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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="">1.8.2.9089</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9090</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">07 January 2023</h4>
<h4 data-toc-skip class="date">12 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 07 January 2023.</p>
generated on 12 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">2023-01-07</td>
<td align="center">2023-01-12</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">2023-01-07</td>
<td align="center">2023-01-12</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">2023-01-07</td>
<td align="center">2023-01-12</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">2015-12-14</td>
<td align="center">P6</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">2015-01-17</td>
<td align="center">P8</td>
<td align="center">Hospital B</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">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2010-02-21</td>
<td align="center">O6</td>
<td align="center">Hospital D</td>
<td align="center">2010-05-21</td>
<td align="center">H1</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">R</td>
<td align="center">F</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2015-06-26</td>
<td align="center">S10</td>
<td align="center">Hospital A</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">R</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2015-10-07</td>
<td align="center">P9</td>
<td align="center">2011-02-02</td>
<td align="center">E4</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">F</td>
</tr>
<tr class="odd">
<td align="center">2016-05-30</td>
<td align="center">J9</td>
<td align="center">Hospital C</td>
<td align="center">Klebsiella pneumoniae</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>
</tr>
<tr class="even">
<td align="center">2014-05-31</td>
<td align="center">J10</td>
<td align="center">Hospital D</td>
<td align="center">2015-11-17</td>
<td align="center">Q2</td>
<td align="center">Hospital B</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2015-11-06</td>
<td align="center">Q6</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia coli</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2016-03-29</td>
<td align="center">E9</td>
<td align="center">Hospital A</td>
<td align="center">Klebsiella 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>
@ -499,16 +499,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,334</td>
<td align="right">51.67%</td>
<td align="right">10,334</td>
<td align="right">51.67%</td>
<td align="right">10,452</td>
<td align="right">52.26%</td>
<td align="right">10,452</td>
<td align="right">52.26%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,666</td>
<td align="right">48.33%</td>
<td align="right">9,548</td>
<td align="right">47.74%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -621,7 +621,7 @@ 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 10,571 'phenotype-based' first isolates (52.9% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,582 'phenotype-based' first isolates (52.9% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 52.9% is suitable for resistance analysis! We can now filter
on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the
@ -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 10,571 isolates for analysis. Now our data looks
<p>So we end up with 10,582 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>
@ -673,47 +673,47 @@ like:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">3</td>
<td align="center">2015-06-26</td>
<td align="center">S10</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="left">2</td>
<td align="center">2010-05-21</td>
<td align="center">H1</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">M</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="left">5</td>
<td align="center">2016-05-30</td>
<td align="center">J9</td>
<td align="center">Hospital C</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="left">3</td>
<td align="center">2011-02-02</td>
<td align="center">E4</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">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">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">9</td>
<td align="center">2012-12-22</td>
<td align="center">Q10</td>
<td align="center">Hospital C</td>
<td align="left">4</td>
<td align="center">2015-11-17</td>
<td align="center">Q2</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">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
@ -721,51 +721,51 @@ like:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">7</td>
<td align="center">2014-02-11</td>
<td align="center">B2</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">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="odd">
<td align="left">8</td>
<td align="center">2012-04-20</td>
<td align="center">K2</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">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">12</td>
<td align="center">2015-09-03</td>
