. The integral clinical
@@ -116,13 +116,11 @@ example_isolates %>%
 #> ℹ Using column mo as input for `mo_fullname()`
 #> ℹ Using column mo as input for `mo_is_gram_negative()`
 #> ℹ Using column mo as input for `mo_is_intrinsic_resistant()`
-#> ℹ Determining intrinsic resistance based on 'EUCAST Expected
+#> ℹ Determining intrinsic resistance based on 'EUCAST Expected Resistant Phenotypes' v1.2 (2023).
-#>   Resistant Phenotypes' v1.2 (2023). This note will be shown
+#>   This note will be shown once per session.
-#>   once per session.
+#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK (amikacin), and KAN
-#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB
+#>   (kanamycin)
-#>   (tobramycin), AMK (amikacin), and KAN (kanamycin)
+#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
 #> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM
 #>   (meropenem)
 #> # A tibble: 35 × 7
 #>    bacteria                     GEN   TOB   AMK   KAN   IPM   MEM  
 #>    <chr>                        <sir> <sir> <sir> <sir> <sir> <sir>
@@ -181,7 +179,7 @@ wisca(example_isolates,
 | Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin |
 |:---|:---|:---|
-| 70% (64.8-75.1%) | 93.6% (92.1-95%) | 89.9% (86.9-92.3%) |
+| 70.2% (64.6-75.4%) | 93.6% (92.1-95%) | 89.9% (87-92.5%) |
 WISCA supports stratification by any clinical variable, so you can
 generate syndrome-specific or ward-specific coverage estimates:
@@ -197,9 +195,9 @@ wisca(example_isolates,
 | Syndromic Group | Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin |
 |:---|:---|:---|:---|
-| Clinical | 74.7% (69-80.3%) | 93.6% (92-95.2%) | 90.4% (86.8-93.1%) |
+| Clinical | 74.7% (68.9-80.8%) | 93.7% (92.1-95.2%) | 90.5% (87-93.2%) |
-| ICU | 56.9% (48.7-66%) | 86.8% (83.6-90%) | 82.8% (78.3-87.3%) |
+| ICU | 57% (48.2-65.7%) | 86.8% (83.4-89.8%) | 83% (78-87.6%) |
-| Outpatient | 57.2% (46-68.2%) | 76.5% (70.3-82.2%) | 67.7% (57.3-77.2%) |
+| Outpatient | 57.2% (46.2-68.9%) | 76.6% (70.1-82.1%) | 67.7% (57.6-77.5%) |
 **For AMR surveillance**, traditional antibiograms remain the right tool
 for tracking resistance per species over time:
@@ -209,8 +207,7 @@ for tracking resistance per species over time:
 antibiogram(example_isolates,
            mo_transform = "gramstain",
            antimicrobials = c("AMC", carbapenems(), "TZP"))
-#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM
+#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
 #>   (meropenem)
 ```
 | Pathogen | Amoxicillin/clavulanic acid | Imipenem | Meropenem | Piperacillin/tazobactam |
@@ -331,16 +328,15 @@ out <- example_isolates %>%
  # calculate AMR using resistance(), over all aminoglycosides and polymyxins:
  summarise(across(c(aminoglycosides(), polymyxins()),
            resistance))
-#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB
+#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK (amikacin), and KAN
-#>   (tobramycin), AMK (amikacin), and KAN (kanamycin)
+#>   (kanamycin)
 #> ℹ For `polymyxins()` using column COL (colistin)
 #> Warning: There was 1 warning in `summarise()`.
-#> ℹ In argument: `across(c(aminoglycosides(), polymyxins()),
+#> ℹ In argument: `across(c(aminoglycosides(), polymyxins()), resistance)`.
 #>   resistance)`.
 #> ℹ In group 3: `ward = "Outpatient"`.
 #> Caused by warning:
-#> ! Introducing NA: only 23 results available for KAN in group:
+#> ! Introducing NA: only 23 results available for KAN in group: ward = "Outpatient" (whilst `minimum =
-#> ward = "Outpatient" (whilst `minimum = 30`).
+#> 30`).
 out
 #> # A tibble: 3 × 6
 #>   ward         GEN   TOB   AMK   KAN   COL
--- a/llms.txt
+++ b/llms.txt
@@ -50,7 +50,7 @@ in scientific research.
 After installing this package, R knows [**~97 000 distinct microbial
 species**](https://amr-for-r.org/reference/microorganisms.md) (updated
-mei 2026) and all [**~620 antimicrobial and antiviral
+May 2026) and all [**~620 antimicrobial and antiviral
 drugs**](https://amr-for-r.org/reference/antimicrobials.md) by name and
 code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED
 CT), and knows all about valid SIR and MIC values. The integral clinical
@@ -116,13 +116,11 @@ example_isolates %>%
 #> ℹ Using column mo as input for `mo_fullname()`
 #> ℹ Using column mo as input for `mo_is_gram_negative()`
 #> ℹ Using column mo as input for `mo_is_intrinsic_resistant()`
-#> ℹ Determining intrinsic resistance based on 'EUCAST Expected
+#> ℹ Determining intrinsic resistance based on 'EUCAST Expected Resistant Phenotypes' v1.2 (2023).
-#>   Resistant Phenotypes' v1.2 (2023). This note will be shown
+#>   This note will be shown once per session.
-#>   once per session.
+#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK (amikacin), and KAN
-#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB
+#>   (kanamycin)
-#>   (tobramycin), AMK (amikacin), and KAN (kanamycin)
+#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
 #> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM
 #>   (meropenem)
 #> # A tibble: 35 × 7
 #>    bacteria                     GEN   TOB   AMK   KAN   IPM   MEM  
 #>    <chr>                        <sir> <sir> <sir> <sir> <sir> <sir>
@@ -181,7 +179,7 @@ wisca(example_isolates,
 | Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin |
 |:---|:---|:---|
-| 70% (64.8-75.1%) | 93.6% (92.1-95%) | 89.9% (86.9-92.3%) |
+| 70.2% (64.6-75.4%) | 93.6% (92.1-95%) | 89.9% (87-92.5%) |
 WISCA supports stratification by any clinical variable, so you can
 generate syndrome-specific or ward-specific coverage estimates:
@@ -197,9 +195,9 @@ wisca(example_isolates,
 | Syndromic Group | Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin |
 |:---|:---|:---|:---|
-| Clinical | 74.7% (69-80.3%) | 93.6% (92-95.2%) | 90.4% (86.8-93.1%) |
+| Clinical | 74.7% (68.9-80.8%) | 93.7% (92.1-95.2%) | 90.5% (87-93.2%) |
-| ICU | 56.9% (48.7-66%) | 86.8% (83.6-90%) | 82.8% (78.3-87.3%) |
+| ICU | 57% (48.2-65.7%) | 86.8% (83.4-89.8%) | 83% (78-87.6%) |
-| Outpatient | 57.2% (46-68.2%) | 76.5% (70.3-82.2%) | 67.7% (57.3-77.2%) |
+| Outpatient | 57.2% (46.2-68.9%) | 76.6% (70.1-82.1%) | 67.7% (57.6-77.5%) |
 **For AMR surveillance**, traditional antibiograms remain the right tool
 for tracking resistance per species over time:
@@ -209,8 +207,7 @@ for tracking resistance per species over time:
 antibiogram(example_isolates,
            mo_transform = "gramstain",
            antimicrobials = c("AMC", carbapenems(), "TZP"))
-#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM
+#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
 #>   (meropenem)
 ```
 | Pathogen | Amoxicillin/clavulanic acid | Imipenem | Meropenem | Piperacillin/tazobactam |
@@ -331,16 +328,15 @@ out <- example_isolates %>%
  # calculate AMR using resistance(), over all aminoglycosides and polymyxins:
  summarise(across(c(aminoglycosides(), polymyxins()),
            resistance))
-#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB
+#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK (amikacin), and KAN
-#>   (tobramycin), AMK (amikacin), and KAN (kanamycin)
+#>   (kanamycin)
 #> ℹ For `polymyxins()` using column COL (colistin)
 #> Warning: There was 1 warning in `summarise()`.
