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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="">1.8.2.9121</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9122</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">12 February 2023</h4>
<h4 data-toc-skip class="date">13 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 12 February 2023.</p>
generated on 13 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">2023-02-12</td>
<td align="center">2023-02-13</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">2023-02-12</td>
<td align="center">2023-02-13</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">2023-02-12</td>
<td align="center">2023-02-13</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -411,69 +411,69 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2016-05-20</td>
<td align="center">F10</td>
<td align="center">2017-03-28</td>
<td align="center">X1</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia coli</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2010-03-06</td>
<td align="center">O2</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2014-08-21</td>
<td align="center">H5</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">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">R</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2010-04-25</td>
<td align="center">G5</td>
<td align="center">Hospital D</td>
<td align="center">2013-12-31</td>
<td align="center">W3</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia coli</td>
<td align="center">I</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">I</td>
<td align="center">M</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2012-08-19</td>
<td align="center">V5</td>
<td align="center">2017-04-25</td>
<td align="center">C6</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">F</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2012-08-20</td>
<td align="center">V8</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">2014-12-18</td>
<td align="center">D2</td>
<td align="center">Hospital B</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">I</td>
<td align="center">F</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2011-10-28</td>
<td align="center">C6</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">2013-02-05</td>
<td align="center">L7</td>
<td align="center">Hospital A</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">M</td>
</tr>
</tbody>
@ -510,16 +510,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,292</td>
<td align="right">51.46%</td>
<td align="right">10,292</td>
<td align="right">51.46%</td>
<td align="right">10,453</td>
<td align="right">52.27%</td>
<td align="right">10,453</td>
<td align="right">52.27%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,708</td>
<td align="right">48.54%</td>
<td align="right">9,547</td>
<td align="right">47.74%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -632,9 +632,9 @@ 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 12,297 'phenotype-based' first isolates (61.5% of total where a</span></span>
<span><span class="co"># =&gt; Found 12,321 'phenotype-based' first isolates (61.6% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 61.5% is suitable for resistance analysis! We can now filter
<p>So only 61.6% 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">
@ -644,7 +644,7 @@ on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html"
<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 12 297 isolates for analysis. Now our data looks
<p>So we end up with 12 321 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>
@ -683,99 +683,99 @@ like:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">2</td>
<td align="center">2014-08-21</td>
<td align="center">H5</td>
<td align="center">Hospital D</td>
<td align="left">1</td>
<td align="center">2017-03-28</td>
<td align="center">X1</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</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">3</td>
<td align="center">2010-04-25</td>
<td align="center">G5</td>
<td align="center">Hospital D</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">5</td>
<td align="center">2012-08-20</td>
<td align="center">V8</td>
<td align="center">Hospital D</td>
<td align="left">2</td>
<td align="center">2010-03-06</td>
<td align="center">O2</td>
<td align="center">Hospital B</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">I</td>
<td align="center">I</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="left">7</td>
<td align="center">2015-05-23</td>
<td align="center">I3</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<tr class="odd">
<td align="left">3</td>
<td align="center">2013-12-31</td>
<td align="center">W3</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</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">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="odd">
<td align="left">13</td>
<td align="center">2015-12-07</td>
<td align="center">V6</td>
<td align="center">Hospital B</td>
<tr class="even">
<td align="left">6</td>
<td align="center">2013-02-05</td>
<td align="center">L7</td>
