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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="">1.8.2.9096</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9098</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">21 January 2023</h4>
<h4 data-toc-skip class="date">23 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 21 January 2023.</p>
generated on 23 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">2023-01-21</td>
<td align="center">2023-01-23</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">2023-01-21</td>
<td align="center">2023-01-23</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">2023-01-21</td>
<td align="center">2023-01-23</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -347,14 +347,15 @@ function.</p>
<span><span class="va">data</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span>
<span> date <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="va">dates</span>, size <span class="op">=</span> <span class="va">sample_size</span>, replace <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span>
<span> patient_id <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="va">patients</span>, size <span class="op">=</span> <span class="va">sample_size</span>, replace <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span>
<span> hospital <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span></span>
<span> <span class="st">"Hospital A"</span>,</span>
<span> <span class="st">"Hospital B"</span>,</span>
<span> <span class="st">"Hospital C"</span>,</span>
<span> <span class="st">"Hospital D"</span></span>
<span> <span class="op">)</span>,</span>
<span> size <span class="op">=</span> <span class="va">sample_size</span>, replace <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> prob <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.30</span>, <span class="fl">0.35</span>, <span class="fl">0.15</span>, <span class="fl">0.20</span><span class="op">)</span></span>
<span> hospital <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span></span>
<span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span></span>
<span> <span class="st">"Hospital A"</span>,</span>
<span> <span class="st">"Hospital B"</span>,</span>
<span> <span class="st">"Hospital C"</span>,</span>
<span> <span class="st">"Hospital D"</span></span>
<span> <span class="op">)</span>,</span>
<span> size <span class="op">=</span> <span class="va">sample_size</span>, replace <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> prob <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.30</span>, <span class="fl">0.35</span>, <span class="fl">0.15</span>, <span class="fl">0.20</span><span class="op">)</span></span>
<span> <span class="op">)</span>,</span>
<span> bacteria <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="va">bacteria</span>,</span>
<span> size <span class="op">=</span> <span class="va">sample_size</span>, replace <span class="op">=</span> <span class="cn">TRUE</span>,</span>
@ -400,70 +401,70 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2013-10-31</td>
<td align="center">J1</td>
<td align="center">2016-03-25</td>
<td align="center">M2</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">I</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2014-11-26</td>
<td align="center">I8</td>
<td align="center">2013-03-28</td>
<td align="center">F10</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2015-03-23</td>
<td align="center">L5</td>
<td align="center">Hospital A</td>
<td align="center">2010-05-31</td>
<td align="center">N4</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2013-01-05</td>
<td align="center">Q3</td>
<td align="center">2014-08-03</td>
<td align="center">V7</td>
<td align="center">Hospital C</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2017-12-24</td>
<td align="center">E9</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2017-04-23</td>
<td align="center">E8</td>
<td align="center">2014-11-23</td>
<td align="center">Z5</td>
<td align="center">Hospital A</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">I</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2015-01-13</td>
<td align="center">X7</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">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
</tbody>
</table>
@ -499,16 +500,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,481</td>
<td align="right">52.41%</td>
<td align="right">10,481</td>
<td align="right">52.41%</td>
<td align="right">10,396</td>
<td align="right">51.98%</td>
<td align="right">10,396</td>
<td align="right">51.98%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,519</td>
<td align="right">47.60%</td>
<td align="right">9,604</td>
<td align="right">48.02%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -621,9 +622,9 @@ takes into account the antimicrobial susceptibility test results using
<span><span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span></span>
<span><span class="co"># 2</span></span>
<span><span class="co"># Including isolates from ICU.</span></span>
<span><span class="co"># =&gt; Found 12,319 'phenotype-based' first isolates (61.6% of total where a</span></span>
<span><span class="co"># =&gt; Found 12,236 'phenotype-based' first isolates (61.2% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 61.6% is suitable for resistance analysis! We can now filter
<p>So only 61.2% 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 +635,7 @@ 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 12,319 isolates for analysis. Now our data looks
<p>So we end up with 12,236 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>
@ -673,13 +674,13 @@ like:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2013-10-31</td>
<td align="center">J1</td>
<td align="left">2</td>