-#> ℹ In argument: `across(c(aminoglycosides(), polymyxins()),
+#> ℹ In argument: `across(c(aminoglycosides(), polymyxins()), resistance)`.
 #>   resistance)`.
 #> ℹ In group 3: `ward = "Outpatient"`.
 #> Caused by warning:
-#> ! Introducing NA: only 23 results available for KAN in group:
+#> ! Introducing NA: only 23 results available for KAN in group: ward = "Outpatient" (whilst `minimum =
-#> ward = "Outpatient" (whilst `minimum = 30`).
+#> 30`).
 out
 #> # A tibble: 3 × 6
 #>   ward         GEN   TOB   AMK   KAN   COL
--- a/news/index.html
+++ b/news/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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -49,10 +49,10 @@
    </div>
    <div class="section level2">
-<h2 class="pkg-version" data-toc-text="3.0.1.9087" id="amr-3019087">AMR 3.0.1.9087<a class="anchor" aria-label="anchor" href="#amr-3019087"></a></h2>
+<h2 class="pkg-version" data-toc-text="3.0.1.9088" id="amr-3019088">AMR 3.0.1.9088<a class="anchor" aria-label="anchor" href="#amr-3019088"></a></h2>
 <p>Planned as v3.1.0, end of September 2026.</p>
 <div class="section level4">
-<h4 id="breaking-changes-3-0-1-9087">Breaking Changes<a class="anchor" aria-label="anchor" href="#breaking-changes-3-0-1-9087"></a></h4>
+<h4 id="breaking-changes-3-0-1-9088">Breaking Changes<a class="anchor" aria-label="anchor" href="#breaking-changes-3-0-1-9088"></a></h4>
 <ul><li>
 <p>The former <em>kingdoms</em> Bacteria and Archaea are now each divided into four kingdoms with new top-level <em>domains</em> ‘Bacteria’ and ‘Archaea’ (Göker and Oren, 2024, DOI: 10.1099/ijsem.0.006242). Following this, a new <code>domain</code> column in the <code>microorganisms</code> data set was added, and more importantly, <code><a href="../reference/mo_property.html">mo_kingdom()</a></code> now returns the formal kingdom (e.g. <code>"Pseudomonadati"</code> instead of <code>"Bacteria"</code>). Use <code><a href="../reference/mo_property.html">mo_domain()</a></code> for the old behaviour. For non-prokaryotic kingdoms (Fungi, Protozoa, etc.), <code>kingdom</code> and <code>domain</code> are identical.</p>
 <table class="table"><colgroup><col width="33%"><col width="29%"><col width="37%"></colgroup><thead><tr><th>
@@ -105,7 +105,7 @@
 <li><p>Faster parallel computing via the <code>future</code> package for <code><a href="../reference/as.sir.html">as.sir()</a></code> and <code><a href="../reference/antibiogram.html">wisca()</a></code>: a non-sequential plan (e.g. <code>future::plan(future::multisession)</code>) must be active before using <code>parallel = TRUE</code>.</p></li>
 </ul></div>
 <div class="section level4">
-<h4 id="new-3-0-1-9087">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9087"></a></h4>
+<h4 id="new-3-0-1-9088">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9088"></a></h4>
 <ul><li>EUCAST 2026 and CLSI 2026 breakpoints: over 5,700 new breakpoints added to the <code>clinical_breakpoints</code> data set; EUCAST 2026 is now the default for all MIC and disk diffusion interpretations</li>
 <li>Wildtype/Non-wildtype (WT/NWT) output when using ECOFF-based interpretation, by setting <code>breakpoint_type = "ECOFF"</code> in <code><a href="../reference/as.sir.html">as.sir()</a></code>; WT/NWT results are fully supported in all resistance/susceptibility functions and plots (<a href="https://github.com/msberends/AMR/issues/254" class="external-link">#254</a>)</li>
 <li>
@@ -122,7 +122,7 @@
 <li>New <code><a href="../reference/antibiogram.html">wisca_plot()</a></code> to assess the susceptibility and incidence distributions from the Monte Carlo simulations</li>
 </ul></div>
 <div class="section level4">
-<h4 id="fixed-3-0-1-9087">Fixed<a class="anchor" aria-label="anchor" href="#fixed-3-0-1-9087"></a></h4>
+<h4 id="fixed-3-0-1-9088">Fixed<a class="anchor" aria-label="anchor" href="#fixed-3-0-1-9088"></a></h4>
 <ul><li>Setting <code>options(AMR_guideline = "EUCAST 2012")</code> or any year-qualified value no longer causes errors or silent wrong behaviour in <code><a href="../reference/interpretive_rules.html">interpretive_rules()</a></code>, <code><a href="../reference/proportion.html">resistance()</a></code>, <code><a href="../reference/proportion.html">susceptibility()</a></code>, <code><a href="../reference/count.html">count_resistant()</a></code>, <code><a href="../reference/count.html">count_susceptible()</a></code>, and SIR plotting/printing functions (<a href="https://github.com/msberends/AMR/issues/298" class="external-link">#298</a>)</li>
 <li>
 <code><a href="../reference/as.sir.html">as.sir()</a></code>
@@ -151,7 +151,7 @@
 </li>
 </ul></div>
 <div class="section level4">
-<h4 id="updated-3-0-1-9087">Updated<a class="anchor" aria-label="anchor" href="#updated-3-0-1-9087"></a></h4>
+<h4 id="updated-3-0-1-9088">Updated<a class="anchor" aria-label="anchor" href="#updated-3-0-1-9088"></a></h4>
 <ul><li>
 <code><a href="../reference/top_n_microorganisms.html">top_n_microorganisms()</a></code>: new <code>property_for_each</code> argument for sub-grouping within top <em>n</em> groups; rank ordering enforced (only lower taxonomic ranks allowed); fixed <code>property = NULL</code> not being accepted; inner filter now tracks original row indices to prevent cross-group contamination</li>
 <li>Taxonomic update for all microorganisms, now updated to June 2026</li>
--- a/news/index.md
+++ b/news/index.md
@@ -1,6 +1,6 @@
 # Changelog
-## AMR 3.0.1.9087
+## AMR 3.0.1.9088
 Planned as v3.1.0, end of September 2026.
