Built site for AMR@2.1.1.9087: 738689b

Built site for AMR@2.1.1.9086: 50a9f8f
2024-12-26 08:06:12 +01:00 · 2024-10-02 08:39:39 +00:00 · 2024-10-02 08:29:15 +00:00
102 changed files with 3399 additions and 851 deletions
--- a/404.html
+++ b/404.html
@ -30,7 +30,7 @@
    <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="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</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/AMRforRGPT.svg
+++ b/AMRforRGPT.svg
--- a/LICENSE-text.html
+++ b/LICENSE-text.html
@ -7,7 +7,7 @@
    <a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</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/android-chrome-192x192.png
+++ b/android-chrome-192x192.png
--- a/android-chrome-512x512.png
+++ b/android-chrome-512x512.png
--- a/apple-touch-icon-120x120.png
+++ b/apple-touch-icon-120x120.png
--- a/apple-touch-icon-152x152.png
+++ b/apple-touch-icon-152x152.png
--- a/apple-touch-icon-180x180.png
+++ b/apple-touch-icon-180x180.png
--- a/apple-touch-icon-60x60.png
+++ b/apple-touch-icon-60x60.png
--- a/apple-touch-icon-76x76.png
+++ b/apple-touch-icon-76x76.png
--- a/apple-touch-icon.png
+++ b/apple-touch-icon.png
--- a/articles/AMR.html
+++ b/articles/AMR.html
@ -29,7 +29,7 @@
    <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="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</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">
@ -87,7 +87,7 @@
 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 30 September 2024.</p>
+generated on 02 October 2024.</p>
 <div class="section level2">
 <h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
 </h2>
@ -143,21 +143,21 @@ make the structure of your data generally look like this:</p>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2024-09-30</td>
+<td align="center">2024-10-02</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">2024-09-30</td>
+<td align="center">2024-10-02</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">2024-09-30</td>
+<td align="center">2024-10-02</td>
 <td align="center">efgh</td>
 <td align="center">Escherichia coli</td>
 <td align="center">R</td>
@ -270,12 +270,12 @@ taxonomic codes. Let’s check this:</p>
 <span><span class="co">#&gt; taxonomic name, and the pathogenicity in humans. See ?mo_matching_score.</span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt; --------------------------------------------------------------------------------</span></span>
-<span><span class="co">#&gt; "E. coli" -&gt; Enterococcus crotali (B_ENTRC_CRTL, 0.650)</span></span>
+<span><span class="co">#&gt; "E. coli" -&gt; Escherichia coli (B_ESCHR_COLI, 0.688)</span></span>
-<span><span class="co">#&gt; Also matched: Escherichia coli (0.598), Enterococcus columbae (0.595),</span></span>
+<span><span class="co">#&gt; Also matched: Enterococcus crotali (0.650), Escherichia coli coli</span></span>
-<span><span class="co">#&gt;               Enterococcus camelliae (0.591), Enterococcus casseliflavus (0.577),</span></span>
+<span><span class="co">#&gt;               (0.643), Escherichia coli expressing (0.611), Enterococcus columbae</span></span>
-<span><span class="co">#&gt;               Escherichia coli coli (0.559), Enterococcus canis (0.556), Enterococcus</span></span>
+<span><span class="co">#&gt;               (0.595), Enterococcus camelliae (0.591), Enterococcus casseliflavus</span></span>
-<span><span class="co">#&gt;               cecorum (0.550), Enterococcus canintestini (0.540), Escherichia coli</span></span>
+<span><span class="co">#&gt;               (0.577), Enterococcus canis (0.556), Enterococcus cecorum (0.550),</span></span>
-<span><span class="co">#&gt;               expressing (0.531), and Enterobacter cowanii (0.522)</span></span>
+<span><span class="co">#&gt;               Enterococcus canintestini (0.540), and Enterobacter cowanii (0.522)</span></span>
 <span><span class="co">#&gt; --------------------------------------------------------------------------------</span></span>
 <span><span class="co">#&gt; "K. pneumoniae" -&gt; Klebsiella pneumoniae (B_KLBSL_PNMN, 0.786)</span></span>
 <span><span class="co">#&gt; Also matched: Klebsiella pneumoniae ozaenae (0.707), Klebsiella</span></span>
@ -333,15 +333,15 @@ dplyr:</p>
 <span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 3,000 × 8</span></span></span>
 <span><span class="co">#&gt;    patient_id hospital date       bacteria     AMX   AMC   CIP   GEN  </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></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> J3         A        2012-11-21 B_ENTRC_CRTL R     I     S     S    </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    </span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> R7         A        2018-04-03 B_KLBSL_PNMN R     I     S     S    </span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> P3         A        2014-09-19 B_ENTRC_CRTL R     S     S     S    </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> P3         A        2014-09-19 B_ESCHR_COLI R     S     S     S    </span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> P10        A        2015-12-10 B_ENTRC_CRTL S     I     S     S    </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> P10        A        2015-12-10 B_ESCHR_COLI S     I     S     S    </span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> B7         A        2015-03-02 B_ENTRC_CRTL S     S     S     S    </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> B7         A        2015-03-02 B_ESCHR_COLI S     S     S     S    </span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> W3         A        2018-03-31 B_STPHY_AURS R     S     R     S    </span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> J8         A        2016-06-14 B_ENTRC_CRTL R     S     S     S    </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> J8         A        2016-06-14 B_ESCHR_COLI R     S     S     S    </span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> M3         A        2015-10-25 B_ENTRC_CRTL R     S     S     S    </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> M3         A        2015-10-25 B_ESCHR_COLI R     S     S     S    </span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> J3         A        2019-06-19 B_ENTRC_CRTL S     S     S     S    </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> J3         A        2019-06-19 B_ESCHR_COLI S     S     S     S    </span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> G6         A        2015-04-27 B_STPHY_AURS S     S     S     S    </span></span>
 <span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,990 more rows</span></span></span></code></pre></div>
 <p>This is basically it for the cleaning, time to start the data
@ -396,9 +396,9 @@ 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 2,764 'phenotype-based' first isolates (92.1% of total where a</span></span>
+<span><span class="co">#&gt; =&gt; Found 2,724 'phenotype-based' first isolates (90.8% of total where a</span></span>
 <span><span class="co">#&gt;    microbial ID was available)</span></span></code></pre></div>
-<p>So only 92% is suitable for resistance analysis! We can now filter on
+<p>So only 91% is suitable for resistance analysis! We can now filter on
 it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the
 <code>dplyr</code> package:</p>
 <div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
@ -408,24 +408,24 @@ 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 2 764 isolates for analysis. Now our data looks
+<p>So we end up with 2 724 isolates for analysis. Now our data looks
 like:</p>
 <div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">our_data_1st</span></span>
-<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,764 × 9</span></span></span>
+<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,724 × 9</span></span></span>
 <span><span class="co">#&gt;    patient_id hospital date       bacteria     AMX   AMC   CIP   GEN   first</span></span>
 <span><span class="co">#&gt;    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>      <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;date&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span></span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> J3         A        2012-11-21 B_ENTRC_CRTL R     I     S     S     TRUE </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>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> R7         A        2018-04-03 B_KLBSL_PNMN R     I     S     S     TRUE </span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> P10        A        2015-12-10 B_ENTRC_CRTL S     I     S     S     TRUE </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> P3         A        2014-09-19 B_ESCHR_COLI R     S     S     S     TRUE </span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> B7         A        2015-03-02 B_ENTRC_CRTL S     S     S     S     TRUE </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</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;"> 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;"> 5</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;"> 6</span> M3         A        2015-10-25 B_ENTRC_CRTL R     S     S     S     TRUE </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</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;"> 7</span> J3         A        2019-06-19 B_ENTRC_CRTL S     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;"> 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;"> 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;"> 9</span> P4         A        2011-06-21 B_ENTRC_CRTL 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;">10</span> Z1         A        2014-09-05 B_ENTRC_CRTL 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: #949494;"># ℹ 2,754 more rows</span></span></span></code></pre></div>
+<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,714 more rows</span></span></span></code></pre></div>
 <p>Time for the analysis.</p>
 </div>
 </div>
@ -438,44 +438,44 @@ 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:2764        Length:2764        Min.   :2011-01-01  </span></span>
+<span><span class="co">#&gt;  Length:2724        Length:2724        Min.   :2011-01-01  </span></span>
-<span><span class="co">#&gt;  Class :character   Class :character   1st Qu.:2013-04-18  </span></span>
+<span><span class="co">#&gt;  Class :character   Class :character   1st Qu.:2013-04-07  </span></span>
-<span><span class="co">#&gt;  Mode  :character   Mode  :character   Median :2015-06-07  </span></span>
+<span><span class="co">#&gt;  Mode  :character   Mode  :character   Median :2015-06-03  </span></span>
-<span><span class="co">#&gt;                                        Mean   :2015-06-16  </span></span>
+<span><span class="co">#&gt;                                        Mean   :2015-06-09  </span></span>
-<span><span class="co">#&gt;                                        3rd Qu.:2017-08-23  </span></span>
+<span><span class="co">#&gt;                                        3rd Qu.:2017-08-11  </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              %S   :42.1% (n=1163)   %S   :53.0% (n=1464)  </span></span>
+<span><span class="co">#&gt;  &lt;NA&gt;  :0              %S   :41.6% (n=1133)   %S   :52.6% (n=1432)  </span></span>
-<span><span class="co">#&gt;  Unique:5              %SDD : 0.0% (n=0)      %SDD : 0.0% (n=0)     </span></span>
+<span><span class="co">#&gt;  Unique:4              %SDD : 0.0% (n=0)      %SDD : 0.0% (n=0)     </span></span>
-<span><span class="co">#&gt;  #1    :B_ESCHR_COLI   %I   :16.2% (n=447)    %I   :12.2% (n=337)   </span></span>
+<span><span class="co">#&gt;  #1    :B_ESCHR_COLI   %I   :16.4% (n=446)    %I   :12.2% (n=333)   </span></span>
-<span><span class="co">#&gt;  #2    :B_STPHY_AURS   %R   :41.8% (n=1154)   %R   :34.8% (n=963)   </span></span>
+<span><span class="co">#&gt;  #2    :B_STPHY_AURS   %R   :42.0% (n=1145)   %R   :35.2% (n=959)   </span></span>
-<span><span class="co">#&gt;  #3    :B_ENTRC_CRTL   %NI  : 0.0% (n=0)      %NI  : 0.0% (n=0)     </span></span>
+<span><span class="co">#&gt;  #3    :B_STRPT_PNMN   %NI  : 0.0% (n=0)      %NI  : 0.0% (n=0)     </span></span>
 <span><span class="co">#&gt;     CIP                    GEN                  first        </span></span>
 <span><span class="co">#&gt;  Class:sir              Class:sir              Mode:logical  </span></span>
-<span><span class="co">#&gt;  %S   :52.9% (n=1462)   %S   :61.5% (n=1699)   TRUE:2764     </span></span>
+<span><span class="co">#&gt;  %S   :52.5% (n=1431)   %S   :61.0% (n=1661)   TRUE:2724     </span></span>
 <span><span class="co">#&gt;  %SDD : 0.0% (n=0)      %SDD : 0.0% (n=0)                    </span></span>
-<span><span class="co">#&gt;  %I   : 6.3% (n=174)    %I   : 3.0% (n=82)                   </span></span>
+<span><span class="co">#&gt;  %I   : 6.5% (n=176)    %I   : 3.0% (n=82)                   </span></span>
-<span><span class="co">#&gt;  %R   :40.8% (n=1128)   %R   :35.6% (n=983)                  </span></span>
+<span><span class="co">#&gt;  %R   :41.0% (n=1117)   %R   :36.0% (n=981)                  </span></span>
 <span><span class="co">#&gt;  %NI  : 0.0% (n=0)      %NI  : 0.0% (n=0)</span></span>
 <span></span>
 <span><span class="fu"><a href="https://pillar.r-lib.org/reference/glimpse.html" class="external-link">glimpse</a></span><span class="op">(</span><span class="va">our_data_1st</span><span class="op">)</span></span>
-<span><span class="co">#&gt; Rows: 2,764</span></span>
+<span><span class="co">#&gt; Rows: 2,724</span></span>
 <span><span class="co">#&gt; Columns: 9</span></span>
-<span><span class="co">#&gt; $ patient_id <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> "J3", "R7", "P10", "B7", "W3", "M3", "J3", "G6", "P4", "Z1"…</span></span>
+<span><span class="co">#&gt; $ patient_id <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> "J3", "R7", "P3", "P10", "B7", "W3", "M3", "J3", "G6", "P4"…</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; $ date       <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> 2012-11-21, 2018-04-03, 2014-09-19, 2015-12-10, 2015-03-02…</span></span>
-<span><span class="co">#&gt; $ bacteria   <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> "B_ENTRC_CRTL", "B_KLBSL_PNMN", "B_ENTRC_CRTL", "B_ENTRC_CRT…</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, S, S, S, S, R, S, S, S, R, R, R, R, S, R,…</span></span>
+<span><span class="co">#&gt; $ AMX        <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> R, R, R, S, S, R, R, S, S, S, S, R, 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, I, S, S, S, S, R, S, S,…</span></span>
+<span><span class="co">#&gt; $ AMC        <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> I, I, S, I, S, S, S, S, S, S, S, S, S, 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; $ CIP        <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> S, S, S, S, S, R, 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, R, 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; $ 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       1877          5          3          3          3 </span></span>
