Built site for AMR: 1.8.2.9043@8dc94a9

2026-10-01 04:13:33 +02:00 · 2022-11-05 08:39:06 +00:00
1 parent b248bcc62a
commit 863a83ee08
@@ -36,7 +36,7 @@
    <a class="navbar-brand me-2" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -38,7 +38,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -395,65 +395,65 @@ data set:</p>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2017-05-11</td>
+<td align="center">2013-01-16</td>
-<td align="center">P2</td>
+<td align="center">B4</td>
-<td align="center">Hospital B</td>
+<td align="center">Hospital A</td>
-<td align="center">Escherichia coli</td>
+<td align="center">Klebsiella pneumoniae</td>
-<td align="center">S</td>
+<td align="center">R</td>
 <td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">F</td>
 </tr>
 <tr class="even">
 <td align="center">2014-09-24</td>
 <td align="center">W9</td>
 <td align="center">Hospital B</td>
 <td align="center">Streptococcus pneumoniae</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">F</td>
 </tr>
 <tr class="odd">
 <td align="center">2015-03-26</td>
 <td align="center">P5</td>
 <td align="center">Hospital B</td>
 <td align="center">Escherichia coli</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">S</td>
 <td align="center">F</td>
 </tr>
 <tr class="even">
 <td align="center">2010-10-29</td>
 <td align="center">B9</td>
 <td align="center">Hospital D</td>
 <td align="center">Escherichia coli</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">M</td>
 </tr>
 <tr class="even">
 <td align="center">2016-04-21</td>
 <td align="center">S8</td>
 <td align="center">Hospital C</td>
 <td align="center">Staphylococcus aureus</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">S</td>
 <td align="center">F</td>
 </tr>
 <tr class="odd">
-<td align="center">2013-04-29</td>
+<td align="center">2013-01-04</td>
-<td align="center">U9</td>
+<td align="center">E1</td>
 <td align="center">Hospital A</td>
 <td align="center">Streptococcus pneumoniae</td>
 <td align="center">R</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">S</td>
 <td align="center">M</td>
 </tr>
 <tr class="even">
 <td align="center">2011-07-13</td>
 <td align="center">Y4</td>
 <td align="center">Hospital C</td>
 <td align="center">Staphylococcus aureus</td>
 <td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
-<td align="center">S</td>
+<td align="center">R</td>
 <td align="center">F</td>
 </tr>
-<tr class="even">
+<tr class="odd">
-<td align="center">2010-07-12</td>
+<td align="center">2013-12-18</td>
-<td align="center">U6</td>
+<td align="center">A10</td>
 <td align="center">Hospital B</td>
 <td align="center">Escherichia coli</td>
 <td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">M</td>
 </tr>
 <tr class="even">
 <td align="center">2013-01-16</td>
 <td align="center">N7</td>
 <td align="center">Hospital A</td>
 <td align="center">Escherichia coli</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
@@ -494,16 +494,16 @@ Longest: 1</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">M</td>
-<td align="right">10,235</td>
+<td align="right">10,495</td>
-<td align="right">51.18%</td>
+<td align="right">52.48%</td>
-<td align="right">10,235</td>
+<td align="right">10,495</td>
-<td align="right">51.18%</td>
+<td align="right">52.48%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">F</td>
-<td align="right">9,765</td>
+<td align="right">9,505</td>
-<td align="right">48.83%</td>
+<td align="right">47.53%</td>
 <td align="right">20,000</td>
 <td align="right">100.00%</td>
 </tr>
@@ -616,10 +616,10 @@ takes into account the antimicrobial susceptibility test results using
 <span><span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span></span>
 <span><span class="co"># 2</span></span>
 <span><span class="co"># Including isolates from ICU.</span></span>
-<span><span class="co"># =&gt; Found 10,603 'phenotype-based' first isolates (53.0% of total where a</span></span>
+<span><span class="co"># =&gt; Found 10,707 'phenotype-based' first isolates (53.5% of total where a</span></span>
 <span><span class="co">#    microbial ID was available)</span></span></code></pre></div>
-<p>So only 53% is suitable for resistance analysis! We can now filter on
+<p>So only 53.5% is suitable for resistance analysis! We can now filter
-it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the
+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="cb15"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
@@ -629,7 +629,7 @@ it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" cl
 <code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">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>
 <span><span class="co"># Including isolates from ICU.</span></span></code></pre></div>
-<p>So we end up with 10,603 isolates for analysis. Now our data looks
+<p>So we end up with 10,707 isolates for analysis. Now our data looks
 like:</p>
 <div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">data_1st</span><span class="op">)</span></span></code></pre></div>
@@ -668,63 +668,31 @@ like:</p>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="left">1</td>
+<td align="left">3</td>
-<td align="center">2017-05-11</td>
+<td align="center">2013-01-04</td>
-<td align="center">P2</td>
+<td align="center">E1</td>
-<td align="center">Hospital B</td>
+<td align="center">Hospital A</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">R</td>
 <td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">F</td>
 <td align="center">Gram-negative</td>
 <td align="center">Escherichia</td>
 <td align="center">coli</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="center">2014-09-24</td>
 <td align="center">W9</td>
 <td align="center">Hospital B</td>
 <td align="center">B_STRPT_PNMN</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">R</td>
-<td align="center">F</td>
+<td align="center">R</td>
 <td align="center">R</td>
 <td align="center">R</td>
 <td align="center">M</td>
 <td align="center">Gram-positive</td>
 <td align="center">Streptococcus</td>
 <td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="odd">
 <td align="left">3</td>
 <td align="center">2015-03-26</td>
 <td align="center">P5</td>
 <td align="center">Hospital B</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">S</td>
 <td align="center">F</td>
 <td align="center">Gram-negative</td>
 <td align="center">Escherichia</td>
 <td align="center">coli</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
-<td align="left">5</td>
+<td align="left">4</td>
-<td align="center">2013-04-29</td>
+<td align="center">2011-07-13</td>
-<td align="center">U9</td>
+<td align="center">Y4</td>
-<td align="center">Hospital A</td>
+<td align="center">Hospital C</td>
 <td align="center">B_STPHY_AURS</td>
 <td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
-<td align="center">S</td>
+<td align="center">R</td>
 <td align="center">F</td>
 <td align="center">Gram-positive</td>
 <td align="center">Staphylococcus</td>
@@ -733,9 +701,9 @@ like:</p>
 </tr>
 <tr class="odd">
 <td align="left">6</td>
-<td align="center">2010-07-12</td>
+<td align="center">2013-01-16</td>
-<td align="center">U6</td>
+<td align="center">N7</td>
-<td align="center">Hospital B</td>
+<td align="center">Hospital A</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">S</td>
 <td align="center">S</td>
@@ -748,19 +716,51 @@ like:</p>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
-<td align="left">10</td>
+<td align="left">7</td>
-<td align="center">2015-03-25</td>
+<td align="center">2013-07-13</td>
-<td align="center">B1</td>
+<td align="center">X9</td>
-<td align="center">Hospital D</td>
+<td align="center">Hospital B</td>
-<td align="center">B_STPHY_AURS</td>
+<td align="center">B_ESCHR_COLI</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">F</td>
 <td align="center">Gram-negative</td>
 <td align="center">Escherichia</td>
 <td align="center">coli</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="odd">
 <td align="left">9</td>
 <td align="center">2014-01-13</td>
 <td align="center">L1</td>
 <td align="center">Hospital B</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">M</td>
-<td align="center">Gram-positive</td>
+<td align="center">Gram-negative</td>
-<td align="center">Staphylococcus</td>
+<td align="center">Escherichia</td>
-<td align="center">aureus</td>
+<td align="center">coli</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
 <td align="left">10</td>
 <td align="center">2017-10-15</td>
 <td align="center">F1</td>
 <td align="center">Hospital B</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">M</td>
 <td align="center">Gram-negative</td>
 <td align="center">Escherichia</td>
 <td align="center">coli</td>
 <td align="center">TRUE</td>
 </tr>
 </tbody>
@@ -796,8 +796,8 @@ readable:</p>
 <code class="sourceCode R"><span><span class="va">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="https://msberends.github.io/cleaner/reference/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></span></code></pre></div>
 <p><strong>Frequency table</strong></p>
 <p>Class: character<br>
-Length: 10,603<br>
+Length: 10,707<br>
-Available: 10,603 (100%, NA: 0 = 0%)<br>
+Available: 10,707 (100%, NA: 0 = 0%)<br>
 Unique: 4</p>
 <p>Shortest: 16<br>
 Longest: 24</p>
@@ -822,33 +822,33 @@ Longest: 24</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">Escherichia coli</td>
-<td align="right">4,603</td>
+<td align="right">4,763</td>
-<td align="right">43.41%</td>
+<td align="right">44.48%</td>
-<td align="right">4,603</td>
+<td align="right">4,763</td>
-<td align="right">43.41%</td>
+<td align="right">44.48%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">Staphylococcus aureus</td>
-<td align="right">2,709</td>
+<td align="right">2,688</td>
-<td align="right">25.55%</td>
+<td align="right">25.11%</td>
-<td align="right">7,312</td>
+<td align="right">7,451</td>
-<td align="right">68.96%</td>
+<td align="right">69.59%</td>
 </tr>
 <tr class="odd">
 <td align="left">3</td>
 <td align="left">Streptococcus pneumoniae</td>
-<td align="right">2,106</td>
+<td align="right">2,091</td>
-<td align="right">19.86%</td>
+<td align="right">19.53%</td>
-<td align="right">9,418</td>
+<td align="right">9,542</td>
-<td align="right">88.82%</td>
+<td align="right">89.12%</td>
 </tr>
 <tr class="even">
 <td align="left">4</td>
 <td align="left">Klebsiella pneumoniae</td>
-<td align="right">1,185</td>
+<td align="right">1,165</td>
-<td align="right">11.18%</td>
+<td align="right">10.88%</td>
-<td align="right">10,603</td>
+<td align="right">10,707</td>
 <td align="right">100.00%</td>
 </tr>
 </tbody>
@@ -897,42 +897,12 @@ antibiotic class they are in:</p>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2014-09-24</td>
+<td align="center">2013-01-04</td>
-<td align="center">W9</td>
+<td align="center">E1</td>
 <td align="center">Hospital B</td>
 <td align="center">B_STRPT_PNMN</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">F</td>
 <td align="center">Gram-positive</td>
 <td align="center">Streptococcus</td>
 <td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
 <td align="center">2014-11-16</td>
 <td align="center">M1</td>
 <td align="center">Hospital A</td>
 <td align="center">B_STRPT_PNMN</td>
 <td align="center">R</td>
 <td align="center">R</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">M</td>
 <td align="center">Gram-positive</td>
 <td align="center">Streptococcus</td>
 <td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="odd">
 <td align="center">2016-07-19</td>
 <td align="center">G10</td>
 <td align="center">Hospital B</td>
 <td align="center">B_STRPT_PNMN</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">R</td>
 <td align="center">M</td>
@@ -942,28 +912,13 @@ antibiotic class they are in:</p>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
-<td align="center">2015-01-12</td>
+<td align="center">2011-07-13</td>
-<td align="center">W8</td>
+<td align="center">Y4</td>
-<td align="center">Hospital A</td>
+<td align="center">Hospital C</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">F</td>
 <td align="center">Gram-negative</td>
 <td align="center">Escherichia</td>
 <td align="center">coli</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="odd">
 <td align="center">2014-10-02</td>
 <td align="center">X5</td>
 <td align="center">Hospital D</td>
