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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="">1.8.2.9081</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9082</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">05 January 2023</h4>
<h4 data-toc-skip class="date">06 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 05 January 2023.</p>
generated on 06 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">2023-01-05</td>
<td align="center">2023-01-06</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">2023-01-05</td>
<td align="center">2023-01-06</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">2023-01-05</td>
<td align="center">2023-01-06</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>
@ -400,66 +400,66 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2015-01-04</td>
<td align="center">C10</td>
<td align="center">2013-11-17</td>
<td align="center">D4</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">I</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">M</td>
</tr>
<tr class="even">
<td align="center">2010-08-21</td>
<td align="center">N3</td>
<td align="center">2014-12-24</td>
<td align="center">S2</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2015-12-21</td>
<td align="center">Q3</td>
<td align="center">Hospital C</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">2014-08-31</td>
<td align="center">Q4</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">S</td>
<td align="center">R</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2015-10-03</td>
<td align="center">C5</td>
<td align="center">2012-08-04</td>
<td align="center">N10</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">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2016-03-16</td>
<td align="center">D5</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2017-12-17</td>
<td align="center">O7</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2014-08-04</td>
<td align="center">2016-10-07</td>
<td align="center">O7</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">Hospital D</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>
@ -499,16 +499,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,374</td>
<td align="right">51.87%</td>
<td align="right">10,374</td>
<td align="right">51.87%</td>
<td align="right">10,466</td>
<td align="right">52.33%</td>
<td align="right">10,466</td>
<td align="right">52.33%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,626</td>
<td align="right">48.13%</td>
<td align="right">9,534</td>
<td align="right">47.67%</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 10,551 'phenotype-based' first isolates (52.8% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,633 'phenotype-based' first isolates (53.2% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 52.8% is suitable for resistance analysis! We can now filter
<p>So only 53.2% is suitable for resistance analysis! We can now filter
on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the
<code>dplyr</code> package:</p>
<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
@ -634,7 +634,7 @@ on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html"
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="co"># Including isolates from ICU.</span></span></code></pre></div>
<p>So we end up with 10,551 isolates for analysis. Now our data looks
<p>So we end up with 10,633 isolates for analysis. Now our data looks
like:</p>
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">data_1st</span><span class="op">)</span></span></code></pre></div>
@ -673,77 +673,13 @@ like:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">4</td>
<td align="center">2015-10-03</td>
<td align="center">C5</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">S</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">6</td>
<td align="center">2014-08-04</td>
<td align="center">O7</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">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">8</td>
<td align="center">2017-05-16</td>
<td align="center">L1</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">S</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="even">
<td align="left">9</td>
<td align="center">2016-05-28</td>
<td align="center">D3</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">S</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">10</td>
<td align="center">2011-02-19</td>
<td align="center">B7</td>
<td align="left">1</td>
<td align="center">2013-11-17</td>
<td align="center">D4</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">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
@ -753,14 +689,78 @@ like:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">11</td>
<td align="center">2014-12-17</td>
<td align="center">L4</td>
<td align="left">2</td>
<td align="center">2014-12-24</td>
<td align="center">S2</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="center">2016-03-16</td>
<td align="center">D5</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">7</td>
