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@ -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="">1.8.2.9063</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9064</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -168,7 +168,7 @@
<h4 data-toc-skip class="author">Dr. Matthijs
Berends</h4>
<h4 data-toc-skip class="date">16 December 2022</h4>
<h4 data-toc-skip class="date">17 December 2022</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/AMR.Rmd" class="external-link"><code>vignettes/AMR.Rmd</code></a></small>
<div class="d-none name"><code>AMR.Rmd</code></div>
@ -180,7 +180,7 @@ Berends</h4>
website update since they are based on randomly created values and the
page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
Markdown</a>. However, the methodology remains unchanged. This page was
generated on 16 December 2022.</p>
generated on 17 December 2022.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@ -236,21 +236,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2022-12-16</td>
<td align="center">2022-12-17</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="center">2022-12-16</td>
<td align="center">2022-12-17</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<tr class="odd">
<td align="center">2022-12-16</td>
<td align="center">2022-12-17</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -400,41 +400,30 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2013-10-19</td>
<td align="center">J10</td>
<td align="center">2011-12-20</td>
<td align="center">L9</td>
<td align="center">Hospital A</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">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2015-10-18</td>
<td align="center">J6</td>
<td align="center">2010-07-06</td>
<td align="center">N2</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2012-11-25</td>
<td align="center">L10</td>
<td align="center">Hospital A</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">M</td>
</tr>
<tr class="even">
<td align="center">2013-07-25</td>
<td align="center">S1</td>
<td align="center">2014-06-14</td>
<td align="center">Z5</td>
<td align="center">Hospital B</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
@ -443,27 +432,38 @@ data set:</p>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2010-09-26</td>
<td align="center">I8</td>
<tr class="even">
<td align="center">2014-12-21</td>
<td align="center">O3</td>
<td align="center">Hospital A</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">F</td>
</tr>
<tr class="odd">
<td align="center">2013-04-17</td>
<td align="center">C4</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia 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">M</td>
</tr>
<tr class="even">
<td align="center">2016-05-07</td>
<td align="center">O7</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">2010-04-22</td>
<td align="center">N3</td>
<td align="center">Hospital D</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">R</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">M</td>
</tr>
</tbody>
</table>
@ -499,18 +499,18 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,479</td>
<td align="right">52.40%</td>
<td align="right">10,479</td>
<td align="right">52.4%</td>
<td align="right">10,365</td>
<td align="right">51.83%</td>
<td align="right">10,365</td>
<td align="right">51.83%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,521</td>
<td align="right">47.61%</td>
<td align="right">9,635</td>
<td align="right">48.18%</td>
<td align="right">20,000</td>
<td align="right">100.0%</td>
<td align="right">100.00%</td>
</tr>
</tbody>
</table>
@ -621,9 +621,9 @@ 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 10,640 'phenotype-based' first isolates (53.2% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,653 'phenotype-based' first isolates (53.3% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 53.2% is suitable for resistance analysis! We can now filter
<p>So only 53.3% is suitable for resistance analysis! We can now filter
on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the
<code>dplyr</code> package:</p>
<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
@ -634,7 +634,7 @@ on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html"
<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 10,640 isolates for analysis. Now our data looks
<p>So we end up with 10,653 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>
@ -673,73 +673,73 @@ like:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">2</td>
<td align="center">2010-07-06</td>
<td align="center">N2</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</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">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">3</td>
<td align="center">2014-06-14</td>
<td align="center">Z5</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">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="odd">
<td align="left">4</td>
