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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="">1.8.2.9094</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9095</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">19 January 2023</h4>
<h4 data-toc-skip class="date">20 January 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>
@ -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 19 January 2023.</p>
generated on 20 January 2023.</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">2023-01-19</td>
<td align="center">2023-01-20</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">2023-01-19</td>
<td align="center">2023-01-20</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">2023-01-19</td>
<td align="center">2023-01-20</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -400,67 +400,67 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2015-07-08</td>
<td align="center">V2</td>
<td align="center">2015-03-26</td>
<td align="center">C9</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">M</td>
</tr>
<tr class="even">
<td align="center">2014-11-12</td>
<td align="center">W8</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2015-01-11</td>
<td align="center">X10</td>
<td align="center">Hospital B</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2017-05-03</td>
<td align="center">F10</td>
<td align="center">Hospital B</td>
<td align="center">Streptococcus pneumoniae</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="odd">
<td align="center">2016-01-28</td>
<td align="center">T4</td>
<td align="center">2017-10-04</td>
<td align="center">V8</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">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2013-03-27</td>
<td align="center">Y3</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2017-11-01</td>
<td align="center">E5</td>
<td align="center">Hospital A</td>
<td align="center">2017-05-25</td>
<td align="center">E8</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">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2016-05-08</td>
<td align="center">H6</td>
<td align="center">Hospital A</td>
<td align="center">2013-12-07</td>
<td align="center">N3</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
@ -499,16 +499,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,473</td>
<td align="right">52.37%</td>
<td align="right">10,473</td>
<td align="right">52.37%</td>
<td align="right">10,275</td>
<td align="right">51.38%</td>
<td align="right">10,275</td>
<td align="right">51.38%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,527</td>
<td align="right">47.64%</td>
<td align="right">9,725</td>
<td align="right">48.63%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -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 10,513 'phenotype-based' first isolates (52.6% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,664 '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 52.6% 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">
@ -634,11 +634,11 @@ 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 10,513 isolates for analysis. Now our data looks
<p>So we end up with 10,664 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>
<table class="table">
<table style="width:100%;" class="table">
<colgroup>
<col width="2%">
<col width="9%">
@ -652,7 +652,7 @@ like:</p>
<col width="6%">
<col width="11%">
<col width="12%">
<col width="7%">
<col width="9%">
<col width="5%">
</colgroup>
<thead><tr class="header">
@ -673,29 +673,13 @@ like:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">3</td>
<td align="center">2016-01-28</td>
<td align="center">T4</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="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">5</td>
<td align="center">2017-11-01</td>
<td align="center">E5</td>
<td align="left">1</td>
<td align="center">2015-03-26</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">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
@ -704,48 +688,32 @@ like:</p>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">7</td>
<td align="center">2017-08-12</td>
<td align="center">B4</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">S</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="left">8</td>
<td align="center">2011-07-01</td>
<td align="center">K2</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</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">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">10</td>
<td align="center">2010-08-12</td>
<td align="center">I2</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">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">12</td>
<td align="center">2011-09-04</td>
<td align="center">E2</td>
<td align="center">2015-07-29</td>
<td align="center">K7</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</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>
@ -753,14 +721,30 @@ like:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">14</td>