<td align="center">2013-03-28</td>
<td align="center">F10</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">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">M</td>
@ -689,60 +690,28 @@ like:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="center">2014-11-26</td>
<td align="center">I8</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="left">3</td>
<td align="center">2010-05-31</td>
<td align="center">N4</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">R</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">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">4</td>
<td align="center">2013-01-05</td>
<td align="center">Q3</td>
<td align="center">2014-08-03</td>
<td align="center">V7</td>
<td align="center">Hospital C</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">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">5</td>
<td align="center">2017-12-24</td>
<td align="center">E9</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">I</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="odd">
<td align="left">7</td>
<td align="center">2014-12-06</td>
<td align="center">Q7</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_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">S</td>
@ -753,15 +722,47 @@ like:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">10</td>
<td align="center">2014-08-11</td>
<td align="center">X6</td>
<td align="left">5</td>
<td align="center">2014-11-23</td>
<td align="center">Z5</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">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">7</td>
<td align="center">2010-07-28</td>
<td align="center">Q2</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">I</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">8</td>
<td align="center">2012-06-28</td>
<td align="center">Z1</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">I</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
@ -801,8 +802,8 @@ readable:</p>
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://msberends.github.io/cleaner/reference/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></span></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 12,319<br>
Available: 12,319 (100%, NA: 0 = 0%)<br>
Length: 12,236<br>
Available: 12,236 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -827,33 +828,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">5,888</td>
<td align="right">47.80%</td>
<td align="right">5,888</td>
<td align="right">47.80%</td>
<td align="right">5,810</td>
<td align="right">47.48%</td>
<td align="right">5,810</td>
<td align="right">47.48%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,213</td>
<td align="right">26.08%</td>
<td align="right">9,101</td>
<td align="right">73.88%</td>
<td align="right">3,302</td>
<td align="right">26.99%</td>
<td align="right">9,112</td>
<td align="right">74.47%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">1,887</td>
<td align="right">15.32%</td>
<td align="right">10,988</td>
<td align="right">89.20%</td>
<td align="right">1,840</td>
<td align="right">15.04%</td>
<td align="right">10,952</td>
<td align="right">89.51%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,331</td>
<td align="right">10.80%</td>
<td align="right">12,319</td>
<td align="right">1,284</td>
<td align="right">10.49%</td>
<td align="right">12,236</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -874,14 +875,14 @@ 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>
@ -902,73 +903,43 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2014-11-26</td>
<td align="center">I8</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">2010-05-31</td>
<td align="center">N4</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">R</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">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">2014-08-11</td>
<td align="center">X6</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">2014-11-23</td>
<td align="center">Z5</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2015-06-18</td>
<td align="center">D8</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="even">
<td align="center">2017-10-11</td>
<td align="center">L2</td>
<td align="center">Hospital B</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">I</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">Klebsiella</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2011-02-28</td>
<td align="center">B10</td>
<td align="center">2015-03-21</td>
<td align="center">K1</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">I</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
@ -977,18 +948,48 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2012-10-28</td>
<td align="center">L6</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">2015-02-07</td>
<td align="center">G7</td>
<td align="center">Hospital C</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="center">2012-10-03</td>
<td align="center">G8</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">R</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2012-11-05</td>
<td align="center">F10</td>
<td align="center">Hospital C</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>
</tbody>
@ -1013,50 +1014,50 @@ 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">1515</td>
<td align="center">1214</td>
<td align="center">3159</td>
<td align="center">5888</td>
<td align="center">1492</td>
<td align="center">1218</td>
<td align="center">3100</td>
<td align="center">5810</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">2728</td>
<td align="center">1171</td>
<td align="center">1989</td>
<td align="center">5888</td>
<td align="center">2743</td>
<td align="center">1143</td>
<td align="center">1924</td>
<td align="center">5810</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">1970</td>
