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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="">1.8.2.9059</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9060</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">09 December 2022</h4>
<h4 data-toc-skip class="date">10 December 2022</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/AMR.Rmd" class="external-link"><code>vignettes/AMR.Rmd</code></a></small>
<div class="d-none name"><code>AMR.Rmd</code></div>
@ -180,7 +180,7 @@ Berends</h4>
website update since they are based on randomly created values and the
page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
Markdown</a>. However, the methodology remains unchanged. This page was
generated on 09 December 2022.</p>
generated on 10 December 2022.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@ -236,21 +236,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2022-12-09</td>
<td align="center">2022-12-10</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="center">2022-12-09</td>
<td align="center">2022-12-10</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<tr class="odd">
<td align="center">2022-12-09</td>
<td align="center">2022-12-10</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -380,12 +380,12 @@ data set:</p>
<col width="13%">
<col width="13%">
<col width="13%">
<col width="26%">
<col width="28%">
<col width="5%">
<col width="5%">
<col width="5%">
<col width="5%">
<col width="9%">
<col width="8%">
</colgroup>
<thead><tr class="header">
<th align="center">date</th>
@ -400,70 +400,70 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2015-07-01</td>
<td align="center">N10</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">2012-03-09</td>
<td align="center">P2</td>
<td align="center">Hospital A</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2017-06-08</td>
<td align="center">T6</td>
<td align="center">2014-07-20</td>
<td align="center">J2</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">R</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2013-05-17</td>
<td align="center">Q7</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2013-01-27</td>
<td align="center">T4</td>
<td align="center">Hospital B</td>
<td align="center">Klebsiella 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="odd">
<td align="center">2013-06-25</td>
<td align="center">X6</td>
<td align="center">2011-01-23</td>
<td align="center">O1</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2017-10-09</td>
<td align="center">U7</td>
<td align="center">2011-12-08</td>
<td align="center">I9</td>
<td align="center">Hospital A</td>
<td align="center">Klebsiella pneumoniae</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">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2010-07-15</td>
<td align="center">J5</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</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>
</tr>
<tr class="even">
<td align="center">2014-12-28</td>
<td align="center">D6</td>
<td align="center">Hospital C</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
</tbody>
</table>
@ -499,16 +499,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,352</td>
<td align="right">51.76%</td>
<td align="right">10,352</td>
<td align="right">51.76%</td>
<td align="right">10,307</td>
<td align="right">51.54%</td>
<td align="right">10,307</td>
<td align="right">51.54%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,648</td>
<td align="right">48.24%</td>
<td align="right">9,693</td>
<td align="right">48.47%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -621,10 +621,10 @@ takes into account the antimicrobial susceptibility test results using
<span><span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span></span>
<span><span class="co"># 2</span></span>
<span><span class="co"># Including isolates from ICU.</span></span>
<span><span class="co"># =&gt; Found 10,610 'phenotype-based' first isolates (53.1% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,602 'phenotype-based' first isolates (53.0% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 53.1% 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 53% 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>
@ -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 10,610 isolates for analysis. Now our data looks
<p>So we end up with 10,602 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 style="width:100%;" class="table">
<table class="table">
<colgroup>
<col width="2%">
<col width="9%">
@ -651,7 +651,7 @@ like:</p>
<col width="3%">
<col width="6%">
<col width="11%">
<col width="12%">
<col width="11%">
<col width="9%">
<col width="5%">
</colgroup>
@ -674,31 +674,31 @@ like:</p>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2015-07-01</td>
<td align="center">N10</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">2012-03-09</td>
<td align="center">P2</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">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">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">2</td>
<td align="center">2017-06-08</td>
<td align="center">T6</td>
<td align="center">2014-07-20</td>
<td align="center">J2</td>
<td align="center">Hospital A</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">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>
@ -706,41 +706,25 @@ like:</p>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="center">2013-05-17</td>