<td align="center">2015-05-09</td>
<td align="center">F7</td>
<td align="left">10</td>
<td align="center">2010-02-06</td>
<td align="center">N9</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">12</td>
<td align="center">2017-12-15</td>
<td align="center">M8</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
@ -768,6 +752,22 @@ like:</p>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">15</td>
<td align="center">2014-01-10</td>
<td align="center">V9</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">S</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>
</tbody>
</table>
<p>Time for the analysis!</p>
@ -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: 10,513<br>
Available: 10,513 (100%, NA: 0 = 0%)<br>
Length: 10,664<br>
Available: 10,664 (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">4,589</td>
<td align="right">43.65%</td>
<td align="right">4,589</td>
<td align="right">43.65%</td>
<td align="right">4,704</td>
<td align="right">44.11%</td>
<td align="right">4,704</td>
<td align="right">44.11%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,637</td>
<td align="right">25.08%</td>
<td align="right">7,226</td>
<td align="right">68.73%</td>
<td align="right">2,741</td>
<td align="right">25.70%</td>
<td align="right">7,445</td>
<td align="right">69.81%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,072</td>
<td align="right">19.71%</td>
<td align="right">9,298</td>
<td align="right">88.44%</td>
<td align="right">2,062</td>
<td align="right">19.34%</td>
<td align="right">9,507</td>
<td align="right">89.15%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,215</td>
<td align="right">11.56%</td>
<td align="right">10,513</td>
<td align="right">1,157</td>
<td align="right">10.85%</td>
<td align="right">10,664</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="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>
@ -902,42 +902,42 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2011-07-01</td>
<td align="center">K2</td>
<td align="center">2015-07-29</td>
<td align="center">K7</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</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">2015-09-30</td>
<td align="center">X1</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</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">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="center">2012-11-09</td>
<td align="center">I6</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2014-06-12</td>
<td align="center">T1</td>
<td align="center">2011-12-11</td>
<td align="center">T5</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">S</td>
<td align="center">R</td>
<td align="center">F</td>
@ -947,9 +947,9 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2013-01-17</td>
<td align="center">D2</td>
<td align="center">Hospital A</td>
<td align="center">2010-01-19</td>
<td align="center">K7</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
@ -962,13 +962,13 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2011-02-13</td>
<td align="center">F3</td>
<td align="center">2013-05-13</td>
<td align="center">F4</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">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
@ -977,18 +977,18 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2011-02-13</td>
<td align="center">N3</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">2010-01-29</td>
<td align="center">W4</td>
<td align="center">Hospital D</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">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">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
</tbody>
@ -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">2119</td>
<td align="center">139</td>
<td align="center">2331</td>
<td align="center">4589</td>
<td align="center">2227</td>
<td align="center">162</td>
<td align="center">2315</td>
<td align="center">4704</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3341</td>
<td align="center">170</td>
<td align="center">1078</td>
<td align="center">4589</td>
<td align="center">3431</td>
<td align="center">174</td>
<td align="center">1099</td>
<td align="center">4704</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3333</td>
<td align="center">3397</td>
<td align="center">0</td>
<td align="center">1256</td>
<td align="center">4589</td>
<td align="center">1307</td>
<td align="center">4704</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4053</td>
<td align="center">4106</td>
<td align="center">0</td>
<td align="center">536</td>
<td align="center">4589</td>
<td align="center">598</td>
<td align="center">4704</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">1215</td>
<td align="center">1215</td>
<td align="center">1157</td>
<td align="center">1157</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">959</td>
<td align="center">49</td>
<td align="center">207</td>
<td align="center">1215</td>
<td align="center">922</td>
<td align="center">47</td>
<td align="center">188</td>
