Built site for AMR: 2.1.0.9002@7cda9e5

2023-10-20 13:01:19 +00:00 · 2023-10-20 13:01:19 +00:00 · 8c3ab46914
parent 9f32027abc
commit 8c3ab46914
92 changed files with 345 additions and 337 deletions
--- a/404.html
+++ b/404.html
@ -36,7 +36,7 @@
    <a class="navbar-brand me-2" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/LICENSE-text.html
+++ b/LICENSE-text.html
@ -10,7 +10,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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
@ -38,7 +38,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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">
@ -204,7 +204,7 @@
 website update since they are based on randomly created values and the
 page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
 Markdown</a>. However, the methodology remains unchanged. This page was
-generated on 20 July 2023.</p>
+generated on 20 October 2023.</p>
 <div class="section level2">
 <h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
 </h2>
@ -260,21 +260,21 @@ make the structure of your data generally look like this:</p>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2023-07-20</td>
+<td align="center">2023-10-20</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">2023-07-20</td>
+<td align="center">2023-10-20</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">2023-07-20</td>
+<td align="center">2023-10-20</td>
 <td align="center">efgh</td>
 <td align="center">Escherichia coli</td>
 <td align="center">R</td>
@ -515,9 +515,9 @@ the methods on the <code><a href="../reference/first_isolate.html">first_isolate
 <span><span class="co">#&gt; ℹ Using column 'patient_id' as input for col_patient_id.</span></span>
 <span><span class="co">#&gt; ℹ Basing inclusion on all antimicrobial results, using a points threshold</span></span>
 <span><span class="co">#&gt;   of 2</span></span>
-<span><span class="co">#&gt; =&gt; Found 2,626 'phenotype-based' first isolates (87.6% within scope and</span></span>
+<span><span class="co">#&gt; =&gt; Found 2,712 'phenotype-based' first isolates (90.4% of total where a</span></span>
-<span><span class="co">#&gt;    87.5% of total where a microbial ID was available)</span></span></code></pre></div>
+<span><span class="co">#&gt;    microbial ID was available)</span></span></code></pre></div>
-<p>So only 88% is suitable for resistance analysis! We can now filter on
+<p>So only 90% 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
 <code>dplyr</code> package:</p>
 <div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
@ -527,11 +527,11 @@ 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 2 626 isolates for analysis. Now our data looks
+<p>So we end up with 2 712 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: 2,626 × 9</span></span></span>
+<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,712 × 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 B_ESCHR_COLI R     I     S     S     TRUE </span></span>
@ -539,12 +539,12 @@ like:</p>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> P10        A        2015-12-10 B_ESCHR_COLI S     I     S     S     TRUE </span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> B7         A        2015-03-02 B_ESCHR_COLI S     S     S     S     TRUE </span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> W3         A        2018-03-31 B_STPHY_AURS R     S     R     S     TRUE </span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> J8         A        2016-06-14 B_ESCHR_COLI R     S     S     S     TRUE </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> M3         A        2015-10-25 B_ESCHR_COLI R     S     S     S     TRUE </span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> M3         A        2015-10-25 B_ESCHR_COLI R     S     S     S     TRUE </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> J3         A        2019-06-19 B_ESCHR_COLI S     S     S     S     TRUE </span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> J3         A        2019-06-19 B_ESCHR_COLI S     S     S     S     TRUE </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> G6         A        2015-04-27 B_STPHY_AURS S     S     S     S     TRUE </span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> G6         A        2015-04-27 B_STPHY_AURS S     S     S     S     TRUE </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> P4         A        2011-06-21 B_ESCHR_COLI S     S     S     S     TRUE </span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> P4         A        2011-06-21 B_ESCHR_COLI S     S     S     S     TRUE </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> Z1         A        2014-09-05 B_ESCHR_COLI S     S     S     S     TRUE </span></span>
-<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,616 more rows</span></span></span></code></pre></div>
+<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,702 more rows</span></span></span></code></pre></div>
 <p>Time for the analysis.</p>
 </div>
 </div>
@ -557,44 +557,44 @@ 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:2626        Length:2626        Min.   :2011-01-01  </span></span>
+<span><span class="co">#&gt;  Length:2712        Length:2712        Min.   :2011-01-01  </span></span>
-<span><span class="co">#&gt;  Class :character   Class :character   1st Qu.:2013-04-14  </span></span>
+<span><span class="co">#&gt;  Class :character   Class :character   1st Qu.:2013-05-03  </span></span>
-<span><span class="co">#&gt;  Mode  :character   Mode  :character   Median :2015-06-05  </span></span>
+<span><span class="co">#&gt;  Mode  :character   Mode  :character   Median :2015-06-16  </span></span>
-<span><span class="co">#&gt;                                        Mean   :2015-06-15  </span></span>
+<span><span class="co">#&gt;                                        Mean   :2015-06-21  </span></span>
-<span><span class="co">#&gt;                                        3rd Qu.:2017-08-23  </span></span>
+<span><span class="co">#&gt;                                        3rd Qu.:2017-08-24  </span></span>
-<span><span class="co">#&gt;                                        Max.   :2020-01-01  </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              %R   :43.2% (n=1134)   %R   :36.1% (n=947)   </span></span>
+<span><span class="co">#&gt;  &lt;NA&gt;  :0              %R   :42.9% (n=1163)   %R   :36.1% (n=978)   </span></span>
-<span><span class="co">#&gt;  Unique:4              %SI  :56.8% (n=1492)   %SI  :63.9% (n=1679)  </span></span>
+<span><span class="co">#&gt;  Unique:4              %SI  :57.1% (n=1549)   %SI  :63.9% (n=1734)  </span></span>
-<span><span class="co">#&gt;  #1    :B_ESCHR_COLI   - %S :41.1% (n=1080)   - %S :52.7% (n=1383)  </span></span>
+<span><span class="co">#&gt;  #1    :B_ESCHR_COLI   - %S :41.0% (n=1112)   - %S :52.0% (n=1409)  </span></span>
-<span><span class="co">#&gt;  #2    :B_STPHY_AURS   - %I :15.7% (n=412)    - %I :11.3% (n=296)   </span></span>
+<span><span class="co">#&gt;  #2    :B_STPHY_AURS   - %I :16.1% (n=437)    - %I :12.0% (n=325)   </span></span>
 <span><span class="co">#&gt;  #3    :B_STRPT_PNMN                                                </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;  %R   :42.0% (n=1102)   %R   :37.0% (n=971)    TRUE:2626     </span></span>
+<span><span class="co">#&gt;  %R   :42.0% (n=1138)   %R   :37.3% (n=1011)   TRUE:2712     </span></span>
-<span><span class="co">#&gt;  %SI  :58.0% (n=1524)   %SI  :63.0% (n=1655)                 </span></span>
+<span><span class="co">#&gt;  %SI  :58.0% (n=1574)   %SI  :62.7% (n=1701)                 </span></span>
-<span><span class="co">#&gt;  - %S :51.9% (n=1362)   - %S :59.9% (n=1574)                 </span></span>
+<span><span class="co">#&gt;  - %S :51.5% (n=1396)   - %S :59.6% (n=1616)                 </span></span>
-<span><span class="co">#&gt;  - %I : 6.2% (n=162)    - %I : 3.1% (n=81)                   </span></span>
+<span><span class="co">#&gt;  - %I : 6.6% (n=178)    - %I : 3.1% (n=85)                   </span></span>
 <span><span class="co">#&gt; </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: 2,626</span></span>
+<span><span class="co">#&gt; Rows: 2,712</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", "R7", "P10", "B7", "W3", "J8", "M3", "J3", "G6", "P4"…</span></span>
+<span><span class="co">#&gt; $ patient_id <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> "J3", "R7", "P10", "B7", "W3", "M3", "J3", "G6", "P4", "Z1"…</span></span>
 <span><span class="co">#&gt; $ hospital   <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> "A", "A", "A", "A", "A", "A", "A", "A", "A", "A", "A", "A",…</span></span>
 <span><span class="co">#&gt; $ date       <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> 2012-11-21, 2018-04-03, 2015-12-10, 2015-03-02, 2018-03-31…</span></span>
 <span><span class="co">#&gt; $ bacteria   <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> "B_ESCHR_COLI", "B_KLBSL_PNMN", "B_ESCHR_COLI", "B_ESCHR_COL…</span></span>
-<span><span class="co">#&gt; $ AMX        <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> R, R, S, S, R, R, R, S, S, S, S, R, S, S, R, R, R, R, I, S,…</span></span>
+<span><span class="co">#&gt; $ AMX        <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> R, R, S, S, R, R, S, S, S, S, R, S, S, S, R, R, R, R, S, R,…</span></span>
-<span><span class="co">#&gt; $ AMC        <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> I, I, I, S, S, S, S, S, S, S, S, S, S, S, S, S, S, R, S, R,…</span></span>
+<span><span class="co">#&gt; $ AMC        <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> I, I, I, S, S, S, S, S, S, S, S, S, I, S, S, S, S, R, S, S,…</span></span>
 <span><span class="co">#&gt; $ CIP        <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> S, S, S, S, R, S, S, S, S, S, S, S, S, S, S, S, S, S, S, S,…</span></span>
-<span><span class="co">#&gt; $ GEN        <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> S, S, S, S, S, S, S, S, S, S, S, R, S, S, S, S, S, S, S, S,…</span></span>
+<span><span class="co">#&gt; $ GEN        <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> S, S, S, S, S, S, S, S, S, S, R, S, S, S, S, S, S, S, S, S,…</span></span>
 <span><span class="co">#&gt; $ first      <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,…</span></span>
 <span></span>
 <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       1808          4          3          3          3 </span></span>
+<span><span class="co">#&gt;        260          3       1852          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">
@ -619,10 +619,10 @@ 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>250</span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;">1</span> Escherichia coli          <span style="text-decoration: underline;">1</span>319</span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;">2</span> Staphylococcus aureus      661</span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;">2</span> Staphylococcus aureus      676</span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;">3</span> Streptococcus pneumoniae   399</span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;">3</span> Streptococcus pneumoniae   400</span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;">4</span> Klebsiella pneumoniae      316</span></span></code></pre></div>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;">4</span> Klebsiella pneumoniae      317</span></span></code></pre></div>
 </div>
 <div class="section level3">
 <h3 id="select-and-filter-with-antibiotic-selectors">Select and filter with antibiotic selectors<a class="anchor" aria-label="anchor" href="#select-and-filter-with-antibiotic-selectors"></a>