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -10,7 +10,7 @@ articles:
  PCA: PCA.html
  WHONET: WHONET.html
  WISCA: WISCA.html
-last_built: 2026-08-20T12:32Z
+last_built: 2026-09-03T12:29Z
 urls:
  reference: https://amr-for-r.org/reference
  article: https://amr-for-r.org/articles
--- a/reference/AMR-deprecated.html
+++ b/reference/AMR-deprecated.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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/reference/AMR-options.html
+++ b/reference/AMR-options.html
@@ -9,7 +9,7 @@ options(AMR_guideline = "CLSI")'><meta property="og:image" content="https://amr-
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/reference/AMR.html
+++ b/reference/AMR.html
@@ -21,7 +21,7 @@ The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -112,7 +112,8 @@ The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish
    <div class="section level2">
    <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2>
    <p><strong>Maintainer</strong>: Matthijs S. Berends <a href="mailto:m.s.berends@umcg.nl">m.s.berends@umcg.nl</a> (<a href="https://orcid.org/0000-0001-7620-1800" class="external-link">ORCID</a>)</p>
-<p>Authors:</p><ul><li><p>Dennis Souverein (<a href="https://orcid.org/0000-0003-0455-0336" class="external-link">ORCID</a>) [contributor]</p></li>
+<p>Authors:</p><ul><li><p>Matthijs S. Berends <a href="mailto:m.s.berends@umcg.nl">m.s.berends@umcg.nl</a> (<a href="https://orcid.org/0000-0001-7620-1800" class="external-link">ORCID</a>)</p></li>
 <li><p>Dennis Souverein (<a href="https://orcid.org/0000-0003-0455-0336" class="external-link">ORCID</a>) [contributor]</p></li>
 <li><p>Erwin E. A. Hassing [contributor]</p></li>
 </ul><p>Other contributors:</p><ul><li><p>Aislinn Cook (<a href="https://orcid.org/0000-0002-9189-7815" class="external-link">ORCID</a>) [contributor]</p></li>
 <li><p>Andrew P. Norgan (<a href="https://orcid.org/0000-0002-2955-2066" class="external-link">ORCID</a>) [contributor]</p></li>
--- a/reference/AMR.md
+++ b/reference/AMR.md
@@ -102,6 +102,9 @@ Useful links:
 Authors:
 - Matthijs S. Berends <m.s.berends@umcg.nl>
  ([ORCID](https://orcid.org/0000-0001-7620-1800))
 - Dennis Souverein ([ORCID](https://orcid.org/0000-0003-0455-0336))
  \[contributor\]
--- a/reference/WHOCC.html
+++ b/reference/WHOCC.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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/reference/WHONET.html
+++ b/reference/WHONET.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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/reference/ab_from_text.html
+++ b/reference/ab_from_text.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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/reference/ab_property.html
+++ b/reference/ab_property.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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/reference/add_custom_antimicrobials.html
+++ b/reference/add_custom_antimicrobials.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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/reference/add_custom_microorganisms.html
+++ b/reference/add_custom_microorganisms.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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/reference/age.html
+++ b/reference/age.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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -112,16 +112,16 @@
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">df</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    birth_date age age_exact age_at_y2k</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1  1999-06-30  27  27.13973          0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1  1999-06-30  27  27.17808          0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2  1968-01-29  58  58.55616         31</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2  1968-01-29  58  58.59452         31</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3  1965-12-05  60  60.70685         34</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3  1965-12-05  60  60.74521         34</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4  1980-03-01  46  46.47123         19</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4  1980-03-01  46  46.50959         19</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5  1949-11-01  76  76.80000         50</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5  1949-11-01  76  76.83836         50</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6  1947-02-14  79  79.51233         52</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6  1947-02-14  79  79.55068         52</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7  1940-02-19  86  86.49863         59</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7  1940-02-19  86  86.53699         59</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8  1988-01-10  38  38.60822         11</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8  1988-01-10  38  38.64658         11</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9  1997-08-27  28  28.98082          2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9  1997-08-27  29  29.01918          2</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1978-01-26  48  48.56438         21</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1978-01-26  48  48.60274         21</span>
 </code></pre></div>
    </div>
  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
--- a/reference/age.md
+++ b/reference/age.md
@@ -81,14 +81,14 @@ df$age_at_y2k <- age(df$birth_date, "2000-01-01")
 df
 #>    birth_date age age_exact age_at_y2k
-#> 1  1999-06-30  27  27.13973          0
+#> 1  1999-06-30  27  27.17808          0
-#> 2  1968-01-29  58  58.55616         31
+#> 2  1968-01-29  58  58.59452         31
-#> 3  1965-12-05  60  60.70685         34
+#> 3  1965-12-05  60  60.74521         34
-#> 4  1980-03-01  46  46.47123         19
+#> 4  1980-03-01  46  46.50959         19
-#> 5  1949-11-01  76  76.80000         50
+#> 5  1949-11-01  76  76.83836         50
-#> 6  1947-02-14  79  79.51233         52
+#> 6  1947-02-14  79  79.55068         52
-#> 7  1940-02-19  86  86.49863         59
+#> 7  1940-02-19  86  86.53699         59
-#> 8  1988-01-10  38  38.60822         11
+#> 8  1988-01-10  38  38.64658         11
-#> 9  1997-08-27  28  28.98082          2
+#> 9  1997-08-27  29  29.01918          2
-#> 10 1978-01-26  48  48.56438         21
+#> 10 1978-01-26  48  48.60274         21
 ```
--- a/reference/age_groups.html
+++ b/reference/age_groups.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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/reference/amr-tidymodels.html
+++ b/reference/amr-tidymodels.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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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">