<td align="center">Hospital A</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">F</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="even">
<td align="left">15</td>
<td align="center">2017-06-15</td>
<td align="center">L5</td>
<tr class="odd">
<td align="left">7</td>
<td align="center">2010-09-28</td>
<td align="center">G1</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">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</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">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">9</td>
<td align="center">2012-08-19</td>
<td align="center">X8</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">I</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">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: 12,297<br>
Available: 12,297 (100%, NA: 0 = 0%)<br>
Length: 12,321<br>
Available: 12,321 (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">5,911</td>
<td align="right">48.07%</td>
<td align="right">5,911</td>
<td align="right">48.07%</td>
<td align="right">5,929</td>
<td align="right">48.12%</td>
<td align="right">5,929</td>
<td align="right">48.12%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,287</td>
<td align="right">26.73%</td>
<td align="right">9,198</td>
<td align="right">74.80%</td>
<td align="right">3,237</td>
<td align="right">26.27%</td>
<td align="right">9,166</td>
<td align="right">74.39%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">1,780</td>
<td align="right">14.48%</td>
<td align="right">10,978</td>
<td align="right">89.27%</td>
<td align="right">1,835</td>
<td align="right">14.89%</td>
<td align="right">11,001</td>
<td align="right">89.29%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,319</td>
<td align="right">10.73%</td>
<td align="right">12,297</td>
<td align="right">1,320</td>
<td align="right">10.71%</td>
<td align="right">12,321</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -884,14 +884,14 @@ antibiotic class they are in:</p>
<col width="9%">
<col width="9%">
<col width="9%">
<col width="11%">
<col width="10%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="6%">
<col width="11%">
<col width="11%">
<col width="12%">
<col width="9%">
<col width="5%">
</colgroup>
@ -912,90 +912,90 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2015-05-23</td>
<td align="center">I3</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">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="even">
<td align="center">2011-10-04</td>
<td align="center">T8</td>
<td align="center">2010-03-06</td>
<td align="center">O2</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">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">I</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">2011-12-01</td>
<td align="center">U8</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">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>
<tr class="even">
<td align="center">2015-07-22</td>
<td align="center">G8</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">I</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">2010-06-18</td>
<td align="center">Z9</td>
<td align="center">2012-08-19</td>
<td align="center">X8</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">I</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>
<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">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2017-02-17</td>
<td align="center">F10</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="even">
<td align="center">2014-10-01</td>
<td align="center">Q6</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">2011-05-23</td>
<td align="center">R7</td>
<td align="center">Hospital B</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">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="odd">
<td align="center">2016-08-09</td>
<td align="center">Y9</td>
<td align="center">Hospital C</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">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">2011-10-07</td>
<td align="center">C4</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">R</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">2771</td>
<td align="center">1193</td>
<td align="center">1947</td>
<td align="center">5911</td>
<td align="center">2773</td>
<td align="center">1159</td>
<td align="center">1997</td>
<td align="center">5929</td>
</tr>
<tr class="even">
<td align="left">1</td>
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">1522</td>
<td align="center">1245</td>
<td align="center">3144</td>
<td align="center">5911</td>
<td align="center">1452</td>
<td align="center">1281</td>
<td align="center">3196</td>
<td align="center">5929</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">2061</td>
<td align="center">1814</td>
<td align="center">2036</td>
<td align="center">5911</td>
<td align="center">2044</td>
<td align="center">1853</td>
<td align="center">2032</td>
<td align="center">5929</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">2057</td>
<td align="center">1807</td>
<td align="center">2047</td>
<td align="center">5911</td>
<td align="center">1881</td>
<td align="center">2001</td>
<td align="center">5929</td>
</tr>
<tr class="odd">