@ -634,7 +634,7 @@ 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/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span>
 <span><span class="co">#&gt; ℹ For aminoglycosides() using column 'GEN' (gentamicin)</span></span>
-<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,626 × 2</span></span></span>
+<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,712 × 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 S    </span></span>
@ -642,18 +642,18 @@ in:</p>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> 2015-12-10 S    </span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> 2015-03-02 S    </span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> 2018-03-31 S    </span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> 2016-06-14 S    </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> 2015-10-25 S    </span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> 2015-10-25 S    </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> 2019-06-19 S    </span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> 2019-06-19 S    </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> 2015-04-27 S    </span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> 2015-04-27 S    </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> 2011-06-21 S    </span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> 2011-06-21 S    </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> 2014-09-05 S    </span></span>
-<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,616 more rows</span></span></span>
+<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,702 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/antibiotic_class_selectors.html">betalactams</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span>
 <span><span class="co">#&gt; ℹ For betalactams() using columns 'AMX' (amoxicillin) and 'AMC'</span></span>
 <span><span class="co">#&gt;   (amoxicillin/clavulanic acid)</span></span>
-<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,626 × 3</span></span></span>
+<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,712 × 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> B_ESCHR_COLI R     I    </span></span>
@ -662,15 +662,15 @@ in:</p>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> B_ESCHR_COLI S     S    </span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> B_STPHY_AURS R     S    </span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> B_ESCHR_COLI R     S    </span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> B_ESCHR_COLI R     S    </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> B_ESCHR_COLI S     S    </span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> B_ESCHR_COLI S     S    </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> B_STPHY_AURS S     S    </span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> B_STPHY_AURS S     S    </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> B_ESCHR_COLI S     S    </span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> B_ESCHR_COLI S     S    </span></span>
-<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,616 more rows</span></span></span>
+<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,702 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: 2,626 × 5</span></span></span>
+<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,712 × 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> B_ESCHR_COLI R     I     S     S    </span></span>
@ -679,17 +679,17 @@ in:</p>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> B_ESCHR_COLI S     S     S     S    </span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> B_STPHY_AURS R     S     R     S    </span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> B_ESCHR_COLI R     S     S     S    </span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> B_ESCHR_COLI R     S     S     S    </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> B_ESCHR_COLI S     S     S     S    </span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> B_ESCHR_COLI S     S     S     S    </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> B_STPHY_AURS S     S     S     S    </span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> B_STPHY_AURS S     S     S     S    </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> B_ESCHR_COLI S     S     S     S    </span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> B_ESCHR_COLI S     S     S     S    </span></span>
-<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,616 more rows</span></span></span>
+<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,702 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/antibiotic_class_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; ℹ For aminoglycosides() using column 'GEN' (gentamicin)</span></span>
-<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 971 × 9</span></span></span>
+<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 1,011 × 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 B_STRPT_PNMN R     S     S     R     TRUE </span></span>
@ -702,45 +702,45 @@ in:</p>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> P5         A        2019-03-09 B_STPHY_AURS S     S     S     R     TRUE </span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> Q8         A        2019-08-10 B_STPHY_AURS S     S     S     R     TRUE </span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> K5         A        2013-03-15 B_STRPT_PNMN S     S     S     R     TRUE </span></span>
-<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 961 more rows</span></span></span>
+<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 1,001 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/antibiotic_class_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; ℹ For betalactams() using columns 'AMX' (amoxicillin) and 'AMC'</span></span>
 <span><span class="co">#&gt;   (amoxicillin/clavulanic acid)</span></span>
-<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 471 × 9</span></span></span>
+<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 483 × 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 B_STRPT_PNMN R     R     S     S     TRUE </span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> R10        A        2013-12-20 B_STPHY_AURS R     R     S     S     TRUE </span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> R7         A        2015-10-25 B_STPHY_AURS R     R     S     S     TRUE </span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> R8         A        2019-10-25 B_STPHY_AURS R     R     S     S     TRUE </span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> I7         A        2015-08-19 B_ESCHR_COLI R     R     S     S     TRUE </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> B6         A        2016-11-20 B_ESCHR_COLI R     R     R     R     TRUE </span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> N3         A        2014-12-29 B_STRPT_PNMN R     R     R     S     TRUE </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> I7         A        2015-08-19 B_ESCHR_COLI R     R     S     S     TRUE </span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> Q2         A        2019-09-22 B_ESCHR_COLI R     R     S     S     TRUE </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> N3         A        2014-12-29 B_STRPT_PNMN R     R     R     S     TRUE </span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> X7         A        2011-03-20 B_ESCHR_COLI R     R     S     R     TRUE </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> Q2         A        2019-09-22 B_ESCHR_COLI R     R     S     S     TRUE </span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> C5         A        2015-08-30 B_KLBSL_PNMN R     R     S     R     TRUE </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> X7         A        2011-03-20 B_ESCHR_COLI R     R     S     R     TRUE </span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> W9         A        2013-10-02 B_ESCHR_COLI R     R     S     S     TRUE </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> V1         A        2018-08-07 B_STPHY_AURS R     R     S     S     TRUE </span></span>
-<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 461 more rows</span></span></span>
+<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 473 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/antibiotic_class_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; ℹ For betalactams() using columns 'AMX' (amoxicillin) and 'AMC'</span></span>
 <span><span class="co">#&gt;   (amoxicillin/clavulanic acid)</span></span>
-<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 471 × 9</span></span></span>
+<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 483 × 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 B_STRPT_PNMN R     R     S     S     TRUE </span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> R10        A        2013-12-20 B_STPHY_AURS R     R     S     S     TRUE </span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> R7         A        2015-10-25 B_STPHY_AURS R     R     S     S     TRUE </span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> R8         A        2019-10-25 B_STPHY_AURS R     R     S     S     TRUE </span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> I7         A        2015-08-19 B_ESCHR_COLI R     R     S     S     TRUE </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> B6         A        2016-11-20 B_ESCHR_COLI R     R     R     R     TRUE </span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> N3         A        2014-12-29 B_STRPT_PNMN R     R     R     S     TRUE </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> I7         A        2015-08-19 B_ESCHR_COLI R     R     S     S     TRUE </span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> Q2         A        2019-09-22 B_ESCHR_COLI R     R     S     S     TRUE </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> N3         A        2014-12-29 B_STRPT_PNMN R     R     R     S     TRUE </span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> X7         A        2011-03-20 B_ESCHR_COLI R     R     S     R     TRUE </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> Q2         A        2019-09-22 B_ESCHR_COLI R     R     S     S     TRUE </span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> C5         A        2015-08-30 B_KLBSL_PNMN R     R     S     R     TRUE </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> X7         A        2011-03-20 B_ESCHR_COLI R     R     S     R     TRUE </span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> W9         A        2013-10-02 B_ESCHR_COLI R     R     S     S     TRUE </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> V1         A        2018-08-07 B_STPHY_AURS R     R     S     S     TRUE </span></span>
-<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 461 more rows</span></span></span></code></pre></div>
+<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 473 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>
@ -1352,7 +1352,7 @@ I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equa
 own:</p>
 <div class="sourceCode" id="cb22"><pre class="downlit sourceCode r">
 <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 class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span></span>
-<span><span class="co">#&gt; [1] 0.4318355</span></span></code></pre></div>
+<span><span class="co">#&gt; [1] 0.4288348</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="cb23"><pre class="downlit sourceCode r">