@@ -202,10 +202,10 @@ may affect the computations for subsequent operations.</p></dd>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">broom       </span> 1.0.13     <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">rsample     </span> 1.3.2 </span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">dials       </span> 1.4.4      <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">tailor      </span> 0.1.0 </span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">infer       </span> 1.1.0      <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">tidyr       </span> 1.3.2 </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">modeldata   </span> 1.5.1      <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">tune        </span> 2.1.0 </span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">modeldata   </span> 1.6.0      <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">tune        </span> 2.1.0 </span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">parsnip     </span> 1.6.0      <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">workflows   </span> 1.3.0 </span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">purrr       </span> 1.2.2      <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">workflowsets</span> 1.1.1 </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">recipes     </span> 1.3.3      <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">yardstick   </span> 1.4.0 </span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">recipes     </span> 1.4.0      <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">yardstick   </span> 1.4.0 </span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ── <span style="font-weight: bold;">Conflicts</span> ───────────────────────────────────────── tidymodels_conflicts() ──</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #BB0000;">✖</span> <span style="color: #0000BB;">purrr</span>::<span style="color: #00BB00;">discard()</span> masks <span style="color: #0000BB;">scales</span>::discard()</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #BB0000;">✖</span> <span style="color: #0000BB;">dplyr</span>::<span style="color: #00BB00;">filter()</span>  masks <span style="color: #0000BB;">stats</span>::filter()</span>
--- a/reference/amr-tidymodels.md
+++ b/reference/amr-tidymodels.md
@@ -181,10 +181,10 @@ if (require("tidymodels")) {
 #> ✔ broom        1.0.13     ✔ rsample      1.3.2 
 #> ✔ dials        1.4.4      ✔ tailor       0.1.0 
 #> ✔ infer        1.1.0      ✔ tidyr        1.3.2 
-#> ✔ modeldata    1.5.1      ✔ tune         2.1.0 
+#> ✔ modeldata    1.6.0      ✔ tune         2.1.0 
 #> ✔ parsnip      1.6.0      ✔ workflows    1.3.0 
 #> ✔ purrr        1.2.2      ✔ workflowsets 1.1.1 
-#> ✔ recipes      1.3.3      ✔ yardstick    1.4.0 
+#> ✔ recipes      1.4.0      ✔ yardstick    1.4.0 
 #> ── Conflicts ───────────────────────────────────────── tidymodels_conflicts() ──
 #> ✖ purrr::discard() masks scales::discard()
 #> ✖ dplyr::filter()  masks stats::filter()
--- a/reference/amr_course.html
+++ b/reference/amr_course.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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/reference/antibiogram.html
+++ b/reference/antibiogram.html
@@ -13,7 +13,7 @@ All antibiogram types adhere to previously described approaches (see Source), an
    <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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/reference/antimicrobial_selectors.html
+++ b/reference/antimicrobial_selectors.html
@@ -17,7 +17,7 @@ my_data_with_all_these_columns %&amp;gt;%
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/reference/antimicrobials.html
+++ b/reference/antimicrobials.html
@@ -9,7 +9,7 @@ The antibiotics data set has been renamed to antimicrobials. The old name will b
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/reference/as.ab.html
+++ b/reference/as.ab.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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/reference/as.av.html
+++ b/reference/as.av.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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/reference/as.disk.html
+++ b/reference/as.disk.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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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">
@@ -62,10 +62,6 @@
 <span><span class="fu">is.disk</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></code></pre></div>
    </div>
    <div class="section level2">
    <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
    <p>An object of class <code>disk</code> (inherits from <code>integer</code>) of length 1.</p>
    </div>
    <div class="section level2">
    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
--- a/reference/as.disk.md
+++ b/reference/as.disk.md
@@ -14,10 +14,6 @@ NA_disk_
 is.disk(x)
 ```
 ## Format
 An object of class `disk` (inherits from `integer`) of length 1.
 ## Arguments
 - x:
--- a/reference/as.mic.html
+++ b/reference/as.mic.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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/reference/as.mo.html
+++ b/reference/as.mo.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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/reference/as.sir.html
+++ b/reference/as.sir.html
@@ -9,7 +9,7 @@ Breakpoints are currently implemented from EUCAST 2011-2026 and CLSI 2011-2026,
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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">
@@ -462,10 +462,10 @@ Breakpoints are currently implemented from EUCAST 2011-2026 and CLSI 2011-2026,
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4 × 18</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   datetime            index method ab_given    mo_given   host_given input_given</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span>              <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>  <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>       <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>      <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>      <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2026-08-20 <span style="color: #949494;">12:34:53</span>     1 MIC    amoxicillin Escherich… human      8          </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2026-09-03 <span style="color: #949494;">12:31:42</span>     1 MIC    amoxicillin Escherich… human      8          </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2026-08-20 <span style="color: #949494;">12:34:53</span>     1 MIC    cipro       Escherich… human      0.256      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2026-09-03 <span style="color: #949494;">12:31:42</span>     1 MIC    cipro       Escherich… human      0.256      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2026-08-20 <span style="color: #949494;">12:34:53</span>     1 DISK   tobra       Escherich… human      16         </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2026-09-03 <span style="color: #949494;">12:31:42</span>     1 DISK   tobra       Escherich… human      16         </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2026-08-20 <span style="color: #949494;">12:34:53</span>     1 DISK   genta       Escherich… human      18         </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2026-09-03 <span style="color: #949494;">12:31:43</span>     1 DISK   genta       Escherich… human      18         </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 11 more variables: ab &lt;ab&gt;, mo &lt;mo&gt;, host &lt;chr&gt;, input &lt;chr&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   outcome &lt;sir&gt;, notes &lt;chr&gt;, guideline &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   breakpoint_S_R &lt;chr&gt;, site &lt;chr&gt;</span></span>
--- a/reference/as.sir.md
+++ b/reference/as.sir.md
@@ -712,10 +712,10 @@ sir_interpretation_history()
 #> # A tibble: 4 × 18
 #>   datetime            index method ab_given    mo_given   host_given input_given
 #>   <dttm>              <int> <chr>  <chr>       <chr>      <chr>      <chr>      
-#> 1 2026-08-20 12:34:53     1 MIC    amoxicillin Escherich… human      8          
+#> 1 2026-09-03 12:31:42     1 MIC    amoxicillin Escherich… human      8          
-#> 2 2026-08-20 12:34:53     1 MIC    cipro       Escherich… human      0.256      
+#> 2 2026-09-03 12:31:42     1 MIC    cipro       Escherich… human      0.256      
-#> 3 2026-08-20 12:34:53     1 DISK   tobra       Escherich… human      16         
