Built site for AMR@3.0.1.9030: e2102c0

2026-03-15 22:47:55 +01:00 · 2026-03-07 17:15:05 +00:00
parent 599302f0bd
commit ab5ce59112
115 changed files with 582 additions and 511 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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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">
@@ -218,18 +218,29 @@ _pkgdown.yml    # pkgdown website configuration</code></pre>
 <code>NEWS.md</code> uses sections <strong>New</strong>, <strong>Fixes</strong>, <strong>Updates</strong> with GitHub issue references (<code>#NNN</code>)</li>
 </ul><div class="section level3">
 <h3 id="version-and-date-bump-required-for-every-pr">Version and date bump required for every PR<a class="anchor" aria-label="anchor" href="#version-and-date-bump-required-for-every-pr"></a></h3>
-<p>Before opening a pull request, always increment the four-digit dev counter by 1 in <strong>both</strong> of these files:</p>
+<p>All PRs are <strong>squash-merged</strong>, so each PR lands as exactly <strong>one commit</strong> on the default branch. Version numbers are kept in sync with the cumulative commit count since the last released tag. Therefore <strong>exactly one version bump is allowed per PR</strong>, regardless of how many intermediate commits are made on the branch.</p>
+<div class="section level4">
+<h4 id="computing-the-correct-version-number">Computing the correct version number<a class="anchor" aria-label="anchor" href="#computing-the-correct-version-number"></a></h4>
+<p>Run the following from the repo root to determine the version string to use:</p>
+<div class="sourceCode" id="cb5"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb5-1"><a href="#cb5-1" tabindex="-1"></a><span class="va">currenttag</span><span class="op">=</span><span class="va">$(</span><span class="fu">git</span> describe <span class="at">--tags</span> <span class="at">--abbrev</span><span class="op">=</span>0 <span class="kw">|</span> <span class="fu">sed</span> <span class="st">'s/v//'</span><span class="va">)</span></span>
+<span id="cb5-2"><a href="#cb5-2" tabindex="-1"></a><span class="va">currenttagfull</span><span class="op">=</span><span class="va">$(</span><span class="fu">git</span> describe <span class="at">--tags</span> <span class="at">--abbrev</span><span class="op">=</span>0<span class="va">)</span></span>
+<span id="cb5-3"><a href="#cb5-3" tabindex="-1"></a><span class="va">defaultbranch</span><span class="op">=</span><span class="va">$(</span><span class="fu">git</span> branch <span class="kw">|</span> <span class="fu">cut</span> <span class="at">-c</span> 3- <span class="kw">|</span> <span class="fu">grep</span> <span class="at">-E</span> <span class="st">'^master$|^main$'</span><span class="va">)</span></span>
+<span id="cb5-4"><a href="#cb5-4" tabindex="-1"></a><span class="va">currentcommit</span><span class="op">=</span><span class="va">$(</span><span class="fu">git</span> rev-list <span class="at">--count</span> <span class="va">${currenttagfull}</span>..<span class="va">${defaultbranch})</span></span>
+<span id="cb5-5"><a href="#cb5-5" tabindex="-1"></a><span class="va">currentversion</span><span class="op">=</span><span class="st">"</span><span class="va">${currenttag}</span><span class="st">.</span><span class="va">$((currentcommit</span> <span class="op">+</span> <span class="dv">9001</span> <span class="op">+</span> <span class="dv">1</span><span class="va">))</span><span class="st">"</span></span>
+<span id="cb5-6"><a href="#cb5-6" tabindex="-1"></a><span class="bu">echo</span> <span class="st">"</span><span class="va">$currentversion</span><span class="st">"</span></span></code></pre></div>
+<p>The <code>+ 1</code> accounts for the fact that this PR’s squash commit is not yet on the default branch. Set <strong>both</strong> of these files to the resulting version string (and only once per PR, even across multiple commits):</p>
 <ol style="list-style-type: decimal"><li>
-<p><strong><code>DESCRIPTION</code></strong> — the <code>Version:</code> field:</p>
-<pre><code>Version: 3.0.1.9021  →  Version: 3.0.1.9022</code></pre>
-</li>
+<strong><code>DESCRIPTION</code></strong> — the <code>Version:</code> field</li>
 <li>
-<p><strong><code>NEWS.md</code></strong> — the top-level heading:</p>
-<pre><code><span><span class="co"># AMR 3.0.1.9021  →  # AMR 3.0.1.9022</span></span></code></pre>
+<strong><code>NEWS.md</code></strong> — the top-level heading <code># AMR &lt;version&gt;</code>
 </li>
-</ol><p>Read the current version from <code>DESCRIPTION</code>, add 1 to the last numeric component, and write the new version to both files in the same commit as the rest of the PR changes.</p>
-<p>Also bump the date to the current date in <strong><code>DESCRIPTION</code></strong>, where it’s in the <code>Date:</code> field in ISO format:</p>
-<pre><code><span><span class="va">Date</span><span class="op">:</span> <span class="fl">2025</span><span class="op">-</span><span class="fl">12</span><span class="op">-</span><span class="fl">31</span></span></code></pre>
+</ol><p>If <code>git describe</code> fails (e.g. no tags exist in the environment), fall back to reading the current version from <code>DESCRIPTION</code> and adding 1 to the last numeric component — but only if no bump has already been made in this PR.</p>
+</div>
+<div class="section level4">
+<h4 id="date-field">Date field<a class="anchor" aria-label="anchor" href="#date-field"></a></h4>
+<p>The <code>Date:</code> field in <code>DESCRIPTION</code> must reflect the date of the <strong>last commit to the PR</strong> (not the first), in ISO format. Update it with every commit so it is always current:</p>
+<pre><code><span><span class="va">Date</span><span class="op">:</span> <span class="fl">2026</span><span class="op">-</span><span class="fl">03</span><span class="op">-</span><span class="fl">07</span></span></code></pre>
+</div>
 </div>
 </div>
 <div class="section level2">
--- a/CLAUDE.md
+++ b/CLAUDE.md
@@ -163,25 +163,45 @@ Version format: `major.minor.patch.dev` (e.g., `3.0.1.9021`)

 ### Version and date bump required for every PR

-Before opening a pull request, always increment the four-digit dev
-counter by 1 in **both** of these files:
+All PRs are **squash-merged**, so each PR lands as exactly **one
+commit** on the default branch. Version numbers are kept in sync with
+the cumulative commit count since the last released tag. Therefore
+**exactly one version bump is allowed per PR**, regardless of how many
+intermediate commits are made on the branch.

-1.  **`DESCRIPTION`** — the `Version:` field:
+#### Computing the correct version number

-        Version: 3.0.1.9021  →  Version: 3.0.1.9022
+Run the following from the repo root to determine the version string to
+use:

-2.  **`NEWS.md`** — the top-level heading:
+``` bash
+currenttag=$(git describe --tags --abbrev=0 | sed 's/v//')
+currenttagfull=$(git describe --tags --abbrev=0)
+defaultbranch=$(git branch | cut -c 3- | grep -E '^master$|^main$')
+currentcommit=$(git rev-list --count ${currenttagfull}..${defaultbranch})
+currentversion="${currenttag}.$((currentcommit + 9001 + 1))"
+echo "$currentversion"
+```

-        # AMR 3.0.1.9021  →  # AMR 3.0.1.9022
+The `+ 1` accounts for the fact that this PR’s squash commit is not yet
+on the default branch. Set **both** of these files to the resulting
+version string (and only once per PR, even across multiple commits):

-Read the current version from `DESCRIPTION`, add 1 to the last numeric
-component, and write the new version to both files in the same commit as
-the rest of the PR changes.
+1.  **`DESCRIPTION`** — the `Version:` field
+2.  **`NEWS.md`** — the top-level heading `# AMR <version>`

-Also bump the date to the current date in **`DESCRIPTION`**, where it’s
-in the `Date:` field in ISO format:
+If `git describe` fails (e.g. no tags exist in the environment), fall
+back to reading the current version from `DESCRIPTION` and adding 1 to
+the last numeric component — but only if no bump has already been made
+in this PR.

-    Date: 2025-12-31
+#### Date field
+
+The `Date:` field in `DESCRIPTION` must reflect the date of the **last
+commit to the PR** (not the first), in ISO format. Update it with every
+commit so it is always current:
+
+    Date: 2026-03-07