 <td align="center">B_STPHY_AURS</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">F</td>
 <td align="center">Gram-positive</td>
@@ -971,13 +926,13 @@ antibiotic class they are in:</p>
 <td align="center">aureus</td>
 <td align="center">TRUE</td>
 </tr>
-<tr class="even">
+<tr class="odd">
-<td align="center">2010-11-15</td>
+<td align="center">2010-11-23</td>
-<td align="center">M5</td>
+<td align="center">B2</td>
-<td align="center">Hospital C</td>
+<td align="center">Hospital B</td>
 <td align="center">B_KLBSL_PNMN</td>
 <td align="center">R</td>
-<td align="center">S</td>
+<td align="center">I</td>
 <td align="center">R</td>
 <td align="center">R</td>
 <td align="center">M</td>
@@ -986,6 +941,51 @@ antibiotic class they are in:</p>
 <td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
 <td align="center">2016-09-07</td>
 <td align="center">I6</td>
 <td align="center">Hospital B</td>
 <td align="center">B_STRPT_PNMN</td>
 <td align="center">R</td>
 <td align="center">R</td>
 <td align="center">R</td>
 <td align="center">R</td>
 <td align="center">M</td>
 <td align="center">Gram-positive</td>
 <td align="center">Streptococcus</td>
 <td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="odd">
 <td align="center">2010-04-16</td>
 <td align="center">T8</td>
 <td align="center">Hospital A</td>
 <td align="center">B_STRPT_PNMN</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">F</td>
 <td align="center">Gram-positive</td>
 <td align="center">Streptococcus</td>
 <td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
 <td align="center">2013-04-19</td>
 <td align="center">G5</td>
 <td align="center">Hospital B</td>
 <td align="center">B_STRPT_PNMN</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">M</td>
 <td align="center">Gram-positive</td>
 <td align="center">Streptococcus</td>
 <td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
 </tbody>
 </table>
 <p>If you want to get a quick glance of the number of isolates in
@@ -1009,50 +1009,50 @@ different bug/drug combinations, you can use the
 <tr class="odd">
 <td align="center">E. coli</td>
 <td align="center">AMX</td>
-<td align="center">2197</td>
+<td align="center">2209</td>
-<td align="center">137</td>
+<td align="center">126</td>
-<td align="center">2269</td>
+<td align="center">2428</td>
-<td align="center">4603</td>
+<td align="center">4763</td>
 </tr>
 <tr class="even">
 <td align="center">E. coli</td>
 <td align="center">AMC</td>
-<td align="center">3391</td>
+<td align="center">3491</td>
-<td align="center">167</td>
+<td align="center">158</td>
-<td align="center">1045</td>
+<td align="center">1114</td>
-<td align="center">4603</td>
+<td align="center">4763</td>
 </tr>
 <tr class="odd">
 <td align="center">E. coli</td>
 <td align="center">CIP</td>
-<td align="center">3413</td>
+<td align="center">3463</td>
 <td align="center">0</td>
-<td align="center">1190</td>
+<td align="center">1300</td>
-<td align="center">4603</td>
+<td align="center">4763</td>
 </tr>
 <tr class="even">
 <td align="center">E. coli</td>
 <td align="center">GEN</td>
-<td align="center">3980</td>
+<td align="center">4154</td>
 <td align="center">0</td>
-<td align="center">623</td>
+<td align="center">609</td>
-<td align="center">4603</td>
+<td align="center">4763</td>
 </tr>
 <tr class="odd">
 <td align="center">K. pneumoniae</td>
 <td align="center">AMX</td>
 <td align="center">0</td>
 <td align="center">0</td>
-<td align="center">1185</td>
+<td align="center">1165</td>
-<td align="center">1185</td>
+<td align="center">1165</td>
 </tr>
 <tr class="even">
 <td align="center">K. pneumoniae</td>
 <td align="center">AMC</td>
-<td align="center">942</td>
+<td align="center">905</td>
-<td align="center">43</td>
+<td align="center">49</td>
-<td align="center">200</td>
+<td align="center">211</td>
-<td align="center">1185</td>
+<td align="center">1165</td>
 </tr>
 </tbody>
 </table>
@@ -1075,34 +1075,34 @@ different bug/drug combinations, you can use the
 <tr class="odd">
 <td align="center">E. coli</td>
 <td align="center">GEN</td>
-<td align="center">3980</td>
+<td align="center">4154</td>
 <td align="center">0</td>
-<td align="center">623</td>
+<td align="center">609</td>
-<td align="center">4603</td>
+<td align="center">4763</td>
 </tr>
 <tr class="even">
 <td align="center">K. pneumoniae</td>
 <td align="center">GEN</td>
-<td align="center">1060</td>
+<td align="center">1057</td>
 <td align="center">0</td>
-<td align="center">125</td>
+<td align="center">108</td>
-<td align="center">1185</td>
+<td align="center">1165</td>
 </tr>
 <tr class="odd">
 <td align="center">S. aureus</td>
 <td align="center">GEN</td>
-<td align="center">2422</td>
+<td align="center">2378</td>
 <td align="center">0</td>
-<td align="center">287</td>
+<td align="center">310</td>
-<td align="center">2709</td>
+<td align="center">2688</td>
 </tr>
 <tr class="even">
 <td align="center">S. pneumoniae</td>
 <td align="center">GEN</td>
 <td align="center">0</td>
 <td align="center">0</td>
-<td align="center">2106</td>
+<td align="center">2091</td>
-<td align="center">2106</td>
+<td align="center">2091</td>
 </tr>
 </tbody>
 </table>
@@ -1134,7 +1134,7 @@ I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equa
 own:</p>
 <div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">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"># [1] 0.5352259</span></span></code></pre></div>
+<span><span class="co"># [1] 0.5443168</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="cb27"><pre class="downlit sourceCode r">
@@ -1149,19 +1149,19 @@ own:</p>
 <tbody>
 <tr class="odd">
 <td align="center">Hospital A</td>
-<td align="center">0.5432099</td>
+<td align="center">0.5446860</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital B</td>
-<td align="center">0.5246981</td>
+<td align="center">0.5468415</td>
 </tr>
 <tr class="odd">
 <td align="center">Hospital C</td>
-<td align="center">0.5336856</td>
+<td align="center">0.5404884</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital D</td>
-<td align="center">0.5419501</td>
+<td align="center">0.5420827</td>
 </tr>
 </tbody>
 </table>
@@ -1186,23 +1186,23 @@ all isolates available for every group (i.e. values S, I or R):</p>
 <tbody>
 <tr class="odd">
 <td align="center">Hospital A</td>
-<td align="center">0.5432099</td>
+<td align="center">0.5446860</td>
-<td align="center">3240</td>
+<td align="center">3312</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital B</td>
-<td align="center">0.5246981</td>
+<td align="center">0.5468415</td>
-<td align="center">3644</td>
+<td align="center">3736</td>
 </tr>
 <tr class="odd">
 <td align="center">Hospital C</td>
-<td align="center">0.5336856</td>
+<td align="center">0.5404884</td>
-<td align="center">1514</td>
+<td align="center">1556</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital D</td>
-<td align="center">0.5419501</td>
+<td align="center">0.5420827</td>
-<td align="center">2205</td>
+<td align="center">2103</td>
 </tr>
 </tbody>
 </table>
@@ -1227,27 +1227,27 @@ therapies very easily:</p>
 <tbody>
 <tr class="odd">
 <td align="center">Escherichia</td>
-<td align="center">0.7729741</td>
+<td align="center">0.7661138</td>
-<td align="center">0.8646535</td>
+<td align="center">0.8721394</td>
-<td align="center">0.9761025</td>
+<td align="center">0.9777451</td>
 </tr>
 <tr class="even">
 <td align="center">Klebsiella</td>
-<td align="center">0.8312236</td>
+<td align="center">0.8188841</td>
-<td align="center">0.8945148</td>
+<td align="center">0.9072961</td>
-<td align="center">0.9746835</td>
+<td align="center">0.9785408</td>
 </tr>
 <tr class="odd">
 <td align="center">Staphylococcus</td>
-<td align="center">0.7958656</td>
+<td align="center">0.7898065</td>
-<td align="center">0.8940568</td>
+<td align="center">0.8846726</td>
-<td align="center">0.9778516</td>
+<td align="center">0.9825149</td>
 </tr>
 <tr class="even">
 <td align="center">Streptococcus</td>
-<td align="center">0.5413105</td>
+<td align="center">0.5538020</td>
 <td align="center">0.0000000</td>
-<td align="center">0.5413105</td>
+<td align="center">0.5538020</td>
 </tr>
 </tbody>
 </table>
@@ -1275,23 +1275,23 @@ classes, use a antibiotic class selector such as
 <tbody>
 <tr class="odd">
 <td align="left">Hospital A</td>
-<td align="right">54.3%</td>
+<td align="right">54.5%</td>
-<td align="right">26.5%</td>
+<td align="right">27.2%</td>
 </tr>
 <tr class="even">
 <td align="left">Hospital B</td>
-<td align="right">52.5%</td>
+<td align="right">54.7%</td>
-<td align="right">25.0%</td>
+<td align="right">26.8%</td>
 </tr>
 <tr class="odd">
 <td align="left">Hospital C</td>
-<td align="right">53.4%</td>
+<td align="right">54.0%</td>
-<td align="right">26.4%</td>
+<td align="right">25.1%</td>
 </tr>
 <tr class="even">
 <td align="left">Hospital D</td>
 <td align="right">54.2%</td>
-<td align="right">27.0%</td>
+<td align="right">25.3%</td>
 </tr>
 </tbody>
 </table>
@@ -1407,16 +1407,18 @@ classes) <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code>:</p>
 <code class="sourceCode R"><span><span class="va">mic_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span></span>
 <span><span class="va">mic_values</span></span>
 <span><span class="co"># Class 'mic'</span></span>
-<span><span class="co">#   [1] 0.125  64     32     0.01   0.25   0.01   1      0.005  4      8     </span></span>
+<span><span class="co">#   [1] 0.125   8       2       8       0.0625  16      8       0.01    0.125  </span></span>
-<span><span class="co">#  [11] 64     0.001  8      0.005  4      0.5    0.005  16     0.001  128   </span></span>
+<span><span class="co">#  [10] 0.005   8       64      8       0.002   0.25    0.5     8       0.125  </span></span>
-<span><span class="co">#  [21] 64     16     64     8      2      2      0.25   128    0.001  &gt;=256 </span></span>
+<span><span class="co">#  [19] 8       &lt;=0.001 0.125   &gt;=256   32      0.025   0.0625  2       4      </span></span>
-<span><span class="co">#  [31] 4      4      8      2      4      16     0.5    2      0.25   0.025 </span></span>
+<span><span class="co">#  [28] 2       0.125   0.002   16      0.125   4       &lt;=0.001 1       0.125  </span></span>
-<span><span class="co">#  [41] 2      8      8      0.005  128    2      0.01   16     1      1     </span></span>
+<span><span class="co">#  [37] 1       128     16      4       1       16      4       32      &lt;=0.001</span></span>
-<span><span class="co">#  [51] 0.002  64     16     32     1      0.025  0.0625 16     64     0.001 </span></span>
+<span><span class="co">#  [46] 2       0.005   0.025   0.005   8       0.25    64      64      8      </span></span>
-<span><span class="co">#  [61] 0.001  0.002  2      0.002  0.025  0.01   0.025  0.01   16     16    </span></span>
+<span><span class="co">#  [55] 8       2       2       0.005   4       4       0.5     4       0.01   </span></span>
-<span><span class="co">#  [71] &gt;=256  64     16     0.25   0.01   64     0.25   64     0.001  0.001 </span></span>
+<span><span class="co">#  [64] 0.25    0.01    0.0625  128     0.01    0.01    1       4       8      </span></span>
-<span><span class="co">#  [81] 64     16     &gt;=256  4      0.25   0.002  0.5    1      128    0.002 </span></span>
+<span><span class="co">#  [73] &gt;=256   0.002   0.5     0.5     128     0.005   16      4       0.125  </span></span>
-<span><span class="co">#  [91] 0.025  0.125  0.025  0.025  0.002  0.25   0.025  64     4      8</span></span></code></pre></div>
+<span><span class="co">#  [82] 8       0.005   0.005   128     0.125   1       0.25    &gt;=256   &gt;=256  </span></span>
 <span><span class="co">#  [91] 0.125   0.25    0.5     0.125   4       32      0.125   0.025   8      </span></span>
 <span><span class="co"># [100] 0.005</span></span></code></pre></div>
 <div class="sourceCode" id="cb37"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="co"># base R:</span></span>
 <span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">mic_values</span><span class="op">)</span></span></code></pre></div>
@@ -1450,10 +1452,10 @@ plotting:</p>
 <code class="sourceCode R"><span><span class="va">disk_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_disk</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span>
 <span><span class="va">disk_values</span></span>