+#> 3 2026-09-03 12:31:42     1 DISK   tobra       Escherich… human      16         
-#> 4 2026-08-20 12:34:53     1 DISK   genta       Escherich… human      18         
+#> 4 2026-09-03 12:31:43     1 DISK   genta       Escherich… human      18         
 #> # ℹ 11 more variables: ab <ab>, mo <mo>, host <chr>, input <chr>,
 #> #   outcome <sir>, notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,
 #> #   breakpoint_S_R <chr>, site <chr>
--- a/reference/atc_online.html
+++ b/reference/atc_online.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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/reference/av_from_text.html
+++ b/reference/av_from_text.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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/reference/av_property.html
+++ b/reference/av_property.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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/reference/availability.html
+++ b/reference/availability.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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/reference/bug_drug_combinations.html
+++ b/reference/bug_drug_combinations.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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/reference/clinical_breakpoints.html
+++ b/reference/clinical_breakpoints.html
@@ -21,7 +21,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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">
@@ -108,7 +108,10 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
 <h3 id="imported-from-whonet">Imported From WHONET<a class="anchor" aria-label="anchor" href="#imported-from-whonet"></a></h3>
-<p>Clinical breakpoints in this package were validated through and imported from <a href="https://whonet.org" class="external-link">WHONET</a>, a free desktop Windows application developed and supported by the WHO Collaborating Centre for Surveillance of Antimicrobial Resistance. More can be read on <a href="https://whonet.org" class="external-link">their website</a>. The developers of WHONET and this <code>AMR</code> package have been in contact about sharing their work. We highly appreciate their great development on the WHONET software.</p>
+<p>Some breakpoints in this package were validated through and imported from <a href="https://whonet.org" class="external-link">WHONET</a>, a free desktop Windows application developed and supported by the WHO Collaborating Centre for Surveillance of Antimicrobial Resistance. More can be read on <a href="https://whonet.org" class="external-link">their website</a>. The developers of WHONET and this <code>AMR</code> package have been in contact about sharing their work. We highly appreciate their great development on the WHONET software.</p>
 <p>From WHONET, imported were:</p><ul><li><p>All CLSI breakpoints, including ECOFF</p></li>
 <li><p>EUCAST breakpoints between  2011 and 2018</p></li>
 </ul><p>EUCAST breakpoints from 2019 onwards, were retrieved directly from <a href="https://www.eucast.org" class="external-link">https://www.eucast.org</a>.</p>
 <p>Our import and reproduction script can be found here: <a href="https://github.com/msberends/AMR/blob/main/data-raw/_reproduction_scripts/reproduction_of_clinical_breakpoints.R" class="external-link">https://github.com/msberends/AMR/blob/main/data-raw/_reproduction_scripts/reproduction_of_clinical_breakpoints.R</a>.</p>
 </div>
--- a/reference/clinical_breakpoints.md
+++ b/reference/clinical_breakpoints.md
@@ -100,7 +100,7 @@ to interpret raw data using a specific breakpoint type, e.g.
 ### Imported From WHONET
-Clinical breakpoints in this package were validated through and imported
+Some breakpoints in this package were validated through and imported
 from [WHONET](https://whonet.org), a free desktop Windows application
 developed and supported by the WHO Collaborating Centre for Surveillance
 of Antimicrobial Resistance. More can be read on [their
@@ -108,6 +108,15 @@ website](https://whonet.org). The developers of WHONET and this `AMR`
 package have been in contact about sharing their work. We highly
 appreciate their great development on the WHONET software.
 From WHONET, imported were:
 - All CLSI breakpoints, including ECOFF
 - EUCAST breakpoints between 2011 and 2018
 EUCAST breakpoints from 2019 onwards, were retrieved directly from
 <https://www.eucast.org>.
 Our import and reproduction script can be found here:
 <https://github.com/msberends/AMR/blob/main/data-raw/_reproduction_scripts/reproduction_of_clinical_breakpoints.R>.
--- a/reference/count.html
+++ b/reference/count.html
@@ -9,7 +9,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/reference/custom_interpretive_rules.html
+++ b/reference/custom_interpretive_rules.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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/reference/custom_mdro_guideline.html
+++ b/reference/custom_mdro_guideline.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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/reference/dosage.html
+++ b/reference/dosage.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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/reference/esbl_isolates.html
+++ b/reference/esbl_isolates.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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/reference/example_isolates.html
+++ b/reference/example_isolates.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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/reference/example_isolates_unclean.html
+++ b/reference/example_isolates_unclean.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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/reference/export_ncbi_biosample.html
+++ b/reference/export_ncbi_biosample.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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/reference/first_isolate.html
+++ b/reference/first_isolate.html
@@ -9,7 +9,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/reference/g.test.html
+++ b/reference/g.test.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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/reference/get_episode.html
+++ b/reference/get_episode.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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/reference/ggplot_pca.html
+++ b/reference/ggplot_pca.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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/reference/ggplot_sir.html
+++ b/reference/ggplot_sir.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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/reference/guess_ab_col.html
+++ b/reference/guess_ab_col.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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/reference/index.html
+++ b/reference/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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/reference/interpretive_rules.html
+++ b/reference/interpretive_rules.html
@@ -9,7 +9,7 @@ To improve the interpretation of the antibiogram before CLSI/EUCAST interpretive
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/reference/intrinsic_resistant.html
+++ b/reference/intrinsic_resistant.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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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">
@@ -60,12 +60,13 @@
    <div class="section level2">
    <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
-    <p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 294 079 observations and 2 variables:</p><ul><li><p><code>mo</code><br> Microorganism ID which occurs in <code><a href="microorganisms.html">microorganisms$mo</a></code>. Names can be retrieved using <code><a href="mo_property.html">mo_name()</a></code>.</p></li>