 ## Internal State

--- 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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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 06 March 2026.</p>
+generated on 07 March 2026.</p>
 <div class="section level2">
 <h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
 </h2>
@@ -147,21 +147,21 @@ make the structure of your data generally look like this:</p>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2026-03-06</td>
+<td align="center">2026-03-07</td>
 <td align="center">abcd</td>
 <td align="center">Escherichia coli</td>
 <td align="center">S</td>
 <td align="center">S</td>
 </tr>
 <tr class="even">
-<td align="center">2026-03-06</td>
+<td align="center">2026-03-07</td>
 <td align="center">abcd</td>
 <td align="center">Escherichia coli</td>
 <td align="center">S</td>
 <td align="center">R</td>
 </tr>
 <tr class="odd">
-<td align="center">2026-03-06</td>
+<td align="center">2026-03-07</td>
 <td align="center">efgh</td>
 <td align="center">Escherichia coli</td>
 <td align="center">R</td>
@@ -407,7 +407,7 @@ the methods on the <code><a href="../reference/first_isolate.html">first_isolate
 <span><span class="co">#&gt; <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">patient_id</span><span style="color: #0000BB;">' as input for </span><span style="color: #0000BB; background-color: #444444;">`col_patient_id`</span><span style="color: #0000BB;">.</span></span></span>
 <span><span class="co">#&gt; <span style="color: #BB0000;">ℹ Basing inclusion on all antimicrobial results, using a points threshold</span></span></span>
 <span><span class="co"><span style="color: #BB0000;">#&gt;   of 2</span></span></span>
-<span><span class="co">#&gt; <span style="color: #BBBBBB;">=&gt; Found </span><span style="color: #BBBBBB; font-weight: bold;">2,730 'phenotype-based' first isolates</span><span style="color: #BBBBBB;"> (91.0% of total where a</span></span></span>
+<span><span class="co">#&gt; <span style="color: #BBBBBB;">=&gt; Found </span><span style="color: #BBBBBB; font-weight: bold;">2,724 'phenotype-based' first isolates</span><span style="color: #BBBBBB;"> (90.8% of total where a</span></span></span>
 <span><span class="co"><span style="color: #BBBBBB;">#&gt;    microbial ID was available)</span></span></span></code></pre></div>
 <p>So only 91% is suitable for resistance analysis! We can now filter on
 it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the
@@ -419,11 +419,11 @@ it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" cl
 <div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">our_data_1st</span> <span class="op">&lt;-</span> <span class="va">our_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
 <span>  <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
-<p>So we end up with 2 730 isolates for analysis. Now our data looks
+<p>So we end up with 2 724 isolates for analysis. Now our data looks
 like:</p>
 <div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">our_data_1st</span></span>
-<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,730 × 9</span></span></span>
+<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,724 × 9</span></span></span>
 <span><span class="co">#&gt;    patient_id hospital date       bacteria     AMX   AMC   CIP   GEN   first</span></span>
 <span><span class="co">#&gt;    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>      <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;date&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span></span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> J3         A        2012-11-21 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;">  R  </span> <span style="color: #080808; background-color: #FFD787;">  I  </span> <span style="color: #080808; background-color: #5FD7AF;">  S  </span> <span style="color: #080808; background-color: #5FD7AF;">  S  </span> TRUE </span></span>
@@ -436,7 +436,7 @@ like:</p>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> J3         A        2019-06-19 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;">  S  </span> <span style="color: #080808; background-color: #5FD7AF;">  S  </span> <span style="color: #080808; background-color: #5FD7AF;">  S  </span> <span style="color: #080808; background-color: #5FD7AF;">  S  </span> TRUE </span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> G6         A        2015-04-27 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #5FD7AF;">  S  </span> <span style="color: #080808; background-color: #5FD7AF;">  S  </span> <span style="color: #080808; background-color: #5FD7AF;">  S  </span> <span style="color: #080808; background-color: #5FD7AF;">  S  </span> TRUE </span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> P4         A        2011-06-21 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;">  S  </span> <span style="color: #080808; background-color: #5FD7AF;">  S  </span> <span style="color: #080808; background-color: #5FD7AF;">  S  </span> <span style="color: #080808; background-color: #5FD7AF;">  S  </span> TRUE </span></span>
-<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,720 more rows</span></span></span></code></pre></div>
+<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,714 more rows</span></span></span></code></pre></div>
 <p>Time for the analysis.</p>
 </div>
 </div>
@@ -449,29 +449,29 @@ impression, as it comes with support for the new <code>mo</code> and
 <div class="sourceCode" id="cb12"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">our_data_1st</span><span class="op">)</span></span>
 <span><span class="co">#&gt;   patient_id          hospital              date           </span></span>
-<span><span class="co">#&gt;  Length:2730        Length:2730        Min.   :2011-01-01  </span></span>
-<span><span class="co">#&gt;  Class :character   Class :character   1st Qu.:2013-04-06  </span></span>
-<span><span class="co">#&gt;  Mode  :character   Mode  :character   Median :2015-06-04  </span></span>
+<span><span class="co">#&gt;  Length:2724        Length:2724        Min.   :2011-01-01  </span></span>
+<span><span class="co">#&gt;  Class :character   Class :character   1st Qu.:2013-04-07  </span></span>
+<span><span class="co">#&gt;  Mode  :character   Mode  :character   Median :2015-06-03  </span></span>
 <span><span class="co">#&gt;                                        Mean   :2015-06-09  </span></span>
-<span><span class="co">#&gt;                                        3rd Qu.:2017-08-14  </span></span>
+<span><span class="co">#&gt;                                        3rd Qu.:2017-08-11  </span></span>
 <span><span class="co">#&gt;                                        Max.   :2019-12-27  </span></span>
 <span><span class="co">#&gt;    bacteria               AMX                    AMC                </span></span>
 <span><span class="co">#&gt;  Class :mo             Class:sir              Class:sir             </span></span>
-<span><span class="co">#&gt;  &lt;NA&gt;  :0              %S   :40.1% (n=1071)   %S   :51.1% (n=1354)  </span></span>
+<span><span class="co">#&gt;  &lt;NA&gt;  :0              %S   :41.6% (n=1133)   %S   :52.6% (n=1432)  </span></span>
 <span><span class="co">#&gt;  Unique:4              %SDD : 0.0% (n=0)      %SDD : 0.0% (n=0)     </span></span>
-<span><span class="co">#&gt;  #1    :B_ESCHR_COLI   %I   :17.0% (n=453)    %I   :12.7% (n=335)   </span></span>
-<span><span class="co">#&gt;  #2    :B_STPHY_AURS   %R   :42.9% (n=1147)   %R   :36.2% (n=959)   </span></span>
+<span><span class="co">#&gt;  #1    :B_ESCHR_COLI   %I   :16.4% (n=446)    %I   :12.2% (n=333)   </span></span>
+<span><span class="co">#&gt;  #2    :B_STPHY_AURS   %R   :42.0% (n=1145)   %R   :35.2% (n=959)   </span></span>
 <span><span class="co">#&gt;  #3    :B_STRPT_PNMN   %NI  : 0.0% (n=0)      %NI  : 0.0% (n=0)     </span></span>
 <span><span class="co">#&gt;     CIP                    GEN                  first        </span></span>
 <span><span class="co">#&gt;  Class:sir              Class:sir              Mode:logical  </span></span>
-<span><span class="co">#&gt;  %S   :52.2% (n=1426)   %S   :60.7% (n=1656)   TRUE:2730     </span></span>
+<span><span class="co">#&gt;  %S   :52.5% (n=1431)   %S   :61.0% (n=1661)   TRUE:2724     </span></span>
 <span><span class="co">#&gt;  %SDD : 0.0% (n=0)      %SDD : 0.0% (n=0)                    </span></span>
-<span><span class="co">#&gt;  %I   : 6.5% (n=178)    %I   : 3.0% (n=83)                   </span></span>
-<span><span class="co">#&gt;  %R   :41.2% (n=1126)   %R   :36.3% (n=991)                  </span></span>
+<span><span class="co">#&gt;  %I   : 6.5% (n=176)    %I   : 3.0% (n=82)                   </span></span>
+<span><span class="co">#&gt;  %R   :41.0% (n=1117)   %R   :36.0% (n=981)                  </span></span>
 <span><span class="co">#&gt;  %NI  : 0.0% (n=0)      %NI  : 0.0% (n=0)</span></span>
 <span></span>
 <span><span class="fu"><a href="https://pillar.r-lib.org/reference/glimpse.html" class="external-link">glimpse</a></span><span class="op">(</span><span class="va">our_data_1st</span><span class="op">)</span></span>
-<span><span class="co">#&gt; Rows: 2,730</span></span>
+<span><span class="co">#&gt; Rows: 2,724</span></span>
 <span><span class="co">#&gt; Columns: 9</span></span>
 <span><span class="co">#&gt; $ patient_id <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> "J3"<span style="color: #949494;">, </span>"R7"<span style="color: #949494;">, </span>"P3"<span style="color: #949494;">, </span>"P10"<span style="color: #949494;">, </span>"B7"<span style="color: #949494;">, </span>"W3"<span style="color: #949494;">, </span>"M3"<span style="color: #949494;">, </span>"J3"<span style="color: #949494;">, </span>"G6"<span style="color: #949494;">, </span>"P4"…</span></span>
 <span><span class="co">#&gt; $ hospital   <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> "A"<span style="color: #949494;">, </span>"A"<span style="color: #949494;">, </span>"A"<span style="color: #949494;">, </span>"A"<span style="color: #949494;">, </span>"A"<span style="color: #949494;">, </span>"A"<span style="color: #949494;">, </span>"A"<span style="color: #949494;">, </span>"A"<span style="color: #949494;">, </span>"A"<span style="color: #949494;">, </span>"A"<span style="color: #949494;">, </span>"A"<span style="color: #949494;">, </span>"A"<span style="color: #949494;">,</span>…</span></span>
@@ -486,7 +486,7 @@ impression, as it comes with support for the new <code>mo</code> and
 <span><span class="co"># number of unique values per column:</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">sapply</a></span><span class="op">(</span><span class="va">our_data_1st</span>, <span class="va">n_distinct</span><span class="op">)</span></span>
 <span><span class="co">#&gt; patient_id   hospital       date   bacteria        AMX        AMC        CIP </span></span>
-<span><span class="co">#&gt;        260          3       1854          4          4          4          3 </span></span>
+<span><span class="co">#&gt;        260          3       1854          4          3          3          3 </span></span>
 <span><span class="co">#&gt;        GEN      first </span></span>
 <span><span class="co">#&gt;          3          1</span></span></code></pre></div>
 <div class="section level3">
@@ -511,9 +511,9 @@ microorganisms:</p>
 <span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 4 × 2</span></span></span>
 <span><span class="co">#&gt;   `mo_name(bacteria)`          n</span></span>
 <span><span class="co">#&gt;   <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>                    <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;">1</span> Escherichia coli          <span style="text-decoration: underline;">1</span>326</span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;">2</span> Staphylococcus aureus      684</span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;">3</span> Streptococcus pneumoniae   401</span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;">1</span> Escherichia coli          <span style="text-decoration: underline;">1</span>321</span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;">2</span> Staphylococcus aureus      682</span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;">3</span> Streptococcus pneumoniae   402</span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;">4</span> Klebsiella pneumoniae      319</span></span></code></pre></div>
 </div>
 <div class="section level3">
@@ -526,7 +526,7 @@ in:</p>
 <code class="sourceCode R"><span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
 <span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">date</span>, <span class="fu"><a href="../reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span>
 <span><span class="co">#&gt; <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #444444;">`aminoglycosides()`</span><span style="color: #0000BB;"> using column '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin)</span></span></span>
-<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,730 × 2</span></span></span>
+<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,724 × 2</span></span></span>
 <span><span class="co">#&gt;    date       GEN  </span></span>
 <span><span class="co">#&gt;    <span style="color: #949494; font-style: italic;">&lt;date&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> 2012-11-21 <span style="color: #080808; background-color: #5FD7AF;">  S  </span></span></span>
@@ -539,13 +539,13 @@ in:</p>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> 2019-06-19 <span style="color: #080808; background-color: #5FD7AF;">  S  </span></span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> 2015-04-27 <span style="color: #080808; background-color: #5FD7AF;">  S  </span></span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> 2011-06-21 <span style="color: #080808; background-color: #5FD7AF;">  S  </span></span></span>
-<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,720 more rows</span></span></span>
+<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,714 more rows</span></span></span>
 <span></span>
 <span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
 <span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">bacteria</span>, <span class="fu"><a href="../reference/antimicrobial_selectors.html">betalactams</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span>
 <span><span class="co">#&gt; <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #444444;">`betalactams()`</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">AMX</span><span style="color: #0000BB;">' (amoxicillin) and '</span><span style="color: #0000BB; font-weight: bold;">AMC</span><span style="color: #0000BB;">'</span></span></span>
 <span><span class="co"><span style="color: #0000BB;">#&gt;   (amoxicillin/clavulanic acid)</span></span></span>
-<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,730 × 3</span></span></span>
+<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,724 × 3</span></span></span>
 <span><span class="co">#&gt;    bacteria     AMX   AMC  </span></span>
 <span><span class="co">#&gt;    <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;">  R  </span> <span style="color: #080808; background-color: #FFD787;">  I  </span></span></span>
@@ -558,11 +558,11 @@ in:</p>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;">  S  </span> <span style="color: #080808; background-color: #5FD7AF;">  S  </span></span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #5FD7AF;">  S  </span> <span style="color: #080808; background-color: #5FD7AF;">  S  </span></span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;">  S  </span> <span style="color: #080808; background-color: #5FD7AF;">  S  </span></span></span>
-<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,720 more rows</span></span></span>
+<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,714 more rows</span></span></span>
 <span></span>
 <span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
 <span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">bacteria</span>, <span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.sir</span><span class="op">)</span><span class="op">)</span></span>
-<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,730 × 5</span></span></span>
+<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,724 × 5</span></span></span>
 <span><span class="co">#&gt;    bacteria     AMX   AMC   CIP   GEN  </span></span>
 <span><span class="co">#&gt;    <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;">  R  </span> <span style="color: #080808; background-color: #FFD787;">  I  </span> <span style="color: #080808; background-color: #5FD7AF;">  S  </span> <span style="color: #080808; background-color: #5FD7AF;">  S  </span></span></span>
@@ -575,13 +575,13 @@ in:</p>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;">  S  </span> <span style="color: #080808; background-color: #5FD7AF;">  S  </span> <span style="color: #080808; background-color: #5FD7AF;">  S  </span> <span style="color: #080808; background-color: #5FD7AF;">  S  </span></span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #5FD7AF;">  S  </span> <span style="color: #080808; background-color: #5FD7AF;">  S  </span> <span style="color: #080808; background-color: #5FD7AF;">  S  </span> <span style="color: #080808; background-color: #5FD7AF;">  S  </span></span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;">  S  </span> <span style="color: #080808; background-color: #5FD7AF;">  S  </span> <span style="color: #080808; background-color: #5FD7AF;">  S  </span> <span style="color: #080808; background-color: #5FD7AF;">  S  </span></span></span>
-<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,720 more rows</span></span></span>
+<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,714 more rows</span></span></span>
 <span></span>
 <span><span class="co"># filtering using AB selectors is also possible:</span></span>
 <span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
 <span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu"><a href="../reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span><span class="op">)</span></span>
 <span><span class="co">#&gt; <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #444444;">`aminoglycosides()`</span><span style="color: #0000BB;"> using column '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin)</span></span></span>
-<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 991 × 9</span></span></span>
+<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 981 × 9</span></span></span>
 <span><span class="co">#&gt;    patient_id hospital date       bacteria     AMX   AMC   CIP   GEN   first</span></span>
 <span><span class="co">#&gt;    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>      <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;date&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span></span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> J5         A        2017-12-25 <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN <span style="color: #080808; background-color: #FF5F5F;">  R  </span> <span style="color: #080808; background-color: #5FD7AF;">  S  </span> <span style="color: #080808; background-color: #5FD7AF;">  S  </span> <span style="color: #080808; background-color: #FF5F5F;">  R  </span> TRUE </span></span>
@@ -594,13 +594,13 @@ in:</p>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> P5         A        2019-03-09 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #5FD7AF;">  S  </span> <span style="color: #080808; background-color: #5FD7AF;">  S  </span> <span style="color: #080808; background-color: #5FD7AF;">  S  </span> <span style="color: #080808; background-color: #FF5F5F;">  R  </span> TRUE </span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> Q8         A        2019-08-10 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #5FD7AF;">  S  </span> <span style="color: #080808; background-color: #5FD7AF;">  S  </span> <span style="color: #080808; background-color: #5FD7AF;">  S  </span> <span style="color: #080808; background-color: #FF5F5F;">  R  </span> TRUE </span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> K5         A        2013-03-15 <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN <span style="color: #080808; background-color: #5FD7AF;">  S  </span> <span style="color: #080808; background-color: #5FD7AF;">  S  </span> <span style="color: #080808; background-color: #5FD7AF;">  S  </span> <span style="color: #080808; background-color: #FF5F5F;">  R  </span> TRUE </span></span>
-<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 981 more rows</span></span></span>
+<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 971 more rows</span></span></span>
 <span></span>
 <span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
 <span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu"><a href="../reference/antimicrobial_selectors.html">betalactams</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span><span class="op">)</span></span>
 <span><span class="co">#&gt; <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #444444;">`betalactams()`</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">AMX</span><span style="color: #0000BB;">' (amoxicillin) and '</span><span style="color: #0000BB; font-weight: bold;">AMC</span><span style="color: #0000BB;">'</span></span></span>
 <span><span class="co"><span style="color: #0000BB;">#&gt;   (amoxicillin/clavulanic acid)</span></span></span>
-<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 461 × 9</span></span></span>
+<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 462 × 9</span></span></span>
 <span><span class="co">#&gt;    patient_id hospital date       bacteria     AMX   AMC   CIP   GEN   first</span></span>
 <span><span class="co">#&gt;    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>      <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;date&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span></span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> M7         A        2013-07-22 <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN <span style="color: #080808; background-color: #FF5F5F;">  R  </span> <span style="color: #080808; background-color: #FF5F5F;">  R  </span> <span style="color: #080808; background-color: #5FD7AF;">  S  </span> <span style="color: #080808; background-color: #5FD7AF;">  S  </span> TRUE </span></span>
@@ -613,13 +613,13 @@ in:</p>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> Q2         A        2019-09-22 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;">  R  </span> <span style="color: #080808; background-color: #FF5F5F;">  R  </span> <span style="color: #080808; background-color: #5FD7AF;">  S  </span> <span style="color: #080808; background-color: #5FD7AF;">  S  </span> TRUE </span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> X7         A        2011-03-20 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;">  R  </span> <span style="color: #080808; background-color: #FF5F5F;">  R  </span> <span style="color: #080808; background-color: #5FD7AF;">  S  </span> <span style="color: #080808; background-color: #FF5F5F;">  R  </span> TRUE </span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> V1         A        2018-08-07 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;">  R  </span> <span style="color: #080808; background-color: #FF5F5F;">  R  </span> <span style="color: #080808; background-color: #5FD7AF;">  S  </span> <span style="color: #080808; background-color: #5FD7AF;">  S  </span> TRUE </span></span>
-<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 451 more rows</span></span></span>
+<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 452 more rows</span></span></span>
 <span></span>
 <span><span class="co"># even works in base R (since R 3.0):</span></span>
 <span><span class="va">our_data_1st</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu"><a href="../reference/antimicrobial_selectors.html">betalactams</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span>, <span class="op">]</span></span>
 <span><span class="co">#&gt; <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #444444;">`betalactams()`</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">AMX</span><span style="color: #0000BB;">' (amoxicillin) and '</span><span style="color: #0000BB; font-weight: bold;">AMC</span><span style="color: #0000BB;">'</span></span></span>
 <span><span class="co"><span style="color: #0000BB;">#&gt;   (amoxicillin/clavulanic acid)</span></span></span>
-<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 461 × 9</span></span></span>
+<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 462 × 9</span></span></span>
 <span><span class="co">#&gt;    patient_id hospital date       bacteria     AMX   AMC   CIP   GEN   first</span></span>
 <span><span class="co">#&gt;    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>      <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;date&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span></span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> M7         A        2013-07-22 <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN <span style="color: #080808; background-color: #FF5F5F;">  R  </span> <span style="color: #080808; background-color: #FF5F5F;">  R  </span> <span style="color: #080808; background-color: #5FD7AF;">  S  </span> <span style="color: #080808; background-color: #5FD7AF;">  S  </span> TRUE </span></span>
@@ -632,7 +632,7 @@ in:</p>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> Q2         A        2019-09-22 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;">  R  </span> <span style="color: #080808; background-color: #FF5F5F;">  R  </span> <span style="color: #080808; background-color: #5FD7AF;">  S  </span> <span style="color: #080808; background-color: #5FD7AF;">  S  </span> TRUE </span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> X7         A        2011-03-20 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;">  R  </span> <span style="color: #080808; background-color: #FF5F5F;">  R  </span> <span style="color: #080808; background-color: #5FD7AF;">  S  </span> <span style="color: #080808; background-color: #FF5F5F;">  R  </span> TRUE </span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> V1         A        2018-08-07 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;">  R  </span> <span style="color: #080808; background-color: #FF5F5F;">  R  </span> <span style="color: #080808; background-color: #5FD7AF;">  S  </span> <span style="color: #080808; background-color: #5FD7AF;">  S  </span> TRUE </span></span>
-<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 451 more rows</span></span></span></code></pre></div>
+<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 452 more rows</span></span></span></code></pre></div>
 </div>
 <div class="section level3">
 <h3 id="generate-antibiograms">Generate antibiograms<a class="anchor" aria-label="anchor" href="#generate-antibiograms"></a>
@@ -1289,7 +1289,7 @@ own:</p>
 <span><span class="co"><span style="color: #0000BB;">#&gt;   category susceptible. Set the </span><span style="color: #0000BB; background-color: #444444;">`guideline`</span><span style="color: #0000BB;"> argument or the </span><span style="color: #0000BB; background-color: #444444;">`AMR_guideline`</span></span></span>
 <span><span class="co"><span style="color: #0000BB;">#&gt;   option to either "CLSI" or "EUCAST", see </span><span style="color: #0000BB; background-color: #444444;">`?AMR-options`</span><span style="color: #0000BB;">.</span></span></span>
 <span><span class="co">#&gt; <span style="color: #0000BB;">ℹ This message will be shown once per session.</span></span></span>
-<span><span class="co">#&gt; [1] 0.4294272</span></span></code></pre></div>
+<span><span class="co">#&gt; [1] 0.4203377</span></span></code></pre></div>
 <p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and
 <code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
 <div class="sourceCode" id="cb24"><pre class="downlit sourceCode r">
@@ -1299,8 +1299,8 @@ own:</p>
 <span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 3 × 2</span></span></span>
 <span><span class="co">#&gt;   hospital amoxicillin</span></span>
 <span><span class="co">#&gt;   <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>          <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;">1</span> A              0.341</span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;">2</span> B              0.586</span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;">1</span> A              0.340</span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;">2</span> B              0.551</span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;">3</span> C              0.370</span></span></code></pre></div>
 </div>
 <div class="section level3">
--- 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 06 March 2026.
+methodology remains unchanged. This page was generated on 07 March 2026.