<td align="center">1842</td>
<td align="center">2076</td>
<td align="center">5888</td>
<td align="center">2024</td>
<td align="center">1859</td>
<td align="center">1927</td>
<td align="center">5810</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">2001</td>
<td align="center">1793</td>
<td align="center">2094</td>
<td align="center">5888</td>
<td align="center">2037</td>
<td align="center">1738</td>
<td align="center">2035</td>
<td align="center">5810</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">1331</td>
<td align="center">1331</td>
<td align="center">1284</td>
<td align="center">1284</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">593</td>
<td align="center">289</td>
<td align="center">449</td>
<td align="center">1331</td>
<td align="center">556</td>
<td align="center">263</td>
<td align="center">465</td>
<td align="center">1284</td>
</tr>
</tbody>
</table>
@ -1078,34 +1079,34 @@ 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">2001</td>
<td align="center">1793</td>
<td align="center">2094</td>
<td align="center">5888</td>
<td align="center">2037</td>
<td align="center">1738</td>
<td align="center">2035</td>
<td align="center">5810</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">471</td>
<td align="center">400</td>
<td align="center">460</td>
<td align="center">1331</td>
<td align="center">429</td>
<td align="center">422</td>
<td align="center">433</td>
<td align="center">1284</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">1094</td>
<td align="center">982</td>
<td align="center">1099</td>
<td align="center">1066</td>
<td align="center">1137</td>
<td align="center">3213</td>
<td align="center">3302</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">1887</td>
<td align="center">1887</td>
<td align="center">1840</td>
<td align="center">1840</td>
</tr>
</tbody>
</table>
@ -1137,7 +1138,7 @@ 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] 0.5826772</span></span></code></pre></div>
<span><span class="co"># [1] 0.5813992</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 +1153,19 @@ own:</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5808320</td>
<td align="center">0.5883615</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5845366</td>
<td align="center">0.5790089</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5761047</td>
<td align="center">0.5716704</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5873016</td>
<td align="center">0.5820106</td>
</tr>
</tbody>
</table>
@ -1189,23 +1190,23 @@ 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">0.5808320</td>
<td align="center">3798</td>
<td align="center">0.5883615</td>
<td align="center">3729</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5845366</td>
<td align="center">4294</td>
<td align="center">0.5790089</td>
<td align="center">4278</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5761047</td>
<td align="center">1833</td>
<td align="center">0.5716704</td>
<td align="center">1772</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5873016</td>
<td align="center">2394</td>
<td align="center">0.5820106</td>
<td align="center">2457</td>
</tr>
</tbody>
</table>
@ -1230,27 +1231,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.6621943</td>
<td align="center">0.6443614</td>
<td align="center">0.8773777</td>
<td align="center">0.6688468</td>
<td align="center">0.6497418</td>
<td align="center">0.8898451</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.6626597</td>
<td align="center">0.6543952</td>
<td align="center">0.8918107</td>
<td align="center">0.6378505</td>
<td align="center">0.6627726</td>
<td align="center">0.8777259</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.6644880</td>
<td align="center">0.6461251</td>
<td align="center">0.8801743</td>
<td align="center">0.6741369</td>
<td align="center">0.6556632</td>
<td align="center">0.8885524</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.4886063</td>
<td align="center">0.4766304</td>
<td align="center">0.0000000</td>
<td align="center">0.4886063</td>
<td align="center">0.4766304</td>
</tr>
</tbody>
</table>
@ -1278,23 +1279,23 @@ classes, use a antibiotic class selector such as
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">58.1%</td>
<td align="right">36.1%</td>
<td align="right">58.8%</td>
<td align="right">36.3%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">58.5%</td>
<td align="right">36.4%</td>
<td align="right">57.9%</td>
<td align="right">35.7%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">57.6%</td>
<td align="right">36.2%</td>
<td align="right">57.2%</td>
<td align="right">36.6%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">58.7%</td>
<td align="right">36.9%</td>
<td align="right">58.2%</td>
<td align="right">36.6%</td>
</tr>
</tbody>
</table>
@ -1410,16 +1411,16 @@ classes) <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code>:</p>
<code class="sourceCode R"><span><span class="va">mic_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span></span>
<span><span class="va">mic_values</span></span>
<span><span class="co"># Class 'mic'</span></span>
<span><span class="co"># [1] 64 0.125 64 4 256 0.01 0.125 2 128 0.002 </span></span>
<span><span class="co"># [11] 2 0.125 0.01 0.01 8 0.0625 0.5 32 0.01 0.0625</span></span>
<span><span class="co"># [21] 8 16 32 16 0.001 0.005 4 128 0.025 128 </span></span>
<span><span class="co"># [31] 2 256 0.5 8 0.25 256 16 0.025 0.001 32 </span></span>
<span><span class="co"># [41] 16 2 16 0.025 1 32 64 4 16 32 </span></span>
<span><span class="co"># [51] 0.005 0.025 0.001 0.025 64 2 0.125 1 0.5 0.125 </span></span>
<span><span class="co"># [61] 16 0.002 0.25 16 0.002 4 0.5 2 128 128 </span></span>
<span><span class="co"># [71] 8 1 0.002 32 0.0625 8 128 0.125 1 0.25 </span></span>