<td align="center">Q7</td>
<td align="center">2011-01-23</td>
<td align="center">O1</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="center">2013-01-27</td>
<td align="center">T4</td>
<td align="center">Hospital B</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</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">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<tr class="even">
<td align="left">9</td>
<td align="center">2011-04-24</td>
<td align="center">K8</td>
<td align="center">Hospital A</td>
<td align="center">2015-07-08</td>
<td align="center">F4</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
@ -752,20 +736,36 @@ like:</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">12</td>
<td align="center">2017-05-31</td>
<td align="center">R4</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">R</td>
<td align="center">S</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">TRUE</td>
</tr>
<tr class="even">
<td align="left">10</td>
<td align="center">2014-08-22</td>
<td align="center">M5</td>
<td align="left">13</td>
<td align="center">2010-09-11</td>
<td align="center">A3</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
</tbody>
@ -801,8 +801,8 @@ readable:</p>
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://msberends.github.io/cleaner/reference/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></span></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 10,610<br>
Available: 10,610 (100%, NA: 0 = 0%)<br>
Length: 10,602<br>
Available: 10,602 (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">4,654</td>
<td align="right">43.86%</td>
<td align="right">4,654</td>
<td align="right">43.86%</td>
<td align="right">4,643</td>
<td align="right">43.79%</td>
<td align="right">4,643</td>
<td align="right">43.79%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,681</td>
<td align="right">25.27%</td>
<td align="right">7,335</td>
<td align="right">69.13%</td>
<td align="right">2,690</td>
<td align="right">25.37%</td>
<td align="right">7,333</td>
<td align="right">69.17%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,113</td>
<td align="right">19.92%</td>
<td align="right">9,448</td>
<td align="right">89.05%</td>
<td align="right">2,056</td>
<td align="right">19.39%</td>
<td align="right">9,389</td>
<td align="right">88.56%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,162</td>
<td align="right">10.95%</td>
<td align="right">10,610</td>
<td align="right">1,213</td>
<td align="right">11.44%</td>
<td align="right">10,602</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -902,25 +902,55 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2011-04-24</td>
<td align="center">K8</td>
<td align="center">2012-03-09</td>
<td align="center">P2</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2015-07-08</td>
<td align="center">F4</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">2012-10-31</td>
<td align="center">S10</td>
<tr class="odd">
<td align="center">2016-01-05</td>
<td align="center">X1</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2012-02-13</td>
<td align="center">U8</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>
@ -932,27 +962,12 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2012-11-07</td>
<td align="center">E6</td>
<td align="center">Hospital A</td>
<td align="center">2014-07-06</td>
<td align="center">P9</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">2014-02-28</td>
<td align="center">Q8</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">I</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
@ -961,34 +976,19 @@ antibiotic class they are in:</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2012-04-14</td>
<td align="center">O4</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2012-07-02</td>
<td align="center">I5</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">2016-03-03</td>
<td align="center">B8</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">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
</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">2202</td>
<td align="center">129</td>
<td align="center">2323</td>
<td align="center">4654</td>
<td align="center">2167</td>
<td align="center">142</td>
<td align="center">2334</td>
<td align="center">4643</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3443</td>
<td align="center">153</td>
<td align="center">1058</td>
<td align="center">4654</td>
<td align="center">3405</td>
<td align="center">162</td>
<td align="center">1076</td>
<td align="center">4643</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3360</td>
<td align="center">3364</td>
<td align="center">0</td>
<td align="center">1294</td>
<td align="center">4654</td>
<td align="center">1279</td>
<td align="center">4643</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4089</td>
<td align="center">4053</td>
<td align="center">0</td>
<td align="center">565</td>
<td align="center">4654</td>
<td align="center">590</td>
<td align="center">4643</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">1162</td>
<td align="center">1162</td>
<td align="center">1213</td>
<td align="center">1213</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">928</td>
<td align="center">43</td>
<td align="center">191</td>
<td align="center">1162</td>
<td align="center">935</td>
<td align="center">36</td>
<td align="center">242</td>