 ## Introduction

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

 |    date    | patient_id |        mo        | AMX | CIP |
 |:----------:|:----------:|:----------------:|:---:|:---:|
-| 2026-03-06 |    abcd    | Escherichia coli |  S  |  S  |
-| 2026-03-06 |    abcd    | Escherichia coli |  S  |  R  |
-| 2026-03-06 |    efgh    | Escherichia coli |  R  |  S  |
+| 2026-03-07 |    abcd    | Escherichia coli |  S  |  S  |
+| 2026-03-07 |    abcd    | Escherichia coli |  S  |  R  |
+| 2026-03-07 |    efgh    | Escherichia coli |  R  |  S  |

 ### Needed R packages

@@ -323,7 +323,7 @@ our_data <- our_data %>%
 #> ℹ Using column 'patient_id' as input for `col_patient_id`.
 #> ℹ Basing inclusion on all antimicrobial results, using a points threshold
 #>   of 2
-#> => Found 2,730 'phenotype-based' first isolates (91.0% of total where a
+#> => Found 2,724 'phenotype-based' first isolates (90.8% of total where a
 #>    microbial ID was available)
 ```

@@ -343,11 +343,11 @@ our_data_1st <- our_data %>%
  filter_first_isolate()
 ```

-So we end up with 2 730 isolates for analysis. Now our data looks like:
+So we end up with 2 724 isolates for analysis. Now our data looks like:

 ``` r
 our_data_1st
-#> # A tibble: 2,730 × 9
+#> # A tibble: 2,724 × 9
 #>    patient_id hospital date       bacteria     AMX   AMC   CIP   GEN   first
 #>    <chr>      <chr>    <date>     <mo>         <sir> <sir> <sir> <sir> <lgl>
 #>  1 J3         A        2012-11-21 B_ESCHR_COLI   R     I     S     S   TRUE 
@@ -360,7 +360,7 @@ our_data_1st
 #>  8 J3         A        2019-06-19 B_ESCHR_COLI   S     S     S     S   TRUE 
 #>  9 G6         A        2015-04-27 B_STPHY_AURS   S     S     S     S   TRUE 
 #> 10 P4         A        2011-06-21 B_ESCHR_COLI   S     S     S     S   TRUE 
-#> # ℹ 2,720 more rows
+#> # ℹ 2,714 more rows
 ```

 Time for the analysis.
@@ -374,29 +374,29 @@ and `sir` classes that we now have in our data set:
 ``` r
 summary(our_data_1st)
 #>   patient_id          hospital              date           
-#>  Length:2730        Length:2730        Min.   :2011-01-01  
-#>  Class :character   Class :character   1st Qu.:2013-04-06  
-#>  Mode  :character   Mode  :character   Median :2015-06-04  
+#>  Length:2724        Length:2724        Min.   :2011-01-01  
+#>  Class :character   Class :character   1st Qu.:2013-04-07  
+#>  Mode  :character   Mode  :character   Median :2015-06-03  
 #>                                        Mean   :2015-06-09  
-#>                                        3rd Qu.:2017-08-14  
+#>                                        3rd Qu.:2017-08-11  
 #>                                        Max.   :2019-12-27  
 #>    bacteria               AMX                    AMC                
 #>  Class :mo             Class:sir              Class:sir             
-#>  <NA>  :0              %S   :40.1% (n=1071)   %S   :51.1% (n=1354)  
+#>  <NA>  :0              %S   :41.6% (n=1133)   %S   :52.6% (n=1432)  
 #>  Unique:4              %SDD : 0.0% (n=0)      %SDD : 0.0% (n=0)     
-#>  #1    :B_ESCHR_COLI   %I   :17.0% (n=453)    %I   :12.7% (n=335)   
-#>  #2    :B_STPHY_AURS   %R   :42.9% (n=1147)   %R   :36.2% (n=959)   
+#>  #1    :B_ESCHR_COLI   %I   :16.4% (n=446)    %I   :12.2% (n=333)   
+#>  #2    :B_STPHY_AURS   %R   :42.0% (n=1145)   %R   :35.2% (n=959)   
 #>  #3    :B_STRPT_PNMN   %NI  : 0.0% (n=0)      %NI  : 0.0% (n=0)     
 #>     CIP                    GEN                  first        
 #>  Class:sir              Class:sir              Mode:logical  
-#>  %S   :52.2% (n=1426)   %S   :60.7% (n=1656)   TRUE:2730     
+#>  %S   :52.5% (n=1431)   %S   :61.0% (n=1661)   TRUE:2724     
 #>  %SDD : 0.0% (n=0)      %SDD : 0.0% (n=0)                    
-#>  %I   : 6.5% (n=178)    %I   : 3.0% (n=83)                   
-#>  %R   :41.2% (n=1126)   %R   :36.3% (n=991)                  
+#>  %I   : 6.5% (n=176)    %I   : 3.0% (n=82)                   
+#>  %R   :41.0% (n=1117)   %R   :36.0% (n=981)                  
 #>  %NI  : 0.0% (n=0)      %NI  : 0.0% (n=0)

 glimpse(our_data_1st)
-#> Rows: 2,730
+#> Rows: 2,724
 #> Columns: 9
 #> $ patient_id <chr> "J3", "R7", "P3", "P10", "B7", "W3", "M3", "J3", "G6", "P4"…
 #> $ hospital   <chr> "A", "A", "A", "A", "A", "A", "A", "A", "A", "A", "A", "A",…
@@ -411,7 +411,7 @@ glimpse(our_data_1st)
 # number of unique values per column:
 sapply(our_data_1st, n_distinct)
 #> patient_id   hospital       date   bacteria        AMX        AMC        CIP 
-#>        260          3       1854          4          4          4          3 
+#>        260          3       1854          4          3          3          3 
 #>        GEN      first 
 #>          3          1
 ```
@@ -438,9 +438,9 @@ our_data_1st %>%
 #> # A tibble: 4 × 2
 #>   `mo_name(bacteria)`          n
 #>   <chr>                    <int>
-#> 1 Escherichia coli          1326
-#> 2 Staphylococcus aureus      684
-#> 3 Streptococcus pneumoniae   401
+#> 1 Escherichia coli          1321
+#> 2 Staphylococcus aureus      682
+#> 3 Streptococcus pneumoniae   402
 #> 4 Klebsiella pneumoniae      319
 ```

@@ -454,7 +454,7 @@ in:
 our_data_1st %>%
  select(date, aminoglycosides())
 #> ℹ For `aminoglycosides()` using column 'GEN' (gentamicin)
-#> # A tibble: 2,730 × 2
+#> # A tibble: 2,724 × 2
 #>    date       GEN  
 #>    <date>     <sir>
 #>  1 2012-11-21   S  
@@ -467,13 +467,13 @@ our_data_1st %>%
 #>  8 2019-06-19   S  
 #>  9 2015-04-27   S  
 #> 10 2011-06-21   S  
-#> # ℹ 2,720 more rows
+#> # ℹ 2,714 more rows

 our_data_1st %>%
  select(bacteria, betalactams())
 #> ℹ For `betalactams()` using columns 'AMX' (amoxicillin) and 'AMC'
 #>   (amoxicillin/clavulanic acid)
-#> # A tibble: 2,730 × 3
+#> # A tibble: 2,724 × 3
 #>    bacteria     AMX   AMC  
 #>    <mo>         <sir> <sir>
 #>  1 B_ESCHR_COLI   R     I  
@@ -486,11 +486,11 @@ our_data_1st %>%
 #>  8 B_ESCHR_COLI   S     S  
 #>  9 B_STPHY_AURS   S     S  
 #> 10 B_ESCHR_COLI   S     S  
-#> # ℹ 2,720 more rows
+#> # ℹ 2,714 more rows

 our_data_1st %>%
  select(bacteria, where(is.sir))
-#> # A tibble: 2,730 × 5
+#> # A tibble: 2,724 × 5
 #>    bacteria     AMX   AMC   CIP   GEN  
 #>    <mo>         <sir> <sir> <sir> <sir>
 #>  1 B_ESCHR_COLI   R     I     S     S  
@@ -503,13 +503,13 @@ our_data_1st %>%
 #>  8 B_ESCHR_COLI   S     S     S     S  
 #>  9 B_STPHY_AURS   S     S     S     S  
 #> 10 B_ESCHR_COLI   S     S     S     S  
-#> # ℹ 2,720 more rows
+#> # ℹ 2,714 more rows

 # filtering using AB selectors is also possible:
 our_data_1st %>%
  filter(any(aminoglycosides() == "R"))
 #> ℹ For `aminoglycosides()` using column 'GEN' (gentamicin)
-#> # A tibble: 991 × 9
+#> # A tibble: 981 × 9
 #>    patient_id hospital date       bacteria     AMX   AMC   CIP   GEN   first
 #>    <chr>      <chr>    <date>     <mo>         <sir> <sir> <sir> <sir> <lgl>
 #>  1 J5         A        2017-12-25 B_STRPT_PNMN   R     S     S     R   TRUE 
@@ -522,13 +522,13 @@ our_data_1st %>%
 #>  8 P5         A        2019-03-09 B_STPHY_AURS   S     S     S     R   TRUE 
 #>  9 Q8         A        2019-08-10 B_STPHY_AURS   S     S     S     R   TRUE 
 #> 10 K5         A        2013-03-15 B_STRPT_PNMN   S     S     S     R   TRUE 
-#> # ℹ 981 more rows
+#> # ℹ 971 more rows

 our_data_1st %>%
  filter(all(betalactams() == "R"))
 #> ℹ For `betalactams()` using columns 'AMX' (amoxicillin) and 'AMC'
 #>   (amoxicillin/clavulanic acid)
-#> # A tibble: 461 × 9
+#> # A tibble: 462 × 9
 #>    patient_id hospital date       bacteria     AMX   AMC   CIP   GEN   first
 #>    <chr>      <chr>    <date>     <mo>         <sir> <sir> <sir> <sir> <lgl>
 #>  1 M7         A        2013-07-22 B_STRPT_PNMN   R     R     S     S   TRUE 
@@ -541,13 +541,13 @@ our_data_1st %>%
 #>  8 Q2         A        2019-09-22 B_ESCHR_COLI   R     R     S     S   TRUE 
 #>  9 X7         A        2011-03-20 B_ESCHR_COLI   R     R     S     R   TRUE 
 #> 10 V1         A        2018-08-07 B_STPHY_AURS   R     R     S     S   TRUE 
-#> # ℹ 451 more rows
+#> # ℹ 452 more rows

 # even works in base R (since R 3.0):
 our_data_1st[all(betalactams() == "R"), ]
 #> ℹ For `betalactams()` using columns 'AMX' (amoxicillin) and 'AMC'
 #>   (amoxicillin/clavulanic acid)
-#> # A tibble: 461 × 9
+#> # A tibble: 462 × 9
 #>    patient_id hospital date       bacteria     AMX   AMC   CIP   GEN   first
 #>    <chr>      <chr>    <date>     <mo>         <sir> <sir> <sir> <sir> <lgl>
 #>  1 M7         A        2013-07-22 B_STRPT_PNMN   R     R     S     S   TRUE 
@@ -560,7 +560,7 @@ our_data_1st[all(betalactams() == "R"), ]
 #>  8 Q2         A        2019-09-22 B_ESCHR_COLI   R     R     S     S   TRUE 
 #>  9 X7         A        2011-03-20 B_ESCHR_COLI   R     R     S     R   TRUE 
 #> 10 V1         A        2018-08-07 B_STPHY_AURS   R     R     S     S   TRUE 
-#> # ℹ 451 more rows
+#> # ℹ 452 more rows
 ```