+<span><span class="co">#&gt;        260          3       1854          4          3          3          3 </span></span>
 <span><span class="co">#&gt;        GEN      first </span></span>
 <span><span class="co">#&gt;          3          1</span></span></code></pre></div>
 <div class="section level3">
@ -487,25 +487,23 @@ microorganisms:</p>
 <div class="sourceCode" id="cb13"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><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/count.html">count</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">bacteria</span><span class="op">)</span>, sort <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
-<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 5 × 2</span></span></span>
+<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>024</span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;">1</span> Escherichia coli          <span style="text-decoration: underline;">1</span>518</span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;">2</span> Staphylococcus aureus      730</span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;">3</span> Enterococcus crotali       494</span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;">3</span> Streptococcus pneumoniae   426</span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;">4</span> Streptococcus pneumoniae   426</span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;">4</span> Klebsiella pneumoniae      326</span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;">5</span> Klebsiella pneumoniae      326</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="../reference/count.html">count</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">bacteria</span><span class="op">)</span>, sort <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
-<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 5 × 2</span></span></span>
+<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           919</span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;">1</span> Escherichia coli          <span style="text-decoration: underline;">1</span>321</span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;">2</span> Staphylococcus aureus      682</span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;">3</span> Enterococcus crotali       442</span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;">3</span> Streptococcus pneumoniae   402</span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;">4</span> Streptococcus pneumoniae   402</span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;">4</span> Klebsiella pneumoniae      319</span></span></code></pre></div>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;">5</span> Klebsiella pneumoniae      319</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>
@ -517,113 +515,113 @@ 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: 2,764 × 2</span></span></span>
+<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,724 × 2</span></span></span>
 <span><span class="co">#&gt;    date       GEN  </span></span>
 <span><span class="co">#&gt;    <span style="color: #949494; font-style: italic;">&lt;date&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> 2012-11-21 S    </span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> 2018-04-03 S    </span></span>
-<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;"> 3</span> 2014-09-19 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;"> 4</span> 2015-12-10 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;"> 5</span> 2015-03-02 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;"> 6</span> 2018-03-31 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;"> 7</span> 2015-10-25 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;"> 8</span> 2019-06-19 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;"> 9</span> 2015-04-27 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: #BCBCBC;">10</span> 2011-06-21 S    </span></span>
-<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,754 more rows</span></span></span>
+<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,714 more rows</span></span></span>
 <span></span>
 <span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
 <span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">bacteria</span>, <span class="fu"><a href="../reference/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: 2,764 × 3</span></span></span>
+<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,724 × 3</span></span></span>
 <span><span class="co">#&gt;    bacteria     AMX   AMC  </span></span>
 <span><span class="co">#&gt;    <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> B_ENTRC_CRTL R     I    </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> B_ESCHR_COLI R     I    </span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> B_KLBSL_PNMN R     I    </span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> B_ENTRC_CRTL S     I    </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> B_ESCHR_COLI R     S    </span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> B_ENTRC_CRTL S     S    </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> B_ESCHR_COLI S     I    </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;"> 5</span> B_ESCHR_COLI S     S    </span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> B_ENTRC_CRTL R     S    </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> B_STPHY_AURS R     S    </span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> B_ENTRC_CRTL S     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;"> 8</span> B_STPHY_AURS 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;"> 9</span> B_ENTRC_CRTL 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;">10</span> B_ENTRC_CRTL 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 2,754 more rows</span></span></span>
+<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,714 more rows</span></span></span>
 <span></span>
 <span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
 <span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">bacteria</span>, <span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.sir</span><span class="op">)</span><span class="op">)</span></span>
-<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,764 × 5</span></span></span>
+<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,724 × 5</span></span></span>
 <span><span class="co">#&gt;    bacteria     AMX   AMC   CIP   GEN  </span></span>
 <span><span class="co">#&gt;    <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> B_ENTRC_CRTL R     I     S     S    </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> B_ESCHR_COLI R     I     S     S    </span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> B_KLBSL_PNMN R     I     S     S    </span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> B_ENTRC_CRTL S     I     S     S    </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> B_ESCHR_COLI R     S     S     S    </span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> B_ENTRC_CRTL S     S     S     S    </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> B_ESCHR_COLI S     I     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;"> 5</span> B_ESCHR_COLI S     S     S     S    </span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> B_ENTRC_CRTL R     S     S     S    </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> B_STPHY_AURS R     S     R     S    </span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> B_ENTRC_CRTL S     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;"> 8</span> B_STPHY_AURS 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;"> 9</span> B_ENTRC_CRTL 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;">10</span> B_ENTRC_CRTL 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 2,754 more rows</span></span></span>
+<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,714 more rows</span></span></span>
 <span></span>
 <span><span class="co"># filtering using AB selectors is also possible:</span></span>
 <span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
 <span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu"><a href="../reference/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: 983 × 9</span></span></span>
+<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 981 × 9</span></span></span>
 <span><span class="co">#&gt;    patient_id hospital date       bacteria     AMX   AMC   CIP   GEN   first</span></span>
 <span><span class="co">#&gt;    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>      <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;date&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span></span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> J5         A        2017-12-25 B_STRPT_PNMN R     S     S     R     TRUE </span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> X1         A        2017-07-04 B_STPHY_AURS R     S     S     R     TRUE </span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> B3         A        2016-07-24 B_ENTRC_CRTL S     S     S     R     TRUE </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> B3         A        2016-07-24 B_ESCHR_COLI S     S     S     R     TRUE </span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> V7         A        2012-04-03 B_ENTRC_CRTL S     S     S     R     TRUE </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> V7         A        2012-04-03 B_ESCHR_COLI S     S     S     R     TRUE </span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> C9         A        2017-03-23 B_ENTRC_CRTL S     S     S     R     TRUE </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> C9         A        2017-03-23 B_ESCHR_COLI S     S     S     R     TRUE </span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> R1         A        2018-06-10 B_STPHY_AURS S     S     S     R     TRUE </span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> S2         A        2013-07-19 B_STRPT_PNMN S     S     S     R     TRUE </span></span>
 <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 973 more rows</span></span></span>
+<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 971 more rows</span></span></span>
 <span></span>
 <span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
 <span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu"><a href="../reference/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: 464 × 9</span></span></span>
+<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 462 × 9</span></span></span>
 <span><span class="co">#&gt;    patient_id hospital date       bacteria     AMX   AMC   CIP   GEN   first</span></span>
 <span><span class="co">#&gt;    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>      <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;date&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span></span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> M7         A        2013-07-22 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> B6         A        2016-11-20 B_ENTRC_CRTL R     R     R     R     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> I7         A        2015-08-19 B_ENTRC_CRTL R     R     S     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> 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> Q2         A        2019-09-22 B_ENTRC_CRTL R     R     S     S     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> X7         A        2011-03-20 B_ENTRC_CRTL 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> 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 454 more rows</span></span></span>
+<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 452 more rows</span></span></span>
 <span></span>
 <span><span class="co"># even works in base R (since R 3.0):</span></span>
 <span><span class="va">our_data_1st</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu"><a href="../reference/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: 464 × 9</span></span></span>
+<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 462 × 9</span></span></span>
 <span><span class="co">#&gt;    patient_id hospital date       bacteria     AMX   AMC   CIP   GEN   first</span></span>
 <span><span class="co">#&gt;    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>      <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;date&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span></span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> M7         A        2013-07-22 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> B6         A        2016-11-20 B_ENTRC_CRTL R     R     R     R     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> I7         A        2015-08-19 B_ENTRC_CRTL R     R     S     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> 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> Q2         A        2019-09-22 B_ENTRC_CRTL R     R     S     S     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> X7         A        2011-03-20 B_ENTRC_CRTL 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> 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 454 more rows</span></span></span></code></pre></div>
+<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 452 more rows</span></span></span></code></pre></div>
 </div>
 <div class="section level3">
 <h3 id="generate-antibiograms">Generate antibiograms<a class="anchor" aria-label="anchor" href="#generate-antibiograms"></a>
@ -1222,7 +1220,7 @@ 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] 0.4175109</span></span></code></pre></div>
+<span><span class="co">#&gt; [1] 0.4203377</span></span></code></pre></div>
 <p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and
 <code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
 <div class="sourceCode" id="cb23"><pre class="downlit sourceCode r">
@ -1232,9 +1230,9 @@ 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              0.342</span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;">1</span> A              0.340</span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;">2</span> B              0.551</span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;">3</span> C              0.362</span></span></code></pre></div>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;">3</span> C              0.370</span></span></code></pre></div>
 <hr>
 <p><em>Author: Dr. Matthijs Berends, 26th Feb 2023</em></p>
 </div>
--- a/articles/AMR_for_Python.html
+++ b/articles/AMR_for_Python.html
@ -29,7 +29,7 @@
    <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="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -91,13 +91,14 @@ antimicrobial resistance (AMR) data analysis, providing extensive
 functionality for working with microbial and antimicrobial properties.