<td align="center">1213</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">4089</td>
<td align="center">4053</td>
<td align="center">0</td>
<td align="center">565</td>
<td align="center">4654</td>
<td align="center">590</td>
<td align="center">4643</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1041</td>
<td align="center">1087</td>
<td align="center">0</td>
<td align="center">121</td>
<td align="center">1162</td>
<td align="center">126</td>
<td align="center">1213</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2383</td>
<td align="center">2392</td>
<td align="center">0</td>
<td align="center">298</td>
<td align="center">2681</td>
<td align="center">2690</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">2113</td>
<td align="center">2113</td>
<td align="center">2056</td>
<td align="center">2056</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] 0.5454288</span></span></code></pre></div>
<span><span class="co"># [1] 0.5470666</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">0.5398258</td>
<td align="center">0.5567929</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5561224</td>
<td align="center">0.5470541</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5287860</td>
<td align="center">0.5369212</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5477338</td>
<td align="center">0.5402844</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">0.5398258</td>
<td align="center">3214</td>
<td align="center">0.5567929</td>
<td align="center">3143</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5561224</td>
<td align="center">3724</td>
<td align="center">0.5470541</td>
<td align="center">3751</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5287860</td>
<td align="center">0.5369212</td>
<td align="center">1598</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5477338</td>
<td align="center">2074</td>
<td align="center">0.5402844</td>
<td align="center">2110</td>
</tr>
</tbody>
</table>
@ -1230,27 +1230,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7726687</td>
<td align="center">0.8785991</td>
<td align="center">0.9804469</td>
<td align="center">0.7682533</td>
<td align="center">0.8729270</td>
<td align="center">0.9763084</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8356282</td>
<td align="center">0.8958692</td>
<td align="center">0.9870912</td>
<td align="center">0.8004946</td>
<td align="center">0.8961253</td>
<td align="center">0.9777411</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7967176</td>
<td align="center">0.8888474</td>
<td align="center">0.9813502</td>
<td align="center">0.7955390</td>
<td align="center">0.8892193</td>
<td align="center">0.9795539</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5224799</td>
<td align="center">0.5330739</td>
<td align="center">0.0000000</td>
<td align="center">0.5224799</td>
<td align="center">0.5330739</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">54.0%</td>
<td align="right">26.8%</td>
<td align="right">55.7%</td>
<td align="right">26.3%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">55.6%</td>
<td align="right">26.8%</td>
<td align="right">54.7%</td>
<td align="right">27.3%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">52.9%</td>
<td align="right">23.8%</td>
<td align="right">53.7%</td>
<td align="right">26.7%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">54.8%</td>
<td align="right">27.0%</td>
<td align="right">54.0%</td>
<td align="right">26.0%</td>
</tr>
</tbody>
</table>
@ -1410,18 +1410,18 @@ classes) <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code>:</p>
<code class="sourceCode R"><span><span class="va">mic_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span></span>
<span><span class="va">mic_values</span></span>
<span><span class="co"># Class 'mic'</span></span>
<span><span class="co"># [1] 0.002 0.002 0.25 0.01 0.5 &lt;=0.001 0.25 &gt;=256 0.0625 </span></span>
<span><span class="co"># [10] 0.25 0.25 16 8 0.002 8 0.5 0.125 0.005 </span></span>
<span><span class="co"># [19] 16 0.01 16 64 0.125 0.005 0.5 16 0.5 </span></span>
<span><span class="co"># [28] 0.01 &gt;=256 0.0625 32 0.005 0.25 128 0.002 2 </span></span>
<span><span class="co"># [37] 1 8 128 &gt;=256 0.025 0.025 32 1 0.005 </span></span>
<span><span class="co"># [46] 0.0625 32 &gt;=256 0.01 4 0.01 16 &lt;=0.001 0.002 </span></span>
<span><span class="co"># [55] 0.002 &gt;=256 2 32 2 0.125 64 &lt;=0.001 0.5 </span></span>
<span><span class="co"># [64] 16 0.01 0.25 4 0.002 0.5 8 2 64 </span></span>
<span><span class="co"># [73] 0.01 0.125 &lt;=0.001 16 0.005 32 0.01 4 1 </span></span>
<span><span class="co"># [82] 1 0.025 128 0.125 8 64 0.125 2 0.125 </span></span>
<span><span class="co"># [91] 2 4 0.0625 &lt;=0.001 &gt;=256 0.25 0.5 0.025 &lt;=0.001</span></span>
<span><span class="co"># [100] 4</span></span></code></pre></div>
<span><span class="co"># [1] 4 &gt;=256 0.25 &lt;=0.001 1 0.002 8 0.025 8 </span></span>
<span><span class="co"># [10] 1 64 0.0625 0.025 16 0.002 1 8 0.01 </span></span>
<span><span class="co"># [19] 0.025 0.01 4 &lt;=0.001 &gt;=256 0.25 0.125 32 4 </span></span>
<span><span class="co"># [28] 64 &lt;=0.001 64 &lt;=0.001 8 4 4 0.0625 0.125 </span></span>
<span><span class="co"># [37] 0.25 4 32 0.5 64 0.002 0.25 0.5 1 </span></span>
<span><span class="co"># [46] 4 0.005 1 32 0.005 0.005 0.125 16 0.025 </span></span>
<span><span class="co"># [55] 32 0.5 32 0.002 8 64 0.5 0.025 2 </span></span>