@ -1362,9 +1362,9 @@ 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              0.343</span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;">1</span> A              0.342</span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;">2</span> B              0.569</span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;">2</span> B              0.564</span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;">3</span> C              0.375</span></span></code></pre></div>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;">3</span> C              0.372</span></span></code></pre></div>
 <hr>
 <p><em>Author: Dr. Matthijs Berends, 26th Feb 2023</em></p>
 </div>
--- a/articles/EUCAST.html
+++ b/articles/EUCAST.html
@ -38,7 +38,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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/MDR.html
+++ b/articles/MDR.html
@ -38,7 +38,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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">
@ -328,7 +328,6 @@ on this data set, we get:</p>
 <span>  <span class="fu"><a href="https://msberends.github.io/cleaner/reference/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="op">)</span> <span class="co"># show frequency table of the result</span></span>
 <span><span class="co">#&gt; Warning: in mdro(): NA introduced for isolates where the available percentage of</span></span>
 <span><span class="co">#&gt; antimicrobial classes was below 50% (set with pct_required_classes)</span></span></code></pre></div>
 <p>(16 isolates had no test results)</p>
 <p><strong>Frequency table</strong></p>
 <p>Class: factor &gt; ordered (numeric)<br>
 Length: 2,000<br>
@ -402,19 +401,19 @@ names or codes, this would have worked exactly the same way:</p>
 <div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span>
 <span><span class="co">#&gt;   rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
-<span><span class="co">#&gt; 1          R         R            S          R            S            I</span></span>
+<span><span class="co">#&gt; 1          R         R            S          R            I            I</span></span>
-<span><span class="co">#&gt; 2          I         I            S          R            I            R</span></span>
+<span><span class="co">#&gt; 2          I         R            R          I            R            R</span></span>
-<span><span class="co">#&gt; 3          R         R            R          R            S            I</span></span>
+<span><span class="co">#&gt; 3          S         R            S          R            R            I</span></span>
-<span><span class="co">#&gt; 4          S         S            I          R            R            R</span></span>
+<span><span class="co">#&gt; 4          S         I            I          I            S            R</span></span>
-<span><span class="co">#&gt; 5          I         R            R          R            I            I</span></span>
+<span><span class="co">#&gt; 5          S         I            R          R            R            S</span></span>
-<span><span class="co">#&gt; 6          I         R            I          R            R            R</span></span>
+<span><span class="co">#&gt; 6          R         R            I          I            R            R</span></span>
 <span><span class="co">#&gt;   kanamycin</span></span>
-<span><span class="co">#&gt; 1         I</span></span>
+<span><span class="co">#&gt; 1         S</span></span>
-<span><span class="co">#&gt; 2         R</span></span>
+<span><span class="co">#&gt; 2         I</span></span>
 <span><span class="co">#&gt; 3         R</span></span>
 <span><span class="co">#&gt; 4         S</span></span>
-<span><span class="co">#&gt; 5         S</span></span>
+<span><span class="co">#&gt; 5         I</span></span>
-<span><span class="co">#&gt; 6         S</span></span></code></pre></div>
+<span><span class="co">#&gt; 6         R</span></span></code></pre></div>
 <p>We can now add the interpretation of MDR-TB to our data set. You can
 use:</p>
 <div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
@ -455,40 +454,40 @@ Unique: 5</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">Mono-resistant</td>
-<td align="right">3234</td>
+<td align="right">3179</td>
-<td align="right">64.68%</td>
+<td align="right">63.58%</td>
-<td align="right">3234</td>
+<td align="right">3179</td>
-<td align="right">64.68%</td>
+<td align="right">63.58%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">Negative</td>
-<td align="right">943</td>
+<td align="right">988</td>
-<td align="right">18.86%</td>
+<td align="right">19.76%</td>
-<td align="right">4177</td>
+<td align="right">4167</td>
-<td align="right">83.54%</td>
+<td align="right">83.34%</td>
 </tr>
 <tr class="odd">
 <td align="left">3</td>
 <td align="left">Multi-drug-resistant</td>
-<td align="right">475</td>
+<td align="right">449</td>
-<td align="right">9.50%</td>
+<td align="right">8.98%</td>
-<td align="right">4652</td>
+<td align="right">4616</td>
-<td align="right">93.04%</td>
+<td align="right">92.32%</td>
 </tr>
 <tr class="even">
 <td align="left">4</td>
 <td align="left">Poly-resistant</td>
-<td align="right">262</td>
+<td align="right">268</td>
-<td align="right">5.24%</td>
+<td align="right">5.36%</td>
-<td align="right">4914</td>
+<td align="right">4884</td>
-<td align="right">98.28%</td>
+<td align="right">97.68%</td>
 </tr>
 <tr class="odd">
 <td align="left">5</td>
 <td align="left">Extensively drug-resistant</td>
-<td align="right">86</td>
+<td align="right">116</td>
-<td align="right">1.72%</td>
+<td align="right">2.32%</td>
 <td align="right">5000</td>
 <td align="right">100.00%</td>
 </tr>
--- a/articles/PCA.html
+++ b/articles/PCA.html
@ -38,7 +38,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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">
@ -307,7 +307,7 @@ 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 1.232e-16</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; 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/WHONET.html
+++ b/articles/WHONET.html
@ -38,7 +38,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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
@ -38,7 +38,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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">
@ -193,7 +193,7 @@
  <main id="main" class="col-md-9"><div class="page-header">
      <img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
-            <h4 data-toc-skip class="date">20 July 2023</h4>
+            <h4 data-toc-skip class="date">20 October 2023</h4>
      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
      <div class="d-none name"><code>datasets.Rmd</code></div>
@ -532,33 +532,33 @@ 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>antibiotics</code>, after
 you load the <code>AMR</code> package.</p>
-<p>It was last updated on 22 February 2023 13:38:57 UTC. Find more info
+<p>It was last updated on 20 October 2023 12:51:48 UTC. Find more info
 about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.rds" class="external-link">original
-R Data Structure (RDS) file</a> (39 kB)<br>
+R Data Structure (RDS) file</a> (44 kB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.txt" class="external-link">tab-separated
 text file</a> (0.1 MB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.xlsx" class="external-link">Microsoft
-Excel workbook</a> (66 kB)<br>
+Excel workbook</a> (72 kB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.feather" class="external-link">Apache
 Feather file</a> (0.1 MB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.parquet" class="external-link">Apache
-Parquet file</a> (97 kB)<br>
+Parquet file</a> (0.1 MB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.xpt" class="external-link">SAS
-transport (XPT) file</a> (1.4 MB)<br>
+transport (XPT) file</a> (1.5 MB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.sav" class="external-link">IBM
-SPSS Statistics data file</a> (0.3 MB)<br>
+SPSS Statistics data file</a> (0.4 MB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.dta" class="external-link">Stata
-DTA file</a> (0.4 MB)</li>
+DTA file</a> (0.5 MB)</li>
 </ul>
 <p>The tab-separated text file and Microsoft Excel workbook, and SAS,
 SPSS and Stata files all contain the ATC codes, common abbreviations,
@ -586,14 +586,14 @@ Names and Codes)</a></li>
 <div class="section level3">
 <h3 id="example-content-1">Example content<a class="anchor" aria-label="anchor" href="#example-content-1"></a>
 </h3>
-<table style="width:100%;" class="table">
+<table class="table">
 <colgroup>
 <col width="1%">
 <col width="2%">
 <col width="8%">
 <col width="7%">
 <col width="7%">
-<col width="13%">
+<col width="12%">
 <col width="17%">
 <col width="6%">
 <col width="13%">
@ -634,7 +634,7 @@ Names and Codes)</a></li>
 <td align="center"></td>
 <td align="center">1.0</td>
 <td align="center">g</td>
-<td align="center">13546-7, 15098-7, 17798-0, …</td>
+<td align="center">101493-5, 11-7, 12-5, …</td>
 </tr>
 <tr class="even">
 <td align="center">AMX</td>
@ -650,7 +650,7 @@ Names and Codes)</a></li>
 <td align="center">g</td>
 <td align="center">3.0</td>
 <td align="center">g</td>
-<td align="center">16365-9, 25274-2, 3344-9, …</td>
+<td align="center">101498-4, 15-8, 16-6, …</td>
 </tr>
 <tr class="odd">
 <td align="center">AMC</td>
@ -683,7 +683,7 @@ inhibitors</td>
 <td align="center">g</td>
 <td align="center">6.0</td>
 <td align="center">g</td>
-<td align="center">21066-6, 3355-5, 33562-0, …</td>
+<td align="center">101477-8, 101478-6, 18864-9, …</td>
 </tr>
 <tr class="odd">
 <td align="center">AZM</td>
@ -699,7 +699,7 @@ inhibitors</td>
 <td align="center">g</td>
 <td align="center">0.5</td>
 <td align="center">g</td>
-<td align="center">16420-2, 25233-8</td>
+<td align="center">100043-9, 16420-2, 16421-0, …</td>
 </tr>
 <tr class="even">
 <td align="center">PEN</td>
@ -732,33 +732,33 @@ column names:<br><em>av</em>, <em>name</em>, <em>atc</em>, <em>cid</em>,
 <em>loinc</em>.</p>
 <p>This data set is in R available as <code>antivirals</code>, after you
 load the <code>AMR</code> package.</p>
-<p>It was last updated on 13 November 2022 07:46:10 UTC. Find more info
+<p>It was last updated on 20 October 2023 12:51:48 UTC. Find more info
 about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.rds" class="external-link">original
-R Data Structure (RDS) file</a> (5 kB)<br>
+R Data Structure (RDS) file</a> (6 kB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.txt" class="external-link">tab-separated
-text file</a> (16 kB)<br>
+text file</a> (17 kB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.xlsx" class="external-link">Microsoft
 Excel workbook</a> (16 kB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.feather" class="external-link">Apache
-Feather file</a> (15 kB)<br>
+Feather file</a> (16 kB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.parquet" class="external-link">Apache
 Parquet file</a> (13 kB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.xpt" class="external-link">SAS
-transport (XPT) file</a> (68 kB)<br>
+transport (XPT) file</a> (73 kB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.sav" class="external-link">IBM
-SPSS Statistics data file</a> (30 kB)<br>
+SPSS Statistics data file</a> (32 kB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.dta" class="external-link">Stata
-DTA file</a> (73 kB)</li>
+DTA file</a> (78 kB)</li>
 </ul>
 <p>The tab-separated text file and Microsoft Excel workbook, and SAS,
 SPSS and Stata files all contain the trade names and LOINC codes as
@ -825,7 +825,7 @@ inhibitors</td>
 <td align="center">g</td>
 <td align="center"></td>
 <td align="center"></td>
-<td align="center">29113-8, 78772-1, 78773-9, …</td>
+<td align="center">29113-8, 30273-7, 30287-7, …</td>
 </tr>
 <tr class="even">
 <td align="center">ACI</td>
@ -880,7 +880,7 @@ inhibitors</td>
 <td align="center">g</td>
 <td align="center"></td>