+    <p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 294 079 observations and 3 variables:</p><ul><li><p><code>mo</code><br> Microorganism ID which occurs in <code><a href="microorganisms.html">microorganisms$mo</a></code>. Names can be retrieved using <code><a href="mo_property.html">mo_name()</a></code>.</p></li>
 <li><p><code>ab</code><br> Antimicrobial ID which occurs in <code><a href="antimicrobials.html">antimicrobials$ab</a></code>. Names can be retrieved using <code><a href="ab_property.html">ab_name()</a></code>.</p></li>
 <li><p><code>version</code><br> Guideline name and version.</p></li>
 </ul></div>
    <div class="section level2">
    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
-    <p>This data set is currently based on <a href="https://www.eucast.org/bacteria/important-additional-information/expert-rules/" class="external-link">'EUCAST Expected Resistant Phenotypes' v1.2</a> (2023).</p>
+    <p>This data set is currently strictly follows <a href="https://www.eucast.org/bacteria/important-additional-information/expert-rules/" class="external-link">'EUCAST Expected Resistant Phenotypes' v1.2</a> (2023). The</p>
 <p>This data set is internally used by:</p><ul><li><p><code><a href="antimicrobial_selectors.html">not_intrinsic_resistant()</a></code> (an <a href="antimicrobial_selectors.html">antimicrobial selector</a>)</p></li>
 <li><p><code><a href="mo_property.html">mo_is_intrinsic_resistant()</a></code></p></li>
 <li><p><code><a href="antibiogram.html">wisca()</a></code> to model \(\beta(1, 9999)\) for resistant bug-drug combinations, per <a href="https://doi.org/10.1093/jac/dkv397" class="external-link">doi:10.1093/jac/dkv397</a></p></li>
@@ -82,19 +83,19 @@
    <div class="section level2">
    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">intrinsic_resistant</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 294,079 × 2</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 294,079 × 3</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>    mo          ab  </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>    mo          ab   version                                    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span>        <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span>        <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>                                      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> <span style="color: #949494;">B_</span>GRAMP     ATM </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> <span style="color: #949494;">B_</span>GRAMP     ATM  'EUCAST Expected Resistant Phenotypes' v1.2</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> <span style="color: #949494;">B_</span>GRAMP     COL </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> <span style="color: #949494;">B_</span>GRAMP     COL  'EUCAST Expected Resistant Phenotypes' v1.2</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> <span style="color: #949494;">B_</span>GRAMP     NAL </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> <span style="color: #949494;">B_</span>GRAMP     NAL  'EUCAST Expected Resistant Phenotypes' v1.2</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> <span style="color: #949494;">B_</span>GRAMP     PLB </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> <span style="color: #949494;">B_</span>GRAMP     PLB  'EUCAST Expected Resistant Phenotypes' v1.2</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> <span style="color: #949494;">B_</span>GRAMP     TEM </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> <span style="color: #949494;">B_</span>GRAMP     TEM  'EUCAST Expected Resistant Phenotypes' v1.2</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> <span style="color: #949494;">B_</span>ANAER-POS ATM </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> <span style="color: #949494;">B_</span>ANAER-POS ATM  'EUCAST Expected Resistant Phenotypes' v1.2</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> <span style="color: #949494;">B_</span>ANAER-POS COL </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> <span style="color: #949494;">B_</span>ANAER-POS COL  'EUCAST Expected Resistant Phenotypes' v1.2</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> <span style="color: #949494;">B_</span>ANAER-POS NAL </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> <span style="color: #949494;">B_</span>ANAER-POS NAL  'EUCAST Expected Resistant Phenotypes' v1.2</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> <span style="color: #949494;">B_</span>ANAER-POS PLB </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> <span style="color: #949494;">B_</span>ANAER-POS PLB  'EUCAST Expected Resistant Phenotypes' v1.2</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> <span style="color: #949494;">B_</span>ANAER-POS TEM </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> <span style="color: #949494;">B_</span>ANAER-POS TEM  'EUCAST Expected Resistant Phenotypes' v1.2</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 294,069 more rows</span></span>
 </code></pre></div>
    </div>
--- a/reference/intrinsic_resistant.md
+++ b/reference/intrinsic_resistant.md
@@ -15,7 +15,7 @@ intrinsic_resistant
 ## Format
 A [tibble](https://tibble.tidyverse.org/reference/tibble.html) with 294
-079 observations and 2 variables:
+079 observations and 3 variables:
 - `mo`  
  Microorganism ID which occurs in
@@ -29,12 +29,15 @@ A [tibble](https://tibble.tidyverse.org/reference/tibble.html) with 294
  Names can be retrieved using
  [`ab_name()`](https://amr-for-r.org/reference/ab_property.md).
 - `version`  
  Guideline name and version.
 ## Details
-This data set is currently based on ['EUCAST Expected Resistant
+This data set is currently strictly follows ['EUCAST Expected Resistant
 Phenotypes'
 v1.2](https://www.eucast.org/bacteria/important-additional-information/expert-rules/)
-(2023).
+(2023). The
 This data set is internally used by:
@@ -68,18 +71,18 @@ repository](https://github.com/msberends/AMR/tree/main/data-raw/datasets).
 ``` r
 intrinsic_resistant
-#> # A tibble: 294,079 × 2
+#> # A tibble: 294,079 × 3
-#>    mo          ab  
+#>    mo          ab   version                                    
-#>    <mo>        <ab>
+#>    <mo>        <ab> <chr>                                      
-#>  1 B_GRAMP     ATM 
+#>  1 B_GRAMP     ATM  'EUCAST Expected Resistant Phenotypes' v1.2
-#>  2 B_GRAMP     COL 
+#>  2 B_GRAMP     COL  'EUCAST Expected Resistant Phenotypes' v1.2
-#>  3 B_GRAMP     NAL 
+#>  3 B_GRAMP     NAL  'EUCAST Expected Resistant Phenotypes' v1.2
-#>  4 B_GRAMP     PLB 
+#>  4 B_GRAMP     PLB  'EUCAST Expected Resistant Phenotypes' v1.2
-#>  5 B_GRAMP     TEM 
+#>  5 B_GRAMP     TEM  'EUCAST Expected Resistant Phenotypes' v1.2
-#>  6 B_ANAER-POS ATM 
+#>  6 B_ANAER-POS ATM  'EUCAST Expected Resistant Phenotypes' v1.2
-#>  7 B_ANAER-POS COL 
+#>  7 B_ANAER-POS COL  'EUCAST Expected Resistant Phenotypes' v1.2
-#>  8 B_ANAER-POS NAL 
+#>  8 B_ANAER-POS NAL  'EUCAST Expected Resistant Phenotypes' v1.2
-#>  9 B_ANAER-POS PLB 
+#>  9 B_ANAER-POS PLB  'EUCAST Expected Resistant Phenotypes' v1.2
-#> 10 B_ANAER-POS TEM 
+#> 10 B_ANAER-POS TEM  'EUCAST Expected Resistant Phenotypes' v1.2
 #> # ℹ 294,069 more rows
 ```
--- a/reference/italicise_taxonomy.html
+++ b/reference/italicise_taxonomy.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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/reference/join.html
+++ b/reference/join.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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/reference/key_antimicrobials.html