<span><span class="co"># [81] 0.002 8 128 16 256 0.125 2 4 1 0.0625</span></span>
<span><span class="co"># [91] 4 0.025 16 0.5 64 0.002 128 0.0625 1 64</span></span></code></pre></div>
<span><span class="co"># [1] 0.001 0.0625 32 0.0625 32 64 &gt;=256 32 4 0.125 </span></span>
<span><span class="co"># [11] 4 32 128 32 0.125 1 0.0625 &gt;=256 16 64 </span></span>
<span><span class="co"># [21] 0.025 64 16 16 &gt;=256 128 0.025 0.005 0.25 1 </span></span>
<span><span class="co"># [31] 0.5 32 0.0625 16 128 0.025 0.25 1 0.005 0.0625</span></span>
<span><span class="co"># [41] 0.025 0.025 0.25 0.002 0.001 2 8 32 0.0625 0.002 </span></span>
<span><span class="co"># [51] 0.001 0.5 0.25 16 0.125 0.005 64 1 0.0625 0.001 </span></span>
<span><span class="co"># [61] 0.025 32 16 &gt;=256 0.005 0.002 16 &gt;=256 1 0.125 </span></span>
<span><span class="co"># [71] 2 0.125 16 16 64 64 0.0625 0.5 1 0.005 </span></span>
<span><span class="co"># [81] 64 0.125 0.025 0.01 0.0625 0.5 0.002 0.25 0.25 128 </span></span>
<span><span class="co"># [91] 4 16 0.002 0.25 32 32 128 128 0.125 0.25</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 +1454,10 @@ 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] 30 20 18 25 20 24 23 23 19 30 23 27 24 19 18 25 21 26 21 26 29 18 25 29 31</span></span>
<span><span class="co"># [26] 19 25 30 19 24 25 26 21 22 28 17 24 17 31 28 20 29 31 21 29 18 25 19 25 22</span></span>
<span><span class="co"># [51] 24 27 29 27 19 26 20 27 24 18 22 22 26 31 19 24 22 29 20 22 31 19 22 21 18</span></span>
<span><span class="co"># [76] 22 17 23 21 20 19 28 21 24 23 25 30 26 26 17 17 20 18 28 24 18 25 29 17 27</span></span></code></pre></div>
<span><span class="co"># [1] 18 29 23 17 30 20 29 20 17 19 22 25 29 30 24 22 29 29 24 17 30 19 25 23 26</span></span>
<span><span class="co"># [26] 20 25 17 20 23 27 19 26 19 26 19 21 19 24 20 18 19 30 17 27 29 21 22 29 21</span></span>
<span><span class="co"># [51] 22 30 20 23 27 30 27 19 24 24 21 24 24 17 21 20 31 27 31 20 22 26 25 29 31</span></span>
<span><span class="co"># [76] 31 18 20 18 17 26 25 24 31 20 18 25 26 19 18 23 31 27 18 18 28 30 26 30 27</span></span></code></pre></div>
<div class="sourceCode" id="cb42"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">disk_values</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></code></pre></div>

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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9096</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9098</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">

58
articles/MDR.html
View File

@ -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="">1.8.2.9096</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9098</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 I I I S I</span></span>
<span><span class="co"># 2 S S I S I I</span></span>
<span><span class="co"># 3 S S S R I S</span></span>
<span><span class="co"># 4 R S S I S S</span></span>
<span><span class="co"># 5 I S I R I R</span></span>
<span><span class="co"># 6 S R S I S R</span></span>
<span><span class="co"># 1 I S R I S S</span></span>
<span><span class="co"># 2 I R R I S I</span></span>
<span><span class="co"># 3 I R S I R I</span></span>
<span><span class="co"># 4 S S I S R I</span></span>
<span><span class="co"># 5 I I R I I S</span></span>
<span><span class="co"># 6 R S S S R I</span></span>
<span><span class="co"># kanamycin</span></span>
<span><span class="co"># 1 R</span></span>
<span><span class="co"># 2 S</span></span>
<span><span class="co"># 1 S</span></span>
<span><span class="co"># 2 R</span></span>
<span><span class="co"># 3 S</span></span>
<span><span class="co"># 4 R</span></span>
<span><span class="co"># 4 I</span></span>
<span><span class="co"># 5 S</span></span>
<span><span class="co"># 6 S</span></span></code></pre></div>
<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">3193</td>
<td align="right">63.86%</td>
<td align="right">3193</td>
<td align="right">63.86%</td>
<td align="right">3130</td>
<td align="right">62.60%</td>
<td align="right">3130</td>
<td align="right">62.60%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">981</td>
<td align="right">19.62%</td>
<td align="right">4174</td>
<td align="right">83.48%</td>
<td align="right">1022</td>
<td align="right">20.44%</td>
<td align="right">4152</td>
<td align="right">83.04%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">472</td>
<td align="right">9.44%</td>
<td align="right">4646</td>
<td align="right">92.92%</td>
<td align="right">476</td>
<td align="right">9.52%</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">262</td>
<td align="right">5.24%</td>
<td align="right">4908</td>
<td align="right">98.16%</td>
<td align="right">269</td>
<td align="right">5.38%</td>
<td align="right">4897</td>
<td align="right">97.94%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">92</td>
<td align="right">1.84%</td>
<td align="right">103</td>
<td align="right">2.06%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

2
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@ -38,7 +38,7 @@
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@ -168,7 +168,7 @@
<h4 data-toc-skip class="author">Dr. Matthijs
Berends</h4>
<h4 data-toc-skip class="date">21 January 2023</h4>
<h4 data-toc-skip class="date">23 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">477,622
online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">478,396
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

2
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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">21 January 2023</h4>
<h4 data-toc-skip class="date">23 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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