 <span><span class="co"># Class 'disk'</span></span>
-<span><span class="co">#   [1] 21 22 20 24 22 19 26 17 18 29 25 23 23 30 27 29 23 27 17 26 28 17 23 22 24</span></span>
+<span><span class="co">#   [1] 31 20 26 28 17 30 25 27 30 18 29 25 25 29 18 27 30 19 21 22 26 23 23 21 20</span></span>
-<span><span class="co">#  [26] 19 17 18 21 18 19 26 23 28 20 26 29 20 29 21 30 23 31 22 31 22 27 20 25 22</span></span>
+<span><span class="co">#  [26] 27 20 17 17 30 26 21 17 30 29 19 25 24 23 17 18 18 18 29 26 30 29 20 19 30</span></span>
-<span><span class="co">#  [51] 19 24 26 29 21 21 23 22 24 31 24 20 17 18 20 21 29 20 18 23 18 17 30 21 18</span></span>
+<span><span class="co">#  [51] 30 27 18 18 23 23 25 23 31 19 30 23 27 21 24 19 26 27 21 29 17 25 29 29 26</span></span>
-<span><span class="co">#  [76] 18 17 23 21 26 29 25 26 30 30 29 29 18 18 23 26 19 29 28 24 28 24 23 17 20</span></span></code></pre></div>
+<span><span class="co">#  [76] 22 28 19 28 26 23 22 29 28 18 29 17 19 29 29 17 27 20 23 21 24 27 25 20 30</span></span></code></pre></div>
 <div class="sourceCode" id="cb43"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="co"># base R:</span></span>
 <span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">disk_values</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></code></pre></div>
@@ -38,7 +38,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -38,7 +38,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -370,19 +370,19 @@ names or codes, this would have worked exactly the same way:</p>
 <div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span>
 <span><span class="co">#   rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
-<span><span class="co"># 1          S         I            S          S            I            R</span></span>
+<span><span class="co"># 1          R         R            S          I            R            S</span></span>
-<span><span class="co"># 2          I         R            I          S            R            R</span></span>
+<span><span class="co"># 2          R         I            S          S            R            S</span></span>
-<span><span class="co"># 3          S         I            I          S            R            R</span></span>
+<span><span class="co"># 3          R         I            S          S            S            S</span></span>
-<span><span class="co"># 4          R         I            S          S            I            I</span></span>
+<span><span class="co"># 4          S         I            S          I            I            I</span></span>
-<span><span class="co"># 5          I         I            R          I            I            I</span></span>
+<span><span class="co"># 5          S         I            S          S            R            S</span></span>
-<span><span class="co"># 6          I         I            S          I            S            I</span></span>
+<span><span class="co"># 6          S         S            S          I            S            S</span></span>
 <span><span class="co">#   kanamycin</span></span>
 <span><span class="co"># 1         S</span></span>
-<span><span class="co"># 2         S</span></span>
+<span><span class="co"># 2         R</span></span>
-<span><span class="co"># 3         S</span></span>
+<span><span class="co"># 3         R</span></span>
-<span><span class="co"># 4         R</span></span>
+<span><span class="co"># 4         I</span></span>
 <span><span class="co"># 5         I</span></span>
-<span><span class="co"># 6         S</span></span></code></pre></div>
+<span><span class="co"># 6         I</span></span></code></pre></div>
 <p>We can now add the interpretation of MDR-TB to our data set. You can
 use:</p>
 <div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
@@ -423,40 +423,40 @@ Unique: 5</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">Mono-resistant</td>
-<td align="right">3206</td>
+<td align="right">3210</td>
-<td align="right">64.12%</td>
+<td align="right">64.20%</td>
-<td align="right">3206</td>
+<td align="right">3210</td>
-<td align="right">64.12%</td>
+<td align="right">64.20%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">Negative</td>
-<td align="right">983</td>
+<td align="right">1040</td>
-<td align="right">19.66%</td>
+<td align="right">20.80%</td>
-<td align="right">4189</td>
+<td align="right">4250</td>
-<td align="right">83.78%</td>
+<td align="right">85.00%</td>
 </tr>
 <tr class="odd">
 <td align="left">3</td>
 <td align="left">Multi-drug-resistant</td>
-<td align="right">464</td>
+<td align="right">427</td>
-<td align="right">9.28%</td>
+<td align="right">8.54%</td>
-<td align="right">4653</td>
+<td align="right">4677</td>
-<td align="right">93.06%</td>
+<td align="right">93.54%</td>
 </tr>
 <tr class="even">
 <td align="left">4</td>
 <td align="left">Poly-resistant</td>
-<td align="right">236</td>
+<td align="right">235</td>
-<td align="right">4.72%</td>
+<td align="right">4.70%</td>
-<td align="right">4889</td>
+<td align="right">4912</td>
-<td align="right">97.78%</td>
+<td align="right">98.24%</td>
 </tr>
 <tr class="odd">
 <td align="left">5</td>
 <td align="left">Extensively drug-resistant</td>
-<td align="right">111</td>
+<td align="right">88</td>
-<td align="right">2.22%</td>
+<td align="right">1.76%</td>
 <td align="right">5000</td>
 <td align="right">100.00%</td>
 </tr>
@@ -38,7 +38,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -38,7 +38,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -38,7 +38,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -38,7 +38,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -191,7 +191,7 @@ column names:<br><em>mo</em>, <em>fullname</em>, <em>status</em>, <em>kingdom</e
 <em>gbif_renamed_to</em>, <em>prevalence</em> and <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 5 November 2022 07:20:03 UTC. Find more info
+<p>It was last updated on 5 November 2022 08:32:50 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>
@@ -490,7 +490,7 @@ column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>a
 <em>iv_ddd</em>, <em>iv_units</em> and <em>loinc</em>.</p>
 <p>This data set is in R available as <code>antibiotics</code>, after
 you load the <code>AMR</code> package.</p>
-<p>It was last updated on 5 November 2022 07:20:03 UTC. Find more info
+<p>It was last updated on 5 November 2022 08:32:50 UTC. Find more info
 about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
@@ -687,7 +687,7 @@ column names:<br><em>atc</em>, <em>cid</em>, <em>name</em>, <em>atc_group</em>,
 <em>iv_ddd</em> and <em>iv_units</em>.</p>
 <p>This data set is in R available as <code>antivirals</code>, after you
 load the <code>AMR</code> package.</p>
-<p>It was last updated on 5 November 2022 07:20:03 UTC. Find more info
+<p>It was last updated on 5 November 2022 08:32:50 UTC. Find more info
 about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
@@ -847,7 +847,7 @@ column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>
 <em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
 <p>This data set is in R available as <code>rsi_translation</code>,
 after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 5 November 2022 07:20:03 UTC. Find more info
+<p>It was last updated on 5 November 2022 08:32:50 UTC. Find more info
 about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
@@ -1020,7 +1020,7 @@ Resistance<a class="anchor" aria-label="anchor" href="#intrinsic_resistant-intri
 column names:<br><em>mo</em> and <em>ab</em>.</p>
 <p>This data set is in R available as <code>intrinsic_resistant</code>,
 after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 5 November 2022 07:20:03 UTC. Find more info
+<p>It was last updated on 5 November 2022 08:32:50 UTC. Find more info
 about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
@@ -1308,7 +1308,7 @@ column names:<br><em>ab</em>, <em>name</em>, <em>type</em>, <em>dose</em>,
 <em>original_txt</em> and <em>eucast_version</em>.</p>
 <p>This data set is in R available as <code>dosage</code>, after you
 load the <code>AMR</code> package.</p>
-<p>It was last updated on 5 November 2022 07:20:03 UTC. Find more info
+<p>It was last updated on 5 November 2022 08:32:50 UTC. Find more info
 about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
@@ -1458,7 +1458,7 @@ column names:<br><em>date</em>, <em>patient</em>, <em>age</em>, <em>gender</em>,
 <em>MUP</em> and <em>RIF</em>.</p>
 <p>This data set is in R available as <code>example_isolates</code>,
 after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 5 November 2022 07:20:03 UTC. Find more info
+<p>It was last updated on 5 November 2022 08:32:50 UTC. Find more info
 about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates.html">here</a>.</p>
 <div class="section level3">
 <h3 id="source-6">Source<a class="anchor" aria-label="anchor" href="#source-6"></a>
@@ -1871,7 +1871,7 @@ column names:<br><em>patient_id</em>, <em>hospital</em>, <em>date</em>,
 <p>This data set is in R available as
 <code>example_isolates_unclean</code>, after you load the
 <code>AMR</code> package.</p>
-<p>It was last updated on 5 November 2022 07:20:03 UTC. Find more info
+<p>It was last updated on 5 November 2022 08:32:50 UTC. Find more info
 about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates_unclean.html">here</a>.</p>
 <div class="section level3">
 <h3 id="source-7">Source<a class="anchor" aria-label="anchor" href="#source-7"></a>
@@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -38,7 +38,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -38,7 +38,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -42,7 +42,7 @@
    <a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -127,10 +127,10 @@
    </div>
    <div class="section level2">
-<h2 class="pkg-version" data-toc-text="1.8.2.9042" id="amr-1829042">AMR 1.8.2.9042<a class="anchor" aria-label="anchor" href="#amr-1829042"></a></h2>
+<h2 class="pkg-version" data-toc-text="1.8.2.9043" id="amr-1829043">AMR 1.8.2.9043<a class="anchor" aria-label="anchor" href="#amr-1829043"></a></h2>
 <p>This version will eventually become v2.0! We’re happy to reach a new major milestone soon!</p>
 <div class="section level4">
-<h4 id="breaking-1-8-2-9042">Breaking<a class="anchor" aria-label="anchor" href="#breaking-1-8-2-9042"></a></h4>
+<h4 id="breaking-1-8-2-9043">Breaking<a class="anchor" aria-label="anchor" href="#breaking-1-8-2-9043"></a></h4>
 <ul><li>Removed all species of the taxonomic kingdom Chromista from the package. This was done for multiple reasons:
 <ul><li>CRAN allows packages to be around 5 MB maximum, some packages are exempted but this package is not one of them</li>
 <li>Chromista are not relevant when it comes to antimicrobial resistance, thus lacking the primary scope of this package</li>
@@ -143,7 +143,7 @@
 <li>Removal of interpretation guidelines older than 10 years, the oldest now included guidelines of EUCAST and CLSI are from 2013</li>
 </ul></div>
 <div class="section level4">
-<h4 id="new-1-8-2-9042">New<a class="anchor" aria-label="anchor" href="#new-1-8-2-9042"></a></h4>
+<h4 id="new-1-8-2-9043">New<a class="anchor" aria-label="anchor" href="#new-1-8-2-9043"></a></h4>
 <ul><li>EUCAST 2022 and CLSI 2022 guidelines have been added for <code><a href="../reference/as.rsi.html">as.rsi()</a></code>. EUCAST 2022 is now the new default guideline for all MIC and disks diffusion interpretations.</li>
 <li>Support for the following languages: Chinese, Greek, Japanese, Polish, Turkish and Ukrainian. We are very grateful for the valuable input by our colleagues from other countries. The <code>AMR</code> package is now available in 16 languages. The automatic language determination will give a note at start-up on systems in supported languages.</li>
 <li>All new algorithm for <code><a href="../reference/as.mo.html">as.mo()</a></code> (and thus all <code>mo_*()</code> functions) while still following our original set-up as described in our paper (DOI 10.18637/jss.v104.i03).
@@ -176,7 +176,7 @@
 </li>
 </ul></div>
 <div class="section level4">
-<h4 id="changed-1-8-2-9042">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-2-9042"></a></h4>
+<h4 id="changed-1-8-2-9043">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-2-9043"></a></h4>
 <ul><li>Fix for using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on certain EUCAST breakpoints for MIC values</li>