 <td align="center"></td>
-<td align="center">29114-6, 31028-4, 78791-1</td>
+<td align="center">29114-6, 30296-8, 30297-6, …</td>
 </tr>
 <tr class="even">
 <td align="center">ASU</td>
--- a/articles/index.html
+++ b/articles/index.html
@ -10,7 +10,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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/other_pkg.html
+++ b/articles/other_pkg.html
@ -38,7 +38,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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/resistance_predict.html
+++ b/articles/resistance_predict.html
@ -38,7 +38,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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/welcome_to_AMR.html
+++ b/articles/welcome_to_AMR.html
@ -38,7 +38,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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
@ -10,7 +10,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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/deps/Fira_Code-0.4.7/uU9eCBsR6Z2vfE9aq3bL0fxyUs4tcw4W_D1sFVQ.woff
+++ b/deps/Fira_Code-0.4.7/uU9eCBsR6Z2vfE9aq3bL0fxyUs4tcw4W_D1sFVQ.woff
--- a/deps/bootstrap-5.2.2/bootstrap.min.css
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--- a/deps/bootstrap-5.2.2/fonts/HI_diYsKILxRpg3hIP6sJ7fM7PqPMcMnZFqUwX28DBKXhM0.woff
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--- a/deps/bootstrap-5.2.2/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk_RkaVQ.woff
+++ b/deps/bootstrap-5.2.2/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk_RkaVQ.woff
--- a/deps/bootstrap-5.2.2/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkxhjaVQ.woff
+++ b/deps/bootstrap-5.2.2/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkxhjaVQ.woff
--- a/deps/bootstrap-5.2.2/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsgH1y4k.woff
+++ b/deps/bootstrap-5.2.2/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsgH1y4k.woff
--- a/deps/bootstrap-5.2.2/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgshZ1y4k.woff
+++ b/deps/bootstrap-5.2.2/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgshZ1y4k.woff
--- a/deps/bootstrap-5.2.2/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsjr0C4k.woff
+++ b/deps/bootstrap-5.2.2/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsjr0C4k.woff
--- a/index.html
+++ b/index.html
@ -42,7 +42,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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">
@ -779,7 +779,7 @@
 <p>Manually, using:</p>
 <div class="sourceCode" id="cb12"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"remotes"</span><span class="op">)</span> <span class="co"># if you haven't already</span></span>
-<span><span class="fu">remotes</span><span class="fu">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html" class="external-link">install_github</a></span><span class="op">(</span><span class="st">"msberends/AMR"</span><span class="op">)</span></span></code></pre></div>
+<span><span class="fu">remotes</span><span class="fu">::</span><span class="fu">install_github</span><span class="op">(</span><span class="st">"msberends/AMR"</span><span class="op">)</span></span></code></pre></div>
 </li>
 <li>
 <p>Automatically, using the <a href="https://ropensci.org/r-universe/" class="external-link">rOpenSci R-universe platform</a>, by adding <a href="https://msberends.r-universe.dev" class="external-link">our R-universe address</a> to your list of repositories (‘repos’):</p>
--- a/news/index.html
+++ b/news/index.html
@ -10,7 +10,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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">
@ -159,8 +159,17 @@
    </div>
    <div class="section level2">
-<h2 class="pkg-version" data-toc-text="2.1.0.9001" id="amr-2109001">AMR 2.1.0.9001<a class="anchor" aria-label="anchor" href="#amr-2109001"></a></h2>
+<h2 class="pkg-version" data-toc-text="2.1.0.9002" id="amr-2109002">AMR 2.1.0.9002<a class="anchor" aria-label="anchor" href="#amr-2109002"></a></h2>
-<ul><li>Fix rounding MICs on latest R beta (‘R-devel’)</li>
+<ul><li>Fix for selecting first isolates using the phenotype-based method
 <ul><li>This included too many isolates when patients had altering antibiograms within the same bacterial species</li>
 <li>See for more info <a href="https://github.com/msberends/AMR/issues/122" class="external-link">our issue </a><a href="https://github.com/msberends/AMR/issues/122" class="external-link">#122</a>
 </li>
 </ul></li>
 <li>Added 1,366 LOINC codes to the <code>antibiotics</code> data set and updated to the latest version (LOINC v2.76)</li>
 <li>MICs can now be used in complex number calculations</li>
 <li>Fix rounding MICs on latest R beta (‘R-devel’)</li>
 <li>Removed unneeded note about the used language when option <code>AMR_locale</code> is set</li>
 <li>Fixed non-ASCII characters in documentation, according to CRAN maintainers</li>
 </ul></div>
    <div class="section level2">
 <h2 class="pkg-version" data-toc-text="2.1.0" id="amr-210">AMR 2.1.0<a class="anchor" aria-label="anchor" href="#amr-210"></a></h2><p class="text-muted">CRAN release: 2023-07-16</p>
@ -364,7 +373,7 @@
 <li>All R and Rmd files in this project are now styled using the <code>styler</code> package</li>
 <li>Set scalar conditional expressions (<code>&amp;&amp;</code> and <code>||</code>) where possible to comply with the upcoming R 4.3</li>
 <li>An enormous lot of code cleaning, fixing some small bugs along the way</li>
-</ul><hr><p>This changelog only contains changes from AMR v2.0 and later. For prior versions, please see <a href="https://github.com/msberends/AMR/blob/v1.8.2/NEWS.md" class="external-link">our archive</a>.</p>
+</ul><hr><p>This changelog only contains changes from AMR v2.0 (January 2023) and later. For prior versions, please see <a href="https://github.com/msberends/AMR/blob/v1.8.2/NEWS.md" class="external-link">our archive</a>.</p>
 </div>
 </div>
  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
--- a/pkgdown.yml
+++ b/pkgdown.yml
@ -11,7 +11,7 @@ articles:
  other_pkg: other_pkg.html
  resistance_predict: resistance_predict.html
  welcome_to_AMR: welcome_to_AMR.html
-last_built: 2023-07-20T06:28Z
+last_built: 2023-10-20T12:57Z
 urls:
  reference: https://msberends.github.io/AMR/reference
  article: https://msberends.github.io/AMR/articles
--- a/reference/AMR-deprecated.html
+++ b/reference/AMR-deprecated.html
@ -10,7 +10,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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
@ -10,7 +10,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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
@ -24,7 +24,7 @@ The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish,
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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/Rplot008.png
+++ b/reference/Rplot008.png
--- a/reference/WHOCC.html
+++ b/reference/WHOCC.html
@ -10,7 +10,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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
@ -10,7 +10,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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
@ -10,7 +10,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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
@ -10,7 +10,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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">
@ -397,7 +397,10 @@
 <span class="r-out co"><span class="r-pr">#&gt;</span> [55] "vetramox"           </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> $loinc</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "16365-9" "25274-2" "3344-9"  "80133-2"</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] "101498-4" "15-8"     "16-6"     "16365-9"  "17-4"     "18-2"    </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  [7] "18861-5"  "18862-3"  "19-0"     "20-8"     "21-6"     "22-4"    </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [13] "25274-2"  "25310-4"  "3344-9"   "55614-2"  "55615-9"  "55616-7" </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [19] "6976-5"   "6977-3"   "80133-2" </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> $ddd</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> $ddd$oral</span>
@ -424,7 +427,10 @@
 <span class="r-in"><span><span class="fu">ab_group</span><span class="op">(</span><span class="st">"J01CA01"</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Beta-lactams/penicillins"</span>
 <span class="r-in"><span><span class="fu">ab_loinc</span><span class="op">(</span><span class="st">"ampicillin"</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "21066-6" "3355-5"  "33562-0" "33919-2" "43883-8" "43884-6" "87604-5"</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] "101477-8" "101478-6" "18864-9"  "18865-6"  "20374-5"  "21066-6" </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  [7] "23618-2"  "27-3"     "28-1"     "29-9"     "30-7"     "31-5"    </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [13] "32-3"     "33-1"     "3355-5"   "33562-0"  "33919-2"  "34-9"    </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [19] "43883-8"  "43884-6"  "6979-9"   "6980-7"   "87604-5" </span>
 <span class="r-in"><span><span class="fu">ab_name</span><span class="op">(</span><span class="st">"21066-6"</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Ampicillin"</span>
 <span class="r-in"><span><span class="fu">ab_name</span><span class="op">(</span><span class="fl">6249</span><span class="op">)</span></span></span>
--- a/reference/add_custom_antimicrobials.html
+++ b/reference/add_custom_antimicrobials.html
@ -10,7 +10,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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
@ -10,7 +10,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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
@ -10,7 +10,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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">
@ -222,16 +222,16 @@
 <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  1957-11-17  65  65.67123         42</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1  1989-08-16  34  34.17808         10</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2  1983-08-04  39  39.95890         16</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2  1963-08-06  60  60.20548         36</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3  1942-11-16  80  80.67397         57</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3  1990-01-19  33  33.75068          9</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4  1948-11-24  74  74.65205         51</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4  1963-12-14  59  59.84932         36</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5  1976-01-30  47  47.46849         23</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5  1972-10-14  51  51.01644         27</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6  1958-02-28  65  65.38904         41</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6  1956-10-07  67  67.03562         43</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7  1993-05-18  30  30.17260          6</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7  1994-01-10  29  29.77534          5</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8  1942-08-16  80  80.92603         57</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8  1932-03-08  91  91.61918         67</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9  1994-05-24  29  29.15616          5</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9  1965-03-23  58  58.57808         34</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1977-08-28  45  45.89315         22</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1986-09-14  37  37.09863         13</span>