 But what if you’re working in Python and still want to benefit from the
 robust features of <code>AMR</code>?</p>
-<p>Luckily, there is no need to port the package to Python! With the
+<p>The best way is to access R directly from Python with the help of
-help of <code>rpy2</code>, a powerful Python package, you can easily
+<code>rpy2</code>, a simple yet powerful Python package. You can easily
-access R from Python and call functions from the <code>AMR</code>
+call functions from the <code>AMR</code> package to process your own
-package to process your own data. This post will guide you through
+data in your own Python environment. This post will guide you through
 setting up <code>rpy2</code> and show you how to use R functions from
 <code>AMR</code> in Python to supercharge your antimicrobial resistance
 analysis.</p>
 <p><a href="https://chatgpt.com/g/g-M4UNLwFi5-amr-for-r-assistant" class="external-link"><img src="../AMRforRGPT.svg" style="min-width: 300px; width: 10%;"></a></p>
 </div>
 <div class="section level2">
 <h2 id="what-is-rpy2">What is <code>rpy2</code>?<a class="anchor" aria-label="anchor" href="#what-is-rpy2"></a>
@ -127,19 +128,44 @@ environment.</li>
 <div class="section level3">
 <h3 id="step-1-install-r">Step 1: Install R<a class="anchor" aria-label="anchor" href="#step-1-install-r"></a>
 </h3>
-<p>Ensure that you have R installed on your system. You can download R
+<p>Ensure that R is installed on your system. R has minimal dependencies
-from <a href="https://cran.r-project.org/" class="external-link">CRAN</a>.</p>
+and is very simple to install:</p>
 <ul>
 <li>
 <strong>Linux</strong>
 <ul>
 <li>Ubuntu / Debian:<br><code>sudo apt install r-base</code>
 </li>
 <li>Fedora:<br><code>sudo dnf install R</code>
 </li>
 <li>CentOS/RHEL:<br><code>sudo yum install R</code>
 </li>
 <li>Arch Linux:<br><code>sudo pacman -S r</code>
 </li>
 </ul>
 </li>
 <li>
 <strong>macOS</strong> (with Homebrew):<br><code>brew install r</code>
 </li>
 <li>
 <strong>Other Systems:</strong><br>
 Visit the <a href="https://cran.r-project.org" class="external-link">CRAN download
 page</a>.</li>
 </ul>
 </div>
 <div class="section level3">
 <h3 id="step-2-install-the-amr-package-in-r">Step 2: Install the <code>AMR</code> package in R<a class="anchor" aria-label="anchor" href="#step-2-install-the-amr-package-in-r"></a>
 </h3>
-<p>Once you have R installed, open your R console and install the
+<p>On Linux and macOS, open Terminal and run:</p>
-<code>AMR</code> package:</p>
+<div class="sourceCode" id="cb1"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="ex">Rscript</span> <span class="at">-e</span> <span class="st">'install.packages("AMR")'</span></span></code></pre></div>
-<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
+<p>For other systems, open your R console and install the
-<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">"AMR"</span><span class="op">)</span></span></code></pre></div>
+<code>AMR</code> package by running:</p>
 <p>You can also install the latest development version of the
 <code>AMR</code> package if needed:</p>
 <div class="sourceCode" id="cb2"><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">"AMR"</span><span class="op">)</span></span></code></pre></div>
 <p>On any system, you can also install the latest development version of
 the <code>AMR</code> package by setting <code>repos</code> to our beta
 channel:</p>
 <div class="sourceCode" id="cb3"><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">"AMR"</span>, repos <span class="op">=</span> <span class="st">"https://msberends.r-universe.dev"</span><span class="op">)</span></span></code></pre></div>
 </div>
 <div class="section level3">
@ -147,58 +173,53 @@ from <a href="https://cran.r-project.org/" class="external-link">CRAN</a>.</p>
 </h3>
 <p>To install <code>rpy2</code>, simply run the following command in
 your terminal:</p>
-<div class="sourceCode" id="cb3"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb3-1"><a href="#cb3-1" tabindex="-1"></a><span class="ex">pip</span> install rpy2</span></code></pre></div>
+<div class="sourceCode" id="cb4"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb4-1"><a href="#cb4-1" tabindex="-1"></a><span class="ex">pip</span> install rpy2</span></code></pre></div>
 </div>
 <div class="section level3">
 <h3 id="step-4-test-rpy2-installation">Step 4: Test <code>rpy2</code> Installation<a class="anchor" aria-label="anchor" href="#step-4-test-rpy2-installation"></a>
 </h3>
 <p>To ensure everything is set up correctly, you can test your
-installation by running the following Python script:</p>
+installation by running the following Python script, which essentially
-<div class="sourceCode" id="cb4"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb4-1"><a href="#cb4-1" tabindex="-1"></a><span class="im">import</span> rpy2.robjects <span class="im">as</span> ro</span>
+runs R in the background:</p>
-<span id="cb4-2"><a href="#cb4-2" tabindex="-1"></a></span>
+<div class="sourceCode" id="cb5"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb5-1"><a href="#cb5-1" tabindex="-1"></a><span class="im">import</span> rpy2.robjects <span class="im">as</span> ro</span>
-<span id="cb4-3"><a href="#cb4-3" tabindex="-1"></a><span class="co"># Test a simple R function from Python</span></span>
+<span id="cb5-2"><a href="#cb5-2" tabindex="-1"></a></span>
-<span id="cb4-4"><a href="#cb4-4" tabindex="-1"></a>ro.r(<span class="st">'1 + 1'</span>)</span></code></pre></div>
+<span id="cb5-3"><a href="#cb5-3" tabindex="-1"></a><span class="co"># Test a simple R function from Python</span></span>
 <span id="cb5-4"><a href="#cb5-4" tabindex="-1"></a>ro.r(<span class="st">'1 + 1'</span>)</span></code></pre></div>
 <p>If this returns <code>2</code>, you’re good to go!</p>
 </div>
 </div>
 <div class="section level2">
-<h2 id="working-with-amr-in-python-using-rpy2">Working with AMR in Python using <code>rpy2</code><a class="anchor" aria-label="anchor" href="#working-with-amr-in-python-using-rpy2"></a>
+<h2 id="working-with-amr-in-python">Working with <code>AMR</code> in Python<a class="anchor" aria-label="anchor" href="#working-with-amr-in-python"></a>
 </h2>
 <p>Now that we have <code>rpy2</code> set up, let’s walk through some
 practical examples of using the <code>AMR</code> package within
 Python.</p>
 <div class="section level3">
-<h3 id="example-1-loading-amr-and-example-data">Example 1: Loading <code>AMR</code> and Example Data<a class="anchor" aria-label="anchor" href="#example-1-loading-amr-and-example-data"></a>
+<h3 id="example-1-converting-taxonomic-data">Example 1: Converting Taxonomic Data<a class="anchor" aria-label="anchor" href="#example-1-converting-taxonomic-data"></a>
 </h3>
 <p>Let’s start by converting taxonomic user input to valid taxonomy
 using the <code>AMR</code> package, from within Python:</p>
-<div class="sourceCode" id="cb5"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb5-1"><a href="#cb5-1" tabindex="-1"></a><span class="im">import</span> pandas <span class="im">as</span> pd</span>
+<div class="sourceCode" id="cb6"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb6-1"><a href="#cb6-1" tabindex="-1"></a><span class="im">import</span> pandas <span class="im">as</span> pd</span>
-<span id="cb5-2"><a href="#cb5-2" tabindex="-1"></a><span class="im">import</span> rpy2.robjects <span class="im">as</span> ro</span>
+<span id="cb6-2"><a href="#cb6-2" tabindex="-1"></a><span class="im">import</span> rpy2.robjects <span class="im">as</span> ro</span>
-<span id="cb5-3"><a href="#cb5-3" tabindex="-1"></a><span class="im">from</span> rpy2.robjects.packages <span class="im">import</span> importr</span>
+<span id="cb6-3"><a href="#cb6-3" tabindex="-1"></a><span class="im">from</span> rpy2.robjects.packages <span class="im">import</span> importr</span>
-<span id="cb5-4"><a href="#cb5-4" tabindex="-1"></a><span class="im">from</span> rpy2.robjects <span class="im">import</span> pandas2ri</span>
+<span id="cb6-4"><a href="#cb6-4" tabindex="-1"></a><span class="im">from</span> rpy2.robjects <span class="im">import</span> pandas2ri</span>
-<span id="cb5-5"><a href="#cb5-5" tabindex="-1"></a></span>
+<span id="cb6-5"><a href="#cb6-5" tabindex="-1"></a></span>
-<span id="cb5-6"><a href="#cb5-6" tabindex="-1"></a><span class="co"># Enable conversion between pandas and R data frames</span></span>
+<span id="cb6-6"><a href="#cb6-6" tabindex="-1"></a><span class="co"># Load the AMR package from R</span></span>
-<span id="cb5-7"><a href="#cb5-7" tabindex="-1"></a>pandas2ri.activate()</span>
+<span id="cb6-7"><a href="#cb6-7" tabindex="-1"></a>amr <span class="op">=</span> importr(<span class="st">'AMR'</span>)</span>
-<span id="cb5-8"><a href="#cb5-8" tabindex="-1"></a></span>
+<span id="cb6-8"><a href="#cb6-8" tabindex="-1"></a></span>
-<span id="cb5-9"><a href="#cb5-9" tabindex="-1"></a><span class="co"># Load the AMR package from R</span></span>
+<span id="cb6-9"><a href="#cb6-9" tabindex="-1"></a><span class="co"># Example user dataset in Python</span></span>
-<span id="cb5-10"><a href="#cb5-10" tabindex="-1"></a>amr <span class="op">=</span> importr(<span class="st">'AMR'</span>)</span>
+<span id="cb6-10"><a href="#cb6-10" tabindex="-1"></a>data <span class="op">=</span> pd.DataFrame({</span>
-<span id="cb5-11"><a href="#cb5-11" tabindex="-1"></a></span>
+<span id="cb6-11"><a href="#cb6-11" tabindex="-1"></a>    <span class="st">'microorganism'</span>: [<span class="st">'E. coli'</span>, <span class="st">'S. aureus'</span>, <span class="st">'P. aeruginosa'</span>, <span class="st">'K. pneumoniae'</span>]</span>
-<span id="cb5-12"><a href="#cb5-12" tabindex="-1"></a><span class="co"># Example user dataset in Python</span></span>
+<span id="cb6-12"><a href="#cb6-12" tabindex="-1"></a>})</span>
-<span id="cb5-13"><a href="#cb5-13" tabindex="-1"></a>data <span class="op">=</span> pd.DataFrame({</span>
+<span id="cb6-13"><a href="#cb6-13" tabindex="-1"></a></span>
-<span id="cb5-14"><a href="#cb5-14" tabindex="-1"></a>    <span class="st">'microorganism'</span>: [<span class="st">'E. coli'</span>, <span class="st">'S. aureus'</span>, <span class="st">'P. aeruginosa'</span>, <span class="st">'K. pneumoniae'</span>]</span>
+<span id="cb6-14"><a href="#cb6-14" tabindex="-1"></a><span class="co"># Apply mo_name() from the AMR package to the 'microorganism' column</span></span>