<td align="center">2013-07-25</td>
<td align="center">S1</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">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="left">9</td>
<td align="center">2010-04-28</td>
<td align="center">E6</td>
<td align="center">Hospital B</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">M</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">10</td>
<td align="center">2014-08-09</td>
<td align="center">X9</td>
<td align="center">2014-12-21</td>
<td align="center">O3</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">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">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</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">11</td>
<td align="center">2013-06-01</td>
<td align="center">A1</td>
<td align="left">6</td>
<td align="center">2010-04-22</td>
<td align="center">N3</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">B_KLBSL_PNMN</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">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">12</td>
<td align="center">2015-02-28</td>
<td align="center">R6</td>
<td align="left">7</td>
<td align="center">2010-09-06</td>
<td align="center">W7</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
@ -753,19 +753,19 @@ like:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">13</td>
<td align="center">2013-01-19</td>
<td align="center">G6</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="left">8</td>
<td align="center">2014-10-08</td>
<td align="center">I6</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</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">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
</tbody>
@ -801,8 +801,8 @@ 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: 10,640<br>
Available: 10,640 (100%, NA: 0 = 0%)<br>
Length: 10,653<br>
Available: 10,653 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -827,33 +827,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">4,656</td>
<td align="right">43.76%</td>
<td align="right">4,656</td>
<td align="right">43.76%</td>
<td align="right">4,579</td>
<td align="right">42.98%</td>
<td align="right">4,579</td>
<td align="right">42.98%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,781</td>
<td align="right">26.14%</td>
<td align="right">7,437</td>
<td align="right">69.90%</td>
<td align="right">2,787</td>
<td align="right">26.16%</td>
<td align="right">7,366</td>
<td align="right">69.14%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,075</td>
<td align="right">19.50%</td>
<td align="right">9,512</td>
<td align="right">89.40%</td>
<td align="right">2,119</td>
<td align="right">19.89%</td>
<td align="right">9,485</td>
<td align="right">89.04%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,128</td>
<td align="right">10.60%</td>
<td align="right">10,640</td>
<td align="right">1,168</td>
<td align="right">10.96%</td>
<td align="right">10,653</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -874,14 +874,14 @@ antibiotic class they are in:</p>
<col width="9%">
<col width="9%">
<col width="9%">
<col width="10%">
<col width="11%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="6%">
<col width="11%">
<col width="12%">
<col width="11%">
<col width="9%">
<col width="5%">
</colgroup>
@ -902,8 +902,8 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2013-07-25</td>
<td align="center">S1</td>
<td align="center">2014-06-14</td>
<td align="center">Z5</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
@ -917,72 +917,72 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2014-08-09</td>
<td align="center">X9</td>
<td align="center">2017-04-17</td>
<td align="center">K4</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">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">2012-01-11</td>
<td align="center">R9</td>
<td align="center">Hospital D</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">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">2015-01-15</td>
<td align="center">V2</td>
<td align="center">2015-12-19</td>
<td align="center">Y3</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</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-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2016-09-20</td>
<td align="center">N8</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">R</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>
<td align="center">aureus</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="center">2015-05-22</td>
<td align="center">B1</td>
<td align="center">2011-05-11</td>
<td align="center">Y3</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="odd">
<td align="center">2014-07-26</td>
<td align="center">Z10</td>
<td align="center">Hospital D</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">2012-12-01</td>
<td align="center">D6</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>