 </code></pre></div>
    </div>
  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
--- a/reference/age_groups-1.png
+++ b/reference/age_groups-1.png
--- a/reference/age_groups.html
+++ b/reference/age_groups.html
@ -10,7 +10,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/antibiogram.html
+++ b/reference/antibiogram.html
@ -10,7 +10,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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/antibiotic_class_selectors.html
+++ b/reference/antibiotic_class_selectors.html
@ -12,7 +12,7 @@ In short, if you have a column name that resembles an antimicrobial drug, it wil
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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">
@ -626,11 +626,11 @@ In short, if you have a column name that resembles an antimicrobial drug, it wil
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 5 × 1</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   kefzol</span>
 <span class="r-out co"><span class="r-pr">#&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> I     </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> R     </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> I     </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> S     </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> I     </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> R     </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> S     </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> I     </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">5</span> I     </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">5</span> S     </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="co"># get AMR for all aminoglycosides e.g., per ward:</span></span></span>
@ -726,8 +726,8 @@ In short, if you have a column name that resembles an antimicrobial drug, it wil
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 3</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   ward         TMP   SXT</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;dbl&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> Clinical   0.627 0.808</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical   0.627 0.807</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU        0.549 0.778</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU        0.551 0.780</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 0.667 0.821</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"># this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):</span></span></span>
--- a/reference/antibiotics.html
+++ b/reference/antibiotics.html
@ -10,7 +10,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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">
@ -189,13 +189,13 @@
 <li><p><code>oral_units</code><br> Units of <code>oral_ddd</code></p></li>
 <li><p><code>iv_ddd</code><br> Defined Daily Dose (DDD), parenteral (intravenous) treatment, currently available for 146 drugs</p></li>
 <li><p><code>iv_units</code><br> Units of <code>iv_ddd</code></p></li>
-<li><p><code>loinc</code><br> All LOINC codes (Logical Observation Identifiers Names and Codes) associated with the name of the antimicrobial drug. Use <code><a href="ab_property.html">ab_loinc()</a></code> to retrieve them quickly, see <code><a href="ab_property.html">ab_property()</a></code>.</p></li>
+<li><p><code>loinc</code><br> All codes associated with the name of the antimicrobial drug from Logical Observation Identifiers Names and Codes (LOINC), Version 2.76 (18 September, 2023). Use <code><a href="ab_property.html">ab_loinc()</a></code> to retrieve them quickly, see <code><a href="ab_property.html">ab_property()</a></code>.</p></li>
 </ul></div>
 <div class="section">
 <h3 id="for-the-antivirals-data-set-a-tibble-with-observations-and-variables-">For the antivirals data set: a <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 120 observations and 11 variables:<a class="anchor" aria-label="anchor" href="#for-the-antivirals-data-set-a-tibble-with-observations-and-variables-"></a></h3>
-<ul><li><p><code>av</code><br> Antibiotic ID as used in this package (such as <code>AMC</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available. <em>This is a unique identifier.</em></p></li>
+<ul><li><p><code>av</code><br> Antiviral ID as used in this package (such as <code>ACI</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available. <em>This is a unique identifier.</em> Combinations are codes that contain a <code>+</code> to indicate this, such as <code>ATA+COBI</code> for atazanavir/cobicistat.</p></li>
 <li><p><code>name</code><br> Official name as used by WHONET/EARS-Net or the WHO. <em>This is a unique identifier.</em></p></li>
 <li><p><code>atc</code><br> ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC</p></li>
 <li><p><code>cid</code><br> Compound ID as found in PubChem. <em>This is a unique identifier.</em></p></li>
@ -205,7 +205,7 @@
 <li><p><code>oral_units</code><br> Units of <code>oral_ddd</code></p></li>
 <li><p><code>iv_ddd</code><br> Defined Daily Dose (DDD), parenteral treatment</p></li>
 <li><p><code>iv_units</code><br> Units of <code>iv_ddd</code></p></li>
-<li><p><code>loinc</code><br> All LOINC codes (Logical Observation Identifiers Names and Codes) associated with the name of the antimicrobial drug.</p></li>
+<li><p><code>loinc</code><br> All codes associated with the name of the antiviral drug from Logical Observation Identifiers Names and Codes (LOINC), Version 2.76 (18 September, 2023). Use <code><a href="av_property.html">av_loinc()</a></code> to retrieve them quickly, see <code><a href="av_property.html">av_property()</a></code>.</p></li>
 </ul></div>
 <p>An object of class <code>tbl_df</code> (inherits from <code>tbl</code>, <code>data.frame</code>) with 120 rows and 11 columns.</p>
@ -214,7 +214,7 @@
    <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
 <ul><li><p>World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology (WHOCC): <a href="https://www.whocc.no/atc_ddd_index/" class="external-link">https://www.whocc.no/atc_ddd_index/</a></p></li>
-<li><p>Logical Observation Identifiers Names and Codes (LOINC), Version 2.73 (8 August, 2022). Accessed from <a href="https://loinc.org" class="external-link">https://loinc.org</a> on October 30th, 2022.</p></li>
+<li><p>Logical Observation Identifiers Names and Codes (LOINC), Version 2.76 (18 September, 2023). Accessed from <a href="https://loinc.org" class="external-link">https://loinc.org</a> on October 19th, 2023.</p></li>
 <li><p>European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: <a href="https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm" class="external-link">https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm</a></p></li>
 </ul></div>
    <div class="section level2">
--- a/reference/as.ab.html
+++ b/reference/as.ab.html
@ -10,7 +10,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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
@ -10,7 +10,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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
@ -10,7 +10,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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
@ -10,7 +10,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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
@ -10,7 +10,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/as.sir.html
+++ b/reference/as.sir.html
@ -14,7 +14,7 @@ All breakpoints used for interpretation are publicly available in the clinical_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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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">
@ -567,19 +567,19 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 13 × 13</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    datetime            index ab_user    mo_user    ab   mo                input</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;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&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> 2023-07-20 <span style="color: #949494;">06:29:57</span>     1 TOB        Escherich… TOB  B_[ORD]_ENTRBCTR 16    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2023-10-20 <span style="color: #949494;">12:58:24</span>     1 TOB        Escherich… TOB  B_[ORD]_ENTRBCTR 16    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2023-07-20 <span style="color: #949494;">06:29:57</span>     1 GEN        Escherich… GEN  B_[ORD]_ENTRBCTR 18    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2023-10-20 <span style="color: #949494;">12:58:24</span>     1 GEN        Escherich… GEN  B_[ORD]_ENTRBCTR 18    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2023-07-20 <span style="color: #949494;">06:29:57</span>     1 CIP        Escherich… CIP  B_[ORD]_ENTRBCTR  0.256</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2023-10-20 <span style="color: #949494;">12:58:24</span>     1 CIP        Escherich… CIP  B_[ORD]_ENTRBCTR  0.256</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2023-07-20 <span style="color: #949494;">06:29:56</span>     1 AMP        Escherich… AMP  B_[ORD]_ENTRBCTR  8    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2023-10-20 <span style="color: #949494;">12:58:24</span>     1 AMP        Escherich… AMP  B_[ORD]_ENTRBCTR  8    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2023-07-20 <span style="color: #949494;">06:29:47</span>     1 AMX        B_STRPT_P… AMX  B_STRPT_PNMN      0.01 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2023-10-20 <span style="color: #949494;">12:58:14</span>     1 AMX        B_STRPT_P… AMX  B_STRPT_PNMN      0.01 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2023-07-20 <span style="color: #949494;">06:29:47</span>     2 AMX        B_STRPT_P… AMX  B_STRPT_PNMN      2    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2023-10-20 <span style="color: #949494;">12:58:14</span>     2 AMX        B_STRPT_P… AMX  B_STRPT_PNMN      2    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2023-07-20 <span style="color: #949494;">06:29:47</span>     3 AMX        B_STRPT_P… AMX  B_STRPT_PNMN      4    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2023-10-20 <span style="color: #949494;">12:58:14</span>     3 AMX        B_STRPT_P… AMX  B_STRPT_PNMN      4    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2023-07-20 <span style="color: #949494;">06:29:47</span>     4 AMX        B_STRPT_P… AMX  B_STRPT_PNMN      8    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2023-10-20 <span style="color: #949494;">12:58:14</span>     4 AMX        B_STRPT_P… AMX  B_STRPT_PNMN      8    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2023-07-20 <span style="color: #949494;">06:29:47</span>     1 AMX        B_STRPT_P… AMX  B_STRPT_PNMN      2    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2023-10-20 <span style="color: #949494;">12:58:14</span>     1 AMX        B_STRPT_P… AMX  B_STRPT_PNMN      2    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2023-07-20 <span style="color: #949494;">06:29:46</span>     1 TOB        Escherich… TOB  B_[ORD]_ENTRBCTR 16    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2023-10-20 <span style="color: #949494;">12:58:13</span>     1 TOB        Escherich… TOB  B_[ORD]_ENTRBCTR 16    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">11</span> 2023-07-20 <span style="color: #949494;">06:29:46</span>     1 GEN        Escherich… GEN  B_[ORD]_ENTRBCTR 18    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">11</span> 2023-10-20 <span style="color: #949494;">12:58:13</span>     1 GEN        Escherich… GEN  B_[ORD]_ENTRBCTR 18    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">12</span> 2023-07-20 <span style="color: #949494;">06:29:46</span>     1 AMP        Escherich… AMP  B_[ORD]_ENTRBCTR 20    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">12</span> 2023-10-20 <span style="color: #949494;">12:58:13</span>     1 AMP        Escherich… AMP  B_[ORD]_ENTRBCTR 20    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">13</span> 2023-07-20 <span style="color: #949494;">06:29:45</span>     1 ampicillin Strep pneu AMP  B_STRPT_PNMN     18    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">13</span> 2023-10-20 <span style="color: #949494;">12:58:13</span>     1 ampicillin Strep pneu AMP  B_STRPT_PNMN     18    </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 6 more variables: outcome &lt;sir&gt;, method &lt;chr&gt;, breakpoint_S_R &lt;chr&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   guideline &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;</span></span>
