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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="">1.8.2.9131</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9132</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -178,7 +178,7 @@
<h4 data-toc-skip class="author">Dr. Matthijs
Berends</h4>
<h4 data-toc-skip class="date">15 February 2023</h4>
<h4 data-toc-skip class="date">17 February 2023</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>
@ -190,7 +190,7 @@ 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 15 February 2023.</p>
generated on 17 February 2023.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@ -246,21 +246,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2023-02-15</td>
<td align="center">2023-02-17</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">2023-02-15</td>
<td align="center">2023-02-17</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">2023-02-15</td>
<td align="center">2023-02-17</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -411,71 +411,71 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2010-08-08</td>
<td align="center">Y8</td>
<td align="center">Hospital B</td>
<td align="center">2013-03-23</td>
<td align="center">C3</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2011-03-02</td>
<td align="center">Q1</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">I</td>
<td align="center">2017-06-18</td>
<td align="center">M9</td>
<td align="center">Hospital B</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2016-04-28</td>
<td align="center">S9</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2014-08-07</td>
<td align="center">T10</td>
<td align="center">2013-10-07</td>
<td align="center">M10</td>
<td align="center">Hospital D</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">I</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>
</tr>
<tr class="odd">
<td align="center">2014-04-21</td>
<td align="center">I3</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">I</td>
<td align="center">I</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2012-08-08</td>
<td align="center">M4</td>
<td align="center">Hospital B</td>
<td align="center">2013-03-21</td>
<td align="center">C9</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2014-12-29</td>
<td align="center">Q10</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2015-08-23</td>
<td align="center">W8</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">F</td>
</tr>
</tbody>
</table>
<p>Now, let’s start the cleaning and the analysis!</p>
@ -510,16 +510,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,421</td>
<td align="right">52.11%</td>
<td align="right">10,421</td>
<td align="right">52.11%</td>
<td align="right">10,408</td>
<td align="right">52.04%</td>
<td align="right">10,408</td>
<td align="right">52.04%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,579</td>
<td align="right">47.90%</td>
<td align="right">9,592</td>
<td align="right">47.96%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -632,10 +632,10 @@ 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 12,198 'phenotype-based' first isolates (61.0% of total where a</span></span>
<span><span class="co"># =&gt; Found 12,380 'phenotype-based' first isolates (61.9% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 61% 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
<p>So only 61.9% 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">
<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>
@ -644,7 +644,7 @@ it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" cl
<div class="sourceCode" id="cb16"><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>
<span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<p>So we end up with 12 198 isolates for analysis. Now our data looks
<p>So we end up with 12 380 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>
@ -684,15 +684,15 @@ like:</p>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2010-08-08</td>
<td align="center">Y8</td>
<td align="center">Hospital B</td>
<td align="center">2013-03-23</td>
<td align="center">C3</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
@ -700,14 +700,46 @@ like:</p>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="center">2011-03-02</td>
<td align="center">Q1</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">I</td>
<td align="center">2017-06-18</td>
<td align="center">M9</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>
<tr class="odd">
<td align="left">4</td>
<td align="center">2013-03-21</td>
<td align="center">C9</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">I</td>
<td align="center">I</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="even">
<td align="left">5</td>
<td align="center">2014-12-29</td>
<td align="center">Q10</td>
<td align="center">Hospital A</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">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
@ -715,47 +747,15 @@ like:</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">4</td>
<td align="center">2014-08-07</td>
<td align="center">T10</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="left">6</td>
<td align="center">2012-08-08</td>
<td align="center">M4</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">I</td>
<td align="center">I</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">7</td>
<td align="center">2017-02-12</td>
<td align="center">O7</td>