 <li>Fix for using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on <code>NA</code> values (e.g. <code>as.rsi(as.disk(NA), ...)</code>)</li>
 <li>Fix for using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on bug-drug combinations with multiple breakpoints for different body sites</li>
@@ -207,7 +207,7 @@
 <li>Fix for <code><a href="../reference/mo_property.html">mo_shortname()</a></code> in case of higher taxonomic ranks (order, class, phylum)</li>
 </ul></div>
 <div class="section level4">
-<h4 id="other-1-8-2-9042">Other<a class="anchor" aria-label="anchor" href="#other-1-8-2-9042"></a></h4>
+<h4 id="other-1-8-2-9043">Other<a class="anchor" aria-label="anchor" href="#other-1-8-2-9043"></a></h4>
 <ul><li>New website to make use of the new Bootstrap 5 and pkgdown 2.0. The website now contains results for all examples and will be automatically regenerated with every change to our repository, using GitHub Actions</li>
 <li>Added Peter Dutey-Magni, Dmytro Mykhailenko, Anton Mymrikov, and Jonas Salm as contributors, to thank them for their valuable input</li>
 <li>All R and Rmd files in this project are now styled using the <code>styler</code> package</li>
@@ -11,7 +11,7 @@ articles:
  datasets: datasets.html
  resistance_predict: resistance_predict.html
  welcome_to_AMR: welcome_to_AMR.html
-last_built: 2022-11-05T07:22Z
+last_built: 2022-11-05T08:35Z
 urls:
  reference: https://msberends.github.io/AMR/reference
  article: https://msberends.github.io/AMR/articles
@@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -62,7 +62,7 @@ Principal component analysis for AMR
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -190,16 +190,16 @@
 <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  1970-09-14  52  52.14247         29</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1  1980-04-25  42  42.53151         19</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2  1973-12-20  48  48.87671         26</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2  1931-08-30  91  91.18356         68</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3  1951-02-05  71  71.74795         48</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3  1943-09-04  79  79.16986         56</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4  1972-09-23  50  50.11781         27</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4  1980-02-23  42  42.69863         19</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5  1999-05-04  23  23.50685          0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5  1973-04-28  49  49.52329         26</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6  1975-09-29  47  47.10137         24</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6  1964-06-28  58  58.35616         35</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7  1981-11-09  40  40.98904         18</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7  1987-05-05  35  35.50411         12</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8  1996-03-20  26  26.63014          3</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8  1998-10-03  24  24.09041          1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9  1970-03-30  52  52.60274         29</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9  1991-07-26  31  31.27945          8</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1999-06-15  23  23.39178          0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1958-05-22  64  64.45753         41</span>
 </code></pre></div>
    </div>
  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
@@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -496,16 +496,16 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 50 × 13</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    datetime            index ab_input   ab_consid…¹ mo_in…² mo_conside…³ guide…⁴</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span>              <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>      <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span>        <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>  </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2022-11-05 <span style="color: #949494;">07:23:25</span>     1 ampicillin AMP         Strep … B_STRPT_PNMN EUCAST…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2022-11-05 <span style="color: #949494;">08:35:59</span>     1 ampicillin AMP         Strep … B_STRPT_PNMN EUCAST…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2022-11-05 <span style="color: #949494;">07:23:25</span>     1 AMP        AMP         Escher… B_ESCHR_COLI EUCAST…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2022-11-05 <span style="color: #949494;">08:35:59</span>     1 AMP        AMP         Escher… B_ESCHR_COLI EUCAST…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2022-11-05 <span style="color: #949494;">07:23:25</span>     1 CIP        CIP         Escher… B_ESCHR_COLI EUCAST…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2022-11-05 <span style="color: #949494;">08:35:59</span>     1 CIP        CIP         Escher… B_ESCHR_COLI EUCAST…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2022-11-05 <span style="color: #949494;">07:23:26</span>     1 GEN        GEN         Escher… B_ESCHR_COLI EUCAST…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2022-11-05 <span style="color: #949494;">08:36:00</span>     1 GEN        GEN         Escher… B_ESCHR_COLI EUCAST…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2022-11-05 <span style="color: #949494;">07:23:26</span>     1 TOB        TOB         Escher… B_ESCHR_COLI EUCAST…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2022-11-05 <span style="color: #949494;">08:36:00</span>     1 TOB        TOB         Escher… B_ESCHR_COLI EUCAST…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2022-11-05 <span style="color: #949494;">07:23:27</span>     1 AMX        AMX         B_STRP… B_STRPT_PNMN EUCAST…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2022-11-05 <span style="color: #949494;">08:36:01</span>     1 AMX        AMX         B_STRP… B_STRPT_PNMN EUCAST…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2022-11-05 <span style="color: #949494;">07:23:28</span>     1 AMX        AMX         B_STRP… B_STRPT_PNMN EUCAST…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2022-11-05 <span style="color: #949494;">08:36:01</span>     1 AMX        AMX         B_STRP… B_STRPT_PNMN EUCAST…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2022-11-05 <span style="color: #949494;">07:23:28</span>     2 AMX        AMX         B_STRP… B_STRPT_PNMN EUCAST…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2022-11-05 <span style="color: #949494;">08:36:01</span>     2 AMX        AMX         B_STRP… B_STRPT_PNMN EUCAST…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2022-11-05 <span style="color: #949494;">07:23:28</span>     3 AMX        AMX         B_STRP… B_STRPT_PNMN EUCAST…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2022-11-05 <span style="color: #949494;">08:36:01</span>     3 AMX        AMX         B_STRP… B_STRPT_PNMN EUCAST…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2022-11-05 <span style="color: #949494;">07:23:28</span>     4 AMX        AMX         B_STRP… B_STRPT_PNMN EUCAST…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2022-11-05 <span style="color: #949494;">08:36:02</span>     4 AMX        AMX         B_STRP… B_STRPT_PNMN EUCAST…</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 40 more rows, 6 more variables: ref_table &lt;chr&gt;, method &lt;chr&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   breakpoint_S &lt;dbl&gt;, breakpoint_R &lt;dbl&gt;, input &lt;dbl&gt;, interpretation &lt;rsi&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   and abbreviated variable names ¹ab_considered, ²mo_input, ³mo_considered,</span></span>
@@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -12,7 +12,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -12,7 +12,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -12,7 +12,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -177,40 +177,43 @@
 <span class="r-in"><span><span class="va">df</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq_len</a></span><span class="op">(</span><span class="fl">2000</span><span class="op">)</span>, size <span class="op">=</span> <span class="fl">200</span><span class="op">)</span>, <span class="op">]</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># indices</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   [1] 10 13 12 30 16 44 61 40 31 51 24 14 27  1 35 14 52 12 11 24 50 35 49 60 10</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   [1] 20 35  5 21 40  9  3 60 33 52 45 42 58 43 38  1 10 12  9 37  3 42 60  7 60</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [26] 53  6  6 61 50  2  4 15 37  8 12 49 36 63 50 17 40 21 39  7 40 61 65 25 38</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [26] 56 59 49 50 32 50 60 58 29 18 57 20 43 52 29 24 45 29 54 37 25 58 42 12 40</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [51] 14 32 32 63 17 29 24 23 45 42 39 30 37 57 49 29 59 14 38 15 14 58 42  4 11</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [51] 59 25  5 52 59 25 59 48  7 48 57 14 59 28 55 49 12 24  6  7 11 38 48  7 37</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [76] 13 12  3 61  2 21 29 36 25 10 54 38 54 36 58 32 51 56 62 63 19 49 59 57 24</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [76] 45 24 56 54 10 47 29 55  7  1 11 35  9 42 16 58 23  2 12 38  3 33 14 17 38</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [101] 63 10 14 63 56 24 62 58 31 13 45 58 50 60 27 50 29 11 20 42  3 10 13 61  5</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [101] 52 22 34 26 10  5 51  6 31 41 30  4 11 25 27 24 54 29 12 32 23 49 20 10 18</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [126] 58 21 51 60 50 12 60 37 52  9 60 34 32 11 57 16 46 30 28 64 59 33 43 23 28</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [126] 13 51 54 31  7 35 50 44 38 16  5 39 30 15 46  3 60 19  3 40 15 45 46 43  8</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [151] 63 10 31 53 25 10 14 55 19 18 17 53 25 25  9 34 52 32 17 10 64 17 63 26 62</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [151]  9 43 39  5  9 18 33 42 55 55 42 56 17 17 34 55 36 26 26 15  1 46 26 53 40</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [176] 58 63 46 29 21 18 22 43 45 47 26 42  5 11 63 53 48 14  9 41 25  2 61 41 36</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [176] 19 59 14 34 25 60 47  5 29 15 19 23 54 28  7 47  9 39 23 22  9 52 24 61 21</span>