 ### Generate antibiograms
@@ -848,7 +848,7 @@ our_data_1st %>% resistance(AMX)
 #>   category susceptible. Set the `guideline` argument or the `AMR_guideline`
 #>   option to either "CLSI" or "EUCAST", see `?AMR-options`.
 #> ℹ This message will be shown once per session.
-#> [1] 0.4294272
+#> [1] 0.4203377
 ```

 Or can be used in conjunction with
@@ -863,8 +863,8 @@ our_data_1st %>%
 #> # A tibble: 3 × 2
 #>   hospital amoxicillin
 #>   <chr>          <dbl>
-#> 1 A              0.341
-#> 2 B              0.586
+#> 1 A              0.340
+#> 2 B              0.551
 #> 3 C              0.370
 ```

--- 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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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">
@@ -198,7 +198,7 @@ function:</p>
 <span><span class="co">#&gt; [1] "Caryophanales"    "Enterobacterales" "Lactobacillales"  "Pseudomonadales"</span></span>
 <span><span class="co">#&gt; Importance of components:</span></span>
 <span><span class="co">#&gt;                           PC1    PC2    PC3     PC4     PC5     PC6       PC7</span></span>
-<span><span class="co">#&gt; Standard deviation     2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 9.577e-17</span></span>
+<span><span class="co">#&gt; Standard deviation     2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 1.232e-16</span></span>
 <span><span class="co">#&gt; Proportion of Variance 0.5799 0.3531 0.0471 0.01435 0.00541 0.00012 0.000e+00</span></span>
 <span><span class="co">#&gt; Cumulative Proportion  0.5799 0.9330 0.9801 0.99446 0.99988 1.00000 1.000e+00</span></span></code></pre></div>
 <pre><code><span><span class="co">#&gt; Groups (n=4, named as 'order'):</span></span>
--- a/articles/PCA.md
+++ b/articles/PCA.md
@@ -117,7 +117,7 @@ summary(pca_result)
 #> [1] "Caryophanales"    "Enterobacterales" "Lactobacillales"  "Pseudomonadales"
 #> Importance of components:
 #>                           PC1    PC2    PC3     PC4     PC5     PC6       PC7
-#> Standard deviation     2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 9.577e-17
+#> Standard deviation     2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 1.232e-16
 #> Proportion of Variance 0.5799 0.3531 0.0471 0.01435 0.00541 0.00012 0.000e+00
 #> Cumulative Proportion  0.5799 0.9330 0.9801 0.99446 0.99988 1.00000 1.000e+00
 ```
--- 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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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">06 March 2026</h4>
+            <h4 data-toc-skip class="date">07 March 2026</h4>
      
      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
      <div class="d-none name"><code>datasets.Rmd</code></div>
@@ -424,7 +424,7 @@ column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>a
 <em>iv_ddd</em>, <em>iv_units</em>, and <em>loinc</em>.</p>
 <p>This data set is in R available as <code>antimicrobials</code>, after
 you load the <code>AMR</code> package.</p>
-<p>It was last updated on 3 March 2026 14:41:08 UTC. Find more info
+<p>It was last updated on 6 March 2026 17:53:42 UTC. Find more info
 about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/antimicrobials.html">data set
 here</a>.</p>
 <p><strong>Direct download links:</strong></p>
--- a/articles/datasets.md
+++ b/articles/datasets.md
@@ -100,7 +100,7 @@ names:
 This data set is in R available as `antimicrobials`, after you load the
 `AMR` package.

-It was last updated on 3 March 2026 14:41:08 UTC. Find more info about
+It was last updated on 6 March 2026 17:53:42 UTC. Find more info about
 the contents, (scientific) source, and structure of this [data set
 here](https://amr-for-r.org/reference/antimicrobials.html).

--- 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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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/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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -49,9 +49,9 @@
    </div>

    <div class="section level2">
-<h2 class="pkg-version" data-toc-text="3.0.1.9026" id="amr-3019026">AMR 3.0.1.9026<a class="anchor" aria-label="anchor" href="#amr-3019026"></a></h2>
+<h2 class="pkg-version" data-toc-text="3.0.1.9030" id="amr-3019030">AMR 3.0.1.9030<a class="anchor" aria-label="anchor" href="#amr-3019030"></a></h2>
 <div class="section level4">
-<h4 id="new-3-0-1-9026">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9026"></a></h4>
+<h4 id="new-3-0-1-9030">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9030"></a></h4>
 <ul><li>Integration with the <strong>tidymodels</strong> framework to allow seamless use of SIR, MIC and disk data in modelling pipelines via <code>recipes</code>
 <ul><li>
 <code><a href="../reference/amr-tidymodels.html">step_mic_log2()</a></code> to transform <code>&lt;mic&gt;</code> columns with log2, and <code><a href="../reference/amr-tidymodels.html">step_sir_numeric()</a></code> to convert <code>&lt;sir&gt;</code> columns to numeric</li>
@@ -84,17 +84,22 @@
 <li>Two new <code>NA</code> objects, <code>NA_ab_</code> and <code>NA_mo_</code>, analogous to base R’s <code>NA_character_</code> and <code>NA_integer_</code>, for use in pipelines that require typed missing values</li>
 </ul></div>
 <div class="section level4">
-<h4 id="fixes-3-0-1-9026">Fixes<a class="anchor" aria-label="anchor" href="#fixes-3-0-1-9026"></a></h4>
-<ul><li>Fixed a bug in <code><a href="../reference/as.ab.html">as.ab()</a></code> where certain AB codes containing “PH” or “TH” (such as <code>ETH</code>, <code>MTH</code>, <code>PHE</code>, <code>PHN</code>, <code>STH</code>, <code>THA</code>, <code>THI1</code>) would incorrectly return <code>NA</code> when combined in a vector with any untranslatable value (<a href="https://github.com/msberends/AMR/issues/245" class="external-link">#245</a>)</li>
+<h4 id="fixes-3-0-1-9030">Fixes<a class="anchor" aria-label="anchor" href="#fixes-3-0-1-9030"></a></h4>
+<ul><li>
+<code><a href="../reference/mdro.html">mdro()</a></code>: when a base beta-lactam drug column is missing but a corresponding drug+inhibitor combination is present in the data and resistant (e.g., piperacillin/tazobactam = R while piperacillin is absent), the base drug is now correctly inferred as resistant. This ensures MDRO classification is not missed due to test-ordering differences in the laboratory. The reverse direction is also valid: susceptibility in a combination does not imply susceptibility in the base drug (the inhibitor may be responsible), so only resistance is propagated. Closes <a href="https://github.com/msberends/AMR/issues/209" class="external-link">#209</a></li>
+<li>Fixed a bug in <code><a href="../reference/as.sir.html">as.sir()</a></code> where values that were purely numeric (e.g., <code>"1"</code>) and matched the broad SIR-matching regex would be incorrectly stripped of all content by the Unicode letter filter</li>
+<li>Fixed a bug in <code><a href="../reference/as.mic.html">as.mic()</a></code> where MIC values in scientific notation (e.g., <code>"1e-3"</code>) were incorrectly handled because the letter <code>e</code> was removed along with other Unicode letters; scientific notation <code>e</code> is now preserved</li>
+<li>Fixed a bug in <code><a href="../reference/as.ab.html">as.ab()</a></code> where certain AB codes containing “PH” or “TH” (such as <code>ETH</code>, <code>MTH</code>, <code>PHE</code>, <code>PHN</code>, <code>STH</code>, <code>THA</code>, <code>THI1</code>) would incorrectly return <code>NA</code> when combined in a vector with any untranslatable value (<a href="https://github.com/msberends/AMR/issues/245" class="external-link">#245</a>)</li>
 <li>Fixed a bug in <code><a href="../reference/antibiogram.html">antibiogram()</a></code> for when no antimicrobials are set</li>
 <li>Fixed a bug in <code><a href="../reference/as.sir.html">as.sir()</a></code> where for numeric input the arguments <code>S</code>, <code>I</code>, and <code>R</code> would not be considered (<a href="https://github.com/msberends/AMR/issues/244" class="external-link">#244</a>)</li>
 <li>Fixed some foreign translations of antimicrobial drugs</li>
 <li>Fixed a bug for printing column names to the console when using <code>mutate_at(vars(...), as.mic)</code> (<a href="https://github.com/msberends/AMR/issues/249" class="external-link">#249</a>)</li>
 <li>Fixed a bug to disregard <code>NI</code> for susceptibility proportion functions</li>
 <li>Fixed Italian translation of CoNS to Stafilococco coagulasi-negativo and CoPS to Stafilococco coagulasi-positivo (<a href="https://github.com/msberends/AMR/issues/256" class="external-link">#256</a>)</li>
+<li>Fixed SIR and MIC coercion of combined values, e.g. <code>as.sir("&lt;= 0.002; S")</code> or <code>as.mic("S; 0.002")</code> (<a href="https://github.com/msberends/AMR/issues/252" class="external-link">#252</a>)</li>
 </ul></div>
 <div class="section level4">
-<h4 id="updates-3-0-1-9026">Updates<a class="anchor" aria-label="anchor" href="#updates-3-0-1-9026"></a></h4>
+<h4 id="updates-3-0-1-9030">Updates<a class="anchor" aria-label="anchor" href="#updates-3-0-1-9030"></a></h4>
 <ul><li>
 <code><a href="../reference/proportion.html">susceptibility()</a></code> and <code><a href="../reference/proportion.html">resistance()</a></code> gained the argument <code>guideline</code>, which defaults to EUCAST, for interpreting the ‘I’ category correctly.</li>
 <li>
--- a/news/index.md
+++ b/news/index.md
@@ -1,6 +1,6 @@
 # Changelog

-## AMR 3.0.1.9026
+## AMR 3.0.1.9030

 #### New

@@ -45,6 +45,24 @@

 #### Fixes

+- [`mdro()`](https://amr-for-r.org/reference/mdro.md): when a base
+  beta-lactam drug column is missing but a corresponding drug+inhibitor
+  combination is present in the data and resistant (e.g.,
+  piperacillin/tazobactam = R while piperacillin is absent), the base
+  drug is now correctly inferred as resistant. This ensures MDRO
+  classification is not missed due to test-ordering differences in the
+  laboratory. The reverse direction is also valid: susceptibility in a
+  combination does not imply susceptibility in the base drug (the
+  inhibitor may be responsible), so only resistance is propagated.
+  Closes [\#209](https://github.com/msberends/AMR/issues/209)
+- Fixed a bug in [`as.sir()`](https://amr-for-r.org/reference/as.sir.md)
+  where values that were purely numeric (e.g., `"1"`) and matched the
+  broad SIR-matching regex would be incorrectly stripped of all content
+  by the Unicode letter filter
+- Fixed a bug in [`as.mic()`](https://amr-for-r.org/reference/as.mic.md)
+  where MIC values in scientific notation (e.g., `"1e-3"`) were
+  incorrectly handled because the letter `e` was removed along with
+  other Unicode letters; scientific notation `e` is now preserved
 - Fixed a bug in [`as.ab()`](https://amr-for-r.org/reference/as.ab.md)
  where certain AB codes containing “PH” or “TH” (such as `ETH`, `MTH`,
  `PHE`, `PHN`, `STH`, `THA`, `THI1`) would incorrectly return `NA` when
@@ -64,6 +82,9 @@
 - Fixed Italian translation of CoNS to Stafilococco coagulasi-negativo
  and CoPS to Stafilococco coagulasi-positivo
  ([\#256](https://github.com/msberends/AMR/issues/256))
+- Fixed SIR and MIC coercion of combined values,
+  e.g. `as.sir("<= 0.002; S")` or `as.mic("S; 0.002")`
+  ([\#252](https://github.com/msberends/AMR/issues/252))

 #### Updates

--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -10,7 +10,7 @@ articles:
  PCA: PCA.html
  WHONET: WHONET.html
  WISCA: WISCA.html
-last_built: 2026-03-06T11:51Z
+last_built: 2026-03-07T17:10Z
 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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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/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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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 +108,7 @@


 <dt id="arg-all-groups">all_groups<a class="anchor" aria-label="anchor" href="#arg-all-groups"></a></dt>
-<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether all antimicrobial groups must be return as a vector for each input value. For example, an antibiotic in the "aminopenicillins" group, is also in the "penicillins" and "beta-lactams" groups. Setting <code>all_groups = TRUE</code> would return all three for such an antibiotic, while <code>all_groups = FALSE</code> (default) only returns the most distinctive group name.</p></dd>
+<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether all antimicrobial groups must be return as a vector for each input value. For example, an antibiotic in the "aminopenicillins" group, is also in the "penicillins" and "beta-lactams" groups. Setting <code>all_groups = TRUE</code> would return all three for such an antibiotic, while <code>all_groups = FALSE</code> (default) only returns the most specific group name.</p></dd>


 <dt id="arg-only-first">only_first<a class="anchor" aria-label="anchor" href="#arg-only-first"></a></dt>
@@ -231,6 +231,8 @@
 <span class="r-out co"><span class="r-pr">#&gt;</span> [93] "zimox"          </span>
 <span class="r-in"><span><span class="fu">ab_group</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Aminopenicillins"</span>
+<span class="r-in"><span><span class="fu">ab_group</span><span class="op">(</span><span class="st">"AMX"</span>, all_groups <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="co"># most specific to most general</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Aminopenicillins" "Penicillins"      "Beta-lactams"    </span>
 <span class="r-in"><span><span class="fu">ab_atc_group1</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Beta-lactam antibacterials, penicillins"</span>
 <span class="r-in"><span><span class="fu">ab_atc_group2</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span></span></span>
--- a/reference/ab_property.md
+++ b/reference/ab_property.md
@@ -79,7 +79,7 @@ set_ab_names(data, ..., property = "name", language = get_AMR_locale(),
  value. For example, an antibiotic in the "aminopenicillins" group, is
  also in the "penicillins" and "beta-lactams" groups. Setting
  `all_groups = TRUE` would return all three for such an antibiotic,
-  while `all_groups = FALSE` (default) only returns the most distinctive
+  while `all_groups = FALSE` (default) only returns the most specific
  group name.

 - only_first:
@@ -239,6 +239,8 @@ ab_tradenames("AMX")
 #> [93] "zimox"          
 ab_group("AMX")
 #> [1] "Aminopenicillins"
+ab_group("AMX", all_groups = TRUE) # most specific to most general
+#> [1] "Aminopenicillins" "Penicillins"      "Beta-lactams"    
 ab_atc_group1("AMX")
 #> [1] "Beta-lactam antibacterials, penicillins"
 ab_atc_group2("AMX")
--- 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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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  1980-02-27  46  46.01918         19</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2  1953-07-26  72  72.61096         46</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3  1949-09-02  76  76.50685         50</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4  1986-08-03  39  39.58904         13</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5  1932-11-19  93  93.29315         67</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6  1949-03-30  76  76.93425         50</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7  1996-06-23  29  29.70137          3</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8  1963-09-16  62  62.46849         36</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9  1952-05-16  73  73.80548         47</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1952-11-14  73  73.30685         47</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1  1999-06-30  26  26.68493          0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2  1968-01-29  58  58.10137         31</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3  1965-12-05  60  60.25205         34</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4  1980-03-01  46  46.01644         19</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5  1949-11-01  76  76.34521         50</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6  1947-02-14  79  79.05753         52</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7  1940-02-19  86  86.04384         59</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8  1988-01-10  38  38.15342         11</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9  1997-08-27  28  28.52603          2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1978-01-26  48  48.10959         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  1980-02-27  46  46.01918         19
-#> 2  1953-07-26  72  72.61096         46
-#> 3  1949-09-02  76  76.50685         50
-#> 4  1986-08-03  39  39.58904         13
-#> 5  1932-11-19  93  93.29315         67
-#> 6  1949-03-30  76  76.93425         50
-#> 7  1996-06-23  29  29.70137          3
-#> 8  1963-09-16  62  62.46849         36
-#> 9  1952-05-16  73  73.80548         47
-#> 10 1952-11-14  73  73.30685         47
+#> 1  1999-06-30  26  26.68493          0
+#> 2  1968-01-29  58  58.10137         31
+#> 3  1965-12-05  60  60.25205         34
+#> 4  1980-03-01  46  46.01644         19
+#> 5  1949-11-01  76  76.34521         50
+#> 6  1947-02-14  79  79.05753         52
+#> 7  1940-02-19  86  86.04384         59
+#> 8  1988-01-10  38  38.15342         11
+#> 9  1997-08-27  28  28.52603          2
+#> 10 1978-01-26  48  48.10959         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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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">
@@ -203,13 +203,13 @@ may affect the computations for subsequent operations.</p></dd>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 7 × 3</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   .metric     .estimator .estimate</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>       <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>          <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> accuracy    binary         0.936</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> recall      binary         0.954</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> precision   binary         0.925</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> sensitivity binary         0.954</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">5</span> specificity binary         0.917</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">6</span> ppv         binary         0.925</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">7</span> npv         binary         0.948</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> accuracy    binary         0.912</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> recall      binary         0.902</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> precision   binary         0.917</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> sensitivity binary         0.902</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">5</span> specificity binary         0.922</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">6</span> ppv         binary         0.917</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">7</span> npv         binary         0.908</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/amr-tidymodels.md
+++ b/reference/amr-tidymodels.md
@@ -182,11 +182,11 @@ if (require("tidymodels")) {
 #> # A tibble: 7 × 3
 #>   .metric     .estimator .estimate
 #>   <chr>       <chr>          <dbl>
-#> 1 accuracy    binary         0.936
-#> 2 recall      binary         0.954
-#> 3 precision   binary         0.925
-#> 4 sensitivity binary         0.954
-#> 5 specificity binary         0.917
-#> 6 ppv         binary         0.925
-#> 7 npv         binary         0.948
+#> 1 accuracy    binary         0.912
+#> 2 recall      binary         0.902
+#> 3 precision   binary         0.917
+#> 4 sensitivity binary         0.902
+#> 5 specificity binary         0.922
+#> 6 ppv         binary         0.917
+#> 7 npv         binary         0.908
 ```
--- a/reference/antibiogram.html
+++ b/reference/antibiogram.html
@@ -9,7 +9,7 @@ Adhering to previously described approaches (see Source) and especially the Baye