<td align="center">2011-09-05</td>
<td align="center">Z1</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">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="odd">
<td align="left">8</td>
<td align="center">2015-09-14</td>
<td align="center">B4</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="left">9</td>
<td align="center">2013-09-14</td>
<td align="center">G4</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">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
@ -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: 10,551<br>
Available: 10,551 (100%, NA: 0 = 0%)<br>
Length: 10,633<br>
Available: 10,633 (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">4,551</td>
<td align="right">43.13%</td>
<td align="right">4,551</td>
<td align="right">43.13%</td>
<td align="right">4,608</td>
<td align="right">43.34%</td>
<td align="right">4,608</td>
<td align="right">43.34%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,712</td>
<td align="right">25.70%</td>
<td align="right">7,263</td>
<td align="right">68.84%</td>
<td align="right">2,724</td>
<td align="right">25.62%</td>
<td align="right">7,332</td>
<td align="right">68.96%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,106</td>
<td align="right">19.96%</td>
<td align="right">9,369</td>
<td align="right">88.80%</td>
<td align="right">2,080</td>
<td align="right">19.56%</td>
<td align="right">9,412</td>
<td align="right">88.52%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,182</td>
<td align="right">11.20%</td>
<td align="right">10,551</td>
<td align="right">1,221</td>
<td align="right">11.48%</td>
<td align="right">10,633</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -874,14 +874,14 @@ antibiotic class they are in:</p>
<col width="9%">
<col width="9%">
<col width="9%">
<col width="10%">
<col width="11%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="6%">
<col width="11%">
<col width="12%">
<col width="11%">
<col width="9%">
<col width="5%">
</colgroup>
@ -902,12 +902,12 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2011-02-19</td>
<td align="center">B7</td>
<td align="center">2013-11-17</td>
<td align="center">D4</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">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
@ -917,13 +917,13 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2013-06-20</td>
<td align="center">U2</td>
<td align="center">2014-12-24</td>
<td align="center">S2</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">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
@ -932,27 +932,42 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2011-08-12</td>
<td align="center">V7</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">2015-09-14</td>
<td align="center">B4</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">2011-02-25</td>
<td align="center">P4</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">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2015-05-21</td>
<td align="center">I4</td>
<tr class="odd">
<td align="center">2015-04-27</td>
<td align="center">C10</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>
@ -961,31 +976,16 @@ antibiotic class they are in:</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2010-01-23</td>
<td align="center">F9</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">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="center">2016-04-22</td>
<td align="center">Y4</td>
<td align="center">Hospital A</td>
<td align="center">2011-03-11</td>
<td align="center">J4</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">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
@ -1013,50 +1013,50 @@ different bug/drug combinations, you can use the
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">2163</td>
<td align="center">127</td>
<td align="center">2261</td>
<td align="center">4551</td>
<td align="center">2140</td>
<td align="center">128</td>
<td align="center">2340</td>
<td align="center">4608</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3376</td>
<td align="center">131</td>
<td align="center">1044</td>
<td align="center">4551</td>
<td align="center">3336</td>
<td align="center">178</td>
<td align="center">1094</td>
<td align="center">4608</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3407</td>
<td align="center">3373</td>
<td align="center">0</td>
<td align="center">1144</td>
<td align="center">4551</td>
<td align="center">1235</td>
<td align="center">4608</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4018</td>
<td align="center">4042</td>
<td align="center">0</td>
<td align="center">533</td>
<td align="center">4551</td>
<td align="center">566</td>
<td align="center">4608</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">1182</td>
<td align="center">1182</td>
<td align="center">1221</td>
<td align="center">1221</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">920</td>
<td align="center">46</td>
<td align="center">216</td>
<td align="center">1182</td>
<td align="center">951</td>