<td align="center">V7</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">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="odd">
<td align="left">13</td>
<td align="center">2012-11-17</td>
<td align="center">U2</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">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="even">
<td align="left">14</td>
<td align="center">2013-07-05</td>
<td align="center">R4</td>
<td align="center">2013-05-07</td>
<td align="center">Y1</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">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>
</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: 10,571<br>
Available: 10,571 (100%, NA: 0 = 0%)<br>
Length: 10,582<br>
Available: 10,582 (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">4,575</td>
<td align="right">43.28%</td>
<td align="right">4,575</td>
<td align="right">43.28%</td>
<td align="right">4,614</td>
<td align="right">43.60%</td>
<td align="right">4,614</td>
<td align="right">43.60%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,719</td>
<td align="right">25.72%</td>
<td align="right">7,294</td>
<td align="right">69.00%</td>
<td align="right">2,700</td>
<td align="right">25.52%</td>
<td align="right">7,314</td>
<td align="right">69.12%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,107</td>
<td align="right">19.93%</td>
<td align="right">9,401</td>
<td align="right">88.93%</td>
<td align="right">2,078</td>
<td align="right">19.64%</td>
<td align="right">9,392</td>
<td align="right">88.75%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,170</td>
<td align="right">11.07%</td>
<td align="right">10,571</td>
<td align="right">1,190</td>
<td align="right">11.25%</td>
<td align="right">10,582</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>
@ -902,27 +902,12 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2015-06-26</td>
<td align="center">S10</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2017-04-26</td>
<td align="center">J4</td>
<td align="center">2010-05-21</td>
<td align="center">H1</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">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
@ -931,39 +916,54 @@ antibiotic class they are in:</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2015-11-17</td>
<td align="center">Q2</td>
<td align="center">Hospital B</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">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2015-03-03</td>
<td align="center">E4</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">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">2015-03-09</td>
<td align="center">W10</td>
<td align="center">2014-02-11</td>
<td align="center">B2</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">R</td>
<td align="center">F</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2013-05-07</td>
<td align="center">Y1</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">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2016-12-05</td>
<td align="center">V8</td>
<td align="center">2015-11-05</td>
<td align="center">Q9</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
@ -977,18 +977,18 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2011-06-19</td>
<td align="center">W7</td>
<td align="center">Hospital C</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">2010-12-16</td>
<td align="center">A4</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">R</td>
<td align="center">F</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">Streptococcus</td>
<td align="center">pneumoniae</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">2133</td>
<td align="center">139</td>
<td align="center">2303</td>
<td align="center">4575</td>
<td align="center">2176</td>
<td align="center">133</td>
<td align="center">2305</td>
<td align="center">4614</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3376</td>
<td align="center">157</td>
<td align="center">1042</td>
<td align="center">4575</td>
<td align="center">3401</td>
<td align="center">161</td>
<td align="center">1052</td>
<td align="center">4614</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3339</td>
<td align="center">3389</td>
<td align="center">0</td>
<td align="center">1236</td>
<td align="center">4575</td>
<td align="center">1225</td>
<td align="center">4614</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">3988</td>
<td align="center">4044</td>
<td align="center">0</td>
<td align="center">587</td>
<td align="center">4575</td>
<td align="center">570</td>
<td align="center">4614</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">1170</td>
<td align="center">1170</td>
<td align="center">1190</td>
<td align="center">1190</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">927</td>
<td align="center">37</td>
<td align="center">206</td>
<td align="center">1170</td>
<td align="center">936</td>
<td align="center">47</td>
<td align="center">207</td>
<td align="center">1190</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">3988</td>
<td align="center">4044</td>
<td align="center">0</td>
<td align="center">587</td>
<td align="center">4575</td>
<td align="center">570</td>