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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">
@@ -587,9 +587,9 @@ Adhering to previously described approaches (see Source) and especially the Baye
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Type:           WISCA with 95% CI</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   `Syndromic Group` `Piperacillin/tazobactam` Piperacillin/tazobactam + Gentam…¹</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>             <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>                     <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>                             </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical          73.5% (68.1-78.6%)        92.3% (90.8-93.8%)                </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU               57.3% (49.8-64.9%)        84.8% (82-87.7%)                  </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient        56.8% (47-67%)            74.4% (68.6-79.7%)                </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical          73.4% (68.3-78.6%)        92.3% (90.7-93.7%)                </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU               57.4% (49.7-65.4%)        84.9% (82.1-87.6%)                </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient        57% (47.4-66.7%)          74.6% (68.8-79.8%)                </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ abbreviated name: ¹`Piperacillin/tazobactam + Gentamicin`</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 1 more variable: `Piperacillin/tazobactam + Tobramycin` &lt;chr&gt;</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Use `ggplot2::autoplot()` or base R `plot()` to create a plot of this antibiogram,</span></span>
@@ -614,9 +614,9 @@ Adhering to previously described approaches (see Source) and especially the Baye
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> |Syndromic Group |Piperacillin/tazobactam |</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> |:---------------|:-----------------------|</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> |Clinical        |73.6% (68.5-78.7%)      |</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> |ICU             |57.4% (49.3-65.8%)      |</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> |Outpatient      |57% (47.1-67.3%)        |</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> |Clinical        |73.5% (68-79%)          |</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> |ICU             |57.7% (49.9-65.3%)      |</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> |Outpatient      |56.9% (46.5-66.8%)      |</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># Generate plots with ggplot2 or base R --------------------------------</span></span></span>
--- a/reference/antibiogram.md
+++ b/reference/antibiogram.md
@@ -777,9 +777,9 @@ antibiogram(example_isolates,
 #> # Type:           WISCA with 95% CI
 #>   `Syndromic Group` `Piperacillin/tazobactam` Piperacillin/tazobactam + Gentam…¹
 #>   <chr>             <chr>                     <chr>                             
-#> 1 Clinical          73.5% (68.1-78.6%)        92.3% (90.8-93.8%)                
-#> 2 ICU               57.3% (49.8-64.9%)        84.8% (82-87.7%)                  
-#> 3 Outpatient        56.8% (47-67%)            74.4% (68.6-79.7%)                
+#> 1 Clinical          73.4% (68.3-78.6%)        92.3% (90.7-93.7%)                
+#> 2 ICU               57.4% (49.7-65.4%)        84.9% (82.1-87.6%)                
+#> 3 Outpatient        57% (47.4-66.7%)          74.6% (68.8-79.8%)                
 #> # ℹ abbreviated name: ¹`Piperacillin/tazobactam + Gentamicin`
 #> # ℹ 1 more variable: `Piperacillin/tazobactam + Tobramycin` <chr>
 #> # Use `ggplot2::autoplot()` or base R `plot()` to create a plot of this antibiogram,
@@ -804,9 +804,9 @@ if (requireNamespace("knitr")) {
 #> 
 #> |Syndromic Group |Piperacillin/tazobactam |
 #> |:---------------|:-----------------------|
-#> |Clinical        |73.6% (68.5-78.7%)      |
-#> |ICU             |57.4% (49.3-65.8%)      |
-#> |Outpatient      |57% (47.1-67.3%)        |
+#> |Clinical        |73.5% (68-79%)          |
+#> |ICU             |57.7% (49.9-65.3%)      |
+#> |Outpatient      |56.9% (46.5-66.8%)      |


 # Generate plots with ggplot2 or base R --------------------------------
--- 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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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.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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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">
@@ -102,7 +102,8 @@


 <dt id="arg-keep-synonyms">keep_synonyms<a class="anchor" aria-label="anchor" href="#arg-keep-synonyms"></a></dt>
-<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. The default is <code>FALSE</code>, which will return a note if old taxonomic names were processed. The default can be set with the package option <code><a href="AMR-options.html">AMR_keep_synonyms</a></code>, i.e. <code>options(AMR_keep_synonyms = TRUE)</code> or <code>options(AMR_keep_synonyms = FALSE)</code>.</p></dd>
+<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate if outdated, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. Do note that the term "synonym" is in this case jargon from the field of microbial taxonomy - it is not in place to denote that e.g. "Streptococcus Group A" is a synonym of <em>S. pyogenes</em>. Though this is practically the case, taxonomically it is not as "Streptococcus Group A" is not even a valid taxonomic name.</p>
+<p>The default is <code>FALSE</code>, which will return a note if outdated taxonomic names were processed. The default can be set with the package option <code><a href="AMR-options.html">AMR_keep_synonyms</a></code>, i.e. <code>options(AMR_keep_synonyms = TRUE)</code> or <code>options(AMR_keep_synonyms = FALSE)</code>.</p></dd>


 <dt id="arg-reference-df">reference_df<a class="anchor" aria-label="anchor" href="#arg-reference-df"></a></dt>
@@ -126,7 +127,7 @@


 <dt id="arg-info">info<a class="anchor" aria-label="anchor" href="#arg-info"></a></dt>
-<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that info must be printed, e.g. a progress bar when more than 25 items are to be coerced, or a list with old taxonomic names. The default is <code>TRUE</code> only in interactive mode.</p></dd>
+<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that info must be printed, e.g. a progress bar when more than 25 items are to be coerced, or a list with outdated taxonomic names. The default is <code>TRUE</code> only in interactive mode.</p></dd>


 <dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
@@ -164,7 +165,7 @@
 <p>To increase the quality of matching, the <code>cleaning_regex</code> argument is used to clean the input. This must be a <a href="https://rdrr.io/r/base/regex.html" class="external-link">regular expression</a> that matches parts of the input that should be removed before the input is matched against the <a href="microorganisms.html">available microbial taxonomy</a>. It will be matched Perl-compatible and case-insensitive. The default value of <code>cleaning_regex</code> is the outcome of the helper function <code>mo_cleaning_regex()</code>.</p>
 <p>There are three helper functions that can be run after using the <code>as.mo()</code> function:</p><ul><li><p>Use <code>mo_uncertainties()</code> to get a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> that prints in a pretty format with all taxonomic names that were guessed. The output contains the matching score for all matches (see <em>Matching Score for Microorganisms</em> below).</p></li>
 <li><p>Use <code>mo_failures()</code> to get a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> <a href="https://rdrr.io/r/base/vector.html" class="external-link">vector</a> with all values that could not be coerced to a valid value.</p></li>
-<li><p>Use <code>mo_renamed()</code> to get a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with all values that could be coerced based on old, previously accepted taxonomic names.</p></li>
+<li><p>Use <code>mo_renamed()</code> to get a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with all values that could be coerced based on outdated, previously accepted taxonomic names.</p></li>
 </ul></div>

 <div class="section">
--- a/reference/as.mo.md
+++ b/reference/as.mo.md
@@ -81,11 +81,17 @@ NA_mo_

 - keep_synonyms:

-  A [logical](https://rdrr.io/r/base/logical.html) to indicate if old,
-  previously valid taxonomic names must be preserved and not be
-  corrected to currently accepted names. The default is `FALSE`, which
-  will return a note if old taxonomic names were processed. The default
-  can be set with the package option
+  A [logical](https://rdrr.io/r/base/logical.html) to indicate if
+  outdated, previously valid taxonomic names must be preserved and not
+  be corrected to currently accepted names. Do note that the term
+  "synonym" is in this case jargon from the field of microbial
+  taxonomy - it is not in place to denote that e.g. "Streptococcus Group
+  A" is a synonym of *S. pyogenes*. Though this is practically the case,
+  taxonomically it is not as "Streptococcus Group A" is not even a valid
+  taxonomic name.
+
+  The default is `FALSE`, which will return a note if outdated taxonomic
+  names were processed. The default can be set with the package option
  [`AMR_keep_synonyms`](https://amr-for-r.org/reference/AMR-options.md),
  i.e. `options(AMR_keep_synonyms = TRUE)` or
  `options(AMR_keep_synonyms = FALSE)`.
@@ -141,8 +147,8 @@ NA_mo_

  A [logical](https://rdrr.io/r/base/logical.html) to indicate that info
  must be printed, e.g. a progress bar when more than 25 items are to be
-  coerced, or a list with old taxonomic names. The default is `TRUE`
-  only in interactive mode.
+  coerced, or a list with outdated taxonomic names. The default is
+  `TRUE` only in interactive mode.

 - ...:

@@ -230,7 +236,7 @@ There are three helper functions that can be run after using the

 - Use `mo_renamed()` to get a
  [data.frame](https://rdrr.io/r/base/data.frame.html) with all values
-  that could be coerced based on old, previously accepted taxonomic
+  that could be coerced based on outdated, previously accepted taxonomic
  names.