@ -1013,50 +1013,50 @@ 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">2215</td>
<td align="center">123</td>
<td align="center">2318</td>
<td align="center">4656</td>
<td align="center">2116</td>
<td align="center">135</td>
<td align="center">2328</td>
<td align="center">4579</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3445</td>
<td align="center">150</td>
<td align="center">1061</td>
<td align="center">4656</td>
<td align="center">3340</td>
<td align="center">172</td>
<td align="center">1067</td>
<td align="center">4579</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3399</td>
<td align="center">3387</td>
<td align="center">0</td>
<td align="center">1257</td>
<td align="center">4656</td>
<td align="center">1192</td>
<td align="center">4579</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4094</td>
<td align="center">3983</td>
<td align="center">0</td>
<td align="center">562</td>
<td align="center">4656</td>
<td align="center">596</td>
<td align="center">4579</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">1128</td>
<td align="center">1128</td>
<td align="center">1168</td>
<td align="center">1168</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">880</td>
<td align="center">52</td>
<td align="center">196</td>
<td align="center">1128</td>
<td align="center">917</td>
<td align="center">35</td>
<td align="center">216</td>
<td align="center">1168</td>
</tr>
</tbody>
</table>
@ -1078,34 +1078,34 @@ 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">4094</td>
<td align="center">3983</td>
<td align="center">0</td>
<td align="center">562</td>
<td align="center">4656</td>
<td align="center">596</td>
<td align="center">4579</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1010</td>
<td align="center">1066</td>
<td align="center">0</td>
<td align="center">118</td>
<td align="center">1128</td>
<td align="center">102</td>
<td align="center">1168</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2431</td>
<td align="center">2468</td>
<td align="center">0</td>
<td align="center">350</td>
<td align="center">2781</td>
<td align="center">319</td>
<td align="center">2787</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">2075</td>
<td align="center">2075</td>
<td align="center">2119</td>
<td align="center">2119</td>
</tr>
</tbody>
</table>
@ -1137,7 +1137,7 @@ I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equa
own:</p>
<div class="sourceCode" id="cb25"><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] 0.5425752</span></span></code></pre></div>
<span><span class="co"># [1] 0.5518633</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="cb26"><pre class="downlit sourceCode r">
@ -1152,19 +1152,19 @@ own:</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5473815</td>
<td align="center">0.5650169</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5484133</td>
<td align="center">0.5469568</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5280255</td>
<td align="center">0.5635802</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5360920</td>
<td align="center">0.5314100</td>
</tr>
</tbody>
</table>
@ -1189,23 +1189,23 @@ 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">0.5473815</td>
<td align="center">3208</td>
<td align="center">0.5650169</td>
<td align="center">3253</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5484133</td>
<td align="center">3687</td>
<td align="center">0.5469568</td>
<td align="center">3631</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5280255</td>
<td align="center">1570</td>
<td align="center">0.5635802</td>
<td align="center">1620</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5360920</td>
<td align="center">2175</td>
<td align="center">0.5314100</td>
<td align="center">2149</td>
</tr>
</tbody>
</table>
@ -1230,27 +1230,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7721220</td>
<td align="center">0.8792955</td>
<td align="center">0.9776632</td>
<td align="center">0.7669797</td>
<td align="center">0.8698406</td>
<td align="center">0.9744486</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8262411</td>
<td align="center">0.8953901</td>
<td align="center">0.9831560</td>
<td align="center">0.8150685</td>
<td align="center">0.9126712</td>
<td align="center">0.9845890</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7907228</td>
<td align="center">0.8741460</td>
<td align="center">0.9816613</td>
<td align="center">0.7865088</td>
<td align="center">0.8855400</td>
<td align="center">0.9788303</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5368675</td>
<td align="center">0.5304389</td>
<td align="center">0.0000000</td>
<td align="center">0.5368675</td>
<td align="center">0.5304389</td>
</tr>
</tbody>
</table>
@ -1278,23 +1278,23 @@ classes, use a antibiotic class selector such as
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">54.7%</td>
<td align="right">26.7%</td>
<td align="right">56.5%</td>