<td align="center">51</td>
<td align="center">219</td>
<td align="center">1221</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">4018</td>
<td align="center">4042</td>
<td align="center">0</td>
<td align="center">533</td>
<td align="center">4551</td>
<td align="center">566</td>
<td align="center">4608</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1073</td>
<td align="center">1121</td>
<td align="center">0</td>
<td align="center">109</td>
<td align="center">1182</td>
<td align="center">100</td>
<td align="center">1221</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2408</td>
<td align="center">2432</td>
<td align="center">0</td>
<td align="center">304</td>
<td align="center">2712</td>
<td align="center">292</td>
<td align="center">2724</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">2106</td>
<td align="center">2106</td>
<td align="center">2080</td>
<td align="center">2080</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] 0.5447825</span></span></code></pre></div>
<span><span class="co"># [1] 0.5483871</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">0.5512346</td>
<td align="center">0.5436433</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5463693</td>
<td align="center">0.5441137</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5256817</td>
<td align="center">0.5588420</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5464268</td>
<td align="center">0.5550395</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">0.5512346</td>
<td align="center">3240</td>
<td align="center">0.5436433</td>
<td align="center">3162</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5463693</td>
<td align="center">3677</td>
<td align="center">0.5441137</td>
<td align="center">3729</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5256817</td>
<td align="center">1577</td>
<td align="center">0.5588420</td>
<td align="center">1589</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5464268</td>
<td align="center">2057</td>
<td align="center">0.5550395</td>
<td align="center">2153</td>
</tr>
</tbody>
</table>
@ -1230,27 +1230,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7705999</td>
<td align="center">0.8828829</td>
<td align="center">0.9817623</td>
<td align="center">0.7625868</td>
<td align="center">0.8771701</td>
<td align="center">0.9743924</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8172589</td>
<td align="center">0.9077834</td>
<td align="center">0.9856176</td>
<td align="center">0.8206388</td>
<td align="center">0.9180999</td>
<td align="center">0.9844390</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7912979</td>
<td align="center">0.8879056</td>
<td align="center">0.9782448</td>
<td align="center">0.7830396</td>
<td align="center">0.8928047</td>
<td align="center">0.9805433</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5251662</td>
<td align="center">0.5447115</td>
<td align="center">0.0000000</td>
<td align="center">0.5251662</td>
<td align="center">0.5447115</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">55.1%</td>
<td align="right">27.0%</td>
<td align="right">54.4%</td>
<td align="right">25.9%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">54.6%</td>
<td align="right">27.7%</td>
<td align="right">54.4%</td>
<td align="right">27.1%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">52.6%</td>
<td align="right">24.6%</td>
<td align="right">55.9%</td>
<td align="right">28.1%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">54.6%</td>
<td align="right">26.5%</td>
<td align="right">55.5%</td>
<td align="right">26.6%</td>
</tr>
</tbody>
</table>
@ -1410,16 +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] 16 4 0.025 1 0.025 0.0625 0.125 2 0.001 &gt;=256 </span></span>
<span><span class="co"># [11] 4 0.025 128 &gt;=256 128 4 0.0625 16 2 0.0625</span></span>
<span><span class="co"># [21] 128 64 0.25 0.5 0.002 2 128 4 0.002 0.025 </span></span>
<span><span class="co"># [31] 128 0.0625 64 32 32 4 &gt;=256 128 0.5 4 </span></span>
<span><span class="co"># [41] 32 16 1 0.002 32 64 0.25 0.025 128 0.5 </span></span>
<span><span class="co"># [51] 0.25 8 0.001 8 0.025 64 0.002 2 0.005 0.5 </span></span>
<span><span class="co"># [61] 0.5 8 0.25 2 8 4 0.002 8 0.002 0.001 </span></span>
<span><span class="co"># [71] 0.025 &gt;=256 128 16 16 4 0.025 0.5 0.005 0.025 </span></span>
<span><span class="co"># [81] 0.5 4 0.005 128 16 16 32 0.002 128 0.25 </span></span>
<span><span class="co"># [91] 2 0.25 0.125 64 16 32 64 128 0.002 0.025</span></span></code></pre></div>
<span><span class="co"># [1] 0.025 2 128 0.0625 0.005 16 0.125 0.5 0.5 64 </span></span>
<span><span class="co"># [11] 0.002 0.025 16 0.0625 2 2 1 0.01 4 0.002 </span></span>
<span><span class="co"># [21] 128 1 0.025 64 128 16 0.01 0.002 2 0.5 </span></span>
<span><span class="co"># [31] 2 8 0.125 0.125 0.005 0.001 0.01 2 0.0625 4 </span></span>
<span><span class="co"># [41] 0.01 32 0.01 32 32 0.25 1 0.25 64 0.5 </span></span>