 ### For Mycologists
--- a/reference/as.sir.html
+++ b/reference/as.sir.html
@@ -9,7 +9,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -424,10 +424,10 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4 × 18</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   datetime            index method ab_given    mo_given   host_given input_given</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span>              <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>  <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>       <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>      <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>      <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2026-03-06 <span style="color: #949494;">11:51:54</span>     1 MIC    amoxicillin Escherich… human      8          </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2026-03-06 <span style="color: #949494;">11:51:54</span>     1 MIC    cipro       Escherich… human      0.256      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2026-03-06 <span style="color: #949494;">11:51:55</span>     1 DISK   tobra       Escherich… human      16         </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2026-03-06 <span style="color: #949494;">11:51:55</span>     1 DISK   genta       Escherich… human      18         </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2026-03-07 <span style="color: #949494;">17:11:21</span>     1 MIC    amoxicillin Escherich… human      8          </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2026-03-07 <span style="color: #949494;">17:11:21</span>     1 MIC    cipro       Escherich… human      0.256      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2026-03-07 <span style="color: #949494;">17:11:22</span>     1 DISK   tobra       Escherich… human      16         </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2026-03-07 <span style="color: #949494;">17:11:22</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>
@@ -634,10 +634,8 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] S    SDD  I    R    NI   &lt;NA&gt; &lt;NA&gt; &lt;NA&gt;</span>
 <span class="r-in"><span><span class="fu">as.sir</span><span class="op">(</span><span class="st">"&lt;= 0.002; S"</span><span class="op">)</span> <span class="co"># will return "S"</span></span></span>
-<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in <span style="background-color: #444444;">`as.sir()`</span>: 1 result truncated (100%) that were invalid antimicrobial</span>
-<span class="r-wrn co"><span class="r-pr">#&gt;</span> interpretations: "&lt;= 0.002; S"</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] &lt;NA&gt;</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] S</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu">as.sir</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">2</span>, <span class="fl">3</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ in </span><span style="color: #0000BB; background-color: #444444;">`as.sir()`</span><span style="color: #0000BB;">: Interpreting input value 1 as "S", 2 as "I", and 3 as "R"</span></span>
--- a/reference/as.sir.md
+++ b/reference/as.sir.md
@@ -660,10 +660,10 @@ sir_interpretation_history()
 #> # A tibble: 4 × 18
 #>   datetime            index method ab_given    mo_given   host_given input_given
 #>   <dttm>              <int> <chr>  <chr>       <chr>      <chr>      <chr>      
-#> 1 2026-03-06 11:51:54     1 MIC    amoxicillin Escherich… human      8          
-#> 2 2026-03-06 11:51:54     1 MIC    cipro       Escherich… human      0.256      
-#> 3 2026-03-06 11:51:55     1 DISK   tobra       Escherich… human      16         
-#> 4 2026-03-06 11:51:55     1 DISK   genta       Escherich… human      18         
+#> 1 2026-03-07 17:11:21     1 MIC    amoxicillin Escherich… human      8          
+#> 2 2026-03-07 17:11:21     1 MIC    cipro       Escherich… human      0.256      
+#> 3 2026-03-07 17:11:22     1 DISK   tobra       Escherich… human      16         
+#> 4 2026-03-07 17:11:22     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>
@@ -870,10 +870,8 @@ as.sir(c("S", "SDD", "I", "R", "NI", "A", "B", "C"))
 #> Class 'sir'
 #> [1] S    SDD  I    R    NI   <NA> <NA> <NA>
 as.sir("<= 0.002; S") # will return "S"
-#> Warning: in `as.sir()`: 1 result truncated (100%) that were invalid antimicrobial
-#> interpretations: "<= 0.002; S"
 #> Class 'sir'
-#> [1] <NA>
+#> [1] S

 as.sir(c(1, 2, 3))
 #> ℹ in `as.sir()`: Interpreting input value 1 as "S", 2 as "I", and 3 as "R"
--- 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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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/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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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_eucast_rules.html
+++ b/reference/custom_eucast_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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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">
@@ -154,28 +154,27 @@
 <span class="r-in"><span><span class="va">df</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq_len</a></span><span class="op">(</span><span class="fl">2000</span><span class="op">)</span>, size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="op">]</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># indices</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   [1] 29 42  9  7 14 28 39 48 29 19 27 10 43 18 22 41 12  8 35 13  3 45  5  4 34</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [26] 37 16 22 23 16 10 41 13  2 44 18 19 38 32 22 35 39 44 38 39 11 23 25 38 26</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [51] 23 25 12 17 23 30 30 33 16 21 36 39 26 11  7  4 16 42 22 46 36 38 31 25 40</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [76]  1 44 38 23 32 44 20 22 15 14 13 42  9 37 29  6 47 24 21 23 43 19 31  1  3</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   [1] 21  7  4 46 15  6 11 27 44 25 20  8 30 25 43 33 13 46  2 44 40 15 33 46  2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [26] 32  4 19 22 45 23 45  9 44 39 16  7 46 10 34 37 45  4 20 11 14  5 19  7 40</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [51]  6 47 31  4 31 42  7 13 29 38 31 18 28  9 43 17 23 41 12  8 35 13  2 45  4</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [76]  3 34 36 15 23 24 15  9 41 12  1 44 17 18 37 32 23 35 38 44 37 38 10 24 26</span>
 <span class="r-in"><span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># TRUE/FALSE</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   [1]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE FALSE  TRUE  TRUE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [13]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [25]  TRUE  TRUE  TRUE FALSE  TRUE FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [37] FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [49] FALSE  TRUE FALSE FALSE FALSE  TRUE FALSE  TRUE FALSE  TRUE FALSE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [61]  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [73]  TRUE FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [85] FALSE FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE  TRUE FALSE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [97] FALSE FALSE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   [1]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [13]  TRUE FALSE  TRUE  TRUE  TRUE FALSE  TRUE FALSE  TRUE FALSE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [25] FALSE  TRUE FALSE  TRUE  TRUE  TRUE  TRUE FALSE  TRUE FALSE  TRUE  TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [37] FALSE FALSE  TRUE  TRUE  TRUE FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [49] FALSE FALSE FALSE  TRUE  TRUE FALSE FALSE  TRUE FALSE FALSE  TRUE  TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [61] FALSE  TRUE  TRUE FALSE FALSE  TRUE FALSE  TRUE  TRUE FALSE  TRUE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [73] FALSE FALSE FALSE  TRUE FALSE  TRUE FALSE FALSE  TRUE FALSE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [85] FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [97] FALSE FALSE FALSE  TRUE</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># filter on results from the third 60-day episode only, using base R</span></span></span>
 <span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, <span class="fl">60</span><span class="op">)</span> <span class="op">==</span> <span class="fl">3</span><span class="op">)</span>, <span class="op">]</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2 × 46</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   date       patient   age gender ward     mo           PEN   OXA   FLC   AMX  </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;date&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>  <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-11-04 304347     62 M      Clinical <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN <span style="color: #080808; background-color: #5FD7AF;">  S  </span> <span style="color: #B2B2B2;">  NA</span>  <span style="color: #B2B2B2;">  NA</span>  <span style="color: #080808; background-color: #5FD7AF;">  S  </span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2002-10-18 E55128     57 F      ICU      <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;">  R  </span> <span style="color: #B2B2B2;">  NA</span>  <span style="color: #080808; background-color: #5FD7AF;">  S  </span> <span style="color: #080808; background-color: #FF5F5F;">  R  </span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 1 × 46</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   date       patient   age gender ward  mo           PEN   OXA   FLC   AMX  </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;date&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>  <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2003-01-06 894506     83 M      ICU   <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN <span style="color: #080808; background-color: #5FD7AF;">  S  </span> <span style="color: #B2B2B2;">  NA</span>  <span style="color: #B2B2B2;">  NA</span>  <span style="color: #080808; background-color: #5FD7AF;">  S  </span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   TOB &lt;sir&gt;, AMK &lt;sir&gt;, KAN &lt;sir&gt;, TMP &lt;sir&gt;, SXT &lt;sir&gt;, NIT &lt;sir&gt;,</span></span>
@@ -209,19 +208,19 @@
 <span class="r-in"><span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">patient</span>, <span class="va">condition</span>, <span class="va">date</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 100 × 4</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups:   patient, condition [96]</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups:   patient, condition [94]</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    patient date       condition new_episode</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;date&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span>      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 022060  2004-05-04 A         TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 060287  2007-03-11 A         TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 0E2483  2007-04-06 C         TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 101305  2006-12-13 A         TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 141061  2014-10-22 A         TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 146F70  2009-08-14 A         TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 15D386  2004-08-01 B         TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 187841  2008-04-22 C         TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 195736  2008-08-29 C         TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 195736  2008-08-29 C         FALSE      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 060287  2007-03-11 A         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 0E2483  2007-11-10 A         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 101305  2006-12-13 A         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 141061  2014-10-22 A         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 151041  2006-02-10 A         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 15D386  2004-08-01 B         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 187841  2008-04-22 A         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 189363  2004-06-22 C         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 208305  2015-09-14 A         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 257844  2011-05-22 A         TRUE       </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 90 more rows</span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
@@ -235,19 +234,19 @@
 <span class="r-in"><span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">patient</span>, <span class="va">ward</span>, <span class="va">date</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 100 × 5</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups:   ward, patient [91]</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups:   ward, patient [89]</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    ward     date       patient new_index new_logical</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;date&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>       <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span>      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> ICU      2004-05-04 022060          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical 2007-03-11 060287          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Clinical 2007-04-06 0E2483          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical 2006-12-13 101305          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Clinical 2014-10-22 141061          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Clinical 2009-08-14 146F70          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> ICU      2004-08-01 15D386          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical 2008-04-22 187841          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Clinical 2008-08-29 195736          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical 2008-08-29 195736          1 FALSE      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical 2007-03-11 060287          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical 2007-11-10 0E2483          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Clinical 2006-12-13 101305          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical 2014-10-22 141061          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Clinical 2006-02-10 151041          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> ICU      2004-08-01 15D386          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Clinical 2008-04-22 187841          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical 2004-06-22 189363          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Clinical 2015-09-14 208305          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical 2011-05-22 257844          1 TRUE       </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 90 more rows</span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
@@ -263,9 +262,9 @@
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 5</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   ward       n_patients n_episodes_365 n_episodes_60 n_episodes_30</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>           <span style="color: #949494; font-style: italic;">&lt;int&gt;</span>          <span style="color: #949494; font-style: italic;">&lt;int&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;int&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical           58             13            37            44</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU                26              7            20            23</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient          7              4             6             7</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical           55             12            34            39</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU                28             10            25            26</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient          6              5             6             6</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># grouping on patients and microorganisms leads to the same</span></span></span>
 <span class="r-in"><span><span class="co"># results as first_isolate() when using 'episode-based':</span></span></span>
@@ -294,19 +293,19 @@
 <span class="r-in"><span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_data.html" class="external-link">group_vars</a></span><span class="op">(</span><span class="va">.</span><span class="op">)</span>, <span class="va">flag_episode</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 100 × 4</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups:   patient, mo, ward [96]</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>    patient mo            ward     flag_episode</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span>          <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span>       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 473F39  <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI  Clinical TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 917895  <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>CPTS  ICU      TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 022060  <span style="color: #949494;">B_</span>ENTRBC<span style="color: #949494;">_</span>CLOC ICU      TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> C36883  <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI  Clinical TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 5DF436  <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS  ICU      TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 971739  <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>CONS  Clinical TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 488175  <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI  Clinical TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 5DB1C8  <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>CPTS  Clinical TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> BC9909  <span style="color: #949494;">B_</span>ENTRBC<span style="color: #949494;">_</span>CLOC Clinical TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 5B78D5  <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS  Clinical TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups:   patient, mo, ward [93]</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>    patient mo            ward       flag_episode</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span>          <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>      <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span>       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 0E2483  <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI  Clinical   TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> F24801  <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>AGLC  ICU        TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> A26548  <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>CONS  ICU        TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 422833  <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FCLS  Clinical   TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> AFD3B1  <span style="color: #BB0000;">  UNKNOWN</span>     Clinical   TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> F35553  <span style="color: #949494;">B_</span>ENTRBC<span style="color: #949494;">_</span>CLOC ICU        TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 316893  <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>CONS  Clinical   TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> B54813  <span style="color: #949494;">B_</span>ENTRC       ICU        TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> E06844  <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS  Outpatient TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> B65162  <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN  Clinical   TRUE        </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 90 more rows</span></span>
 <span class="r-in"><span><span class="co"># }</span></span></span>
 </code></pre></div>
--- a/reference/get_episode.md
+++ b/reference/get_episode.md
@@ -178,28 +178,27 @@ x
 df <- example_isolates[sample(seq_len(2000), size = 100), ]

 get_episode(df$date, episode_days = 60) # indices
-#>   [1] 29 42  9  7 14 28 39 48 29 19 27 10 43 18 22 41 12  8 35 13  3 45  5  4 34
-#>  [26] 37 16 22 23 16 10 41 13  2 44 18 19 38 32 22 35 39 44 38 39 11 23 25 38 26
-#>  [51] 23 25 12 17 23 30 30 33 16 21 36 39 26 11  7  4 16 42 22 46 36 38 31 25 40
-#>  [76]  1 44 38 23 32 44 20 22 15 14 13 42  9 37 29  6 47 24 21 23 43 19 31  1  3
+#>   [1] 21  7  4 46 15  6 11 27 44 25 20  8 30 25 43 33 13 46  2 44 40 15 33 46  2
+#>  [26] 32  4 19 22 45 23 45  9 44 39 16  7 46 10 34 37 45  4 20 11 14  5 19  7 40
+#>  [51]  6 47 31  4 31 42  7 13 29 38 31 18 28  9 43 17 23 41 12  8 35 13  2 45  4
+#>  [76]  3 34 36 15 23 24 15  9 41 12  1 44 17 18 37 32 23 35 38 44 37 38 10 24 26
 is_new_episode(df$date, episode_days = 60) # TRUE/FALSE
-#>   [1]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE FALSE  TRUE  TRUE  TRUE
-#>  [13]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE
-#>  [25]  TRUE  TRUE  TRUE FALSE  TRUE FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE
-#>  [37] FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE  TRUE
-#>  [49] FALSE  TRUE FALSE FALSE FALSE  TRUE FALSE  TRUE FALSE  TRUE FALSE  TRUE
-#>  [61]  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE
-#>  [73]  TRUE FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE  TRUE
-#>  [85] FALSE FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE  TRUE FALSE FALSE FALSE
-#>  [97] FALSE FALSE FALSE FALSE
+#>   [1]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE
+#>  [13]  TRUE FALSE  TRUE  TRUE  TRUE FALSE  TRUE FALSE  TRUE FALSE FALSE FALSE
+#>  [25] FALSE  TRUE FALSE  TRUE  TRUE  TRUE  TRUE FALSE  TRUE FALSE  TRUE  TRUE
+#>  [37] FALSE FALSE  TRUE  TRUE  TRUE FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE
+#>  [49] FALSE FALSE FALSE  TRUE  TRUE FALSE FALSE  TRUE FALSE FALSE  TRUE  TRUE
+#>  [61] FALSE  TRUE  TRUE FALSE FALSE  TRUE FALSE  TRUE  TRUE FALSE  TRUE FALSE
+#>  [73] FALSE FALSE FALSE  TRUE FALSE  TRUE FALSE FALSE  TRUE FALSE FALSE FALSE
+#>  [85] FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
+#>  [97] FALSE FALSE FALSE  TRUE