 <span class="r-in"><span></span></span>
--- a/reference/atc_online.html
+++ b/reference/atc_online.html
@ -10,7 +10,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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
@ -10,7 +10,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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
@ -10,7 +10,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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">
@ -355,7 +355,8 @@
 <span class="r-in"><span><span class="fu">av_group</span><span class="op">(</span><span class="st">"J05AB01"</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Nucleosides and nucleotides excl. reverse transcriptase inhibitors"</span>
 <span class="r-in"><span><span class="fu">av_loinc</span><span class="op">(</span><span class="st">"abacavir"</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "29113-8" "78772-1" "78773-9" "79134-3" "80118-3"</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "29113-8" "30273-7" "30287-7" "30303-2" "78772-1" "78773-9" "79134-3"</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [8] "80118-3"</span>
 <span class="r-in"><span><span class="fu">av_name</span><span class="op">(</span><span class="st">"29113-8"</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Abacavir"</span>
 <span class="r-in"><span><span class="fu">av_name</span><span class="op">(</span><span class="fl">135398513</span><span class="op">)</span></span></span>
--- a/reference/availability.html
+++ b/reference/availability.html
@ -10,7 +10,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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
@ -10,7 +10,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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
@ -10,7 +10,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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
@ -12,7 +12,7 @@ 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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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
@ -10,7 +10,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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
@ -10,7 +10,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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/eucast_rules.html
+++ b/reference/eucast_rules.html
@ -12,7 +12,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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
@ -10,7 +10,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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
@ -10,7 +10,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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
@ -12,7 +12,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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">
@ -361,9 +361,9 @@
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Basing inclusion on all antimicrobial results, using a points threshold</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   of 2</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Excluding 16 isolates with a microbial ID 'UNKNOWN' (in column 'mo')</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Found 1,379 'phenotype-based' first isolates (69.0% of total where a</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Found 1,373 'phenotype-based' first isolates (68.7% of total where a</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>    microbial ID was available)</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 1,379 × 46</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 1,373 × 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> 2002-01-02 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA   </span>
@ -376,7 +376,7 @@
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2002-01-22 F35553     50 M      ICU      B_PROTS_MRBL R     NA    NA    NA   </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2002-02-03 481442     76 M      ICU      B_STPHY_CONS R     NA    S     NA   </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2002-02-05 023456     50 M      Clinical B_STPHY_HMNS S     NA    S     NA   </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 1,369 more rows</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 1,363 more rows</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>
@ -387,7 +387,7 @@
 <span class="r-in"><span><span class="co"># get all first Gram-negatives</span></span></span>
 <span class="r-in"><span><span class="va">example_isolates</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">first_isolate</span><span class="op">(</span>info <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span> <span class="op">&amp;</span> <span class="fu"><a href="mo_property.html">mo_is_gram_negative</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>, <span class="op">]</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Using column 'mo' as input for mo_is_gram_negative()</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 437 × 46</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 434 × 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> 2002-01-02 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA   </span>
@ -400,7 +400,7 @@
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2002-03-16 4FC193     69 M      Clinical B_PSDMN_AERG R     NA    NA    R    </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2002-04-01 496896     46 F      ICU      B_ESCHR_COLI R     NA    NA    NA   </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2002-04-23 EE2510     69 F      ICU      B_ESCHR_COLI R     NA    NA    NA   </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 427 more rows</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 424 more rows</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>
@ -417,9 +417,9 @@
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Basing inclusion on all antimicrobial results, using a points threshold</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   of 2</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Excluding 16 isolates with a microbial ID 'UNKNOWN' (in column 'mo')</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Found 1,379 'phenotype-based' first isolates (69.0% of total where a</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Found 1,373 'phenotype-based' first isolates (68.7% of total where a</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>    microbial ID was available)</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 1,379 × 46</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 1,373 × 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> 2002-01-02 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA   </span>
@ -432,7 +432,7 @@
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2002-01-22 F35553     50 M      ICU      B_PROTS_MRBL R     NA    NA    NA   </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2002-02-03 481442     76 M      ICU      B_STPHY_CONS R     NA    S     NA   </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2002-02-05 023456     50 M      Clinical B_STPHY_HMNS S     NA    S     NA   </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 1,369 more rows</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 1,363 more rows</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>
@ -444,7 +444,7 @@
 <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>
 <span class="r-in"><span>    <span class="fu">filter_first_isolate</span><span class="op">(</span>info <span class="op">=</span> <span class="cn">FALSE</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: 1,379 × 46</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 1,373 × 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> 2002-01-02 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA   </span>
@ -457,7 +457,7 @@
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2002-01-22 F35553     50 M      ICU      B_PROTS_MRBL R     NA    NA    NA   </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2002-02-03 481442     76 M      ICU      B_STPHY_CONS R     NA    S     NA   </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2002-02-05 023456     50 M      Clinical B_STPHY_HMNS S     NA    S     NA   </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 1,369 more rows</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 1,363 more rows</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>
@ -477,18 +477,18 @@
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Group: ward = "Clinical"</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Excluding 9 isolates with a microbial ID 'UNKNOWN' (in column 'mo')</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Found 861 'phenotype-based' first isolates (69.8% of total where a</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Found 857 'phenotype-based' first isolates (69.4% of total where a</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>    microbial ID was available)</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Group: ward = "ICU"</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Excluding 6 isolates with a microbial ID 'UNKNOWN' (in column 'mo')</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Found 449 'phenotype-based' first isolates (69.6% within scope and 69.5%</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Found 447 'phenotype-based' first isolates (69.2% of total where a</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>    of total where a microbial ID was available)</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>    microbial ID was available)</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Group: ward = "Outpatient"</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Excluding 1 isolates with a microbial ID 'UNKNOWN' (in column 'mo')</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Found 98 'phenotype-based' first isolates (82.4% within scope and 81.7%</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Found 98 'phenotype-based' first isolates (81.7% of total where a</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>    of total where a microbial ID was available)</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>    microbial ID was available)</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2,000 × 5</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups:   ward [3]</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    ward     date       patient mo           first</span>
--- a/reference/g.test.html
+++ b/reference/g.test.html
@ -10,7 +10,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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