<td align="left">6</td>
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">564</td>
<td align="center">294</td>
<td align="center">461</td>
<td align="center">1319</td>
<td align="center">589</td>
<td align="center">282</td>
<td align="center">449</td>
<td align="center">1320</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">1319</td>
<td align="center">1319</td>
<td align="center">1320</td>
<td align="center">1320</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">2057</td>
<td align="center">1807</td>
<td align="center">2047</td>
<td align="center">5911</td>
<td align="center">1881</td>
<td align="center">2001</td>
<td align="center">5929</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">454</td>
<td align="center">417</td>
<td align="center">448</td>
<td align="center">1319</td>
<td align="center">460</td>
<td align="center">405</td>
<td align="center">455</td>
<td align="center">1320</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">1142</td>
<td align="center">1151</td>
<td align="center">1041</td>
<td align="center">1104</td>
<td align="center">3287</td>
<td align="center">1045</td>
<td align="center">3237</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">1780</td>
<td align="center">1780</td>
<td align="center">1835</td>
<td align="center">1835</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] 0.58128</span></span></code></pre></div>
<span><span class="co"># [1] 0.5912669</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">0.5788164</td>
<td align="center">0.5871212</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5898375</td>
<td align="center">0.5979070</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5721206</td>
<td align="center">0.5780315</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5766096</td>
<td align="center">0.5957361</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">0.5788164</td>
<td align="center">3616</td>
<td align="center">0.5871212</td>
<td align="center">3696</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5898375</td>
<td align="center">4369</td>
<td align="center">0.5979070</td>
<td align="center">4300</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5721206</td>
<td align="center">1858</td>
<td align="center">0.5780315</td>
<td align="center">1839</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5766096</td>
<td align="center">2454</td>
<td align="center">0.5957361</td>
<td align="center">2486</td>
</tr>
</tbody>
</table>
@ -1247,27 +1247,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.6706141</td>
<td align="center">0.6536965</td>
<td align="center">0.8820842</td>
<td align="center">0.6631810</td>
<td align="center">0.6625063</td>
<td align="center">0.8891887</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.6504928</td>
<td align="center">0.6603487</td>
<td align="center">0.8885519</td>
<td align="center">0.6598485</td>
<td align="center">0.6553030</td>
<td align="center">0.8818182</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.6671737</td>
<td align="center">0.6641314</td>
<td align="center">0.8910861</td>
<td align="center">0.6663577</td>
<td align="center">0.6771702</td>
<td align="center">0.8884770</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.4747191</td>
<td align="center">0.4621253</td>
<td align="center">0.0000000</td>
<td align="center">0.4747191</td>
<td align="center">0.4621253</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">57.9%</td>
<td align="right">36.2%</td>
<td align="right">58.7%</td>
<td align="right">36.6%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">59.0%</td>
<td align="right">36.5%</td>
<td align="right">59.8%</td>
<td align="right">36.8%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">57.2%</td>
<td align="right">35.1%</td>
<td align="right">57.8%</td>
<td align="right">36.5%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">57.7%</td>
<td align="right">35.9%</td>
<td align="right">59.6%</td>
<td align="right">36.4%</td>
</tr>
</tbody>
</table>
@ -1427,18 +1427,18 @@ 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] 4 0.5 0.5 32 0.005 0.025 2 128 0.025 </span></span>
<span><span class="co"># [10] 2 16 0.002 0.5 &gt;=256 &lt;=0.001 &gt;=256 0.002 0.0625 </span></span>
<span><span class="co"># [19] 0.025 0.005 16 128 0.005 8 0.25 128 0.25 </span></span>
<span><span class="co"># [28] 2 0.002 128 64 8 &gt;=256 8 0.025 &gt;=256 </span></span>
<span><span class="co"># [37] 0.5 0.01 0.25 8 0.0625 0.025 &gt;=256 0.005 2 </span></span>
<span><span class="co"># [46] 128 &gt;=256 0.005 0.5 &gt;=256 &lt;=0.001 0.005 0.0625 1 </span></span>
<span><span class="co"># [55] 0.5 0.125 16 0.002 0.005 16 4 0.01 0.25 </span></span>
<span><span class="co"># [64] 64 0.0625 0.002 32 0.5 4 8 128 32 </span></span>
<span><span class="co"># [73] 1 1 0.002 2 0.0625 &lt;=0.001 0.0625 &gt;=256 2 </span></span>
<span><span class="co"># [82] 8 0.125 0.0625 2 0.125 128 1 &gt;=256 4 </span></span>
<span><span class="co"># [91] 16 0.25 0.125 1 0.0625 0.125 &gt;=256 0.005 &lt;=0.001</span></span>
<span><span class="co"># [100] &gt;=256</span></span></code></pre></div>
<span><span class="co"># [1] 64 0.01 2 0.01 0.0625 32 &lt;=0.001 0.01 8 </span></span>