<span><span class="co"># [51] 2 128 0.005 1 0.0625 64 0.125 1 0.5 0.5 </span></span>
<span><span class="co"># [61] 0.5 2 0.125 256 128 16 64 0.25 2 0.01 </span></span>
<span><span class="co"># [71] 0.025 0.125 0.005 16 1 8 0.001 0.125 32 256 </span></span>
<span><span class="co"># [81] 0.5 16 0.005 4 1 16 256 8 0.25 0.01 </span></span>
<span><span class="co"># [91] 0.5 16 0.002 32 128 16 1 0.001 16 32</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>
@ -1453,10 +1453,10 @@ plotting:</p>
<code class="sourceCode R"><span><span class="va">disk_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_disk</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span>
<span><span class="va">disk_values</span></span>
<span><span class="co"># Class 'disk'</span></span>
<span><span class="co"># [1] 20 28 30 24 19 25 22 30 26 17 22 31 28 31 19 19 24 30 22 17 30 20 30 27 31</span></span>
<span><span class="co"># [26] 28 17 23 28 20 23 25 22 19 24 18 29 30 19 17 27 20 17 24 25 25 26 17 26 24</span></span>
<span><span class="co"># [51] 30 29 29 25 31 23 29 24 28 31 31 26 25 19 31 30 26 28 30 29 30 27 28 29 28</span></span>
<span><span class="co"># [76] 19 31 29 25 18 29 27 18 22 24 21 20 17 25 30 27 29 28 19 27 25 18 17 25 31</span></span></code></pre></div>
<span><span class="co"># [1] 21 18 31 26 31 22 21 22 22 27 21 28 24 29 30 27 31 22 30 31 25 29 30 22 22</span></span>
<span><span class="co"># [26] 20 29 18 31 28 18 19 18 25 30 28 25 20 22 20 17 20 21 24 19 23 25 19 30 30</span></span>
<span><span class="co"># [51] 23 24 23 17 17 17 25 24 26 17 24 19 31 27 24 21 27 21 25 31 22 24 22 19 24</span></span>
<span><span class="co"># [76] 23 24 18 29 24 21 28 19 26 23 24 18 20 31 31 26 19 24 17 18 27 25 26 28 25</span></span></code></pre></div>
<div class="sourceCode" id="cb42"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">disk_values</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></code></pre></div>

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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="">1.8.2.9081</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9082</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="">1.8.2.9081</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9082</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">
@ -375,18 +375,18 @@ 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 I R I S R</span></span>
<span><span class="co"># 2 R R I S R I</span></span>
<span><span class="co"># 3 R I I S I I</span></span>
<span><span class="co"># 4 R I I R I R</span></span>
<span><span class="co"># 5 S R I I I S</span></span>
<span><span class="co"># 6 I I I R R S</span></span>
<span><span class="co"># 1 I S I S R S</span></span>
<span><span class="co"># 2 S S R S R S</span></span>
<span><span class="co"># 3 I R S I R I</span></span>
<span><span class="co"># 4 R R S S R S</span></span>
<span><span class="co"># 5 S R R S I R</span></span>
<span><span class="co"># 6 I I I S I I</span></span>
<span><span class="co"># kanamycin</span></span>
<span><span class="co"># 1 I</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 I</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"># 4 R</span></span>
<span><span class="co"># 5 R</span></span>
<span><span class="co"># 6 R</span></span></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can
use:</p>
@ -428,40 +428,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3164</td>
<td align="right">63.28%</td>
<td align="right">3164</td>
<td align="right">63.28%</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">1005</td>
<td align="right">20.10%</td>
<td align="right">4169</td>
<td align="right">83.38%</td>
<td align="right">983</td>
<td align="right">19.66%</td>
<td align="right">4177</td>
<td align="right">83.54%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">485</td>
<td align="right">9.70%</td>
<td align="right">4654</td>
<td align="right">93.08%</td>
<td align="right">492</td>
<td align="right">9.84%</td>
<td align="right">4669</td>
<td align="right">93.38%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">248</td>
<td align="right">4.96%</td>
<td align="right">4902</td>
<td align="right">98.04%</td>
<td align="right">235</td>
<td align="right">4.70%</td>
<td align="right">4904</td>
<td align="right">98.08%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">98</td>
<td align="right">1.96%</td>
<td align="right">96</td>
<td align="right">1.92%</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="">1.8.2.9081</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9082</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="">1.8.2.9081</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">05 January 2023</h4>
<h4 data-toc-skip class="date">06 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>
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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">05 January 2023</h4>
<h4 data-toc-skip class="date">06 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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