@ -10,7 +10,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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">
@ -263,27 +263,28 @@
 <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">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># indices</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   [1]  9 11 43  7 14 38  8 24 28 41 33 28 43 43 18 11  2 43 11 35 19  8 44 34 29</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   [1]  9 15 34 37 30 16 14 46  8 15 32 36 48 41 28 26 30 17  4 10 12 21 45 35 42</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [26] 27  5 19 13  1 15 37 28 21 22  1 44 22  6 17 23 39 26 25 14 11 30 20 43 20</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [26] 46 30 44 20 23 35 34  3 16 18 12 27 44  1 42 41 32 22 13 40 17 21 24 23 38</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [51] 40  1  6 11  9 12 34  4 20  6 24 23 18  6 37  5 17 42 18  2 38 26 10 31 10</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [51] 46  7 45 40 11  3  2 29  9 33 28  8 18 37 40 36 43 31 13 42 48 38  9 40 47</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [76]  8 24 23 42  5 34 36 19 16 22 26 40 11 14 24 26 41  3 33 14 32  4 15 11 37</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [76] 35 14 40 14 43 42 19  6 19 12 39 31 17  5 16 10 25 47 16 14  7 31 12 46 22</span>
 <span class="r-in"><span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</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  TRUE  TRUE  TRUE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   [1]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE FALSE  TRUE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [13] FALSE FALSE  TRUE FALSE  TRUE FALSE FALSE  TRUE  TRUE FALSE  TRUE  TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [13]  TRUE  TRUE  TRUE  TRUE FALSE  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  TRUE  TRUE  TRUE FALSE  TRUE  TRUE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [25]  TRUE FALSE FALSE  TRUE  TRUE  TRUE FALSE FALSE  TRUE FALSE  TRUE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [37] FALSE FALSE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE FALSE FALSE  TRUE  TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [37]  TRUE FALSE  TRUE FALSE FALSE FALSE  TRUE  TRUE  TRUE FALSE FALSE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [49] FALSE FALSE  TRUE FALSE FALSE FALSE FALSE  TRUE FALSE  TRUE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [49] FALSE  TRUE FALSE  TRUE FALSE FALSE  TRUE FALSE  TRUE  TRUE FALSE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [61] FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [61] FALSE FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [73]  TRUE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE  TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [73] FALSE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [85] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE  TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [85] FALSE  TRUE FALSE FALSE  TRUE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  [97] FALSE FALSE FALSE FALSE</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: 1 × 46</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> 2003-01-14 553529     89 F      Clinical B_ESCHR_COLI R     NA    NA    NA   </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-06-23 798871     82 M      Clinical B_ENTRC_FCLS NA    NA    NA    NA   </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2002-07-28 F54261     69 M      Clinical B_STPHY_CONS R     NA    S     NA   </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>
@ -317,19 +318,19 @@
 <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 [95]</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups:   patient, condition [99]</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> 004531  2013-12-02 A         TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 005088  2007-08-22 C         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 008218  2009-04-27 B         TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 067927  2002-02-14 B         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 018637  2005-09-28 B         TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 122506  2007-08-10 A         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 05C73F  2006-01-12 B         TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 122506  2007-08-11 A         FALSE      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 062027  2015-09-21 A         TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 149442  2002-08-31 B         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 082622  2014-02-08 B         TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 164466  2009-10-07 B         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 0E2483  2007-08-10 C         TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 175532  2012-10-11 A         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 101305  2006-12-13 B         TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 175532  2010-04-10 C         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 125492  2016-05-13 C         TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 195736  2015-01-02 A         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 141061  2014-10-22 C         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>
@ -343,19 +344,19 @@
 <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 [92]</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups:   ward, patient [99]</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>    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: #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> Clinical   2013-12-02 004531          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical 2013-12-02 004531          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical   2007-08-22 005088          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical 2009-04-27 008218          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> ICU        2002-02-14 067927          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Clinical 2005-09-28 018637          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical   2007-08-10 122506          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical 2006-01-12 05C73F          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Clinical   2007-08-11 122506          1 FALSE      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> ICU      2015-09-21 062027          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> ICU        2002-08-31 149442          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> ICU      2014-02-08 082622          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Clinical   2009-10-07 164466          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> ICU      2007-08-10 0E2483          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical   2012-10-11 175532          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical 2006-12-13 101305          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> ICU        2010-04-10 175532          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> ICU      2016-05-13 125492          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Outpatient 2015-01-02 195736          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical 2014-10-22 141061          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>
@ -371,9 +372,9 @@
 <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           52             13            34            43</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical           61             15            40            49</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU                34             10            24            30</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU                34              9            24            28</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient          6              4             5             6</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient          4              2             4             4</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>
@ -402,19 +403,19 @@
 <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 [97]</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups:   patient, mo, ward [100]</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>    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: #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> 219024  B_ESCHR_COLI Clinical TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 984417    UNKNOWN    Clinical   TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 990867  B_STPHY_AURS Clinical TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> E19253  B_STPHY_CONS Clinical   TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> F5F794  B_STPHY_AURS ICU      TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 004531  B_STPHY_AURS Clinical   TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> F76709  B_KLBSL_OXYT Clinical TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> AC8303  B_STPHY_HMLY Clinical   TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 690B42  B_ESCHR_COLI ICU      TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 662978  B_ESCHR_COLI Clinical   TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 384779  B_STPHY_CPTS Clinical TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 34B622  B_KLBSL_OXYT Clinical   TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 400169  B_STPHY_EPDR ICU      TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 578848  B_STPHY_CONS Clinical   TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> A22120  B_STRPT_MITS Clinical TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 647993  B_STPHY_AURS ICU        TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 473F39  B_ESCHR_COLI Clinical TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> F76709  B_ESCHR_COLI Outpatient TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 483195  B_ESCHR_COLI ICU      TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 413267  B_STPHY_EPDR ICU        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/ggplot_pca.html
+++ b/reference/ggplot_pca.html
@ -10,7 +10,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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-8.png
+++ b/reference/ggplot_sir-8.png
--- a/reference/ggplot_sir.html
+++ b/reference/ggplot_sir.html
@ -10,7 +10,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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
@ -10,7 +10,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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
@ -10,7 +10,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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
@ -10,7 +10,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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
@ -10,7 +10,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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
@ -10,7 +10,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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
@ -10,7 +10,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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">
@ -311,7 +311,7 @@
 <span class="r-in"><span>  <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">my_patients</span><span class="op">$</span><span class="va">first_regular</span>, na.rm <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