-<span id="cb5-15"><a href="#cb5-15" tabindex="-1"></a>})</span>
+<span id="cb6-15"><a href="#cb6-15" tabindex="-1"></a>ro.globalenv[<span class="st">'r_data'</span>] <span class="op">=</span> data</span>
-<span id="cb5-16"><a href="#cb5-16" tabindex="-1"></a></span>
+<span id="cb6-16"><a href="#cb6-16" tabindex="-1"></a>ro.r(<span class="st">'r_data$mo_name &lt;- mo_name(r_data$microorganism)'</span>)</span>
-<span id="cb5-17"><a href="#cb5-17" tabindex="-1"></a><span class="co"># Convert the Python DataFrame to an R DataFrame</span></span>
+<span id="cb6-17"><a href="#cb6-17" tabindex="-1"></a></span>
-<span id="cb5-18"><a href="#cb5-18" tabindex="-1"></a>r_data <span class="op">=</span> pandas2ri.py2rpy(data)</span>
+<span id="cb6-18"><a href="#cb6-18" tabindex="-1"></a><span class="co"># Retrieve and print the modified R DataFrame in Python</span></span>
-<span id="cb5-19"><a href="#cb5-19" tabindex="-1"></a></span>
+<span id="cb6-19"><a href="#cb6-19" tabindex="-1"></a>result <span class="op">=</span> ro.r(<span class="st">'r_data'</span>)</span>
-<span id="cb5-20"><a href="#cb5-20" tabindex="-1"></a><span class="co"># Apply mo_name() from the AMR package to the 'microorganism' column</span></span>
+<span id="cb6-20"><a href="#cb6-20" tabindex="-1"></a>result <span class="op">=</span> pandas2ri.rpy2py(result)</span>
-<span id="cb5-21"><a href="#cb5-21" tabindex="-1"></a>ro.globalenv[<span class="st">'r_data'</span>] <span class="op">=</span> r_data</span>
+<span id="cb6-21"><a href="#cb6-21" tabindex="-1"></a><span class="bu">print</span>(result)</span></code></pre></div>
 <span id="cb5-22"><a href="#cb5-22" tabindex="-1"></a>ro.r(<span class="st">'r_data$mo_name &lt;- mo_name(r_data$microorganism)'</span>)</span>
 <span id="cb5-23"><a href="#cb5-23" tabindex="-1"></a></span>
 <span id="cb5-24"><a href="#cb5-24" tabindex="-1"></a><span class="co"># Retrieve and print the modified R DataFrame in Python</span></span>
 <span id="cb5-25"><a href="#cb5-25" tabindex="-1"></a>result <span class="op">=</span> ro.r(<span class="st">'as.data.frame(r_data)'</span>)</span>
 <span id="cb5-26"><a href="#cb5-26" tabindex="-1"></a>result <span class="op">=</span> pandas2ri.rpy2py(result)</span>
 <span id="cb5-27"><a href="#cb5-27" tabindex="-1"></a><span class="bu">print</span>(result)</span></code></pre></div>
 <p>In this example, a Python dataset with microorganism names like
 <em>E. coli</em> and <em>S. aureus</em> is passed to the R function
 <code><a href="../reference/mo_property.html">mo_name()</a></code>. The result is an updated <code>DataFrame</code>
@ -212,12 +233,12 @@ that includes the standardised microorganism names based on the
 generating an antibiogram, a table that summarises the antimicrobial
 susceptibility of bacterial isolates. Here’s how you can generate an
 antibiogram from Python:</p>
-<div class="sourceCode" id="cb6"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb6-1"><a href="#cb6-1" tabindex="-1"></a><span class="co"># Run an antibiogram in R from Python</span></span>
+<div class="sourceCode" id="cb7"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb7-1"><a href="#cb7-1" tabindex="-1"></a><span class="co"># Run an antibiogram in R from Python</span></span>
-<span id="cb6-2"><a href="#cb6-2" tabindex="-1"></a>ro.r(<span class="st">'result &lt;- antibiogram(example_isolates, antibiotics = c(aminoglycosides(), carbapenems()))'</span>)</span>
+<span id="cb7-2"><a href="#cb7-2" tabindex="-1"></a>ro.r(<span class="st">'result &lt;- antibiogram(example_isolates, antibiotics = c(aminoglycosides(), carbapenems()))'</span>)</span>
-<span id="cb6-3"><a href="#cb6-3" tabindex="-1"></a></span>
+<span id="cb7-3"><a href="#cb7-3" tabindex="-1"></a></span>
-<span id="cb6-4"><a href="#cb6-4" tabindex="-1"></a><span class="co"># Retrieve the result in Python</span></span>
+<span id="cb7-4"><a href="#cb7-4" tabindex="-1"></a><span class="co"># Retrieve the result in Python</span></span>
-<span id="cb6-5"><a href="#cb6-5" tabindex="-1"></a>result <span class="op">=</span> ro.r(<span class="st">'as.data.frame(result)'</span>)</span>
+<span id="cb7-5"><a href="#cb7-5" tabindex="-1"></a>result <span class="op">=</span> ro.r(<span class="st">'as.data.frame(result)'</span>)</span>
-<span id="cb6-6"><a href="#cb6-6" tabindex="-1"></a><span class="bu">print</span>(result)</span></code></pre></div>
+<span id="cb7-6"><a href="#cb7-6" tabindex="-1"></a><span class="bu">print</span>(result)</span></code></pre></div>
 <p>In this example, we generate an antibiogram by selecting
 aminoglycosides and carbapenems, two classes of antibiotics, and then
 convert the resulting R data frame into a Python-readable format.</p>
@ -227,12 +248,12 @@ convert the resulting R data frame into a Python-readable format.</p>
 </h3>
 <p>Let’s say you want to filter the dataset for Gram-negative bacteria
 and display their resistance to certain antibiotics:</p>
-<div class="sourceCode" id="cb7"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb7-1"><a href="#cb7-1" tabindex="-1"></a><span class="co"># Filter for Gram-negative bacteria with intrinsic resistance to cefotaxime</span></span>
+<div class="sourceCode" id="cb8"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb8-1"><a href="#cb8-1" tabindex="-1"></a><span class="co"># Filter for Gram-negative bacteria with intrinsic resistance to cefotaxime</span></span>
-<span id="cb7-2"><a href="#cb7-2" tabindex="-1"></a>ro.r(<span class="st">'result &lt;- example_isolates[which(mo_is_gram_negative() &amp; mo_is_intrinsic_resistant(ab = "cefotax")), c("bacteria", aminoglycosides(), carbapenems())]'</span>)</span>
+<span id="cb8-2"><a href="#cb8-2" tabindex="-1"></a>ro.r(<span class="st">'result &lt;- example_isolates[which(mo_is_gram_negative() &amp; mo_is_intrinsic_resistant(ab = "cefotax")), c("bacteria", aminoglycosides(), carbapenems())]'</span>)</span>
-<span id="cb7-3"><a href="#cb7-3" tabindex="-1"></a></span>
+<span id="cb8-3"><a href="#cb8-3" tabindex="-1"></a></span>
-<span id="cb7-4"><a href="#cb7-4" tabindex="-1"></a><span class="co"># Retrieve the filtered result in Python</span></span>
+<span id="cb8-4"><a href="#cb8-4" tabindex="-1"></a><span class="co"># Retrieve the filtered result in Python</span></span>
-<span id="cb7-5"><a href="#cb7-5" tabindex="-1"></a>result <span class="op">=</span> ro.r(<span class="st">'as.data.frame(result)'</span>)</span>
+<span id="cb8-5"><a href="#cb8-5" tabindex="-1"></a>result <span class="op">=</span> ro.r(<span class="st">'as.data.frame(result)'</span>)</span>
-<span id="cb7-6"><a href="#cb7-6" tabindex="-1"></a><span class="bu">print</span>(result)</span></code></pre></div>
+<span id="cb8-6"><a href="#cb8-6" tabindex="-1"></a><span class="bu">print</span>(result)</span></code></pre></div>
 <p>This example uses the AMR functions
 <code><a href="../reference/mo_property.html">mo_is_gram_negative()</a></code> and
 <code><a href="../reference/mo_property.html">mo_is_intrinsic_resistant()</a></code> to filter the dataset and
@ -243,12 +264,12 @@ returns a subset of bacteria with resistance data.</p>
 </h3>
 <p>You can easily customise the antibiogram by passing different
 antibiotics or microorganism transformations, as shown below:</p>
-<div class="sourceCode" id="cb8"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb8-1"><a href="#cb8-1" tabindex="-1"></a><span class="co"># Customise the antibiogram with different settings</span></span>
+<div class="sourceCode" id="cb9"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb9-1"><a href="#cb9-1" tabindex="-1"></a><span class="co"># Customise the antibiogram with different settings</span></span>
-<span id="cb8-2"><a href="#cb8-2" tabindex="-1"></a>ro.r(<span class="st">'result &lt;- antibiogram(example_isolates, antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"), mo_transform = "gramstain")'</span>)</span>
+<span id="cb9-2"><a href="#cb9-2" tabindex="-1"></a>ro.r(<span class="st">'result &lt;- antibiogram(example_isolates, antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"), mo_transform = "gramstain")'</span>)</span>
-<span id="cb8-3"><a href="#cb8-3" tabindex="-1"></a></span>
+<span id="cb9-3"><a href="#cb9-3" tabindex="-1"></a></span>
-<span id="cb8-4"><a href="#cb8-4" tabindex="-1"></a><span class="co"># Retrieve and print the result</span></span>
+<span id="cb9-4"><a href="#cb9-4" tabindex="-1"></a><span class="co"># Retrieve and print the result</span></span>
-<span id="cb8-5"><a href="#cb8-5" tabindex="-1"></a>result <span class="op">=</span> ro.r(<span class="st">'as.data.frame(result)'</span>)</span>
+<span id="cb9-5"><a href="#cb9-5" tabindex="-1"></a>result <span class="op">=</span> ro.r(<span class="st">'as.data.frame(result)'</span>)</span>
-<span id="cb8-6"><a href="#cb8-6" tabindex="-1"></a><span class="bu">print</span>(result)</span></code></pre></div>
+<span id="cb9-6"><a href="#cb9-6" tabindex="-1"></a><span class="bu">print</span>(result)</span></code></pre></div>
 <p>Here, we use piperacillin/tazobactam (TZP) in combination with
 tobramycin (TOB) and gentamicin (GEN) to see how they perform against
 various Gram-negative bacteria.</p>
--- a/articles/EUCAST.html
+++ b/articles/EUCAST.html
@ -29,7 +29,7 @@
    <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="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</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
@ -29,7 +29,7 @@
    <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="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/articles/PCA.html
+++ b/articles/PCA.html
@ -29,7 +29,7 @@
    <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="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/articles/WHONET.html
+++ b/articles/WHONET.html
@ -29,7 +29,7 @@
    <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="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</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
@ -29,7 +29,7 @@
    <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="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</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">
@ -76,7 +76,7 @@
  <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">30 September 2024</h4>