<span><span class="co"># [64] 32 0.5 4 0.0625 0.002 0.002 0.01 0.005 2 </span></span>
<span><span class="co"># [73] 4 0.002 0.5 64 0.125 32 0.01 4 &lt;=0.001</span></span>
<span><span class="co"># [82] 0.025 1 &lt;=0.001 0.25 0.0625 0.002 4 8 0.5 </span></span>
<span><span class="co"># [91] 0.25 128 32 0.025 0.125 32 32 32 0.5 </span></span>
<span><span class="co"># [100] 0.002</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 +1455,10 @@ 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] 23 30 18 26 21 18 21 17 30 30 30 22 23 17 26 18 30 27 26 31 26 30 23 22 17</span></span>
<span><span class="co"># [26] 27 27 26 30 17 18 19 26 29 29 24 20 30 27 22 18 31 26 24 26 22 30 23 20 22</span></span>
<span><span class="co"># [51] 17 22 17 31 18 19 31 17 24 17 31 28 28 20 23 18 25 21 31 30 21 25 25 30 20</span></span>
<span><span class="co"># [76] 22 30 27 24 26 29 19 23 20 31 24 19 22 27 29 28 18 29 26 22 19 20 24 19 27</span></span></code></pre></div>
<span><span class="co"># [1] 24 24 29 30 27 19 20 20 20 19 24 26 19 21 24 28 30 25 25 22 30 29 18 30 18</span></span>
<span><span class="co"># [26] 25 21 23 31 30 26 17 23 21 27 27 24 28 25 22 18 25 29 25 30 30 23 30 23 26</span></span>
<span><span class="co"># [51] 26 20 31 20 18 27 26 22 22 20 30 23 20 26 22 31 21 22 23 25 24 23 23 18 18</span></span>
<span><span class="co"># [76] 17 19 25 17 27 25 17 26 21 24 30 31 30 18 19 30 23 17 27 30 18 21 26 28 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="">1.8.2.9059</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9060</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">

56
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="">1.8.2.9059</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9060</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 S S R R R S</span></span>
<span><span class="co"># 2 R R I I R R</span></span>
<span><span class="co"># 3 S S R I R I</span></span>
<span><span class="co"># 4 S I R I R R</span></span>
<span><span class="co"># 5 R S R R I I</span></span>
<span><span class="co"># 6 S S S R I I</span></span>
<span><span class="co"># 1 R R S S S R</span></span>
<span><span class="co"># 2 S I I R R R</span></span>
<span><span class="co"># 3 R I S S S R</span></span>
<span><span class="co"># 4 I R S R I I</span></span>
<span><span class="co"># 5 S R R R R I</span></span>
<span><span class="co"># 6 R I S R I R</span></span>
<span><span class="co"># kanamycin</span></span>
<span><span class="co"># 1 R</span></span>
<span><span class="co"># 2 I</span></span>
<span><span class="co"># 3 R</span></span>
<span><span class="co"># 2 R</span></span>
<span><span class="co"># 3 I</span></span>
<span><span class="co"># 4 S</span></span>
<span><span class="co"># 5 S</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">3228</td>
<td align="right">64.56%</td>
<td align="right">3228</td>
<td align="right">64.56%</td>
<td align="right">3194</td>
<td align="right">63.88%</td>
<td align="right">3194</td>
<td align="right">63.88%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">968</td>
<td align="right">19.36%</td>
<td align="right">4196</td>
<td align="right">83.92%</td>
<td align="right">952</td>
<td align="right">19.04%</td>
<td align="right">4146</td>
<td align="right">82.92%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">452</td>
<td align="right">9.04%</td>
<td align="right">4648</td>
<td align="right">92.96%</td>
<td align="right">488</td>
<td align="right">9.76%</td>
<td align="right">4634</td>
<td align="right">92.68%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">244</td>
<td align="right">4.88%</td>
<td align="right">4892</td>
<td align="right">97.84%</td>
<td align="right">264</td>
<td align="right">5.28%</td>
<td align="right">4898</td>
<td align="right">97.96%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">108</td>
<td align="right">2.16%</td>
<td align="right">102</td>
<td align="right">2.04%</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="">1.8.2.9059</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9060</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="">1.8.2.9059</small>
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@ -168,7 +168,7 @@
<h4 data-toc-skip class="author">Dr. Matthijs
Berends</h4>
<h4 data-toc-skip class="date">09 December 2022</h4>
<h4 data-toc-skip class="date">10 December 2022</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/SPSS.Rmd" class="external-link"><code>vignettes/SPSS.Rmd</code></a></small>
<div class="d-none name"><code>SPSS.Rmd</code></div>

2
articles/WHONET.html
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9060</small>
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4
articles/datasets.html
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9060</small>
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@ -166,7 +166,7 @@
<main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
<h4 data-toc-skip class="date">09 December 2022</h4>
<h4 data-toc-skip class="date">10 December 2022</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<div class="d-none name"><code>datasets.Rmd</code></div>

2
articles/index.html
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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articles/resistance_predict.html
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9060</small>
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