<td align="center">4614</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1055</td>
<td align="center">1065</td>
<td align="center">0</td>
<td align="center">115</td>
<td align="center">1170</td>
<td align="center">125</td>
<td align="center">1190</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2407</td>
<td align="center">2393</td>
<td align="center">0</td>
<td align="center">312</td>
<td align="center">2719</td>
<td align="center">307</td>
<td align="center">2700</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">2107</td>
<td align="center">2107</td>
<td align="center">2078</td>
<td align="center">2078</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] 0.5429004</span></span></code></pre></div>
<span><span class="co"># [1] 0.5426195</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">0.5397836</td>
<td align="center">0.5490875</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5503731</td>
<td align="center">0.5438596</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5403882</td>
<td align="center">0.5260078</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5360577</td>
<td align="center">0.5427757</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">0.5397836</td>
<td align="center">3142</td>
<td align="center">0.5490875</td>
<td align="center">3178</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5503731</td>
<td align="center">3752</td>
<td align="center">0.5438596</td>
<td align="center">3762</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5403882</td>
<td align="center">1597</td>
<td align="center">0.5260078</td>
<td align="center">1538</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5360577</td>
<td align="center">2080</td>
<td align="center">0.5427757</td>
<td align="center">2104</td>
</tr>
</tbody>
</table>
@ -1230,27 +1230,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7722404</td>
<td align="center">0.8716940</td>
<td align="center">0.9768306</td>
<td align="center">0.7719983</td>
<td align="center">0.8764629</td>
<td align="center">0.9809276</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8239316</td>
<td align="center">0.9017094</td>
<td align="center">0.9769231</td>
<td align="center">0.8260504</td>
<td align="center">0.8949580</td>
<td align="center">0.9798319</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.8006620</td>
<td align="center">0.8852519</td>
<td align="center">0.9764619</td>
<td align="center">0.8025926</td>
<td align="center">0.8862963</td>
<td align="center">0.9796296</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5372568</td>
<td align="center">0.5442733</td>
<td align="center">0.0000000</td>
<td align="center">0.5372568</td>
<td align="center">0.5442733</td>
</tr>
</tbody>
</table>
@ -1278,22 +1278,22 @@ 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">54.9%</td>
<td align="right">27.4%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">55.0%</td>
<td align="right">26.8%</td>
<td align="right">54.4%</td>
<td align="right">25.6%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">54.0%</td>
<td align="right">24.9%</td>
<td align="right">52.6%</td>
<td align="right">24.8%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">53.6%</td>
<td align="right">54.3%</td>
<td align="right">24.9%</td>
</tr>
</tbody>
@ -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] 0.005 0.0625 0.001 128 32 4 8 32 0.125 64 </span></span>
<span><span class="co"># [11] 0.5 16 0.125 8 0.25 0.5 16 0.5 1 0.005 </span></span>
<span><span class="co"># [21] 0.025 16 0.005 0.01 2 2 0.002 0.025 0.005 64 </span></span>
<span><span class="co"># [31] 128 4 0.0625 2 128 128 32 2 0.125 2 </span></span>
<span><span class="co"># [41] 0.0625 0.25 1 2 0.125 0.5 &gt;=256 0.005 0.001 8 </span></span>
<span><span class="co"># [51] 16 16 0.0625 8 &gt;=256 128 1 &gt;=256 4 4 </span></span>
<span><span class="co"># [61] 128 0.002 0.25 0.005 0.005 4 8 0.002 0.001 &gt;=256 </span></span>
<span><span class="co"># [71] 0.125 0.0625 0.001 0.25 128 64 0.125 32 16 128 </span></span>
<span><span class="co"># [81] 0.002 4 0.001 0.001 0.005 0.025 0.001 &gt;=256 0.0625 &gt;=256 </span></span>
<span><span class="co"># [91] 2 0.5 0.0625 8 1 0.5 0.01 0.001 8 0.5</span></span></code></pre></div>
<span><span class="co"># [1] 0.001 0.125 0.01 0.002 32 0.01 8 64 0.0625 0.002 </span></span>
<span><span class="co"># [11] 0.025 0.25 128 0.125 4 8 0.125 4 0.025 32 </span></span>
<span><span class="co"># [21] 64 0.125 8 0.005 0.5 0.002 32 0.5 0.25 32 </span></span>
<span><span class="co"># [31] 0.025 128 0.25 0.001 0.01 256 16 0.002 16 0.0625</span></span>
<span><span class="co"># [41] 0.125 0.001 0.025 8 4 4 0.01 0.5 2 64 </span></span>
<span><span class="co"># [51] 2 256 0.5 2 0.001 16 16 0.125 64 4 </span></span>
<span><span class="co"># [61] 8 16 0.5 0.125 0.001 0.5 0.001 2 32 8 </span></span>
<span><span class="co"># [71] 0.125 8 0.01 0.5 2 0.01 32 1 0.002 0.01 </span></span>
<span><span class="co"># [81] 0.5 8 0.5 0.5 0.25 0.005 0.001 16 32 0.005 </span></span>
<span><span class="co"># [91] 64 0.125 16 1 0.01 0.002 0.5 16 8 0.005</span></span></code></pre></div>