+            <h4 data-toc-skip class="date">02 October 2024</h4>
      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
      <div class="d-none name"><code>datasets.Rmd</code></div>
@ -108,7 +108,7 @@ column names:<br><em>mo</em>, <em>fullname</em>, <em>status</em>, <em>kingdom</e
 <em>snomed</em>.</p>
 <p>This data set is in R available as <code>microorganisms</code>, after
 you load the <code>AMR</code> package.</p>
-<p>It was last updated on 30 September 2024 16:46:55 UTC. Find more info
+<p>It was last updated on 2 October 2024 08:20:05 UTC. Find more info
 about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
@ -286,7 +286,7 @@ Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a hre
 <td align="center"></td>
 <td align="center">11158430</td>
 <td align="center"></td>
-<td align="center">1.15</td>
+<td align="center">1</td>
 <td align="center">407310004, 407251000, 407281008, …</td>
 </tr>
 <tr class="even">
@ -314,7 +314,7 @@ Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a hre
 <td align="center"></td>
 <td align="center"></td>
 <td align="center"></td>
-<td align="center">1.15</td>
+<td align="center">1</td>
 <td align="center"></td>
 </tr>
 <tr class="odd">
@ -342,7 +342,7 @@ Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a hre
 <td align="center">5427575</td>
 <td align="center"></td>
 <td align="center"></td>
-<td align="center">1.15</td>
+<td align="center">1</td>
 <td align="center">419388003</td>
 </tr>
 <tr class="even">
@ -370,7 +370,7 @@ Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a hre
 <td align="center"></td>
 <td align="center"></td>
 <td align="center"></td>
-<td align="center">1.50</td>
+<td align="center">1</td>
 <td align="center"></td>
 </tr>
 <tr class="odd">
@ -398,7 +398,7 @@ Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a hre
 <td align="center">11286021</td>
 <td align="center"></td>
 <td align="center"></td>
-<td align="center">1.15</td>
+<td align="center">1</td>
 <td align="center">1095001000112106, 715307006, 737528008, …</td>
 </tr>
 <tr class="even">
@ -426,7 +426,7 @@ Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a hre
 <td align="center">12233256</td>
 <td align="center">11286021</td>
 <td align="center"></td>
-<td align="center">1.15</td>
+<td align="center">1</td>
 <td align="center"></td>
 </tr>
 </tbody>
--- a/articles/index.html
+++ b/articles/index.html
@ -7,7 +7,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</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
@ -29,7 +29,7 @@
    <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="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</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
@ -29,7 +29,7 @@
    <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="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</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
@ -29,7 +29,7 @@
    <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="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/authors.html
+++ b/authors.html
@ -7,7 +7,7 @@
    <a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</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/browserconfig.xml
+++ b/browserconfig.xml
@ -1,10 +0,0 @@
 <?xml version="1.0" encoding="utf-8"?>
 <browserconfig>
    <msapplication>
        <tile>
            <square150x150logo src="/mstile-150x150.png?v=newlogo"/>
            <square310x310logo src="/mstile-310x310.png?v=newlogo"/>
            <TileColor>#128f76</TileColor>
        </tile>
    </msapplication>
 </browserconfig>
--- a/extra.css
+++ b/extra.css
@ -66,8 +66,31 @@
  --bs-dropdown-link-hover-color: var(--amr-green-light) !important;
  --bs-dropdown-link-hover-bg: var(--amr-green-dark) !important;
  --bs-dropdown-link-active-color: white !important;
 }
 /* Python page */
 body.amr-for-python * {
  --amr-green-light: #FFD43B; /* Python yellow */
  --amr-green-light-rgb: 255, 212, 59;
  --amr-green-dark: #306998; /* Python blue */
  --amr-green-dark-rgb: 48, 105, 152;
  --amr-green-middle: #b1bc5e; /* Adjusted middle yellow */
  --amr-green-middle-rgb: 177, 188, 94;
  --bs-success: var(--amr-green-dark) !important;
  --bs-light: var(--amr-green-light) !important;
  --bs-info: var(--amr-green-middle) !important;
  --bs-link-color: var(--amr-green-dark) !important;
  --bs-link-color-rgb: var(--amr-green-dark-rgb) !important;
  --bs-primary: var(--amr-green-dark) !important;
  --bs-primary-color: var(--amr-green-dark) !important;
  --bs-primary-rgb: var(--amr-green-dark-rgb) !important;
  --bs-secondary-color: var(--amr-green-dark) !important;
  --bs-navbar-active-color: var(--amr-green-light) !important;
  --bs-dropdown-bg: var(--amr-green-dark) !important;
  --bs-dropdown-link-hover-color: var(--amr-green-light) !important;
  --bs-dropdown-link-hover-bg: var(--amr-green-dark) !important;
 }
 .nav-text.text-muted,
 .bg-primary .navbar-nav .show>.nav-link,
 .bg-primary .navbar-nav .nav-link.active,
--- a/extra.js
+++ b/extra.js
@ -52,7 +52,7 @@ $(document).ready(function() {
  // make Python part more fancy - prepare for CSS
  if (window.location.href.includes('AMR_for_Python')) {
    $('body').addClass('amr-for-python');
-    $('img[src="logo.svg"]').attr('src', 'logo_python.svg');
+    $('img[src="../logo.svg"]').attr('src', '../logo_python.svg');
  }
  // add doctoral titles to authors
--- a/favicon-16x16.png
+++ b/favicon-16x16.png
--- a/favicon-32x32.png
+++ b/favicon-32x32.png
--- a/favicon.ico
+++ b/favicon.ico
--- a/index.html
+++ b/index.html
@ -32,7 +32,7 @@
    <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="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -91,6 +91,7 @@
 <li>100% free of costs and dependencies, highly suitable for places with <strong>limited resources</strong>
 </li>
 </ul>
 <p><a href="https://chatgpt.com/g/g-M4UNLwFi5-amr-for-r-assistant" class="external-link"><img src="AMRforRGPT.svg" style="min-width: 300px; width: 10%;"></a></p>
 <div style="display: flex; font-size: 0.8em;">
 <p style="text-align:left; width: 50%;">
 <small><a href="https://msberends.github.io/AMR/">https://msberends.github.io/AMR</a></small>
--- a/logo_python.svg
+++ b/logo_python.svg
--- a/mstile-150x150.png
+++ b/mstile-150x150.png
--- a/mstile-310x310.png
+++ b/mstile-310x310.png
--- a/news/index.html
+++ b/news/index.html
@ -7,7 +7,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</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">
@ -47,18 +47,18 @@
    </div>
    <div class="section level2">
-<h2 class="pkg-version" data-toc-text="2.1.1.9084" id="amr-2119084">AMR 2.1.1.9084<a class="anchor" aria-label="anchor" href="#amr-2119084"></a></h2>
+<h2 class="pkg-version" data-toc-text="2.1.1.9087" id="amr-2119087">AMR 2.1.1.9087<a class="anchor" aria-label="anchor" href="#amr-2119087"></a></h2>
 <p><em>(this beta version will eventually become v3.0. We’re happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using <a href="https://msberends.github.io/AMR/#latest-development-version">the instructions here</a>.)</em></p>
 <div class="section level5">
-<h5 id="a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9084">A New Milestone: AMR v3.0 with One Health Support (= Human + Veterinary + Environmental)<a class="anchor" aria-label="anchor" href="#a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9084"></a></h5>
+<h5 id="a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9087">A New Milestone: AMR v3.0 with One Health Support (= Human + Veterinary + Environmental)<a class="anchor" aria-label="anchor" href="#a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9087"></a></h5>
 <p>This package now supports not only tools for AMR data analysis in clinical settings, but also for veterinary and environmental microbiology. This was made possible through a collaboration with the <a href="https://www.upei.ca/avc" class="external-link">University of Prince Edward Island’s Atlantic Veterinary College</a>, Canada. To celebrate this great improvement of the package, we also updated the package logo to reflect this change.</p>
 </div>
 <div class="section level3">
-<h3 id="breaking-2-1-1-9084">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9084"></a></h3>
+<h3 id="breaking-2-1-1-9087">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9087"></a></h3>
 <ul><li>Removed all functions and references that used the deprecated <code>rsi</code> class, which were all replaced with their <code>sir</code> equivalents over a year ago</li>
 </ul></div>
 <div class="section level3">
-<h3 id="new-2-1-1-9084">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9084"></a></h3>
+<h3 id="new-2-1-1-9087">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9087"></a></h3>
 <ul><li>
 <strong>One Health implementation</strong>
 <ul><li>Function <code><a href="../reference/as.sir.html">as.sir()</a></code> now has extensive support for veterinary breakpoints from CLSI. Use <code>breakpoint_type = "animal"</code> and set the <code>host</code> argument to a variable that contains animal species names.</li>
@ -95,7 +95,7 @@
 </ul></li>
 </ul></div>
 <div class="section level3">
-<h3 id="changed-2-1-1-9084">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9084"></a></h3>
+<h3 id="changed-2-1-1-9087">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9087"></a></h3>
 <ul><li>SIR interpretation
 <ul><li>It is now possible to use column names for argument <code>ab</code>, <code>mo</code>, and <code>uti</code>: <code>as.sir(..., ab = "column1", mo = "column2", uti = "column3")</code>. This greatly improves the flexibility for users.</li>
 <li>Users can now set their own criteria (using regular expressions) as to what should be considered S, I, R, SDD, and NI.</li>
@ -146,13 +146,13 @@
 <li>Improved algorithm of <code><a href="../reference/first_isolate.html">first_isolate()</a></code> when using the phenotype-based method, to prioritise records with the highest availability of SIR values</li>
 </ul></div>
 <div class="section level3">
-<h3 id="other-2-1-1-9084">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9084"></a></h3>
+<h3 id="other-2-1-1-9087">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9087"></a></h3>
 <ul><li>Greatly updated and expanded documentation</li>
 <li>Added Larisse Bolton, Jordan Stull, Matthew Saab, and Javier Sanchez as contributors, to thank them for their valuable input</li>