<td align="center">Hospital B</td>
<td align="center">2015-08-23</td>
<td align="center">W8</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">R</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
@ -763,19 +763,19 @@ like:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">8</td>
<td align="center">2011-02-09</td>
<td align="center">K4</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="left">7</td>
<td align="center">2014-08-05</td>
<td align="center">R2</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">I</td>
<td align="center">R</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">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
</tbody>
@ -811,8 +811,8 @@ 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: 12,198<br>
Available: 12,198 (100%, NA: 0 = 0%)<br>
Length: 12,380<br>
Available: 12,380 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -837,33 +837,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">5,861</td>
<td align="right">48.05%</td>
<td align="right">5,861</td>
<td align="right">48.05%</td>
<td align="right">5,922</td>
<td align="right">47.84%</td>
<td align="right">5,922</td>
<td align="right">47.84%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,183</td>
<td align="right">26.09%</td>
<td align="right">9,044</td>
<td align="right">74.14%</td>
<td align="right">3,262</td>
<td align="right">26.35%</td>
<td align="right">9,184</td>
<td align="right">74.18%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">1,850</td>
<td align="right">15.17%</td>
<td align="right">10,894</td>
<td align="right">89.31%</td>
<td align="right">1,854</td>
<td align="right">14.98%</td>
<td align="right">11,038</td>
<td align="right">89.16%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,304</td>
<td align="right">10.69%</td>
<td align="right">12,198</td>
<td align="right">1,342</td>
<td align="right">10.84%</td>
<td align="right">12,380</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -912,42 +912,12 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2011-03-02</td>
<td align="center">Q1</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</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">TRUE</td>
</tr>
<tr class="even">
<td align="center">2014-08-07</td>
<td align="center">T10</td>
<td align="center">Hospital D</td>
<td align="center">2017-06-18</td>
<td align="center">M9</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="center">2011-02-09</td>
<td align="center">K4</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
@ -957,23 +927,23 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2016-05-14</td>
<td align="center">P6</td>
<td align="center">Hospital C</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">2014-08-05</td>
<td align="center">R2</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</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="odd">
<td align="center">2010-02-23</td>
<td align="center">W6</td>
<td align="center">2011-08-22</td>
<td align="center">S8</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
@ -987,15 +957,45 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2014-05-10</td>
<td align="center">R2</td>
<td align="center">2013-07-23</td>
<td align="center">C7</td>
<td align="center">Hospital A</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">M</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="center">2012-03-19</td>
<td align="center">H6</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">R</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="center">2010-03-15</td>
<td align="center">A3</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">R</td>
<td align="center">F</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
@ -1025,46 +1025,46 @@ different bug/drug combinations, you can use the
<td align="left">2</td>
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">2766</td>
<td align="center">1144</td>
<td align="center">1951</td>
<td align="center">5861</td>
<td align="center">2776</td>
<td align="center">1183</td>
<td align="center">1963</td>
<td align="center">5922</td>
</tr>
<tr class="even">
<td align="left">1</td>
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">1499</td>
<td align="center">1230</td>
<td align="center">3132</td>
<td align="center">5861</td>
<td align="center">1534</td>
<td align="center">1264</td>
<td align="center">3124</td>
<td align="center">5922</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">2070</td>
<td align="center">1784</td>
<td align="center">2007</td>
<td align="center">5861</td>
<td align="center">2035</td>
<td align="center">1845</td>
<td align="center">2042</td>
<td align="center">5922</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">2005</td>
<td align="center">1804</td>
<td align="center">2052</td>
<td align="center">5861</td>
<td align="center">2048</td>
<td align="center">1829</td>
<td align="center">2045</td>
<td align="center">5922</td>
</tr>
<tr class="odd">
<td align="left">6</td>
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">573</td>
<td align="center">595</td>
<td align="center">281</td>
<td align="center">450</td>
<td align="center">1304</td>
<td align="center">466</td>
<td align="center">1342</td>
</tr>
<tr class="even">
<td align="left">5</td>
@ -1072,8 +1072,8 @@ different bug/drug combinations, you can use the
<td align="center">AMX</td>
<td align="center">0</td>
<td align="center">0</td>
<td align="center">1304</td>