<span><span class="co"># [10] 0.005 64 64 8 128 0.002 32 16 32 </span></span>
<span><span class="co"># [19] 2 2 0.25 64 64 32 64 128 128 </span></span>
<span><span class="co"># [28] 2 0.0625 0.25 0.5 4 0.025 0.25 0.125 8 </span></span>
<span><span class="co"># [37] &lt;=0.001 0.5 0.01 0.0625 8 32 0.0625 0.5 64 </span></span>
<span><span class="co"># [46] 0.025 0.5 0.005 1 2 4 0.005 0.5 64 </span></span>
<span><span class="co"># [55] 0.0625 256 0.025 0.125 0.125 0.125 0.25 4 0.5 </span></span>
<span><span class="co"># [64] 128 4 0.002 0.5 1 0.005 2 8 0.005 </span></span>
<span><span class="co"># [73] 0.002 1 256 256 0.025 32 0.01 0.25 0.005 </span></span>
<span><span class="co"># [82] 2 0.025 1 128 64 1 32 16 64 </span></span>
<span><span class="co"># [91] 0.0625 0.025 0.5 256 &lt;=0.001 16 &lt;=0.001 32 128 </span></span>
<span><span class="co"># [100] 8</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 +1472,10 @@ 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 26 26 27 23 17 20 22 22 20 21 22 31 21 21 23 17 23 17 31 23 19 31 20 29</span></span>
<span><span class="co"># [26] 22 27 18 20 24 25 29 23 23 30 28 28 29 30 21 24 19 17 30 17 17 21 17 28 20</span></span>
<span><span class="co"># [51] 24 19 18 17 27 19 29 21 17 27 20 18 30 21 17 30 29 24 21 18 28 18 24 25 31</span></span>
<span><span class="co"># [76] 27 24 29 22 19 17 25 26 27 29 24 28 22 19 30 31 18 19 24 22 27 20 22 26 18</span></span></code></pre></div>
<span><span class="co"># [1] 24 25 28 31 31 21 29 27 17 27 27 22 27 31 27 24 29 17 30 17 23 20 22 17 24</span></span>
<span><span class="co"># [26] 28 31 28 26 26 22 28 22 26 30 25 21 17 27 25 17 28 25 18 29 21 25 19 30 31</span></span>
<span><span class="co"># [51] 27 18 29 22 20 23 31 19 30 28 21 21 25 28 21 29 25 24 20 17 19 26 26 24 23</span></span>
<span><span class="co"># [76] 17 30 17 17 29 19 18 28 19 25 31 21 29 28 26 28 28 25 22 22 18 21 31 19 29</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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@ -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="">1.8.2.9121</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9122</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">

54
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="">1.8.2.9121</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9122</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 S S I I S</span></span>
<span><span class="co"># 2 R S I R S R</span></span>
<span><span class="co"># 3 I S S S S I</span></span>
<span><span class="co"># 4 I I R I I S</span></span>
<span><span class="co"># 5 I S R I S R</span></span>
<span><span class="co"># 6 S S S I I S</span></span>
<span><span class="co"># 1 R I S R R S</span></span>
<span><span class="co"># 2 I R I S R S</span></span>
<span><span class="co"># 3 R R I I S I</span></span>
<span><span class="co"># 4 I I R R S I</span></span>
<span><span class="co"># 5 R I I I R I</span></span>
<span><span class="co"># 6 S S I R R 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"># 3 R</span></span>
<span><span class="co"># 3 S</span></span>
<span><span class="co"># 4 I</span></span>
<span><span class="co"># 5 I</span></span>
<span><span class="co"># 6 R</span></span></code></pre></div>
<span><span class="co"># 6 S</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">3220</td>
<td align="right">64.40%</td>
<td align="right">3220</td>
<td align="right">64.40%</td>
<td align="right">3214</td>
<td align="right">64.28%</td>
<td align="right">3214</td>
<td align="right">64.28%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">941</td>
<td align="right">18.82%</td>
<td align="right">4161</td>
<td align="right">83.22%</td>
<td align="right">1018</td>
<td align="right">20.36%</td>
<td align="right">4232</td>
<td align="right">84.64%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">474</td>
<td align="right">9.48%</td>
<td align="right">4635</td>
<td align="right">92.70%</td>
<td align="right">439</td>
<td align="right">8.78%</td>
<td align="right">4671</td>
<td align="right">93.42%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">238</td>
<td align="right">4.76%</td>
<td align="right">4873</td>
<td align="right">97.46%</td>
<td align="right">228</td>
<td align="right">4.56%</td>
<td align="right">4899</td>
<td align="right">97.98%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">127</td>
<td align="right">2.54%</td>
<td align="right">101</td>
<td align="right">2.02%</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>
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@ -38,7 +38,7 @@
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@ -178,7 +178,7 @@
<h4 data-toc-skip class="author">Dr. Matthijs
Berends</h4>
<h4 data-toc-skip class="date">12 February 2023</h4>
<h4 data-toc-skip class="date">13 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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<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">12 February 2023</h4>
<h4 data-toc-skip class="date">13 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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