 <li>Stopped support for SAS (<code>.xpt</code>) files, since their file structure and extremely inefficient and requires more disk space than GitHub allows in a single commit.</li>
 </ul></div>
 <div class="section level3">
-<h3 id="older-versions-2-1-1-9084">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9084"></a></h3>
+<h3 id="older-versions-2-1-1-9087">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9087"></a></h3>
 <p>This changelog only contains changes from AMR v3.0 (October 2024) and later.</p>
 <ul><li>For prior v2 versions, please see <a href="https://github.com/msberends/AMR/blob/v2.1.1/NEWS.md" class="external-link">our v2 archive</a>.</li>
 <li>For prior v1 versions, please see <a href="https://github.com/msberends/AMR/blob/v1.8.2/NEWS.md" class="external-link">our v1 archive</a>.</li>
--- a/pkgdown.yml
+++ b/pkgdown.yml
@ -12,7 +12,7 @@ articles:
  resistance_predict: resistance_predict.html
  welcome_to_AMR: welcome_to_AMR.html
  WHONET: WHONET.html
-last_built: 2024-09-30T21:17Z
+last_built: 2024-10-02T08:36Z
 urls:
  reference: https://msberends.github.io/AMR/reference
  article: https://msberends.github.io/AMR/articles
--- a/reference/AMR-options.html
+++ b/reference/AMR-options.html
@ -7,7 +7,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/AMR.html
+++ b/reference/AMR.html
@ -21,7 +21,7 @@ The AMR package is available in English, 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="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/WHOCC.html
+++ b/reference/WHOCC.html
@ -7,7 +7,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/WHONET.html
+++ b/reference/WHONET.html
@ -7,7 +7,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/ab_from_text.html
+++ b/reference/ab_from_text.html
@ -7,7 +7,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/ab_property.html
+++ b/reference/ab_property.html
@ -7,7 +7,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/add_custom_antimicrobials.html
+++ b/reference/add_custom_antimicrobials.html
@ -7,7 +7,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/add_custom_microorganisms.html
+++ b/reference/add_custom_microorganisms.html
@ -7,7 +7,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/age.html
+++ b/reference/age.html
@ -7,7 +7,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -110,16 +110,16 @@
 <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  1965-12-05  58  58.81967         34</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1  1965-12-05  58  58.82514         34</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2  1980-03-01  44  44.58197         19</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2  1980-03-01  44  44.58743         19</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3  1949-11-01  74  74.91257         50</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3  1949-11-01  74  74.91803         50</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4  1947-02-14  77  77.62568         52</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4  1947-02-14  77  77.63115         52</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5  1940-02-19  84  84.61202         59</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5  1940-02-19  84  84.61749         59</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6  1988-01-10  36  36.72131         11</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6  1988-01-10  36  36.72678         11</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7  1997-08-27  27  27.09290          2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7  1997-08-27  27  27.09836          2</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8  1978-01-26  46  46.67760         21</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8  1978-01-26  46  46.68306         21</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9  1972-06-17  52  52.28689         27</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9  1972-06-17  52  52.29235         27</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1986-08-10  38  38.13934         13</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1986-08-10  38  38.14481         13</span>
 </code></pre></div>
    </div>
  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
--- a/reference/age_groups.html
+++ b/reference/age_groups.html
@ -7,7 +7,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</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
@ -7,7 +7,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</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
@ -9,7 +9,7 @@ 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="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</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/antibiotics.html
+++ b/reference/antibiotics.html
@ -7,7 +7,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/as.ab.html
+++ b/reference/as.ab.html
@ -7,7 +7,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/as.av.html
+++ b/reference/as.av.html
@ -7,7 +7,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/as.disk.html
+++ b/reference/as.disk.html
@ -7,7 +7,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</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-2.png
+++ b/reference/as.mic-2.png
--- a/reference/as.mic-3.png
+++ b/reference/as.mic-3.png
--- a/reference/as.mic-4.png
+++ b/reference/as.mic-4.png
--- a/reference/as.mic.html
+++ b/reference/as.mic.html
@ -7,7 +7,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/as.mo.html
+++ b/reference/as.mo.html
@ -7,7 +7,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</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">
@ -244,7 +244,7 @@
 <li><p>Any <em>non-bacterial</em> genus, species or subspecies of which the genus is present in the following list, has <code>prevalence = 1.25</code> in the <a href="microorganisms.html">microorganisms</a> data set: <em>Absidia</em>, <em>Acanthamoeba</em>, <em>Acremonium</em>, <em>Actinomucor</em>, <em>Aedes</em>, <em>Alternaria</em>, <em>Amoeba</em>, <em>Ancylostoma</em>, <em>Angiostrongylus</em>, <em>Anisakis</em>, <em>Anopheles</em>, <em>Apophysomyces</em>, <em>Arthroderma</em>, <em>Aspergillus</em>, <em>Aureobasidium</em>, <em>Basidiobolus</em>, <em>Beauveria</em>, <em>Bipolaris</em>, <em>Blastobotrys</em>, <em>Blastocystis</em>, <em>Blastomyces</em>, <em>Candida</em>, <em>Capillaria</em>, <em>Chaetomium</em>, <em>Chilomastix</em>, <em>Chrysonilia</em>, <em>Chrysosporium</em>, <em>Cladophialophora</em>, <em>Cladosporium</em>, <em>Clavispora</em>, <em>Coccidioides</em>, <em>Cokeromyces</em>, <em>Conidiobolus</em>, <em>Coniochaeta</em>, <em>Contracaecum</em>, <em>Cordylobia</em>, <em>Cryptococcus</em>, <em>Cryptosporidium</em>, <em>Cunninghamella</em>, <em>Curvularia</em>, <em>Cyberlindnera</em>, <em>Debaryozyma</em>, <em>Demodex</em>, <em>Dermatobia</em>, <em>Dientamoeba</em>, <em>Diphyllobothrium</em>, <em>Dirofilaria</em>, <em>Echinostoma</em>, <em>Entamoeba</em>, <em>Enterobius</em>, <em>Epidermophyton</em>, <em>Exidia</em>, <em>Exophiala</em>, <em>Exserohilum</em>, <em>Fasciola</em>, <em>Fonsecaea</em>, <em>Fusarium</em>, <em>Geotrichum</em>, <em>Giardia</em>, <em>Graphium</em>, <em>Haloarcula</em>, <em>Halobacterium</em>, <em>Halococcus</em>, <em>Hansenula</em>, <em>Hendersonula</em>, <em>Heterophyes</em>, <em>Histomonas</em>, <em>Histoplasma</em>, <em>Hortaea</em>, <em>Hymenolepis</em>, <em>Hypomyces</em>, <em>Hysterothylacium</em>, <em>Kloeckera</em>, <em>Kluyveromyces</em>, <em>Kodamaea</em>, <em>Lacazia</em>, <em>Leishmania</em>, <em>Lichtheimia</em>, <em>Lodderomyces</em>, <em>Lomentospora</em>, <em>Madurella</em>, <em>Malassezia</em>, <em>Malbranchea</em>, <em>Metagonimus</em>, <em>Meyerozyma</em>, <em>Microsporidium</em>, <em>Microsporum</em>, <em>Millerozyma</em>, <em>Mortierella</em>, <em>Mucor</em>, <em>Mycocentrospora</em>, <em>Nannizzia</em>, <em>Necator</em>, <em>Nectria</em>, <em>Ochroconis</em>, <em>Oesophagostomum</em>, <em>Oidiodendron</em>, <em>Opisthorchis</em>, <em>Paecilomyces</em>, <em>Paracoccidioides</em>, <em>Pediculus</em>, <em>Penicillium</em>, <em>Phaeoacremonium</em>, <em>Phaeomoniella</em>, <em>Phialophora</em>, <em>Phlebotomus</em>, <em>Phoma</em>, <em>Pichia</em>, <em>Piedraia</em>, <em>Pithomyces</em>, <em>Pityrosporum</em>, <em>Pneumocystis</em>, <em>Pseudallescheria</em>, <em>Pseudoscopulariopsis</em>, <em>Pseudoterranova</em>, <em>Pulex</em>, <em>Purpureocillium</em>, <em>Quambalaria</em>, <em>Rhinocladiella</em>, <em>Rhizomucor</em>, <em>Rhizopus</em>, <em>Rhodotorula</em>, <em>Saccharomyces</em>, <em>Saksenaea</em>, <em>Saprochaete</em>, <em>Sarcoptes</em>, <em>Scedosporium</em>, <em>Schistosoma</em>, <em>Schizosaccharomyces</em>, <em>Scolecobasidium</em>, <em>Scopulariopsis</em>, <em>Scytalidium</em>, <em>Spirometra</em>, <em>Sporobolomyces</em>, <em>Sporopachydermia</em>, <em>Sporothrix</em>, <em>Sporotrichum</em>, <em>Stachybotrys</em>, <em>Strongyloides</em>, <em>Syncephalastrum</em>, <em>Syngamus</em>, <em>Taenia</em>, <em>Talaromyces</em>, <em>Teleomorph</em>, <em>Toxocara</em>, <em>Trichinella</em>, <em>Trichobilharzia</em>, <em>Trichoderma</em>, <em>Trichomonas</em>, <em>Trichophyton</em>, <em>Trichosporon</em>, <em>Trichostrongylus</em>, <em>Trichuris</em>, <em>Tritirachium</em>, <em>Trombicula</em>, <em>Trypanosoma</em>, <em>Tunga</em>, <em>Ulocladium</em>, <em>Ustilago</em>, <em>Verticillium</em>, <em>Wallemia</em>, <em>Wangiella</em>, <em>Wickerhamomyces</em>, <em>Wuchereria</em>, <em>Yarrowia</em>, or <em>Zygosaccharomyces</em>;</p></li>
 <li><p>All other records have <code>prevalence = 2.0</code> in the <a href="microorganisms.html">microorganisms</a> data set.</p></li>
 </ul><p>When calculating the matching score, all characters in \(x\) and \(n\) are ignored that are other than A-Z, a-z, 0-9, spaces and parentheses.</p>
-<p>All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., <code>"E. coli"</code> will return the microbial ID of <em>Escherichia coli</em> (\(m = 0.598\), a highly prevalent microorganism found in humans) and not <em>Entamoeba coli</em> (\(m = 0.381\), a less prevalent microorganism in humans), although the latter would alphabetically come first.</p>