<td align="center">1157</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">4053</td>
<td align="center">4106</td>
<td align="center">0</td>
<td align="center">536</td>
<td align="center">4589</td>
<td align="center">598</td>
<td align="center">4704</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1109</td>
<td align="center">1047</td>
<td align="center">0</td>
<td align="center">106</td>
<td align="center">1215</td>
<td align="center">110</td>
<td align="center">1157</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2328</td>
<td align="center">2407</td>
<td align="center">0</td>
<td align="center">309</td>
<td align="center">2637</td>
<td align="center">334</td>
<td align="center">2741</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">2072</td>
<td align="center">2072</td>
<td align="center">2062</td>
<td align="center">2062</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] 0.5497955</span></span></code></pre></div>
<span><span class="co"># [1] 0.5381658</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">0.5437933</td>
<td align="center">0.5460547</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5506739</td>
<td align="center">0.5252972</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5457454</td>
<td align="center">0.5231231</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5605034</td>
<td align="center">0.5592912</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">0.5437933</td>
<td align="center">3174</td>
<td align="center">0.5460547</td>
<td align="center">3181</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5506739</td>
<td align="center">3710</td>
<td align="center">0.5252972</td>
<td align="center">3617</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5457454</td>
<td align="center">1563</td>
<td align="center">0.5231231</td>
<td align="center">1665</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5605034</td>
<td align="center">2066</td>
<td align="center">0.5592912</td>
<td align="center">2201</td>
</tr>
</tbody>
</table>
@ -1230,27 +1230,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7650904</td>
<td align="center">0.8831990</td>
<td align="center">0.9797341</td>
<td align="center">0.7663690</td>
<td align="center">0.8728741</td>
<td align="center">0.9770408</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8296296</td>
<td align="center">0.9127572</td>
<td align="center">0.9901235</td>
<td align="center">0.8375108</td>
<td align="center">0.9049265</td>
<td align="center">0.9870354</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.8058400</td>
<td align="center">0.8828214</td>
<td align="center">0.9821767</td>
<td align="center">0.7986136</td>
<td align="center">0.8781467</td>
<td align="center">0.9788398</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5342664</td>
<td align="center">0.5446169</td>
<td align="center">0.0000000</td>
<td align="center">0.5342664</td>
<td align="center">0.5446169</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">54.4%</td>
<td align="right">25.0%</td>
<td align="right">54.6%</td>
<td align="right">26.2%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">55.1%</td>
<td align="right">25.9%</td>
<td align="right">52.5%</td>
<td align="right">25.7%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">54.6%</td>
<td align="right">27.3%</td>
<td align="right">52.3%</td>
<td align="right">24.7%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">56.1%</td>
<td align="right">28.0%</td>
<td align="right">55.9%</td>
<td align="right">27.4%</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] 64 0.005 16 0.025 2 &lt;=0.001 8 0.0625 0.01 </span></span>
<span><span class="co"># [10] 1 0.005 32 0.25 16 4 4 0.002 0.01 </span></span>
<span><span class="co"># [19] 0.01 16 &lt;=0.001 0.5 &lt;=0.001 0.005 2 1 64 </span></span>
<span><span class="co"># [28] 0.0625 0.125 0.002 0.025 0.25 8 0.025 0.0625 0.5 </span></span>
<span><span class="co"># [37] 0.002 256 0.25 1 0.025 64 256 0.125 8 </span></span>
<span><span class="co"># [46] 0.01 0.025 32 0.025 0.0625 8 0.5 2 0.5 </span></span>
<span><span class="co"># [55] 16 64 32 0.025 64 0.01 0.25 0.002 0.5 </span></span>
<span><span class="co"># [64] 128 0.5 0.25 0.005 4 1 &lt;=0.001 256 2 </span></span>
<span><span class="co"># [73] 4 256 2 0.005 0.002 4 16 0.002 16 </span></span>
<span><span class="co"># [82] 256 0.25 0.025 256 4 0.125 1 &lt;=0.001 0.5 </span></span>
<span><span class="co"># [91] 32 4 0.25 0.5 0.002 0.025 0.005 2 1 </span></span>
<span><span class="co"># [100] 4</span></span></code></pre></div>
<span><span class="co"># [1] &gt;=256 0.005 64 0.025 0.5 0.0625 0.025 128 1 &gt;=256 </span></span>
<span><span class="co"># [11] &gt;=256 0.025 0.025 0.001 0.25 1 0.005 2 &gt;=256 64 </span></span>
<span><span class="co"># [21] 0.01 2 0.001 64 32 2 0.0625 0.005 0.125 0.001 </span></span>
<span><span class="co"># [31] 0.5 2 0.25 0.0625 0.125 128 0.0625 0.0625 2 32 </span></span>
<span><span class="co"># [41] 128 0.002 &gt;=256 0.25 32 64 0.01 0.025 16 0.005 </span></span>