<td align="right">27.3%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">54.8%</td>
<td align="right">26.7%</td>
<td align="right">54.7%</td>
<td align="right">27.0%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">52.8%</td>
<td align="right">26.9%</td>
<td align="right">56.4%</td>
<td align="right">28.1%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">53.6%</td>
<td align="right">24.7%</td>
<td align="right">53.1%</td>
<td align="right">25.5%</td>
</tr>
</tbody>
</table>
@ -1410,18 +1410,16 @@ 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] 0.25 32 0.025 16 256 32 0.5 64 64 </span></span>
<span><span class="co"># [10] 0.0625 1 0.25 4 128 16 4 0.125 4 </span></span>
<span><span class="co"># [19] 1 0.25 0.5 32 0.0625 0.0625 32 32 0.25 </span></span>
<span><span class="co"># [28] 0.002 0.01 1 0.005 0.0625 32 64 0.01 0.125 </span></span>
<span><span class="co"># [37] 0.25 0.005 2 &lt;=0.001 32 0.25 &lt;=0.001 64 2 </span></span>
<span><span class="co"># [46] 2 64 2 8 16 0.5 64 0.5 8 </span></span>
<span><span class="co"># [55] 0.25 256 2 128 128 0.025 0.25 0.5 0.5 </span></span>
<span><span class="co"># [64] 16 16 0.005 128 16 1 0.5 2 0.005 </span></span>
<span><span class="co"># [73] 0.002 0.125 1 0.25 128 0.25 64 0.125 0.005 </span></span>
<span><span class="co"># [82] 0.25 0.5 0.0625 8 128 0.25 0.0625 0.025 4 </span></span>
<span><span class="co"># [91] &lt;=0.001 2 16 &lt;=0.001 32 0.01 16 0.002 16 </span></span>
<span><span class="co"># [100] 4</span></span></code></pre></div>
<span><span class="co"># [1] 128 32 0.002 0.005 0.01 32 0.25 128 32 &gt;=256 </span></span>
<span><span class="co"># [11] 0.005 0.125 16 2 0.01 4 &gt;=256 4 0.01 0.001 </span></span>
<span><span class="co"># [21] 16 &gt;=256 32 0.25 16 0.001 128 0.001 8 0.0625</span></span>
<span><span class="co"># [31] 16 16 1 16 0.125 16 8 2 &gt;=256 2 </span></span>
<span><span class="co"># [41] 0.002 0.01 0.5 16 1 0.0625 0.01 0.025 0.002 0.0625</span></span>
<span><span class="co"># [51] 0.25 64 0.01 0.125 0.0625 0.005 0.0625 &gt;=256 0.0625 32 </span></span>
<span><span class="co"># [61] 1 0.002 0.125 32 0.002 128 0.01 8 0.25 8 </span></span>
<span><span class="co"># [71] 0.005 &gt;=256 2 0.01 32 4 &gt;=256 2 0.002 0.01 </span></span>
<span><span class="co"># [81] 1 16 0.025 16 4 0.5 32 32 64 0.25 </span></span>
<span><span class="co"># [91] 0.01 &gt;=256 0.01 16 0.025 16 1 0.005 0.25 0.025</span></span></code></pre></div>
<div class="sourceCode" id="cb36"><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>
@ -1455,10 +1453,10 @@ 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] 20 17 23 30 29 24 31 18 21 23 21 21 25 19 19 29 20 30 19 27 21 26 29 22 31</span></span>
<span><span class="co"># [26] 20 30 31 23 31 26 31 29 21 20 28 19 20 23 21 25 22 21 17 20 21 25 26 23 23</span></span>
<span><span class="co"># [51] 19 18 18 21 27 31 31 25 27 27 22 28 17 21 22 30 22 19 28 23 23 31 30 27 29</span></span>
<span><span class="co"># [76] 19 26 27 26 30 24 23 21 29 28 31 17 21 17 19 31 28 17 24 26 25 17 23 27 18</span></span></code></pre></div>
<span><span class="co"># [1] 18 29 28 22 20 28 25 20 28 23 23 31 24 26 31 31 30 20 29 20 31 29 28 29 25</span></span>
<span><span class="co"># [26] 28 26 23 27 22 21 23 17 25 30 30 29 28 25 28 19 17 28 18 31 20 29 29 23 23</span></span>
<span><span class="co"># [51] 19 25 29 20 27 29 19 24 22 24 31 22 25 29 18 31 17 23 26 19 24 31 29 31 28</span></span>
<span><span class="co"># [76] 31 22 27 30 27 30 22 22 27 23 24 28 25 26 24 29 20 26 20 29 29 22 19 25 26</span></span></code></pre></div>
<div class="sourceCode" id="cb42"><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>

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2
articles/EUCAST.html
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@ -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="">1.8.2.9063</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9064</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

58
articles/MDR.html
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@ -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="">1.8.2.9063</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9064</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -375,19 +375,19 @@ 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 I S S S S R</span></span>
<span><span class="co"># 2 I S S R I R</span></span>
<span><span class="co"># 3 I S S I I S</span></span>
<span><span class="co"># 4 R R I R I S</span></span>
<span><span class="co"># 5 S S R R I I</span></span>
<span><span class="co"># 6 I S S R I R</span></span>
<span><span class="co"># 1 R R I I S I</span></span>
<span><span class="co"># 2 S I S I R R</span></span>
<span><span class="co"># 3 R I S I R S</span></span>
<span><span class="co"># 4 I R S I I R</span></span>
<span><span class="co"># 5 R R R R S I</span></span>
<span><span class="co"># 6 R I S S I I</span></span>
<span><span class="co"># kanamycin</span></span>