+<p>All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., <code>"E. coli"</code> will return the microbial ID of <em>Escherichia coli</em> (\(m = 0.688\), a highly prevalent microorganism found in humans) and not <em>Entamoeba coli</em> (\(m = 0.381\), a less prevalent microorganism in humans), although the latter would alphabetically come first.</p>
    </div>
    <div class="section level2">
    <h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2>
@ -316,7 +316,7 @@
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># All mo_* functions use as.mo() internally too (see ?mo_property):</span></span></span>
 <span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_genus</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Enterococcus"</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Escherichia"</span>
 <span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="st">"ESCO"</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Gram-negative"</span>
 <span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span><span class="st">"ESCCOL"</span>, ab <span class="op">=</span> <span class="st">"vanco"</span><span class="op">)</span></span></span>
--- a/reference/as.sir.html
+++ b/reference/as.sir.html
@ -21,7 +21,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
    <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="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</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">
@ -751,7 +751,7 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
 <span class="r-msg co"><span class="r-pr">#&gt;</span> 2024...</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>  OK </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>      microorganism amoxicillin cipro tobra genta ERY</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1 Escherichia coli           8     S  &lt;NA&gt;  &lt;NA&gt;   R</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1 Escherichia coli           8  &lt;NA&gt;     S     S   R</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co">## Using base R ------------------------------------------------</span></span></span>
@ -785,16 +785,16 @@ 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: 57 × 16</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    datetime            index ab_given mo_given host_given ab   mo              </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span>              <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>      <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span>            </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2024-09-30 <span style="color: #949494;">21:18:40</span>     4 AMX      B_STRPT… human      AMX  B_STRPT_PNMN    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2024-10-02 <span style="color: #949494;">08:37:04</span>     4 AMX      B_STRPT… human      AMX  B_STRPT_PNMN    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2024-09-30 <span style="color: #949494;">21:18:47</span>     4 genta    Escheri… human      GEN  B_[ORD]_ENTRBCTR</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2024-10-02 <span style="color: #949494;">08:37:11</span>     4 genta    Escheri… human      GEN  B_[ORD]_ENTRBCTR</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2024-09-30 <span style="color: #949494;">21:18:47</span>     4 genta    Escheri… human      GEN  B_[ORD]_ENTRBCTR</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2024-10-02 <span style="color: #949494;">08:37:11</span>     4 genta    Escheri… human      GEN  B_[ORD]_ENTRBCTR</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2024-09-30 <span style="color: #949494;">21:18:48</span>     4 genta    Escheri… cattle     GEN  B_ESCHR_COLI    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2024-10-02 <span style="color: #949494;">08:37:12</span>     4 genta    Escheri… cattle     GEN  B_ESCHR_COLI    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2024-09-30 <span style="color: #949494;">21:18:48</span>     4 genta    Escheri… cattle     GEN  B_ESCHR_COLI    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2024-10-02 <span style="color: #949494;">08:37:12</span>     4 genta    Escheri… cattle     GEN  B_ESCHR_COLI    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2024-09-30 <span style="color: #949494;">21:18:40</span>     3 AMX      B_STRPT… human      AMX  B_STRPT_PNMN    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2024-10-02 <span style="color: #949494;">08:37:04</span>     3 AMX      B_STRPT… human      AMX  B_STRPT_PNMN    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2024-09-30 <span style="color: #949494;">21:18:47</span>     3 tobra    Escheri… human      TOB  B_[ORD]_ENTRBCTR</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2024-10-02 <span style="color: #949494;">08:37:11</span>     3 tobra    Escheri… human      TOB  B_[ORD]_ENTRBCTR</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2024-09-30 <span style="color: #949494;">21:18:47</span>     3 tobra    Escheri… human      TOB  B_[ORD]_ENTRBCTR</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2024-10-02 <span style="color: #949494;">08:37:11</span>     3 tobra    Escheri… human      TOB  B_[ORD]_ENTRBCTR</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2024-09-30 <span style="color: #949494;">21:18:48</span>     3 tobra    Escheri… horses     TOB  B_ESCHR_COLI    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2024-10-02 <span style="color: #949494;">08:37:12</span>     3 tobra    Escheri… horses     TOB  B_ESCHR_COLI    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2024-09-30 <span style="color: #949494;">21:18:48</span>     3 tobra    Escheri… horses     TOB  B_ESCHR_COLI    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2024-10-02 <span style="color: #949494;">08:37:12</span>     3 tobra    Escheri… horses     TOB  B_ESCHR_COLI    </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 47 more rows</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 9 more variables: host &lt;chr&gt;, method &lt;chr&gt;, input &lt;dbl&gt;, outcome &lt;sir&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   notes &lt;chr&gt;, guideline &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;,</span></span>
--- a/reference/atc_online.html
+++ b/reference/atc_online.html
@ -7,7 +7,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/av_from_text.html
+++ b/reference/av_from_text.html
@ -7,7 +7,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/av_property.html
+++ b/reference/av_property.html
@ -7,7 +7,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/availability.html
+++ b/reference/availability.html
@ -7,7 +7,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/bug_drug_combinations.html
+++ b/reference/bug_drug_combinations.html
@ -7,7 +7,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/clinical_breakpoints.html
+++ b/reference/clinical_breakpoints.html
@ -21,7 +21,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/count.html
+++ b/reference/count.html
@ -9,7 +9,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/custom_eucast_rules.html
+++ b/reference/custom_eucast_rules.html
@ -7,7 +7,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/dosage.html
+++ b/reference/dosage.html
@ -7,7 +7,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</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
@ -9,7 +9,7 @@ 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="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/example_isolates.html
+++ b/reference/example_isolates.html
@ -7,7 +7,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/example_isolates_unclean.html
+++ b/reference/example_isolates_unclean.html
@ -7,7 +7,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/export_ncbi_biosample.html
+++ b/reference/export_ncbi_biosample.html
@ -7,7 +7,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/first_isolate.html
+++ b/reference/first_isolate.html
@ -9,7 +9,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/g.test.html
+++ b/reference/g.test.html
@ -7,7 +7,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/get_episode.html
+++ b/reference/get_episode.html
@ -7,7 +7,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/ggplot_pca.html
+++ b/reference/ggplot_pca.html
@ -7,7 +7,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/ggplot_sir.html
+++ b/reference/ggplot_sir.html
@ -7,7 +7,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/guess_ab_col.html
+++ b/reference/guess_ab_col.html
@ -7,7 +7,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/index.html
+++ b/reference/index.html
@ -7,7 +7,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/intrinsic_resistant.html
+++ b/reference/intrinsic_resistant.html
@ -7,7 +7,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/italicise_taxonomy.html
+++ b/reference/italicise_taxonomy.html
@ -7,7 +7,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/join.html
+++ b/reference/join.html
@ -7,7 +7,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/key_antimicrobials.html
+++ b/reference/key_antimicrobials.html
@ -7,7 +7,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/kurtosis.html
+++ b/reference/kurtosis.html
@ -7,7 +7,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/like.html
+++ b/reference/like.html
@ -7,7 +7,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/mdro.html
+++ b/reference/mdro.html
@ -7,7 +7,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/mean_amr_distance.html
+++ b/reference/mean_amr_distance.html
@ -7,7 +7,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/microorganisms.codes.html
+++ b/reference/microorganisms.codes.html
@ -7,7 +7,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/microorganisms.groups.html
+++ b/reference/microorganisms.groups.html
@ -7,7 +7,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/microorganisms.html
+++ b/reference/microorganisms.html
@ -9,7 +9,7 @@ This data set is carefully crafted, yet made 100% reproducible from public and a
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/mo_matching_score.html
+++ b/reference/mo_matching_score.html
@ -7,7 +7,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</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">
@ -97,7 +97,7 @@