 <span class="r-in"><span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># TRUE/FALSE</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   [1] FALSE  TRUE  TRUE  TRUE FALSE  TRUE FALSE FALSE  TRUE FALSE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   [1]  TRUE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [13] FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [13]  TRUE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [25] FALSE FALSE  TRUE FALSE  TRUE FALSE FALSE FALSE  TRUE  TRUE  TRUE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [25] FALSE  TRUE FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE  TRUE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [37] FALSE FALSE FALSE  TRUE FALSE  TRUE  TRUE  TRUE  TRUE FALSE FALSE  TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [37] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [49] FALSE FALSE  TRUE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [49] FALSE  TRUE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [61] FALSE FALSE FALSE FALSE  TRUE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [61]  TRUE FALSE  TRUE  TRUE FALSE FALSE  TRUE  TRUE FALSE FALSE  TRUE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [73] FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [73]  TRUE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [85] FALSE  TRUE  TRUE FALSE FALSE  TRUE FALSE  TRUE  TRUE FALSE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [85]  TRUE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [97] FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [97] FALSE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [109] FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE  TRUE  TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [109]  TRUE  TRUE  TRUE  TRUE FALSE FALSE  TRUE FALSE  TRUE FALSE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [121]  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [121] FALSE  TRUE FALSE FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE  TRUE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [133] FALSE  TRUE FALSE  TRUE  TRUE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [133]  TRUE FALSE  TRUE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [145]  TRUE FALSE  TRUE  TRUE  TRUE  TRUE FALSE  TRUE FALSE FALSE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [145] FALSE  TRUE  TRUE FALSE  TRUE  TRUE FALSE FALSE  TRUE FALSE FALSE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [157] FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE  TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [157] FALSE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE  TRUE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [169]  TRUE FALSE FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE  TRUE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [169]  TRUE FALSE FALSE FALSE FALSE  TRUE FALSE  TRUE FALSE  TRUE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [181]  TRUE  TRUE FALSE  TRUE  TRUE FALSE FALSE  TRUE FALSE FALSE  TRUE  TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [181] FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [193] FALSE FALSE FALSE  TRUE FALSE FALSE  TRUE  TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [193] FALSE  TRUE  TRUE FALSE  TRUE FALSE  TRUE FALSE</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># filter on results from the third 60-day episode only, using base R</span></span></span>
 <span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, <span class="fl">60</span><span class="op">)</span> <span class="op">==</span> <span class="fl">3</span><span class="op">)</span>, <span class="op">]</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2 × 46</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 5 × 46</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   date       patient   age gender ward     mo           PEN   OXA   FLC   AMX  </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   date       patient   age gender ward      mo           PEN   OXA   FLC   AMX  </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;date&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>  <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;date&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>  <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-07-21 955940     82 F      Clinical B_PSDMN_AERG R     NA    NA    R    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-11-12 CF9318     29 M      ICU       B_STPHY_CONS R     NA    R     R    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2002-06-23 798871     82 M      Clinical B_ENTRC_FCLS NA    NA    NA    NA   </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2002-11-11 D80753     74 F      Outpatie… B_STPHY_CONS R     NA    S     NA   </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2002-11-28 600057     88 M      Outpatie… B_STPHY_AURS R     NA    S     R    </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2002-12-13 285137     78 F      ICU       B_ESCHR_COLI R     NA    NA    NA   </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">5</span> 2002-11-04 304347     62 M      Clinical  B_STRPT_PNMN S     NA    NA    S    </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 36 more variables: AMC &lt;rsi&gt;, AMP &lt;rsi&gt;, TZP &lt;rsi&gt;, CZO &lt;rsi&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   FEP &lt;rsi&gt;, CXM &lt;rsi&gt;, FOX &lt;rsi&gt;, CTX &lt;rsi&gt;, CAZ &lt;rsi&gt;, CRO &lt;rsi&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   GEN &lt;rsi&gt;, TOB &lt;rsi&gt;, AMK &lt;rsi&gt;, KAN &lt;rsi&gt;, TMP &lt;rsi&gt;, SXT &lt;rsi&gt;,</span></span>
@@ -246,16 +249,16 @@
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups:   condition [3]</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    patient date       condition new_episode</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;date&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span>      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 419655  2004-02-21 A         FALSE      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 561303  2006-08-11 B         TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 021648  2004-08-21 B         FALSE      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> F54287  2010-07-05 C         FALSE      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> D27410  2004-06-04 B         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 6BC362  2003-04-21 C         TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> E95747  2008-06-30 A         FALSE      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 557456  2006-10-24 B         FALSE      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 838434  2005-06-20 A         FALSE      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> F56314  2011-10-17 B         FALSE      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 634DF2  2012-03-12 A         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 406502  2004-02-29 B         FALSE      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 872108  2016-12-27 B         FALSE      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> CF9318  2002-11-12 C         FALSE      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> B26873  2011-01-09 A         FALSE      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 8DD375  2017-09-12 C         FALSE      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> F462F5  2008-08-29 B         FALSE      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 650870  2009-11-12 C         TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 545388  2013-12-05 B         FALSE      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 0DBF93  2015-10-12 A         FALSE      </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 190 more rows</span></span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@@ -267,19 +270,19 @@
 <span class="r-in"><span>    <span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 200 × 5</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups:   ward, patient [186]</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups:   ward, patient [180]</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    ward       date       patient new_index new_logical</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>      <span style="color: #949494; font-style: italic;">&lt;date&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>       <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span>      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> ICU        2004-02-21 419655          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical   2006-08-11 561303          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical   2004-08-21 021648          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical   2010-07-05 F54287          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Outpatient 2004-06-04 D27410          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> ICU        2003-04-21 6BC362          1 FALSE      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical   2008-06-30 E95747          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> ICU        2006-10-24 557456          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Clinical   2005-06-20 838434          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Outpatient 2011-10-17 F56314          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> ICU        2012-03-12 634DF2          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Clinical   2004-02-29 406502          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Clinical   2016-12-27 872108          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> ICU        2002-11-12 CF9318          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical   2011-01-09 B26873          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> ICU        2017-09-12 8DD375          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Clinical   2008-08-29 F462F5          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Outpatient 2009-11-12 650870          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical   2013-12-05 545388          2 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical   2015-10-12 0DBF93          1 TRUE       </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 190 more rows</span></span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@@ -294,9 +297,9 @@
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 5</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   ward       n_patients n_episodes_365 n_episodes_60 n_episodes_30</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>           <span style="color: #949494; font-style: italic;">&lt;int&gt;</span>          <span style="color: #949494; font-style: italic;">&lt;int&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;int&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical          131             13            53            75</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical          106             14            49            72</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU                44             10            27            36</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU                60             10            36            42</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient         11              7            10            10</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient         14              8            11            12</span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span>  <span class="co"># grouping on patients and microorganisms leads to the same</span></span></span>
@@ -326,19 +329,19 @@
 <span class="r-in"><span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_data.html" class="external-link">group_vars</a></span><span class="op">(</span><span class="va">.</span><span class="op">)</span>, <span class="va">flag_episode</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 200 × 4</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups:   patient, mo, ward [193]</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups:   patient, mo, ward [189]</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    patient mo           ward       flag_episode</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>      <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span>       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 419655  B_STRPT_PNMN ICU        TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 561303  B_STPHY_CONS Clinical   TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 021648  B_ESCHR_COLI Clinical   TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> F54287  B_STRPT_ANGN Clinical   TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> D27410  B_BCTRD_FRGL Outpatient TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 6BC362  B_ENTRC      ICU        TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> E95747  B_KLBSL_PNMN Clinical   TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 557456  B_BCTRD_FRGL ICU        TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 838434  B_STPHY_CONS Clinical   TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> F56314  B_ESCHR_COLI Outpatient TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 634DF2  B_STRPT_PNMN ICU        TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 406502  B_STRPT_PNMN Clinical   TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 872108  B_ESCHR_COLI Clinical   TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> CF9318  B_STPHY_CONS ICU        TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> B26873  B_ESCHR_COLI Clinical   TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 8DD375  B_ESCHR_COLI ICU        TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> F462F5  B_STRPT_PNMN Clinical   TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 650870  B_ESCHR_COLI Outpatient TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 545388  B_STPHY_CPTS Clinical   TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 0DBF93  B_STPHY_EPDR Clinical   TRUE        </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 190 more rows</span></span>