<td align="center">1304</td>
<td align="center">1342</td>
<td align="center">1342</td>
</tr>
</tbody>
</table>
@ -1095,34 +1095,34 @@ 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">2005</td>
<td align="center">1804</td>
<td align="center">2052</td>
<td align="center">5861</td>
<td align="center">2048</td>
<td align="center">1829</td>
<td align="center">2045</td>
<td align="center">5922</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">411</td>
<td align="center">441</td>
<td align="center">452</td>
<td align="center">1304</td>
<td align="center">472</td>
<td align="center">436</td>
<td align="center">434</td>
<td align="center">1342</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">1092</td>
<td align="center">1014</td>
<td align="center">1077</td>
<td align="center">3183</td>
<td align="center">1107</td>
<td align="center">1029</td>
<td align="center">1126</td>
<td align="center">3262</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">1850</td>
<td align="center">1850</td>
<td align="center">1854</td>
<td align="center">1854</td>
</tr>
</tbody>
</table>
@ -1154,7 +1154,7 @@ 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] 0.5823086</span></span></code></pre></div>
<span><span class="co"># [1] 0.5808562</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">
@ -1169,19 +1169,19 @@ own:</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5925926</td>
<td align="center">0.5816024</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5784499</td>
<td align="center">0.5940042</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5731311</td>
<td align="center">0.5499199</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5802005</td>
<td align="center">0.5802964</td>
</tr>
</tbody>
</table>
@ -1206,23 +1206,23 @@ 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">0.5925926</td>
<td align="center">3726</td>
<td align="center">0.5816024</td>
<td align="center">3707</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5784499</td>
<td align="center">4232</td>
<td align="center">0.5940042</td>
<td align="center">4303</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5731311</td>
<td align="center">1846</td>
<td align="center">0.5499199</td>
<td align="center">1873</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5802005</td>
<td align="center">2394</td>
<td align="center">0.5802964</td>
<td align="center">2497</td>
</tr>
</tbody>
</table>
@ -1247,27 +1247,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.6671217</td>
<td align="center">0.6498891</td>
<td align="center">0.8846613</td>
<td align="center">0.6685241</td>
<td align="center">0.6546775</td>
<td align="center">0.8850051</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.6549080</td>
<td align="center">0.6533742</td>
<td align="center">0.8788344</td>
<td align="center">0.6527571</td>
<td align="center">0.6766021</td>
<td align="center">0.8971684</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.6830035</td>
<td align="center">0.6616400</td>
<td align="center">0.8850141</td>
<td align="center">0.6686082</td>
<td align="center">0.6548130</td>
<td align="center">0.8868792</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.4837838</td>
<td align="center">0.4778857</td>
<td align="center">0.0000000</td>
<td align="center">0.4837838</td>
<td align="center">0.4778857</td>
</tr>
</tbody>
</table>
@ -1295,23 +1295,23 @@ classes, use a antibiotic class selector such as
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">59.3%</td>
<td align="right">36.3%</td>
<td align="right">58.2%</td>
<td align="right">35.3%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">57.8%</td>
<td align="right">35.5%</td>
<td align="right">59.4%</td>
<td align="right">37.5%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">57.3%</td>
<td align="right">35.6%</td>
<td align="right">55.0%</td>
<td align="right">34.5%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">58.0%</td>
<td align="right">35.6%</td>
<td align="right">36.5%</td>
</tr>
</tbody>
</table>
@ -1427,18 +1427,16 @@ 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] 0.01 &gt;=256 0.5 64 64 &gt;=256 0.005 1 &gt;=256 </span></span>
<span><span class="co"># [10] 16 4 32 1 2 64 0.0625 0.0625 8 </span></span>
<span><span class="co"># [19] 64 2 0.01 8 1 0.002 0.5 0.5 0.002 </span></span>
<span><span class="co"># [28] 0.0625 0.005 32 2 0.01 1 4 64 8 </span></span>
<span><span class="co"># [37] 0.125 32 0.125 0.002 &gt;=256 0.005 0.002 2 8 </span></span>
<span><span class="co"># [46] &gt;=256 &gt;=256 0.01 32 0.002 64 0.5 8 2 </span></span>
<span><span class="co"># [55] 0.25 4 0.002 0.002 0.125 8 0.25 &lt;=0.001 32 </span></span>
<span><span class="co"># [64] &lt;=0.001 &lt;=0.001 0.002 &gt;=256 0.002 0.5 0.125 0.01 &lt;=0.001</span></span>
<span><span class="co"># [73] 2 8 0.01 0.25 128 0.025 128 0.25 0.005 </span></span>
<span><span class="co"># [82] 0.01 0.002 32 32 1 0.5 &gt;=256 2 0.025 </span></span>
<span><span class="co"># [91] 4 8 4 0.25 0.5 0.5 1 0.01 32 </span></span>
<span><span class="co"># [100] 0.5</span></span></code></pre></div>
<span><span class="co"># [1] 32 64 0.002 2 16 8 128 0.025 0.0625 0.001 </span></span>
<span><span class="co"># [11] 0.0625 0.005 16 128 4 0.025 0.01 128 0.001 16 </span></span>
<span><span class="co"># [21] 128 0.025 4 0.002 0.01 64 4 0.125 &gt;=256 128 </span></span>
<span><span class="co"># [31] 1 0.002 0.005 64 0.25 0.025 16 32 32 1 </span></span>