<span><span class="co"># [51] 0.002 0.125 0.5 64 0.002 &gt;=256 0.5 0.5 0.0625 1 </span></span>
<span><span class="co"># [61] 4 &gt;=256 0.005 2 128 128 32 0.25 1 4 </span></span>
<span><span class="co"># [71] 8 4 0.002 128 0.025 32 8 0.5 0.001 0.025 </span></span>
<span><span class="co"># [81] 8 32 1 0.025 0.5 0.001 0.25 0.002 0.002 64 </span></span>
<span><span class="co"># [91] 1 0.002 0.025 128 128 2 0.01 0.002 16 4</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] 31 19 20 30 23 18 21 26 31 22 20 27 23 21 25 29 24 31 27 24 28 30 30 24 25</span></span>
<span><span class="co"># [26] 23 31 20 17 17 25 22 26 17 28 25 27 30 18 17 22 25 19 21 30 23 21 18 18 30</span></span>
<span><span class="co"># [51] 21 20 30 19 24 31 30 23 19 26 28 19 20 27 17 26 26 23 18 27 31 24 20 19 31</span></span>
<span><span class="co"># [76] 17 23 19 19 30 23 25 21 22 25 27 18 27 22 17 23 27 21 22 27 30 31 19 23 27</span></span></code></pre></div>
<span><span class="co"># [1] 17 29 22 22 20 26 28 25 21 24 26 31 19 28 26 18 21 24 23 23 31 22 26 31 18</span></span>
<span><span class="co"># [26] 20 29 18 21 29 25 31 23 29 26 24 28 28 23 22 21 18 17 20 21 30 29 27 29 26</span></span>
<span><span class="co"># [51] 31 29 22 29 24 19 26 27 30 23 30 22 30 23 31 26 19 23 29 22 24 28 21 17 17</span></span>
<span><span class="co"># [76] 25 24 30 21 30 17 27 19 19 25 23 26 26 22 25 30 18 24 29 20 29 20 24 25 24</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="">1.8.2.9094</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9095</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">

60
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="">1.8.2.9094</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9095</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 I S</span></span>
<span><span class="co"># 2 R R I S R I</span></span>
<span><span class="co"># 3 S I R I S I</span></span>
<span><span class="co"># 4 R I R S S I</span></span>
<span><span class="co"># 5 I S R R R S</span></span>
<span><span class="co"># 6 S R S S S S</span></span>
<span><span class="co"># 1 R I I I R I</span></span>
<span><span class="co"># 2 I R I I R S</span></span>
<span><span class="co"># 3 R S I S S I</span></span>
<span><span class="co"># 4 S R S R I I</span></span>
<span><span class="co"># 5 S R R R I I</span></span>
<span><span class="co"># 6 R I S S S R</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 R</span></span>
<span><span class="co"># 4 S</span></span>
<span><span class="co"># 1 I</span></span>
<span><span class="co"># 2 I</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 I</span></span></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can
use:</p>
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
@ -428,40 +428,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3209</td>
<td align="right">64.18%</td>
<td align="right">3209</td>
<td align="right">64.18%</td>
<td align="right">3201</td>
<td align="right">64.02%</td>
<td align="right">3201</td>
<td align="right">64.02%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">1005</td>
<td align="right">20.10%</td>
<td align="right">4214</td>
<td align="right">84.28%</td>
<td align="right">981</td>
<td align="right">19.62%</td>
<td align="right">4182</td>
<td align="right">83.64%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">417</td>
<td align="right">8.34%</td>
<td align="right">4631</td>
<td align="right">92.62%</td>
<td align="right">441</td>
<td align="right">8.82%</td>
<td align="right">4623</td>
<td align="right">92.46%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">265</td>
<td align="right">5.30%</td>
<td align="right">4896</td>
<td align="right">97.92%</td>
<td align="right">258</td>
<td align="right">5.16%</td>
<td align="right">4881</td>
<td align="right">97.62%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">104</td>
<td align="right">2.08%</td>
<td align="right">119</td>
<td align="right">2.38%</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="">1.8.2.9094</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9095</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="">1.8.2.9094</small>
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<h4 data-toc-skip class="author">Dr. Matthijs
Berends</h4>
<h4 data-toc-skip class="date">19 January 2023</h4>
<h4 data-toc-skip class="date">20 January 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>
<div class="d-none name"><code>SPSS.Rmd</code></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="">1.8.2.9094</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>
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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">19 January 2023</h4>
<h4 data-toc-skip class="date">20 January 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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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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