 <span class="r-in"><span><span class="co"># }</span></span></span>
 </code></pre></div>
@@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -297,10 +297,12 @@
 <span class="r-in"><span></span></span>
 <span class="r-in"><span>  <span class="co"># old base R plotting method:</span></span></span>
 <span class="r-in"><span>  <span class="fu"><a href="https://rdrr.io/r/stats/biplot.html" class="external-link">biplot</a></span><span class="op">(</span><span class="va">pca_result</span><span class="op">)</span></span></span>
 <span class="r-in"><span>  <span class="co"># new ggplot2 plotting method using this package:</span></span></span>
 <span class="r-in"><span>  <span class="fu">ggplot_pca</span><span class="op">(</span><span class="va">pca_result</span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span>  <span class="co"># new ggplot2 plotting method using this package:</span></span></span>
 <span class="r-in"><span>  <span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>    <span class="fu">ggplot_pca</span><span class="op">(</span><span class="va">pca_result</span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span>    <span class="co"># still extendible with any ggplot2 function</span></span></span>
 <span class="r-in"><span>    <span class="fu">ggplot_pca</span><span class="op">(</span><span class="va">pca_result</span><span class="op">)</span> <span class="op">+</span></span></span>
 <span class="r-in"><span>      <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/scale_viridis.html" class="external-link">scale_colour_viridis_d</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span></span>
 <span class="r-in"><span>      <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">labs</a></span><span class="op">(</span>title <span class="op">=</span> <span class="st">"Title here"</span><span class="op">)</span></span></span>
@@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -167,9 +167,9 @@
    <div class="section level2">
    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 3.031603</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 3.017006</span>
 <span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span>, excess <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.02766519</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.02228581</span>
 </code></pre></div>
    </div>
  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
@@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -195,11 +195,10 @@
    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">x</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 4       0.025   16      1       64      1       4       0.0625  &lt;=0.002</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 64    16    &gt;=128 0.025 32    64    0.125 0.005 8     0.005</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.005  </span>
 <span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1]  0.6331668 -0.8186885  1.0297441  0.2365895  1.4263214  0.2365895</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1]  0.8826792  0.5471212  1.0504581 -1.0169023  0.7149002  0.8826792</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [7]  0.6331668 -0.5565652 -1.5412239 -1.2791005</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [7] -0.6273316 -1.4064731  0.3793422 -1.4064731</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">y</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
 <span class="r-in"><span>  id <span class="op">=</span> <span class="va">LETTERS</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span></span>
@@ -209,38 +208,38 @@
 <span class="r-in"><span>  tobr <span class="op">=</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span>, ab <span class="op">=</span> <span class="st">"tobr"</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">y</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>    id amox   cipr gent tobr</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>    id amox   cipr  gent  tobr</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1   A    4   0.25    4    2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1   A   16 &lt;=0.25   &gt;=8     1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2   B   16  0.125  &lt;=2  &gt;=8</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2   B   32    &gt;=2   &gt;=8 &lt;=0.5</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3   C    4    &gt;=1  &lt;=2  &lt;=1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3   C   32      1   &gt;=8     1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4   D    8  0.125  &gt;=8  &lt;=1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4   D  &lt;=1      1     1     2</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5   E    4    &gt;=1  &lt;=2  &gt;=8</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5   E    4    &gt;=2   &gt;=8   &gt;=4</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6   F    8    &gt;=1  &gt;=8  &lt;=1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6   F    4 &lt;=0.25   &gt;=8     1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7   G    4  0.125    4  &gt;=8</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7   G    8 &lt;=0.25 &lt;=0.5   &gt;=4</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8   H    8 0.0625  &lt;=2  &gt;=8</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8   H  &lt;=1    &gt;=2     1     1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9   I    8 0.0625  &gt;=8  &gt;=8</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9   I  &lt;=1 &lt;=0.25     4     1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10  J    8 0.0625  &gt;=8    4</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10  J   32 &lt;=0.25   &gt;=8     1</span>
 <span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   "id" and "tobr"</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>NAs introduced by coercion</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] -0.35825689  0.32811868 -0.50858606 -0.04827254  0.02773665  0.39214262</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1]  0.00491141  0.39299678  0.47548368 -0.32590689  0.81532985 -0.23108238</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [7] -0.14751347 -0.18908497  0.34124511  0.16247088</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [7] -0.22244389 -0.40839379 -0.62380306  0.12290831</span>
 <span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op">&lt;-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu">where</span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   "tobr"</span>
 <span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>    id amox   cipr gent tobr amr_distance</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>    id amox   cipr  gent  tobr amr_distance</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3   C    4    &gt;=1  &lt;=2  &lt;=1  -0.50858606</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9   I  &lt;=1 &lt;=0.25     4     1  -0.62380306</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1   A    4   0.25    4    2  -0.35825689</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8   H  &lt;=1    &gt;=2     1     1  -0.40839379</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8   H    8 0.0625  &lt;=2  &gt;=8  -0.18908497</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4   D  &lt;=1      1     1     2  -0.32590689</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7   G    4  0.125    4  &gt;=8  -0.14751347</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6   F    4 &lt;=0.25   &gt;=8     1  -0.23108238</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4   D    8  0.125  &gt;=8  &lt;=1  -0.04827254</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7   G    8 &lt;=0.25 &lt;=0.5   &gt;=4  -0.22244389</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5   E    4    &gt;=1  &lt;=2  &gt;=8   0.02773665</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1   A   16 &lt;=0.25   &gt;=8     1   0.00491141</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10  J    8 0.0625  &gt;=8    4   0.16247088</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10  J   32 &lt;=0.25   &gt;=8     1   0.12290831</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2   B   16  0.125  &lt;=2  &gt;=8   0.32811868</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2   B   32    &gt;=2   &gt;=8 &lt;=0.5   0.39299678</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9   I    8 0.0625  &gt;=8  &gt;=8   0.34124511</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3   C   32      1   &gt;=8     1   0.47548368</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6   F    8    &gt;=1  &gt;=8  &lt;=1   0.39214262</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5   E    4    &gt;=2   &gt;=8   &gt;=4   0.81532985</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="va">y</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@@ -252,17 +251,17 @@
 <span class="r-in"><span><span class="op">}</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   "tobr"</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>    id amox   cipr gent tobr amr_distance check_id_C</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>    id amox   cipr  gent  tobr amr_distance check_id_C</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1   C    4    &gt;=1  &lt;=2  &lt;=1  -0.50858606  0.0000000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1   C   32      1   &gt;=8     1   0.47548368  0.0000000</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2   A    4   0.25    4    2  -0.35825689  0.1503292</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2   B   32    &gt;=2   &gt;=8 &lt;=0.5   0.39299678  0.0824869</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3   H    8 0.0625  &lt;=2  &gt;=8  -0.18908497  0.3195011</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3   E    4    &gt;=2   &gt;=8   &gt;=4   0.81532985  0.3398462</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4   G    4  0.125    4  &gt;=8  -0.14751347  0.3610726</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4   J   32 &lt;=0.25   &gt;=8     1   0.12290831  0.3525754</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5   D    8  0.125  &gt;=8  &lt;=1  -0.04827254  0.4603135</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5   A   16 &lt;=0.25   &gt;=8     1   0.00491141  0.4705723</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6   E    4    &gt;=1  &lt;=2  &gt;=8   0.02773665  0.5363227</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6   G    8 &lt;=0.25 &lt;=0.5   &gt;=4  -0.22244389  0.6979276</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7   J    8 0.0625  &gt;=8    4   0.16247088  0.6710569</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7   F    4 &lt;=0.25   &gt;=8     1  -0.23108238  0.7065661</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8   B   16  0.125  &lt;=2  &gt;=8   0.32811868  0.8367047</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8   D  &lt;=1      1     1     2  -0.32590689  0.8013906</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9   I    8 0.0625  &gt;=8  &gt;=8   0.34124511  0.8498312</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9   H  &lt;=1    &gt;=2     1     1  -0.40839379  0.8838775</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10  F    8    &gt;=1  &gt;=8  &lt;=1   0.39214262  0.9007287</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10  I  &lt;=1 &lt;=0.25     4     1  -0.62380306  1.0992867</span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="co"># support for groups</span></span></span>