+++ b/reference/key_antimicrobials.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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/reference/kurtosis.html
+++ b/reference/kurtosis.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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/reference/like.html
+++ b/reference/like.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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/reference/mdro.html
+++ b/reference/mdro.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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/reference/mean_amr_distance.html
+++ b/reference/mean_amr_distance.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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/reference/microorganisms.codes.html
+++ b/reference/microorganisms.codes.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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/reference/microorganisms.groups.html
+++ b/reference/microorganisms.groups.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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/reference/microorganisms.html
+++ b/reference/microorganisms.html
@@ -9,7 +9,7 @@ This data set is carefully crafted, yet made 100% reproducible from public and a
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/reference/mo_matching_score.html
+++ b/reference/mo_matching_score.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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/reference/mo_property.html
+++ b/reference/mo_property.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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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">
@@ -375,15 +375,15 @@
 <li><p><code>mo_ref("Enterobacter aerogenes")</code> will return <code>"Tindall et al., 2017"</code> (with a note about the renaming)</p></li>
 <li><p><code>mo_ref("Enterobacter aerogenes", keep_synonyms = TRUE)</code> will return <code>"Hormaeche et al., 1960"</code> (with a once-per-session warning that the name is outdated)</p></li>
 </ul><p><code>mo_ref()</code> returns the abbreviated authority of the nomenclatural act that created the queried name combination. When <code>keep_synonyms = FALSE</code> (default), this is the authority of the currently accepted name. When <code>keep_synonyms = TRUE</code>, this is the authority under which the queried (possibly outdated) name was published. Emendations (changes to the species description without a name change) are not reflected; only the combination or original description authority is returned.</p>
-<p>The short name (<code>mo_shortname()</code>) returns the first character of the genus and the full species, such as <code>"E. coli"</code>, for species and subspecies. Exceptions are abbreviations of staphylococci (such as <em>"CoNS"</em>, Coagulase-Negative Staphylococci) and beta-haemolytic streptococci (such as <em>"GBS"</em>, Group B Streptococci). Please bear in mind that e.g. <em>E. coli</em> could mean <em>Escherichia coli</em> (kingdom of Bacteria) as well as <em>Entamoeba coli</em> (kingdom of Protozoa). Returning to the full name will be done using <code><a href="as.mo.html">as.mo()</a></code> internally, giving priority to bacteria and human pathogens, i.e. <code>"E. coli"</code> will always be considered <em>Escherichia coli</em>. As a result, <code>mo_fullname(mo_shortname("Entamoeba coli"))</code> returns <code>"Escherichia coli"</code>.</p>
+<p>The short name (<code>mo_shortname()</code>) returns the first character of the genus and the full species, such as <code>"E. coli"</code>, for species and subspecies. Exceptions are abbreviations of staphylococci (such as <em>"CoNS"</em>, Coagulase-Negative Staphylococci) and beta-haemolytic streptococci (such as <em>"GBS"</em>, Group B Streptococci). Please bear in mind that e.g. <em>E. coli</em> could mean <em>Escherichia coli</em> (domain of Bacteria) as well as <em>Entamoeba coli</em> (domain of Protozoa). Returning to the full name will be done using <code><a href="as.mo.html">as.mo()</a></code> internally, giving priority to bacteria and human pathogens, i.e. <code>"E. coli"</code> will always be considered <em>Escherichia coli</em>. As a result, <code>mo_fullname(mo_shortname("Entamoeba coli"))</code> returns <code>"Escherichia coli"</code>.</p>
 <p>Following the formal introduction of the new kingdom rank into prokaryotic nomenclature in 2024 (<a href="https://doi.org/10.1099/ijsem.0.006242" class="external-link">doi:10.1099/ijsem.0.006242</a>
 ), <code>mo_kingdom()</code> and <code>mo_domain()</code> return different results for bacteria and archaea: <code>mo_kingdom()</code> returns the new formal kingdom (e.g. "Pseudomonadati", "Bacillati"), while <code>mo_domain()</code> returns the new domain (e.g. "Bacteria", "Archaea"). For non-prokaryotic organisms, both functions return identical results.</p>
 <p>Determination of human pathogenicity (<code>mo_pathogenicity()</code>) is strongly based on Bartlett <em>et al.</em> (2022, <a href="https://doi.org/10.1099/mic.0.001269" class="external-link">doi:10.1099/mic.0.001269</a>
 ). This function returns a <a href="https://rdrr.io/pkg/data.table/man/fctr.html" class="external-link">factor</a> with the levels <em>Pathogenic</em>, <em>Potentially pathogenic</em>, <em>Non-pathogenic</em>, and <em>Unknown</em>.</p>
-<p>Determination of the Gram stain (<code>mo_gramstain()</code> is based on the taxonomic kingdom and phylum. Originally, Cavalier-Smith defined the so-called subkingdoms Negibacteria and Posibacteria (2002, <a href="https://pubmed.ncbi.nlm.nih.gov/11837318/" class="external-link">PMID 11837318</a>), and only considered these phyla as Posibacteria: Actinobacteria, Chloroflexi, Firmicutes, and Tenericutes. These phyla were later renamed to Actinomycetota, Chloroflexota, Bacillota, and Mycoplasmatota (2021, <a href="https://pubmed.ncbi.nlm.nih.gov/34694987/" class="external-link">PMID 34694987</a>). Bacteria in these phyla are considered Gram-positive in this <code>AMR</code> package, except for members of the class Negativicutes (within phylum Bacillota) which are Gram-negative. All other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value <code>NA</code>. Functions <code>mo_is_gram_negative()</code> and <code>mo_is_gram_positive()</code> always return <code>TRUE</code> or <code>FALSE</code> (or <code>NA</code> when the input is <code>NA</code> or the MO code is <code>UNKNOWN</code>), thus always return <code>FALSE</code> for species outside the taxonomic kingdom of Bacteria.</p>
+<p>Determination of the Gram stain (<code>mo_gramstain()</code> is based on the taxonomic domain and phylum. Originally, Cavalier-Smith defined the so-called subkingdoms Negibacteria and Posibacteria (2002, <a href="https://pubmed.ncbi.nlm.nih.gov/11837318/" class="external-link">PMID 11837318</a>), and only considered these phyla as Posibacteria: Actinobacteria, Chloroflexi, Firmicutes, and Tenericutes. These phyla were later renamed to Actinomycetota, Chloroflexota, Bacillota, and Mycoplasmatota (2021, <a href="https://pubmed.ncbi.nlm.nih.gov/34694987/" class="external-link">PMID 34694987</a>). Bacteria in these phyla are considered Gram-positive in this <code>AMR</code> package, except for members of the class Negativicutes (within phylum Bacillota) which are Gram-negative. All other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value <code>NA</code>. Functions <code>mo_is_gram_negative()</code> and <code>mo_is_gram_positive()</code> always return <code>TRUE</code> or <code>FALSE</code> (or <code>NA</code> when the input is <code>NA</code> or the MO code is <code>UNKNOWN</code>), thus always return <code>FALSE</code> for species outside the taxonomic kingdom of Bacteria.</p>