<div class="sourceCode" id="cb36"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">mic_values</span><span class="op">)</span></span></code></pre></div>
@ -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] 28 22 28 23 22 31 27 19 23 22 18 17 29 23 28 20 21 31 28 17 22 30 31 24 29</span></span>
<span><span class="co"># [26] 24 23 19 17 21 26 30 26 29 25 23 31 29 20 31 26 26 19 26 22 24 28 28 28 27</span></span>
<span><span class="co"># [51] 28 18 17 19 22 19 25 20 19 17 24 20 26 22 26 18 18 27 24 30 27 24 24 26 30</span></span>
<span><span class="co"># [76] 26 21 22 27 22 24 27 24 28 20 29 17 28 26 20 21 29 18 24 20 22 28 22 29 21</span></span></code></pre></div>
<span><span class="co"># [1] 19 25 22 29 26 26 28 19 29 20 24 24 17 31 24 25 27 27 22 21 31 27 23 18 30</span></span>
<span><span class="co"># [26] 21 26 29 17 29 31 21 24 31 19 24 27 31 27 29 23 20 31 18 29 25 30 21 25 30</span></span>
<span><span class="co"># [51] 18 23 22 23 19 19 23 24 23 26 17 21 24 27 29 29 27 26 29 17 22 17 29 21 31</span></span>
<span><span class="co"># [76] 21 22 17 19 28 29 17 27 17 25 18 25 26 28 31 30 24 29 21 31 26 31 23 24 28</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="">1.8.2.9089</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9090</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="">1.8.2.9089</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9090</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 R R I S R</span></span>
<span><span class="co"># 2 S I R S S I</span></span>
<span><span class="co"># 3 I I R I S I</span></span>
<span><span class="co"># 4 R R I R I I</span></span>
<span><span class="co"># 5 I R S R R I</span></span>
<span><span class="co"># 6 I S S R S R</span></span>
<span><span class="co"># 1 S R I I R R</span></span>
<span><span class="co"># 2 S S S R I S</span></span>
<span><span class="co"># 3 S I I S R R</span></span>
<span><span class="co"># 4 I R S R I I</span></span>
<span><span class="co"># 5 I I I S R R</span></span>
<span><span class="co"># 6 I R S S R S</span></span>
<span><span class="co"># kanamycin</span></span>
<span><span class="co"># 1 I</span></span>
<span><span class="co"># 2 I</span></span>
<span><span class="co"># 3 I</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"># 5 I</span></span>
<span><span class="co"># 6 S</span></span></code></pre></div>
<span><span class="co"># 5 S</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>
<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">3145</td>
<td align="right">62.90%</td>
<td align="right">3145</td>
<td align="right">62.90%</td>
<td align="right">3204</td>
<td align="right">64.08%</td>
<td align="right">3204</td>
<td align="right">64.08%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">1012</td>
<td align="right">20.24%</td>
<td align="right">4157</td>
<td align="right">83.14%</td>
<td align="right">989</td>
<td align="right">19.78%</td>
<td align="right">4193</td>
<td align="right">83.86%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">506</td>
<td align="right">10.12%</td>
<td align="right">4663</td>
<td align="right">93.26%</td>
<td align="right">435</td>
<td align="right">8.70%</td>
<td align="right">4628</td>
<td align="right">92.56%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">253</td>
<td align="right">5.06%</td>
<td align="right">4916</td>
<td align="right">98.32%</td>
<td align="right">262</td>
<td align="right">5.24%</td>
<td align="right">4890</td>
<td align="right">97.80%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">84</td>
<td align="right">1.68%</td>
<td align="right">110</td>
<td align="right">2.20%</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="">1.8.2.9089</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9090</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">

6
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="">1.8.2.9089</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9090</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">07 January 2023</h4>
<h4 data-toc-skip class="date">12 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>
@ -247,7 +247,7 @@ data using a custom made website. The webdesign knowledge needed
<li>
<p><strong>R has a huge community.</strong></p>
<p>Many R users just ask questions on websites like <a href="https://stackoverflow.com" class="external-link">StackOverflow.com</a>, the largest
online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">476,194
online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">476,873
R-related questions</a> have already been asked on this platform (that
covers questions and answers for any programming language). In my own
experience, most questions are answered within a couple of

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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -38,7 +38,7 @@
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@ -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">07 January 2023</h4>
<h4 data-toc-skip class="date">12 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 @@
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