 # filter on results from the third 60-day episode only, using base R
 df[which(get_episode(df$date, 60) == 3), ]
-#> # A tibble: 2 × 46
-#>   date       patient   age gender ward     mo           PEN   OXA   FLC   AMX  
-#>   <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir>
-#> 1 2002-11-04 304347     62 M      Clinical B_STRPT_PNMN   S     NA    NA    S  
-#> 2 2002-10-18 E55128     57 F      ICU      B_STPHY_AURS   R     NA    S     R  
+#> # A tibble: 1 × 46
+#>   date       patient   age gender ward  mo           PEN   OXA   FLC   AMX  
+#>   <date>     <chr>   <dbl> <chr>  <chr> <mo>         <sir> <sir> <sir> <sir>
+#> 1 2003-01-06 894506     83 M      ICU   B_STRPT_PNMN   S     NA    NA    S  
 #> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>,
 #> #   CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>,
 #> #   TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>,
@@ -233,19 +232,19 @@ if (require("dplyr")) {
    arrange(patient, condition, date)
 }
 #> # A tibble: 100 × 4
-#> # Groups:   patient, condition [96]
+#> # Groups:   patient, condition [94]
 #>    patient date       condition new_episode
 #>    <chr>   <date>     <chr>     <lgl>      
-#>  1 022060  2004-05-04 A         TRUE       
-#>  2 060287  2007-03-11 A         TRUE       
-#>  3 0E2483  2007-04-06 C         TRUE       
-#>  4 101305  2006-12-13 A         TRUE       
-#>  5 141061  2014-10-22 A         TRUE       
-#>  6 146F70  2009-08-14 A         TRUE       
-#>  7 15D386  2004-08-01 B         TRUE       
-#>  8 187841  2008-04-22 C         TRUE       
-#>  9 195736  2008-08-29 C         TRUE       
-#> 10 195736  2008-08-29 C         FALSE      
+#>  1 060287  2007-03-11 A         TRUE       
+#>  2 0E2483  2007-11-10 A         TRUE       
+#>  3 101305  2006-12-13 A         TRUE       
+#>  4 141061  2014-10-22 A         TRUE       
+#>  5 151041  2006-02-10 A         TRUE       
+#>  6 15D386  2004-08-01 B         TRUE       
+#>  7 187841  2008-04-22 A         TRUE       
+#>  8 189363  2004-06-22 C         TRUE       
+#>  9 208305  2015-09-14 A         TRUE       
+#> 10 257844  2011-05-22 A         TRUE       
 #> # ℹ 90 more rows

 if (require("dplyr")) {
@@ -259,19 +258,19 @@ if (require("dplyr")) {
    arrange(patient, ward, date)
 }
 #> # A tibble: 100 × 5
-#> # Groups:   ward, patient [91]
+#> # Groups:   ward, patient [89]
 #>    ward     date       patient new_index new_logical
 #>    <chr>    <date>     <chr>       <int> <lgl>      
-#>  1 ICU      2004-05-04 022060          1 TRUE       
-#>  2 Clinical 2007-03-11 060287          1 TRUE       
-#>  3 Clinical 2007-04-06 0E2483          1 TRUE       
-#>  4 Clinical 2006-12-13 101305          1 TRUE       
-#>  5 Clinical 2014-10-22 141061          1 TRUE       
-#>  6 Clinical 2009-08-14 146F70          1 TRUE       
-#>  7 ICU      2004-08-01 15D386          1 TRUE       
-#>  8 Clinical 2008-04-22 187841          1 TRUE       
-#>  9 Clinical 2008-08-29 195736          1 TRUE       
-#> 10 Clinical 2008-08-29 195736          1 FALSE      
+#>  1 Clinical 2007-03-11 060287          1 TRUE       
+#>  2 Clinical 2007-11-10 0E2483          1 TRUE       
+#>  3 Clinical 2006-12-13 101305          1 TRUE       
+#>  4 Clinical 2014-10-22 141061          1 TRUE       
+#>  5 Clinical 2006-02-10 151041          1 TRUE       
+#>  6 ICU      2004-08-01 15D386          1 TRUE       
+#>  7 Clinical 2008-04-22 187841          1 TRUE       
+#>  8 Clinical 2004-06-22 189363          1 TRUE       
+#>  9 Clinical 2015-09-14 208305          1 TRUE       
+#> 10 Clinical 2011-05-22 257844          1 TRUE       
 #> # ℹ 90 more rows

 if (require("dplyr")) {
@@ -287,9 +286,9 @@ if (require("dplyr")) {
 #> # A tibble: 3 × 5
 #>   ward       n_patients n_episodes_365 n_episodes_60 n_episodes_30
 #>   <chr>           <int>          <int>         <int>         <int>
-#> 1 Clinical           58             13            37            44
-#> 2 ICU                26              7            20            23
-#> 3 Outpatient          7              4             6             7
+#> 1 Clinical           55             12            34            39
+#> 2 ICU                28             10            25            26
+#> 3 Outpatient          6              5             6             6

 # grouping on patients and microorganisms leads to the same
 # results as first_isolate() when using 'episode-based':
@@ -318,19 +317,19 @@ if (require("dplyr")) {
    select(group_vars(.), flag_episode)
 }
 #> # A tibble: 100 × 4
-#> # Groups:   patient, mo, ward [96]
-#>    patient mo            ward     flag_episode
-#>    <chr>   <mo>          <chr>    <lgl>       
-#>  1 473F39  B_ESCHR_COLI  Clinical TRUE        
-#>  2 917895  B_STPHY_CPTS  ICU      TRUE        
-#>  3 022060  B_ENTRBC_CLOC ICU      TRUE        
-#>  4 C36883  B_ESCHR_COLI  Clinical TRUE        
-#>  5 5DF436  B_STPHY_AURS  ICU      TRUE        
-#>  6 971739  B_STPHY_CONS  Clinical TRUE        
-#>  7 488175  B_ESCHR_COLI  Clinical TRUE        
-#>  8 5DB1C8  B_STPHY_CPTS  Clinical TRUE        
-#>  9 BC9909  B_ENTRBC_CLOC Clinical TRUE        
-#> 10 5B78D5  B_STPHY_AURS  Clinical TRUE        
+#> # Groups:   patient, mo, ward [93]
+#>    patient mo            ward       flag_episode
+#>    <chr>   <mo>          <chr>      <lgl>       
+#>  1 0E2483  B_ESCHR_COLI  Clinical   TRUE        
+#>  2 F24801  B_STRPT_AGLC  ICU        TRUE        
+#>  3 A26548  B_STPHY_CONS  ICU        TRUE        
+#>  4 422833  B_ENTRC_FCLS  Clinical   TRUE        
+#>  5 AFD3B1    UNKNOWN     Clinical   TRUE        
+#>  6 F35553  B_ENTRBC_CLOC ICU        TRUE        
+#>  7 316893  B_STPHY_CONS  Clinical   TRUE        
+#>  8 B54813  B_ENTRC       ICU        TRUE        
+#>  9 E06844  B_STPHY_AURS  Outpatient TRUE        
+#> 10 B65162  B_STRPT_PNMN  Clinical   TRUE        
 #> # ℹ 90 more rows
 # }
 ```
--- 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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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
@@ -13,7 +13,7 @@ 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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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/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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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">
@@ -91,9 +91,9 @@
    <div class="section level2">
    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2.985485</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2.985614</span>
 <span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span>, excess <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.01413942</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.01547453</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/kurtosis.md
+++ b/reference/kurtosis.md
@@ -45,7 +45,7 @@ kurtosis(x, na.rm = FALSE, excess = FALSE)