 <span class="r-in"><span>  <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -12,7 +12,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -12,7 +12,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -178,41 +178,43 @@
    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 0.125 0.01  2     0.5   8     1     2     2     0.5   0.5   0.001 4    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 16      16      0.125   0.0625  256     0.125   256     &lt;=0.001 0.025  </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [13] 0.002 0.25  1     0.005 64    64    0.5   4     128   0.002 0.01  64   </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.005   16      0.01    0.5     0.002   128     0.0625  0.025   0.5    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 32   </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 0.01    0.125   128     1       128     0.005   4      </span>
 <span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 21 40 49 45 11 23 49 42 12  7 44 50 23 47 41 27 47 50 33 18 18 38 21 40 12</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 49 27 35 49 28 36 14 43 14 22 36 45 40 39 42 16 25 31 44 21 43 28 17 21 47</span>
 <span class="r-in"><span><span class="fu">random_rsi</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'rsi'</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] R R I R R I I R I S I R S S R S I I R S S I R R I</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] S S S S I R R R R S R I R I S R I S S R R I I R I</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># \donttest{</span></span></span>
 <span class="r-in"><span><span class="co"># make the random generation more realistic by setting a bug and/or drug:</span></span></span>
 <span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 0.0625-64</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 16    0.025 128   0.5   0.002 4     0.125 0.125 0.5   8     0.01  0.001</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 0.0625  0.005   1       0.0625  4       0.5     2       8       2      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [13] 8     2     64    0.5   0.5   0.025 0.01  8     0.125 0.5   0.5   2    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [10] &gt;=64    &gt;=64    1       1       4       16      2       &lt;=0.001 0.005  </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 4    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 0.125   0.025   0.002   8       0.5     0.125   1      </span>
 <span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-16</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 4  16 2  2  2  8  8  2  4  1  2  1  1  4  1  1  16 8  16 4  2  8  1  2  4 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 16    16    2     2     8     &gt;=32  4     &lt;=0.5 &lt;=0.5 16    &lt;=0.5 8    </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [13] 2     2     1     2     1     &lt;=0.5 2     2     1     1     16    4    </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [25] &lt;=0.5</span>
 <span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-4</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 4       0.25    0.125   0.0625  0.125   0.125   4       1       2      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 1      8      16     4      0.25   1      4      2      0.125  4     </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.25    0.125   0.5     &lt;=0.025 0.25    2       &lt;=0.025 0.125   4      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 2      8      0.0625 0.0625 16     8      0.0625 1      1      0.25  </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 0.0625  4       0.25    2       &lt;=0.025 0.25    0.25   </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 0.5    0.25   0.25   0.25   1     </span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 8-50</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1]  8 31 45 32 40 26 48 46 43 10 41 45 33 23 41 25 26 18 16 16 49 26 14 21 10</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 26 31  9 31 44 38 45 43 14 30 14 46 25 17 36 30 34 25 11 29 29 12 23 21 44</span>
 <span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 11-17</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 13 15 13 13 17 14 11 15 11 12 15 15 15 12 14 13 16 16 15 14 15 16 16 16 16</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 17 13 13 13 17 13 17 14 15 11 12 15 16 16 11 12 14 11 11 11 17 15 16 11 11</span>
 <span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 12-27</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 19 22 23 20 25 24 26 24 27 18 22 21 22 26 25 24 15 15 22 20 22 22 20 25 21</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 27 19 22 23 16 22 27 21 26 19 16 16 18 26 25 23 19 16 17 27 26 16 23 16 20</span>
 <span class="r-in"><span><span class="co"># }</span></span></span>
 </code></pre></div>
    </div>
@@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -12,7 +12,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -166,7 +166,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
    <div class="section level2">
    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">skewness</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Uniform.html" class="external-link">runif</a></span><span class="op">(</span><span class="fl">1000</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.01389271</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.002367023</span>
 </code></pre></div>
    </div>
  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
@@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -1 +1 @@
-[{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"How to conduct AMR data analysis","text":"Conducting AMR data analysis unfortunately requires -depth knowledge different scientific fields, makes hard right. least, requires: Good questions (always start !) thorough understanding (clinical) epidemiology, understand clinical epidemiological relevance possible bias results thorough understanding (clinical) microbiology/infectious diseases, understand microorganisms causal infections implications pharmaceutical treatment, well understanding intrinsic acquired microbial resistance Experience data analysis microbiological tests results, understand determination limitations MIC values interpretations RSI values Availability biological taxonomy microorganisms probably normalisation factors pharmaceuticals, defined daily doses (DDD) Available (inter-)national guidelines, profound methods apply course, instantly provide knowledge experience. AMR package, aimed providing (1) tools simplify antimicrobial resistance data cleaning, transformation analysis, (2) methods easily incorporate international guidelines (3) scientifically reliable reference data, including requirements mentioned . AMR package enables standardised reproducible AMR data analysis, application evidence-based rules, determination first isolates, translation various codes microorganisms antimicrobial agents, determination (multi-drug) resistant microorganisms, calculation antimicrobial resistance, prevalence future trends.","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"preparation","dir":"Articles","previous_headings":"","what":"Preparation","title":"How to conduct AMR data analysis","text":"tutorial, create fake demonstration data work . can skip Cleaning data already data ready. start analysis, try make structure data generally look like :","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"needed-r-packages","dir":"Articles","previous_headings":"Preparation","what":"Needed R packages","title":"How to conduct AMR data analysis","text":"many uses R, need additional packages AMR data analysis. package works closely together tidyverse packages dplyr ggplot2 RStudio. tidyverse tremendously improves way conduct data science - allows natural way writing syntaxes creating beautiful plots R. also use cleaner package, can used cleaning data creating frequency tables.","code":"library(dplyr) library(ggplot2) library(AMR) library(cleaner)  # (if not yet installed, install with:) # install.packages(c(\"dplyr\", \"ggplot2\", \"AMR\", \"cleaner\"))"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"creation-of-data","dir":"Articles","previous_headings":"","what":"Creation of data","title":"How to conduct AMR data analysis","text":"create fake example data use analysis. AMR data analysis, need least: patient ID, name code microorganism, date antimicrobial results (antibiogram). also include specimen type (e.g. filter blood urine), ward type (e.g. filter ICUs). additional columns (like hospital name, patients gender even [well-defined] clinical properties) can comparative analysis, tutorial demonstrate .","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"patients","dir":"Articles","previous_headings":"Creation of data","what":"Patients","title":"How to conduct AMR data analysis","text":"start patients, need unique list patients. LETTERS object available R - ’s vector 26 characters: Z. patients object just created now vector length 260, values (patient IDs) varying A1 Z10. Now also set gender patients, putting ID gender table: first 135 patient IDs now male, 125 female.","code":"patients <- unlist(lapply(LETTERS, paste0, 1:10)) patients_table <- data.frame(   patient_id = patients,   gender = c(     rep(\"M\", 135),     rep(\"F\", 125)   ) )"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"dates","dir":"Articles","previous_headings":"Creation of data","what":"Dates","title":"How to conduct AMR data analysis","text":"Let’s pretend data consists blood cultures isolates 1 January 2010 1 January 2018. dates object now contains days date range.","code":"dates <- seq(as.Date(\"2010-01-01\"), as.Date(\"2018-01-01\"), by = \"day\")"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"microorganisms","dir":"Articles","previous_headings":"Creation of data > Dates","what":"Microorganisms","title":"How to conduct AMR data analysis","text":"tutorial, uses four different microorganisms: Escherichia coli, Staphylococcus aureus, Streptococcus pneumoniae, Klebsiella pneumoniae:","code":"bacteria <- c(   \"Escherichia coli\", \"Staphylococcus aureus\",   \"Streptococcus pneumoniae\", \"Klebsiella pneumoniae\" )"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"put-everything-together","dir":"Articles","previous_headings":"CreatLine truncated
+[{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"How to conduct AMR data analysis","text":"Conducting AMR data analysis unfortunately requires -depth knowledge different scientific fields, makes hard right. least, requires: Good questions (always start !) thorough understanding (clinical) epidemiology, understand clinical epidemiological relevance possible bias results thorough understanding (clinical) microbiology/infectious diseases, understand microorganisms causal infections implications pharmaceutical treatment, well understanding intrinsic acquired microbial resistance Experience data analysis microbiological tests results, understand determination limitations MIC values interpretations RSI values Availability biological taxonomy microorganisms probably normalisation factors pharmaceuticals, defined daily doses (DDD) Available (inter-)national guidelines, profound methods apply course, instantly provide knowledge experience. AMR package, aimed providing (1) tools simplify antimicrobial resistance data cleaning, transformation analysis, (2) methods easily incorporate international guidelines (3) scientifically reliable reference data, including requirements mentioned . AMR package enables standardised reproducible AMR data analysis, application evidence-based rules, determination first isolates, translation various codes microorganisms antimicrobial agents, determination (multi-drug) resistant microorganisms, calculation antimicrobial resistance, prevalence future trends.","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"preparation","dir":"Articles","previous_headings":"","what":"Preparation","title":"How to conduct AMR data analysis","text":"tutorial, create fake demonstration data work . can skip Cleaning data already data ready. start analysis, try make structure data generally look like :","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"needed-r-packages","dir":"Articles","previous_headings":"Preparation","what":"Needed R packages","title":"How