<span><span class="co"># 1 I</span></span>
<span><span class="co"># 1 S</span></span>
<span><span class="co"># 2 I</span></span>
<span><span class="co"># 3 S</span></span>
<span><span class="co"># 3 R</span></span>
<span><span class="co"># 4 I</span></span>
<span><span class="co"># 5 R</span></span>
<span><span class="co"># 6 S</span></span></code></pre></div>
<span><span class="co"># 5 S</span></span>
<span><span class="co"># 6 R</span></span></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can
use:</p>
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
@ -428,40 +428,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3281</td>
<td align="right">65.62%</td>
<td align="right">3281</td>
<td align="right">65.62%</td>
<td align="right">3211</td>
<td align="right">64.22%</td>
<td align="right">3211</td>
<td align="right">64.22%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">959</td>
<td align="right">19.18%</td>
<td align="right">4240</td>
<td align="right">84.80%</td>
<td align="right">993</td>
<td align="right">19.86%</td>
<td align="right">4204</td>
<td align="right">84.08%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">425</td>
<td align="right">8.50%</td>
<td align="right">4665</td>
<td align="right">93.30%</td>
<td align="right">431</td>
<td align="right">8.62%</td>
<td align="right">4635</td>
<td align="right">92.70%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">235</td>
<td align="right">4.70%</td>
<td align="right">4900</td>
<td align="right">98.00%</td>
<td align="right">243</td>
<td align="right">4.86%</td>
<td align="right">4878</td>
<td align="right">97.56%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">100</td>
<td align="right">2.00%</td>
<td align="right">122</td>
<td align="right">2.44%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

2
articles/PCA.html
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@ -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="">1.8.2.9063</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9064</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

4
articles/SPSS.html
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@ -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="">1.8.2.9063</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9064</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -168,7 +168,7 @@
<h4 data-toc-skip class="author">Dr. Matthijs
Berends</h4>
<h4 data-toc-skip class="date">16 December 2022</h4>
<h4 data-toc-skip class="date">17 December 2022</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/SPSS.Rmd" class="external-link"><code>vignettes/SPSS.Rmd</code></a></small>
<div class="d-none name"><code>SPSS.Rmd</code></div>

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articles/WHONET.html
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@ -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="">1.8.2.9063</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9064</small>
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articles/datasets.html
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@ -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="">1.8.2.9063</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9064</small>
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@ -166,7 +166,7 @@
<main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
<h4 data-toc-skip class="date">16 December 2022</h4>
<h4 data-toc-skip class="date">17 December 2022</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<div class="d-none name"><code>datasets.Rmd</code></div>
@ -187,7 +187,7 @@ of the data sets look like.</p>
<h2 id="microorganisms-full-microbial-taxonomy">
<code>microorganisms</code>: Full Microbial Taxonomy<a class="anchor" aria-label="anchor" href="#microorganisms-full-microbial-taxonomy"></a>
</h2>
<p>A data set with 52,144 rows and 22 columns, containing the following
<p>A data set with 52,140 rows and 22 columns, containing the following
column names:<br><em>mo</em>, <em>fullname</em>, <em>status</em>, <em>kingdom</em>,
<em>phylum</em>, <em>class</em>, <em>order</em>, <em>family</em>,
<em>genus</em>, <em>species</em>, <em>subspecies</em>, <em>rank</em>,
@ -196,7 +196,7 @@ 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 16 December 2022 15:10:43 UTC. Find more info
<p>It was last updated on 17 December 2022 13:31:33 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>
@ -273,7 +273,7 @@ Set Name ‘Microoganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href
</tr>
<tr class="even">
<td align="center">Bacteria</td>
<td align="center">36,478</td>
<td align="center">36,474</td>
</tr>
<tr class="odd">
<td align="center">Fungi</td>

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articles/index.html
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9063</small>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9063</small>
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