 <span class="r-in"><span>  <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">my_patients</span><span class="op">$</span><span class="va">first_weighted</span>, na.rm <span class="op">=</span> <span class="cn">TRUE</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> [1] 1395</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1376</span>
 <span class="r-in"><span><span class="co"># }</span></span></span>
 </code></pre></div>
    </div>
--- a/reference/kurtosis.html
+++ b/reference/kurtosis.html
@ -10,7 +10,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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">
@ -199,9 +199,9 @@
    <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] 3.004586</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2.966658</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] 0.0308963</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.08087365</span>
 </code></pre></div>
    </div>
  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
--- a/reference/like.html
+++ b/reference/like.html
@ -10,7 +10,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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
@ -10,7 +10,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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
@ -10,7 +10,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/microorganisms.codes.html
+++ b/reference/microorganisms.codes.html
@ -10,7 +10,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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
@ -10,7 +10,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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
@ -10,7 +10,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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">
@ -175,7 +175,7 @@
 <li><p><code>status</code> <br> Status of the taxon, either "accepted" or "synonym"</p></li>
 <li><p><code>kingdom</code>, <code>phylum</code>, <code>class</code>, <code>order</code>, <code>family</code>, <code>genus</code>, <code>species</code>, <code>subspecies</code><br> Taxonomic rank of the microorganism</p></li>
 <li><p><code>rank</code><br> Text of the taxonomic rank of the microorganism, such as <code>"species"</code> or <code>"genus"</code></p></li>
-<li><p><code>ref</code><br> Author(s) and year of related scientific publication. This contains only the <em>first surname</em> and year of the <em>latest</em> authors, e.g. "Wallis <em>et al.</em> 2006 <em>emend.</em> Smith and Jones 2018" becomes "Smith <em>et al.</em>, 2018". This field is directly retrieved from the source specified in the column <code>source</code>. Moreover, accents were removed to comply with CRAN that only allows ASCII characters, e.g. "Váňová" becomes "Vanova".</p></li>
+<li><p><code>ref</code><br> Author(s) and year of related scientific publication. This contains only the <em>first surname</em> and year of the <em>latest</em> authors, e.g. "Wallis <em>et al.</em> 2006 <em>emend.</em> Smith and Jones 2018" becomes "Smith <em>et al.</em>, 2018". This field is directly retrieved from the source specified in the column <code>source</code>. Moreover, accents were removed to comply with CRAN that only allows ASCII characters.</p></li>
 <li><p><code>lpsn</code><br> Identifier ('Record number') of the List of Prokaryotic names with Standing in Nomenclature (LPSN). This will be the first/highest LPSN identifier to keep one identifier per row. For example, <em>Acetobacter ascendens</em> has LPSN Record number 7864 and 11011. Only the first is available in the <code>microorganisms</code> data set.</p></li>
 <li><p><code>oxygen_tolerance</code> <br> Oxygen tolerance, either "aerobe", "anaerobe", "anaerobe/microaerophile", "facultative anaerobe", "likely facultative anaerobe", or "microaerophile". These data were retrieved from BacDive (see <em>Source</em>). Items that contain "likely" are missing from BacDive and were extrapolated from other species within the same genus to guess the oxygen tolerance. Currently 73.4% of all ~37 000 bacteria in the data set contain an oxygen tolerance.</p></li>
 <li><p><code>lpsn_parent</code><br> LPSN identifier of the parent taxon</p></li>
--- a/reference/mo_matching_score.html
+++ b/reference/mo_matching_score.html
@ -10,7 +10,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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
@ -10,7 +10,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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_source.html
+++ b/reference/mo_source.html
@ -12,7 +12,7 @@ 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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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
@ -10,7 +10,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/plot.html
+++ b/reference/plot.html
@ -10,7 +10,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/proportion.html
+++ b/reference/proportion.html
@ -12,7 +12,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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">
@ -276,10 +276,10 @@ resistance() should be used to calculate resistance, susceptibility() should be
    </div>
    <div class="section level2">
    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
-    <p>The function <code>resistance()</code> is equal to the function <code>proportion_R()</code>. The function <code>susceptibility()</code> is equal to the function <code>proportion_SI()</code>.</p>
+    <p><strong>Remember that you should filter your data to let it contain only first isolates!</strong> This is needed to exclude duplicates and to reduce selection bias. Use <code><a href="first_isolate.html">first_isolate()</a></code> to determine them in your data set with one of the four available algorithms.</p>
 <p>The function <code>resistance()</code> is equal to the function <code>proportion_R()</code>. The function <code>susceptibility()</code> is equal to the function <code>proportion_SI()</code>.</p>
 <p>Use <code>sir_confidence_interval()</code> to calculate the confidence interval, which relies on <code><a href="https://rdrr.io/r/stats/binom.test.html" class="external-link">binom.test()</a></code>, i.e., the Clopper-Pearson method. This function returns a vector of length 2 at default for antimicrobial <em>resistance</em>. Change the <code>side</code> argument to "left"/"min" or "right"/"max" to return a single value, and change the <code>ab_result</code> argument to e.g. <code>c("S", "I")</code> to test for antimicrobial <em>susceptibility</em>, see Examples.</p>
-<p><strong>Remember that you should filter your data to let it contain only first isolates!</strong> This is needed to exclude duplicates and to reduce selection bias. Use <code><a href="first_isolate.html">first_isolate()</a></code> to determine them in your data set with one of the four available algorithms.</p>
+<p>These functions are not meant to count isolates, but to calculate the proportion of resistance/susceptibility. Use the <code><a href="count.html">count_*()</a></code> functions to count isolates. The function <code>susceptibility()</code> is essentially equal to <code><a href="count.html">count_susceptible()</a></code><code>/</code><code><a href="count.html">count_all()</a></code>. <em>Low counts can influence the outcome - the <code>proportion_*()</code> functions may camouflage this, since they only return the proportion (albeit dependent on the <code>minimum</code> argument).</em></p>
 <p>These functions are not meant to count isolates, but to calculate the proportion of resistance/susceptibility. Use the <code><a href="count.html">count()</a></code> functions to count isolates. The function <code>susceptibility()</code> is essentially equal to <code>count_susceptible() / count_all()</code>. <em>Low counts can influence the outcome - the <code>proportion</code> functions may camouflage this, since they only return the proportion (albeit being dependent on the <code>minimum</code> argument).</em></p>
 <p>The function <code>proportion_df()</code> takes any variable from <code>data</code> that has an <code><a href="as.sir.html">sir</a></code> class (created with <code><a href="as.sir.html">as.sir()</a></code>) and calculates the proportions S, I, and R. It also supports grouped variables. The function <code>sir_df()</code> works exactly like <code>proportion_df()</code>, but adds the number of isolates.</p>
    </div>
    <div class="section level2">
--- a/reference/random.html
+++ b/reference/random.html
@ -10,7 +10,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/resistance_predict.html
+++ b/reference/resistance_predict.html
@ -10,7 +10,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/skewness.html
+++ b/reference/skewness.html
@ -12,7 +12,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
    <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">skewness</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Uniform.html" class="external-link">runif</a></span><span class="op">(</span><span class="fl">1000</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.02181457</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.01149408</span>
 </code></pre></div>
    </div>
  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
--- a/reference/translate.html
+++ b/reference/translate.html
@ -10,7 +10,7 @@
    <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="">2.1.0.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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">
@ -215,7 +215,7 @@
 <span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># setting another language</span></span></span>
-<span class="r-in"><span><span class="fu">set_AMR_locale</span><span class="op">(</span><span class="st">"Spanish"</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="fu">set_AMR_locale</span><span class="op">(</span><span class="st">"Dutch"</span><span class="op">)</span></span></span>
 <span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
 <span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_name</a></span><span class="op">(</span><span class="st">"Ciprofloxacin"</span><span class="op">)</span></span></span>
 <span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
@ -223,15 +223,7 @@
 <span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># setting yet another language</span></span></span>
-<span class="r-in"><span><span class="fu">set_AMR_locale</span><span class="op">(</span><span class="st">"Greek"</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="fu">set_AMR_locale</span><span class="op">(</span><span class="st">"German"</span><span class="op">)</span></span></span>
 <span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
 <span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_name</a></span><span class="op">(</span><span class="st">"Ciprofloxacin"</span><span class="op">)</span></span></span>
 <span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
 <span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"Coagulase-negative Staphylococcus (CoNS)"</span><span class="op">)</span></span></span>
 <span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># setting yet another language</span></span></span>
 <span class="r-in"><span><span class="fu">set_AMR_locale</span><span class="op">(</span><span class="st">"Ukrainian"</span><span class="op">)</span></span></span>
 <span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
 <span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_name</a></span><span class="op">(</span><span class="st">"Ciprofloxacin"</span><span class="op">)</span></span></span>
 <span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
--- a/search.json
+++ b/search.json