to conduct AMR data analysis","text":"many uses R, need additional packages AMR data analysis. package works closely together tidyverse packages dplyr ggplot2 RStudio. tidyverse tremendously improves way conduct data science - allows natural way writing syntaxes creating beautiful plots R. also use cleaner package, can used cleaning data creating frequency tables.","code":"library(dplyr) library(ggplot2) library(AMR) library(cleaner)  # (if not yet installed, install with:) # install.packages(c(\"dplyr\", \"ggplot2\", \"AMR\", \"cleaner\"))"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"creation-of-data","dir":"Articles","previous_headings":"","what":"Creation of data","title":"How to conduct AMR data analysis","text":"create fake example data use analysis. AMR data analysis, need least: patient ID, name code microorganism, date antimicrobial results (antibiogram). also include specimen type (e.g. filter blood urine), ward type (e.g. filter ICUs). additional columns (like hospital name, patients gender even [well-defined] clinical properties) can comparative analysis, tutorial demonstrate .","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"patients","dir":"Articles","previous_headings":"Creation of data","what":"Patients","title":"How to conduct AMR data analysis","text":"start patients, need unique list patients. LETTERS object available R - ’s vector 26 characters: Z. patients object just created now vector length 260, values (patient IDs) varying A1 Z10. Now also set gender patients, putting ID gender table: first 135 patient IDs now male, 125 female.","code":"patients <- unlist(lapply(LETTERS, paste0, 1:10)) patients_table <- data.frame(   patient_id = patients,   gender = c(     rep(\"M\", 135),     rep(\"F\", 125)   ) )"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"dates","dir":"Articles","previous_headings":"Creation of data","what":"Dates","title":"How to conduct AMR data analysis","text":"Let’s pretend data consists blood cultures isolates 1 January 2010 1 January 2018. dates object now contains days date range.","code":"dates <- seq(as.Date(\"2010-01-01\"), as.Date(\"2018-01-01\"), by = \"day\")"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"microorganisms","dir":"Articles","previous_headings":"Creation of data > Dates","what":"Microorganisms","title":"How to conduct AMR data analysis","text":"tutorial, uses four different microorganisms: Escherichia coli, Staphylococcus aureus, Streptococcus pneumoniae, Klebsiella pneumoniae:","code":"bacteria <- c(   \"Escherichia coli\", \"Staphylococcus aureus\",   \"Streptococcus pneumoniae\", \"Klebsiella pneumoniae\" )"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"put-everything-together","dir":"Articles","previous_headings":"CreatLine truncated
		`@@ -1 +1 @@`
			[{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"How to conduct AMR data analysis","text":"Conducting AMR data analysis unfortunately requires -depth knowledge different scientific fields, makes hard right. least, requires: Good questions (always start !) thorough understanding (clinical) epidemiology, understand clinical epidemiological relevance possible bias results thorough understanding (clinical) microbiology/infectious diseases, understand microorganisms causal infections implications pharmaceutical treatment, well understanding intrinsic acquired microbial resistance Experience data analysis microbiological tests results, understand determination limitations MIC values interpretations RSI values Availability biological taxonomy microorganisms probably normalisation factors pharmaceuticals, defined daily doses (DDD) Available (inter-)national guidelines, profound methods apply course, instantly provide knowledge experience. AMR package, aimed providing (1) tools simplify antimicrobial resistance data cleaning, transformation analysis, (2) methods easily incorporate international guidelines (3) scientifically reliable reference data, including requirements mentioned . AMR package enables standardised reproducible AMR data analysis, application evidence-based rules, determination first isolates, translation various codes microorganisms antimicrobial agents, determination (multi-drug) resistant microorganisms, calculation antimicrobial resistance, prevalence future trends.","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"preparation","dir":"Articles","previous_headings":"","what":"Preparation","title":"How to conduct AMR data analysis","text":"tutorial, create fake demonstration data work . can skip Cleaning data already data ready. start analysis, try make structure data generally look like :","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"needed-r-packages","dir":"Articles","previous_headings":"Preparation","what":"Needed R packages","title":"How to conduct AMR data analysis","text":"many uses R, need additional packages AMR data analysis. package works closely together tidyverse packages dplyr ggplot2 RStudio. tidyverse tremendously improves way conduct data science - allows natural way writing syntaxes creating beautiful plots R. also use cleaner package, can used cleaning data creating frequency tables.","code":"library(dplyr) library(ggplot2) library(AMR) library(cleaner) # (if not yet installed, install with:) # install.packages(c(\"dplyr\", \"ggplot2\", \"AMR\", \"cleaner\"))"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"creation-of-data","dir":"Articles","previous_headings":"","what":"Creation of data","title":"How to conduct AMR data analysis","text":"create fake example data use analysis. AMR data analysis, need least: patient ID, name code microorganism, date antimicrobial results (antibiogram). also include specimen type (e.g. filter blood urine), ward type (e.g. filter ICUs). additional columns (like hospital name, patients gender even [well-defined] clinical properties) can comparative analysis, tutorial demonstrate .","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"patients","dir":"Articles","previous_headings":"Creation of data","what":"Patients","title":"How to conduct AMR data analysis","text":"start patients, need unique list patients. LETTERS object available R - ’s vector 26 characters: Z. patients object just created now vector length 260, values (patient IDs) varying A1 Z10. Now also set gender patients, putting ID gender table: first 135 patient IDs now male, 125 female.","code":"patients <- unlist(lapply(LETTERS, paste0, 1:10)) patients_table <- data.frame( patient_id = patients, gender = c( rep(\"M\", 135), rep(\"F\", 125) ) )"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"dates","dir":"Articles","previous_headings":"Creation of data","what":"Dates","title":"How to conduct AMR data analysis","text":"Let’s pretend data consists blood cultures isolates 1 January 2010 1 January 2018. dates object now contains days date range.","code":"dates <- seq(as.Date(\"2010-01-01\"), as.Date(\"2018-01-01\"), by = \"day\")"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"microorganisms","dir":"Articles","previous_headings":"Creation of data > Dates","what":"Microorganisms","title":"How to conduct AMR data analysis","text":"tutorial, uses four different microorganisms: Escherichia coli, Staphylococcus aureus, Streptococcus pneumoniae, Klebsiella pneumoniae:","code":"bacteria <- c( \"Escherichia coli\", \"Staphylococcus aureus\", \"Streptococcus pneumoniae\", \"Klebsiella pneumoniae\" )"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"put-everything-together","dir":"Articles","previous_headings":"CreatLine truncated				[{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"How to conduct AMR data analysis","text":"Conducting AMR data analysis unfortunately requires -depth knowledge different scientific fields, makes hard right. least, requires: Good questions (always start !) thorough understanding (clinical) epidemiology, understand clinical epidemiological relevance possible bias results thorough understanding (clinical) microbiology/infectious diseases, understand microorganisms causal infections implications pharmaceutical treatment, well understanding intrinsic acquired microbial resistance Experience data analysis microbiological tests results, understand determination limitations MIC values interpretations RSI values Availability biological taxonomy microorganisms probably normalisation factors pharmaceuticals, defined daily doses (DDD) Available (inter-)national guidelines, profound methods apply course, instantly provide knowledge experience. AMR package, aimed providing (1) tools simplify antimicrobial resistance data cleaning, transformation analysis, (2) methods easily incorporate international guidelines (3) scientifically reliable reference data, including requirements mentioned . AMR package enables standardised reproducible AMR data analysis, application evidence-based rules, determination first isolates, translation various codes microorganisms antimicrobial agents, determination (multi-drug) resistant microorganisms, calculation antimicrobial resistance, prevalence future trends.","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"preparation","dir":"Articles","previous_headings":"","what":"Preparation","title":"How to conduct AMR data analysis","text":"tutorial, create fake demonstration data work . can skip Cleaning data already data ready. start analysis, try make structure data generally look like :","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"needed-r-packages","dir":"Articles","previous_headings":"Preparation","what":"Needed R packages","title":"How to conduct AMR data analysis","text":"many uses R, need additional packages AMR data analysis. package works closely together tidyverse packages dplyr ggplot2 RStudio. tidyverse tremendously improves way conduct data science - allows natural way writing syntaxes creating beautiful plots R. also use cleaner package, can used cleaning data creating frequency tables.","code":"library(dplyr) library(ggplot2) library(AMR) library(cleaner) # (if not yet installed, install with:) # install.packages(c(\"dplyr\", \"ggplot2\", \"AMR\", \"cleaner\"))"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"creation-of-data","dir":"Articles","previous_headings":"","what":"Creation of data","title":"How to conduct AMR data analysis","text":"create fake example data use analysis. AMR data analysis, need least: patient ID, name code microorganism, date antimicrobial results (antibiogram). also include specimen type (e.g. filter blood urine), ward type (e.g. filter ICUs). additional columns (like hospital name, patients gender even [well-defined] clinical properties) can comparative analysis, tutorial demonstrate .","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"patients","dir":"Articles","previous_headings":"Creation of data","what":"Patients","title":"How to conduct AMR data analysis","text":"start patients, need unique list patients. LETTERS object available R - ’s vector 26 characters: Z. patients object just created now vector length 260, values (patient IDs) varying A1 Z10. Now also set gender patients, putting ID gender table: first 135 patient IDs now male, 125 female.","code":"patients <- unlist(lapply(LETTERS, paste0, 1:10)) patients_table <- data.frame( patient_id = patients, gender = c( rep(\"M\", 135), rep(\"F\", 125) ) )"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"dates","dir":"Articles","previous_headings":"Creation of data","what":"Dates","title":"How to conduct AMR data analysis","text":"Let’s pretend data consists blood cultures isolates 1 January 2010 1 January 2018. dates object now contains days date range.","code":"dates <- seq(as.Date(\"2010-01-01\"), as.Date(\"2018-01-01\"), by = \"day\")"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"microorganisms","dir":"Articles","previous_headings":"Creation of data > Dates","what":"Microorganisms","title":"How to conduct AMR data analysis","text":"tutorial, uses four different microorganisms: Escherichia coli, Staphylococcus aureus, Streptococcus pneumoniae, Klebsiella pneumoniae:","code":"bacteria <- c( \"Escherichia coli\", \"Staphylococcus aureus\", \"Streptococcus pneumoniae\", \"Klebsiella pneumoniae\" )"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"put-everything-together","dir":"Articles","previous_headings":"CreatLine truncated