-<p>Determination of yeasts (<code>mo_is_yeast()</code>) is based on the taxonomic kingdom and class. <em>Budding yeasts</em> are yeasts that reproduce asexually through a process called budding, where a new cell develops from a small protrusion on the parent cell. Taxonomically, these are members of the phylum Ascomycota, class Saccharomycetes (also called Hemiascomycetes) or Pichiomycetes. <em>True yeasts</em> quite specifically refers to yeasts in the underlying order Saccharomycetales (such as <em>Saccharomyces cerevisiae</em>). Thus, for all microorganisms that are member of the taxonomic class Saccharomycetes or Pichiomycetes, the function will return <code>TRUE</code>. It returns <code>FALSE</code> otherwise (or <code>NA</code> when the input is <code>NA</code> or the MO code is <code>UNKNOWN</code>).</p>
+<p>Determination of yeasts (<code>mo_is_yeast()</code>) is based on the taxonomic domain and class. <em>Budding yeasts</em> are yeasts that reproduce asexually through a process called budding, where a new cell develops from a small protrusion on the parent cell. Taxonomically, these are members of the phylum Ascomycota, class Saccharomycetes (also called Hemiascomycetes) or Pichiomycetes. <em>True yeasts</em> quite specifically refers to yeasts in the underlying order Saccharomycetales (such as <em>Saccharomyces cerevisiae</em>). Thus, for all microorganisms that are member of the taxonomic class Saccharomycetes or Pichiomycetes, the function will return <code>TRUE</code>. It returns <code>FALSE</code> otherwise (or <code>NA</code> when the input is <code>NA</code> or the MO code is <code>UNKNOWN</code>).</p>
 <p>Determination of intrinsic resistance (<code>mo_is_intrinsic_resistant()</code>) is based on the <a href="intrinsic_resistant.html">intrinsic_resistant</a> data set, which is based on <a href="https://www.eucast.org/bacteria/important-additional-information/expert-rules/" class="external-link">'EUCAST Expected Resistant Phenotypes' v1.2</a> (2023). The <code>mo_is_intrinsic_resistant()</code> function can be vectorised over both argument <code>x</code> (input for microorganisms) and <code>ab</code> (input for antimicrobials).</p>
-<p>Determination of both bacterial oxygen tolerance (<code>mo_oxygen_tolerance()</code>) and morphology (<code>mo_morphology()</code>) are  based on BacDive, see <em>Source</em>. The function <code>mo_is_anaerobic()</code> only returns <code>TRUE</code> if the oxygen tolerance is <code>"anaerobe"</code>, indicating an obligate anaerobic species or genus. It always returns <code>FALSE</code> for species outside the taxonomic kingdom of Bacteria.</p>
+<p>Determination of both bacterial oxygen tolerance (<code>mo_oxygen_tolerance()</code>) and morphology (<code>mo_morphology()</code>) are  based on BacDive, see <em>Source</em>. The function <code>mo_is_anaerobic()</code> only returns <code>TRUE</code> if the oxygen tolerance is <code>"anaerobe"</code>, indicating an obligate anaerobic species or genus. It always returns <code>FALSE</code> for species outside the taxonomic domain of Bacteria.</p>
 <p>The function <code>mo_url()</code> will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species. <a href="https://www.mycobank.org" class="external-link">This MycoBank URL</a> is used for fungi wherever available , <a href="https://www.mycobank.org" class="external-link">this LPSN URL</a> for bacteria wherever available, and <a href="https://www.gbif.org" class="external-link">this GBIF link</a> otherwise.</p>
 <p>SNOMED codes (<code>mo_snomed()</code>) was last updated on 16th of July, 2024. See <em>Source</em> and the <a href="microorganisms.html">microorganisms</a> data set for more info.</p>
 <p>Old taxonomic names (so-called 'synonyms') can be retrieved with <code>mo_synonyms()</code> (which will have the scientific reference as <a href="https://rdrr.io/r/base/names.html" class="external-link">name</a>), the current taxonomic name can be retrieved with <code>mo_current()</code>. Both functions return full names.</p>
--- a/reference/mo_property.md
+++ b/reference/mo_property.md
@@ -400,9 +400,9 @@ genus and the full species, such as `"E. coli"`, for species and
 subspecies. Exceptions are abbreviations of staphylococci (such as
 *"CoNS"*, Coagulase-Negative Staphylococci) and beta-haemolytic
 streptococci (such as *"GBS"*, Group B Streptococci). Please bear in
-mind that e.g. *E. coli* could mean *Escherichia coli* (kingdom of
+mind that e.g. *E. coli* could mean *Escherichia coli* (domain of
-Bacteria) as well as *Entamoeba coli* (kingdom of Protozoa). Returning
+Bacteria) as well as *Entamoeba coli* (domain of Protozoa). Returning to
-to the full name will be done using
+the full name will be done using
 [`as.mo()`](https://amr-for-r.org/reference/as.mo.md) internally, giving
 priority to bacteria and human pathogens, i.e. `"E. coli"` will always
 be considered *Escherichia coli*. As a result,
@@ -426,7 +426,7 @@ function returns a
 *Pathogenic*, *Potentially pathogenic*, *Non-pathogenic*, and *Unknown*.
 Determination of the Gram stain (`mo_gramstain()` is based on the
-taxonomic kingdom and phylum. Originally, Cavalier-Smith defined the
+taxonomic domain and phylum. Originally, Cavalier-Smith defined the
 so-called subkingdoms Negibacteria and Posibacteria (2002, [PMID
 11837318](https://pubmed.ncbi.nlm.nih.gov/11837318/)), and only
 considered these phyla as Posibacteria: Actinobacteria, Chloroflexi,
@@ -443,7 +443,7 @@ is `UNKNOWN`), thus always return `FALSE` for species outside the
 taxonomic kingdom of Bacteria.
 Determination of yeasts (`mo_is_yeast()`) is based on the taxonomic
-kingdom and class. *Budding yeasts* are yeasts that reproduce asexually
+domain and class. *Budding yeasts* are yeasts that reproduce asexually
 through a process called budding, where a new cell develops from a small
 protrusion on the parent cell. Taxonomically, these are members of the
 phylum Ascomycota, class Saccharomycetes (also called Hemiascomycetes)
@@ -468,7 +468,7 @@ Determination of both bacterial oxygen tolerance
 on BacDive, see *Source*. The function `mo_is_anaerobic()` only returns
 `TRUE` if the oxygen tolerance is `"anaerobe"`, indicating an obligate
 anaerobic species or genus. It always returns `FALSE` for species
-outside the taxonomic kingdom of Bacteria.
+outside the taxonomic domain of Bacteria.
 The function `mo_url()` will return the direct URL to the online
 database entry, which also shows the scientific reference of the
--- a/reference/mo_source.html
+++ b/reference/mo_source.html
@@ -9,7 +9,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/reference/pca.html
+++ b/reference/pca.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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/reference/plot.html
+++ b/reference/plot.html
@@ -9,7 +9,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/reference/proportion.html
+++ b/reference/proportion.html
@@ -9,7 +9,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/reference/random.html
+++ b/reference/random.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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/reference/resistance_predict.html
+++ b/reference/resistance_predict.html
@@ -9,7 +9,7 @@ NOTE: These functions are deprecated and will be removed in a future version. Us
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/reference/skewness.html
+++ b/reference/skewness.html
@@ -9,7 +9,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/reference/top_n_microorganisms.html
+++ b/reference/top_n_microorganisms.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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/reference/translate.html
+++ b/reference/translate.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="">3.0.1.9087</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/search.json
+++ b/search.json