 ``` r
 kurtosis(rnorm(10000))
-#> [1] 2.985485
+#> [1] 2.985614
 kurtosis(rnorm(10000), excess = TRUE)
-#> [1] 0.01413942
+#> [1] 0.01547453
 ```
--- 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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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">
@@ -110,31 +110,31 @@
    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">sir</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_sir</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">sir</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] R I R I I S R S I I</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] S R S R I I R R R S</span>
 <span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">sir</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1]  1.449138 -0.621059  1.449138 -0.621059 -0.621059 -0.621059  1.449138</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [8] -0.621059 -0.621059 -0.621059</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] -0.9486833  0.9486833 -0.9486833  0.9486833 -0.9486833 -0.9486833</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [7]  0.9486833  0.9486833  0.9486833 -0.9486833</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">mic</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">mic</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 0.25     0.5      8        2        0.004    4        1        0.001   </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [9] 0.004    &lt;=0.0005</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 0.5      &lt;=0.0001 0.25     0.0005   0.001    0.0002   8        &lt;=0.0001</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [9] &lt;=0.0001 0.004   </span>
 <span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">mic</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1]  0.2626139  0.4520471  1.2097801  0.8309136 -0.8675039  1.0203468</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [7]  0.6414804 -1.2463704 -0.8675039 -1.4358036</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1]  1.18999891 -0.86809178  1.02250714 -0.47918793 -0.31169616 -0.70060001</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [7]  1.85996599 -0.86809178 -0.86809178  0.02328738</span>
 <span class="r-in"><span><span class="co"># equal to the Z-score of their log2:</span></span></span>
 <span class="r-in"><span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span> <span class="op">-</span> <span class="fu"><a href="https://rdrr.io/r/base/mean.html" class="external-link">mean</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="fu"><a href="https://rdrr.io/r/stats/sd.html" class="external-link">sd</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1]  0.2626139  0.4520471  1.2097801  0.8309136 -0.8675039  1.0203468</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [7]  0.6414804 -1.2463704 -0.8675039 -1.4358036</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1]  1.18999891 -0.86809178  1.02250714 -0.47918793 -0.31169616 -0.70060001</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [7]  1.85996599 -0.86809178 -0.86809178  0.02328738</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">disk</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_disk</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">disk</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 49 38 33 31 17 42 43 46 37 46</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 20 45 31 26 23 38 44 41 20 49</span>
 <span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">disk</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1]  1.14152462 -0.02113934 -0.54962296 -0.76101641 -2.24077054  0.40164755</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [7]  0.50734427  0.82443445 -0.12683607  0.82443445</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] -1.2414143  1.0239402 -0.2446583 -0.6977292 -0.9695717  0.3896410</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [7]  0.9333261  0.6614835 -1.2414143  1.3863970</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">y</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
 <span class="r-in"><span>  id <span class="op">=</span> <span class="va">LETTERS</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span></span>
@@ -145,35 +145,35 @@
 <span class="r-in"><span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">y</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    id amox cipr gent tobr</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1   A    S   28  &gt;=2    8</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2   B    R   33    1    8</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3   C    R   32    1    8</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4   D    I   25    1   16</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5   E    I   19  0.5   16</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6   F    S   23  0.5    8</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7   G    R   27  0.5   16</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8   H    S   29  0.5    8</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9   I    R   32    1    8</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10  J    R   32  0.5   16</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1   A    R   33   16  &lt;=1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2   B    S   32  &lt;=8   32</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3   C    S   27   16   32</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4   D    I   33  &lt;=8    8</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5   E    I   22  &lt;=8    2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6   F    R   32  &lt;=8    4</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7   G    S   31   16    8</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8   H    I   31  &lt;=8  &lt;=1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9   I    R   28   16    2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10  J    S   22   16    4</span>
 <span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">  and "tobr"</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1]  0.06974787  0.45859464  0.40418392  0.03309016 -0.65092262 -0.91740267</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [7]  0.25870477 -0.59093836  0.40418392  0.53075837</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1]  0.52677313  0.16501937  0.34372779 -0.05155946 -0.97765805  0.26901032</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [7]  0.30452889 -0.58337098  0.36899264 -0.36546366</span>
 <span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op">&lt;-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu"><a href="as.mic.html">is.mic</a></span><span class="op">(</span><span class="va">y</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Calculating mean AMR distance based on columns "gent" and "tobr"</span></span>
 <span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    id amox cipr gent tobr amr_distance</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6   F    S   23  0.5    8   -0.8163565</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8   H    S   29  0.5    8   -0.8163565</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2   B    R   33    1    8   -0.1012596</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3   C    R   32    1    8   -0.1012596</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9   I    R   32    1    8   -0.1012596</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5   E    I   19  0.5   16    0.1518893</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7   G    R   27  0.5   16    0.1518893</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10  J    R   32  0.5   16    0.1518893</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1   A    S   28  &gt;=2    8    0.6138374</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4   D    I   25    1   16    0.8669863</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8   H    I   31  &lt;=8  &lt;=1   -1.0808937</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5   E    I   22  &lt;=8    2   -0.8051882</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6   F    R   32  &lt;=8    4   -0.5294827</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4   D    I   33  &lt;=8    8   -0.2537773</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1   A    R   33   16  &lt;=1   -0.1322104</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9   I    R   28   16    2    0.1434951</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2   B    S   32  &lt;=8   32    0.2976337</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10  J    S   22   16    4    0.4192006</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7   G    S   31   16    8    0.6949060</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3   C    S   27   16   32    1.2463170</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="va">y</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@@ -186,16 +186,16 @@
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">  and "tobr"</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    id amox cipr gent tobr amr_distance check_id_C</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1   C    R   32    1    8   0.40418392 0.00000000</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2   I    R   32    1    8   0.40418392 0.00000000</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3   B    R   33    1    8   0.45859464 0.05441072</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4   J    R   32  0.5   16   0.53075837 0.12657445</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5   G    R   27  0.5   16   0.25870477 0.14547915</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6   A    S   28  &gt;=2    8   0.06974787 0.33443605</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7   D    I   25    1   16   0.03309016 0.37109376</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8   H    S   29  0.5    8  -0.59093836 0.99512228</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9   E    I   19  0.5   16  -0.65092262 1.05510655</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10  F    S   23  0.5    8  -0.91740267 1.32158659</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1   C    S   27   16   32   0.34372779 0.00000000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2   I    R   28   16    2   0.36899264 0.02526485</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3   G    S   31   16    8   0.30452889 0.03919890</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4   F    R   32  &lt;=8    4   0.26901032 0.07471748</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5   B    S   32  &lt;=8   32   0.16501937 0.17870842</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6   A    R   33   16  &lt;=1   0.52677313 0.18304534</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7   D    I   33  &lt;=8    8  -0.05155946 0.39528726</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8   J    S   22   16    4  -0.36546366 0.70919145</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9   H    I   31  &lt;=8  &lt;=1  -0.58337098 0.92709877</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10  E    I   22  &lt;=8    2  -0.97765805 1.32138584</span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="co"># support for groups</span></span></span>
 <span class="r-in"><span>  <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
--- a/reference/mean_amr_distance.md
+++ b/reference/mean_amr_distance.md
@@ -85,31 +85,31 @@ suspicious.
 sir <- random_sir(10)
 sir
 #> Class 'sir'
-#>  [1] R I R I I S R S I I
+#>  [1] S R S R I I R R R S
 mean_amr_distance(sir)
-#>  [1]  1.449138 -0.621059  1.449138 -0.621059 -0.621059 -0.621059  1.449138
-#>  [8] -0.621059 -0.621059 -0.621059
+#>  [1] -0.9486833  0.9486833 -0.9486833  0.9486833 -0.9486833 -0.9486833
+#>  [7]  0.9486833  0.9486833  0.9486833 -0.9486833

 mic <- random_mic(10)
 mic
 #> Class 'mic'
-#>  [1] 0.25     0.5      8        2        0.004    4        1        0.001   
-#>  [9] 0.004    <=0.0005
+#>  [1] 0.5      <=0.0001 0.25     0.0005   0.001    0.0002   8        <=0.0001
+#>  [9] <=0.0001 0.004   
 mean_amr_distance(mic)
-#>  [1]  0.2626139  0.4520471  1.2097801  0.8309136 -0.8675039  1.0203468
-#>  [7]  0.6414804 -1.2463704 -0.8675039 -1.4358036
+#>  [1]  1.18999891 -0.86809178  1.02250714 -0.47918793 -0.31169616 -0.70060001
+#>  [7]  1.85996599 -0.86809178 -0.86809178  0.02328738
 # equal to the Z-score of their log2:
 (log2(mic) - mean(log2(mic))) / sd(log2(mic))
-#>  [1]  0.2626139  0.4520471  1.2097801  0.8309136 -0.8675039  1.0203468
-#>  [7]  0.6414804 -1.2463704 -0.8675039 -1.4358036
+#>  [1]  1.18999891 -0.86809178  1.02250714 -0.47918793 -0.31169616 -0.70060001
+#>  [7]  1.85996599 -0.86809178 -0.86809178  0.02328738

 disk <- random_disk(10)
 disk
 #> Class 'disk'
-#>  [1] 49 38 33 31 17 42 43 46 37 46
+#>  [1] 20 45 31 26 23 38 44 41 20 49
 mean_amr_distance(disk)
-#>  [1]  1.14152462 -0.02113934 -0.54962296 -0.76101641 -2.24077054  0.40164755
-#>  [7]  0.50734427  0.82443445 -0.12683607  0.82443445
+#>  [1] -1.2414143  1.0239402 -0.2446583 -0.6977292 -0.9695717  0.3896410
+#>  [7]  0.9333261  0.6614835 -1.2414143  1.3863970

 y <- data.frame(
  id = LETTERS[1:10],
@@ -120,35 +120,35 @@ y <- data.frame(
 )
 y
 #>    id amox cipr gent tobr
-#> 1   A    S   28  >=2    8
-#> 2   B    R   33    1    8
-#> 3   C    R   32    1    8
-#> 4   D    I   25    1   16
-#> 5   E    I   19  0.5   16
-#> 6   F    S   23  0.5    8
-#> 7   G    R   27  0.5   16
-#> 8   H    S   29  0.5    8
-#> 9   I    R   32    1    8
-#> 10  J    R   32  0.5   16
+#> 1   A    R   33   16  <=1
+#> 2   B    S   32  <=8   32
+#> 3   C    S   27   16   32
+#> 4   D    I   33  <=8    8
+#> 5   E    I   22  <=8    2
+#> 6   F    R   32  <=8    4
+#> 7   G    S   31   16    8
+#> 8   H    I   31  <=8  <=1
+#> 9   I    R   28   16    2
+#> 10  J    S   22   16    4
 mean_amr_distance(y)
 #> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",
 #>   and "tobr"
-#>  [1]  0.06974787  0.45859464  0.40418392  0.03309016 -0.65092262 -0.91740267
-#>  [7]  0.25870477 -0.59093836  0.40418392  0.53075837
+#>  [1]  0.52677313  0.16501937  0.34372779 -0.05155946 -0.97765805  0.26901032
+#>  [7]  0.30452889 -0.58337098  0.36899264 -0.36546366
 y$amr_distance <- mean_amr_distance(y, is.mic(y))
 #> ℹ Calculating mean AMR distance based on columns "gent" and "tobr"
 y[order(y$amr_distance), ]
 #>    id amox cipr gent tobr amr_distance
-#> 6   F    S   23  0.5    8   -0.8163565
-#> 8   H    S   29  0.5    8   -0.8163565
-#> 2   B    R   33    1    8   -0.1012596
-#> 3   C    R   32    1    8   -0.1012596
-#> 9   I    R   32    1    8   -0.1012596
-#> 5   E    I   19  0.5   16    0.1518893
-#> 7   G    R   27  0.5   16    0.1518893
-#> 10  J    R   32  0.5   16    0.1518893
-#> 1   A    S   28  >=2    8    0.6138374
-#> 4   D    I   25    1   16    0.8669863
+#> 8   H    I   31  <=8  <=1   -1.0808937
+#> 5   E    I   22  <=8    2   -0.8051882
+#> 6   F    R   32  <=8    4   -0.5294827
+#> 4   D    I   33  <=8    8   -0.2537773
+#> 1   A    R   33   16  <=1   -0.1322104
+#> 9   I    R   28   16    2    0.1434951
+#> 2   B    S   32  <=8   32    0.2976337
+#> 10  J    S   22   16    4    0.4192006
+#> 7   G    S   31   16    8    0.6949060
+#> 3   C    S   27   16   32    1.2463170

 if (require("dplyr")) {
  y %>%
@@ -161,16 +161,16 @@ if (require("dplyr")) {
 #> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",
 #>   and "tobr"
 #>    id amox cipr gent tobr amr_distance check_id_C
-#> 1   C    R   32    1    8   0.40418392 0.00000000
-#> 2   I    R   32    1    8   0.40418392 0.00000000
-#> 3   B    R   33    1    8   0.45859464 0.05441072
-#> 4   J    R   32  0.5   16   0.53075837 0.12657445
-#> 5   G    R   27  0.5   16   0.25870477 0.14547915
-#> 6   A    S   28  >=2    8   0.06974787 0.33443605
-#> 7   D    I   25    1   16   0.03309016 0.37109376
-#> 8   H    S   29  0.5    8  -0.59093836 0.99512228
-#> 9   E    I   19  0.5   16  -0.65092262 1.05510655
-#> 10  F    S   23  0.5    8  -0.91740267 1.32158659
+#> 1   C    S   27   16   32   0.34372779 0.00000000
+#> 2   I    R   28   16    2   0.36899264 0.02526485
+#> 3   G    S   31   16    8   0.30452889 0.03919890
+#> 4   F    R   32  <=8    4   0.26901032 0.07471748
+#> 5   B    S   32  <=8   32   0.16501937 0.17870842
+#> 6   A    R   33   16  <=1   0.52677313 0.18304534
+#> 7   D    I   33  <=8    8  -0.05155946 0.39528726
+#> 8   J    S   22   16    4  -0.36546366 0.70919145
+#> 9   H    I   31  <=8  <=1  -0.58337098 0.92709877
+#> 10  E    I   22  <=8    2  -0.97765805 1.32138584
 if (require("dplyr")) {
  # support for groups
  example_isolates %>%
--- 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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -179,7 +179,8 @@


 <dt id="arg-keep-synonyms">keep_synonyms<a class="anchor" aria-label="anchor" href="#arg-keep-synonyms"></a></dt>
-<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. The default is <code>FALSE</code>, which will return a note if old taxonomic names were processed. The default can be set with the package option <code><a href="AMR-options.html">AMR_keep_synonyms</a></code>, i.e. <code>options(AMR_keep_synonyms = TRUE)</code> or <code>options(AMR_keep_synonyms = FALSE)</code>.</p></dd>
+<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate if outdated, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. Do note that the term "synonym" is in this case jargon from the field of microbial taxonomy - it is not in place to denote that e.g. "Streptococcus Group A" is a synonym of <em>S. pyogenes</em>. Though this is practically the case, taxonomically it is not as "Streptococcus Group A" is not even a valid taxonomic name.</p>
+<p>The default is <code>FALSE</code>, which will return a note if outdated taxonomic names were processed. The default can be set with the package option <code><a href="AMR-options.html">AMR_keep_synonyms</a></code>, i.e. <code>options(AMR_keep_synonyms = TRUE)</code> or <code>options(AMR_keep_synonyms = FALSE)</code>.</p></dd>


 <dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
@@ -367,7 +368,7 @@
 <span class="r-in"><span><span class="fu">mo_mycobank</span><span class="op">(</span><span class="st">"Candida krusei"</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "337013"</span>
 <span class="r-in"><span><span class="fu">mo_mycobank</span><span class="op">(</span><span class="st">"Candida krusei"</span>, keep_synonyms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
-<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Function <span style="background-color: #444444;">`as.mo()`</span> returned one old taxonomic name. Use <span style="background-color: #444444;">`as.mo(...,</span></span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Function <span style="background-color: #444444;">`as.mo()`</span> returned one outdated taxonomic name. Use <span style="background-color: #444444;">`as.mo(...,</span></span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="background-color: #444444;">keep_synonyms = FALSE)`</span> to clean the input to currently accepted taxonomic</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> names, or set the R option <span style="background-color: #444444;">`AMR_keep_synonyms`</span> to <span style="background-color: #444444;">`FALSE`</span>. This warning</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> will be shown once per session.</span>
--- a/reference/mo_property.md
+++ b/reference/mo_property.md
@@ -139,11 +139,17 @@ mo_property(x, property = "fullname", language = get_AMR_locale(),

 - keep_synonyms:

-  A [logical](https://rdrr.io/r/base/logical.html) to indicate if old,
-  previously valid taxonomic names must be preserved and not be
-  corrected to currently accepted names. The default is `FALSE`, which
-  will return a note if old taxonomic names were processed. The default
-  can be set with the package option
+  A [logical](https://rdrr.io/r/base/logical.html) to indicate if
+  outdated, previously valid taxonomic names must be preserved and not
+  be corrected to currently accepted names. Do note that the term
+  "synonym" is in this case jargon from the field of microbial
+  taxonomy - it is not in place to denote that e.g. "Streptococcus Group
+  A" is a synonym of *S. pyogenes*. Though this is practically the case,
+  taxonomically it is not as "Streptococcus Group A" is not even a valid
+  taxonomic name.
+
+  The default is `FALSE`, which will return a note if outdated taxonomic
+  names were processed. The default can be set with the package option
  [`AMR_keep_synonyms`](https://amr-for-r.org/reference/AMR-options.md),
  i.e. `options(AMR_keep_synonyms = TRUE)` or
  `options(AMR_keep_synonyms = FALSE)`.
@@ -479,7 +485,7 @@ mo_mycobank("Candida albicans")
 mo_mycobank("Candida krusei")
 #> [1] "337013"
 mo_mycobank("Candida krusei", keep_synonyms = TRUE)
-#> Warning: Function `as.mo()` returned one old taxonomic name. Use `as.mo(...,
+#> Warning: Function `as.mo()` returned one outdated taxonomic name. Use `as.mo(...,
 #> keep_synonyms = FALSE)` to clean the input to currently accepted taxonomic
 #> names, or set the R option `AMR_keep_synonyms` to `FALSE`. This warning
 #> will be shown once per session.
--- 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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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-1.png
+++ b/reference/plot-1.png
--- a/reference/plot-10.png
+++ b/reference/plot-10.png
--- a/reference/plot-12.png
+++ b/reference/plot-12.png
--- a/reference/plot-13.png
+++ b/reference/plot-13.png
--- a/reference/plot-14.png
+++ b/reference/plot-14.png
--- a/reference/plot-15.png
+++ b/reference/plot-15.png
--- a/reference/plot-16.png
+++ b/reference/plot-16.png
--- a/reference/plot-17.png
+++ b/reference/plot-17.png
--- a/reference/plot-18.png
+++ b/reference/plot-18.png
--- a/reference/plot-19.png
+++ b/reference/plot-19.png
--- a/reference/plot-2.png
+++ b/reference/plot-2.png
--- a/Show More
+++ b/Show More