 <li><p>Any <em>non-bacterial</em> genus, species or subspecies of which the genus is present in the following list, has <code>prevalence = 1.25</code> in the <a href="microorganisms.html">microorganisms</a> data set: <em>Absidia</em>, <em>Acanthamoeba</em>, <em>Acremonium</em>, <em>Actinomucor</em>, <em>Aedes</em>, <em>Alternaria</em>, <em>Amoeba</em>, <em>Ancylostoma</em>, <em>Angiostrongylus</em>, <em>Anisakis</em>, <em>Anopheles</em>, <em>Apophysomyces</em>, <em>Arthroderma</em>, <em>Aspergillus</em>, <em>Aureobasidium</em>, <em>Basidiobolus</em>, <em>Beauveria</em>, <em>Bipolaris</em>, <em>Blastobotrys</em>, <em>Blastocystis</em>, <em>Blastomyces</em>, <em>Candida</em>, <em>Capillaria</em>, <em>Chaetomium</em>, <em>Chilomastix</em>, <em>Chrysonilia</em>, <em>Chrysosporium</em>, <em>Cladophialophora</em>, <em>Cladosporium</em>, <em>Clavispora</em>, <em>Coccidioides</em>, <em>Cokeromyces</em>, <em>Conidiobolus</em>, <em>Coniochaeta</em>, <em>Contracaecum</em>, <em>Cordylobia</em>, <em>Cryptococcus</em>, <em>Cryptosporidium</em>, <em>Cunninghamella</em>, <em>Curvularia</em>, <em>Cyberlindnera</em>, <em>Debaryozyma</em>, <em>Demodex</em>, <em>Dermatobia</em>, <em>Dientamoeba</em>, <em>Diphyllobothrium</em>, <em>Dirofilaria</em>, <em>Echinostoma</em>, <em>Entamoeba</em>, <em>Enterobius</em>, <em>Epidermophyton</em>, <em>Exidia</em>, <em>Exophiala</em>, <em>Exserohilum</em>, <em>Fasciola</em>, <em>Fonsecaea</em>, <em>Fusarium</em>, <em>Geotrichum</em>, <em>Giardia</em>, <em>Graphium</em>, <em>Haloarcula</em>, <em>Halobacterium</em>, <em>Halococcus</em>, <em>Hansenula</em>, <em>Hendersonula</em>, <em>Heterophyes</em>, <em>Histomonas</em>, <em>Histoplasma</em>, <em>Hortaea</em>, <em>Hymenolepis</em>, <em>Hypomyces</em>, <em>Hysterothylacium</em>, <em>Kloeckera</em>, <em>Kluyveromyces</em>, <em>Kodamaea</em>, <em>Lacazia</em>, <em>Leishmania</em>, <em>Lichtheimia</em>, <em>Lodderomyces</em>, <em>Lomentospora</em>, <em>Madurella</em>, <em>Malassezia</em>, <em>Malbranchea</em>, <em>Metagonimus</em>, <em>Meyerozyma</em>, <em>Microsporidium</em>, <em>Microsporum</em>, <em>Millerozyma</em>, <em>Mortierella</em>, <em>Mucor</em>, <em>Mycocentrospora</em>, <em>Nannizzia</em>, <em>Necator</em>, <em>Nectria</em>, <em>Ochroconis</em>, <em>Oesophagostomum</em>, <em>Oidiodendron</em>, <em>Opisthorchis</em>, <em>Paecilomyces</em>, <em>Paracoccidioides</em>, <em>Pediculus</em>, <em>Penicillium</em>, <em>Phaeoacremonium</em>, <em>Phaeomoniella</em>, <em>Phialophora</em>, <em>Phlebotomus</em>, <em>Phoma</em>, <em>Pichia</em>, <em>Piedraia</em>, <em>Pithomyces</em>, <em>Pityrosporum</em>, <em>Pneumocystis</em>, <em>Pseudallescheria</em>, <em>Pseudoscopulariopsis</em>, <em>Pseudoterranova</em>, <em>Pulex</em>, <em>Purpureocillium</em>, <em>Quambalaria</em>, <em>Rhinocladiella</em>, <em>Rhizomucor</em>, <em>Rhizopus</em>, <em>Rhodotorula</em>, <em>Saccharomyces</em>, <em>Saksenaea</em>, <em>Saprochaete</em>, <em>Sarcoptes</em>, <em>Scedosporium</em>, <em>Schistosoma</em>, <em>Schizosaccharomyces</em>, <em>Scolecobasidium</em>, <em>Scopulariopsis</em>, <em>Scytalidium</em>, <em>Spirometra</em>, <em>Sporobolomyces</em>, <em>Sporopachydermia</em>, <em>Sporothrix</em>, <em>Sporotrichum</em>, <em>Stachybotrys</em>, <em>Strongyloides</em>, <em>Syncephalastrum</em>, <em>Syngamus</em>, <em>Taenia</em>, <em>Talaromyces</em>, <em>Teleomorph</em>, <em>Toxocara</em>, <em>Trichinella</em>, <em>Trichobilharzia</em>, <em>Trichoderma</em>, <em>Trichomonas</em>, <em>Trichophyton</em>, <em>Trichosporon</em>, <em>Trichostrongylus</em>, <em>Trichuris</em>, <em>Tritirachium</em>, <em>Trombicula</em>, <em>Trypanosoma</em>, <em>Tunga</em>, <em>Ulocladium</em>, <em>Ustilago</em>, <em>Verticillium</em>, <em>Wallemia</em>, <em>Wangiella</em>, <em>Wickerhamomyces</em>, <em>Wuchereria</em>, <em>Yarrowia</em>, or <em>Zygosaccharomyces</em>;</p></li>
 <li><p>All other records have <code>prevalence = 2.0</code> in the <a href="microorganisms.html">microorganisms</a> data set.</p></li>
 </ul><p>When calculating the matching score, all characters in \(x\) and \(n\) are ignored that are other than A-Z, a-z, 0-9, spaces and parentheses.</p>
-<p>All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., <code>"E. coli"</code> will return the microbial ID of <em>Escherichia coli</em> (\(m = 0.598\), a highly prevalent microorganism found in humans) and not <em>Entamoeba coli</em> (\(m = 0.381\), a less prevalent microorganism in humans), although the latter would alphabetically come first.</p>
+<p>All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., <code>"E. coli"</code> will return the microbial ID of <em>Escherichia coli</em> (\(m = 0.688\), a highly prevalent microorganism found in humans) and not <em>Entamoeba coli</em> (\(m = 0.381\), a less prevalent microorganism in humans), although the latter would alphabetically come first.</p>
    </div>
    <div class="section level2">
    <h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2>
@ -113,18 +113,18 @@
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu"><a href="as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mo'</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] B_ENTRC_CRTL</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] B_ESCHR_COLI</span>
 <span class="r-in"><span><span class="fu"><a href="as.mo.html">mo_uncertainties</a></span><span class="op">(</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Matching scores are based on the resemblance between the input and the full</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> taxonomic name, and the pathogenicity in humans. See ?mo_matching_score.</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> --------------------------------------------------------------------------------</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> "E. coli" -&gt; Enterococcus crotali (B_ENTRC_CRTL, 0.650)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> "E. coli" -&gt; Escherichia coli (B_ESCHR_COLI, 0.688)</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Also matched: Escherichia coli (0.598), Enterococcus columbae (0.595),</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Also matched: Enterococcus crotali (0.650), Escherichia coli coli</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>               Enterococcus camelliae (0.591), Enterococcus casseliflavus (0.577),</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>               (0.643), Escherichia coli expressing (0.611), Enterococcus columbae</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>               Escherichia coli coli (0.559), Enterococcus canis (0.556), Enterococcus</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>               (0.595), Enterococcus camelliae (0.591), Enterococcus casseliflavus</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>               cecorum (0.550), Enterococcus canintestini (0.540), Escherichia coli</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>               (0.577), Enterococcus canis (0.556), Enterococcus cecorum (0.550),</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>               expressing (0.531), and Enterobacter cowanii (0.522)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>               Enterococcus canintestini (0.540), and Enterobacter cowanii (0.522)</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Only the first 10 other matches of each record are shown. Run</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> print(mo_uncertainties(), n = ...) to view more entries, or save</span>
@ -134,7 +134,7 @@
 <span class="r-in"><span>  x <span class="op">=</span> <span class="st">"E. coli"</span>,</span></span>
 <span class="r-in"><span>  n <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Escherichia coli"</span>, <span class="st">"Entamoeba coli"</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] 0.5978261 0.3809524</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.6875000 0.3809524</span>
 </code></pre></div>
    </div>
  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
--- a/reference/mo_property.html
+++ b/reference/mo_property.html
@ -7,7 +7,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</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
@ -9,7 +9,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/pca.html
+++ b/reference/pca.html
@ -7,7 +7,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/plot.html
+++ b/reference/plot.html
@ -9,7 +9,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/proportion.html
+++ b/reference/proportion.html
@ -9,7 +9,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/random.html
+++ b/reference/random.html
@ -7,7 +7,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</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-4.png
+++ b/reference/resistance_predict-4.png
--- a/reference/resistance_predict.html
+++ b/reference/resistance_predict.html
@ -7,7 +7,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</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">
@ -263,8 +263,7 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
 <span class="r-in"><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">data</span><span class="op">)</span></span></span>
 <span class="r-in"><span>  <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">data</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
-<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error:</span> in resistance_predict(): the data provided in argument x must contain rows and columns (current</span>
+<span class="r-plt img"><img src="resistance_predict-4.png" alt="" width="700" height="433"></span>
 <span class="r-err co"><span class="r-pr">#&gt;</span> dimensions: 0x46)</span>
 <span class="r-in"><span><span class="co"># }</span></span></span>
 </code></pre></div>
    </div>
--- a/reference/skewness.html
+++ b/reference/skewness.html
@ -9,7 +9,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/translate.html
+++ b/reference/translate.html
@ -7,7 +7,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</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">
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--- a/Show More
+++ b/Show More
Author	SHA1	Message	Date
github-actions	74bb1abb0c	Built site for AMR@2.1.1.9087: `738689b`	2024-10-02 08:39:39 +00:00
github-actions	4762d07c22	Built site for AMR@2.1.1.9086: `50a9f8f`	2024-10-02 08:29:15 +00:00