<span><span class="co"># [41] 8 2 32 16 0.0625 16 8 &gt;=256 &gt;=256 0.25 </span></span>
<span><span class="co"># [51] 64 0.25 128 16 0.0625 0.001 4 0.0625 0.005 0.5 </span></span>
<span><span class="co"># [61] 64 0.0625 0.025 0.001 0.001 0.005 0.0625 0.025 0.25 1 </span></span>
<span><span class="co"># [71] 0.125 0.002 8 0.125 0.001 0.001 0.01 16 8 32 </span></span>
<span><span class="co"># [81] 0.002 0.01 1 0.01 1 0.0625 0.025 0.01 1 1 </span></span>
<span><span class="co"># [91] 0.025 0.125 8 4 32 &gt;=256 4 0.001 4 0.005</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>
@ -1472,10 +1470,10 @@ 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] 24 28 29 21 30 30 22 20 23 25 31 28 24 20 25 18 17 21 28 24 19 31 28 25 17</span></span>
<span><span class="co"># [26] 30 31 25 26 18 29 27 29 24 23 31 18 22 22 31 20 24 27 18 18 29 27 30 25 27</span></span>
<span><span class="co"># [51] 17 29 20 26 24 18 26 28 22 30 29 20 26 28 30 24 19 19 26 17 22 22 17 30 24</span></span>
<span><span class="co"># [76] 17 27 20 23 23 18 30 27 21 24 19 25 23 24 20 18 30 20 23 22 25 18 30 28 21</span></span></code></pre></div>
<span><span class="co"># [1] 26 25 22 31 23 25 21 17 28 29 23 26 21 19 29 21 25 27 25 28 28 30 23 26 17</span></span>
<span><span class="co"># [26] 29 27 25 28 21 26 28 24 27 31 22 21 23 18 29 26 30 30 28 18 25 20 30 29 17</span></span>
<span><span class="co"># [51] 18 21 27 24 29 21 24 22 26 27 18 25 28 31 19 18 18 28 19 22 18 27 28 31 21</span></span>
<span><span class="co"># [76] 31 18 17 27 20 26 24 17 26 23 19 20 18 25 26 26 24 24 29 30 19 19 23 31 25</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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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="">1.8.2.9131</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9132</small>
<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="">1.8.2.9131</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9132</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -385,19 +385,19 @@ 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 R R R I S I</span></span>
<span><span class="co"># 2 S I R S I I</span></span>
<span><span class="co"># 3 R S R I R R</span></span>
<span><span class="co"># 4 I I I I R R</span></span>
<span><span class="co"># 5 I R I R S R</span></span>
<span><span class="co"># 6 S R S I I I</span></span>
<span><span class="co"># 1 I S I I R R</span></span>
<span><span class="co"># 2 S I R S S R</span></span>
<span><span class="co"># 3 I I I R R S</span></span>
<span><span class="co"># 4 R R I R R I</span></span>
<span><span class="co"># 5 S R S R I I</span></span>
<span><span class="co"># 6 S S I R I I</span></span>
<span><span class="co"># kanamycin</span></span>
<span><span class="co"># 1 S</span></span>
<span><span class="co"># 2 R</span></span>
<span><span class="co"># 3 S</span></span>
<span><span class="co"># 1 I</span></span>
<span><span class="co"># 2 S</span></span>
<span><span class="co"># 3 I</span></span>
<span><span class="co"># 4 I</span></span>
<span><span class="co"># 5 S</span></span>
<span><span class="co"># 6 S</span></span></code></pre></div>
<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">
@ -438,40 +438,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3198</td>
<td align="right">63.96%</td>
<td align="right">3198</td>
<td align="right">63.96%</td>
<td align="right">3173</td>
<td align="right">63.46%</td>
<td align="right">3173</td>
<td align="right">63.46%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">997</td>
<td align="right">19.94%</td>
<td align="right">4195</td>
<td align="right">83.90%</td>
<td align="right">1003</td>
<td align="right">20.06%</td>
<td align="right">4176</td>
<td align="right">83.52%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">438</td>
<td align="right">8.76%</td>
<td align="right">4633</td>
<td align="right">92.66%</td>
<td align="right">462</td>
<td align="right">9.24%</td>
<td align="right">4638</td>
<td align="right">92.76%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">257</td>
<td align="right">5.14%</td>
<td align="right">4890</td>
<td align="right">97.80%</td>
<td align="right">255</td>
<td align="right">5.10%</td>
<td align="right">4893</td>
<td align="right">97.86%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">110</td>
<td align="right">2.20%</td>
<td align="right">107</td>
<td align="right">2.14%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

2
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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="">1.8.2.9131</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9132</small>
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@ -38,7 +38,7 @@
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<h4 data-toc-skip class="author">Dr. Matthijs
Berends</h4>
<h4 data-toc-skip class="date">15 February 2023</h4>
<h4 data-toc-skip class="date">17 February 2023</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>
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articles/datasets.html
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<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">15 February 2023</h4>
<h4 data-toc-skip class="date">17 February 2023</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<div class="d-none name"><code>datasets.Rmd</code></div>

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