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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="">1.8.2.9051</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9052</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">14 November 2022</h4>
<h4 data-toc-skip class="date">17 November 2022</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/AMR.Rmd" class="external-link"><code>vignettes/AMR.Rmd</code></a></small>
<div class="d-none name"><code>AMR.Rmd</code></div>
@ -180,7 +180,7 @@ Berends</h4>
website update since they are based on randomly created values and the
page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
Markdown</a>. However, the methodology remains unchanged. This page was
generated on 14 November 2022.</p>
generated on 17 November 2022.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@ -236,21 +236,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2022-11-14</td>
<td align="center">2022-11-17</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="center">2022-11-14</td>
<td align="center">2022-11-17</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<tr class="odd">
<td align="center">2022-11-14</td>
<td align="center">2022-11-17</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>
@ -400,71 +400,71 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2011-09-28</td>
<td align="center">W5</td>
<td align="center">2015-12-23</td>
<td align="center">L8</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2013-01-09</td>
<td align="center">A10</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">2014-07-14</td>
<td align="center">M7</td>
<td align="center">Hospital B</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">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2010-03-15</td>
<td align="center">W2</td>
<td align="center">2010-06-02</td>
<td align="center">F6</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">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2012-05-12</td>
<td align="center">A5</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2010-01-24</td>
<td align="center">W4</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">S</td>
<td align="center">R</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2012-08-18</td>
<td align="center">P7</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">2010-11-08</td>
<td align="center">J2</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">M</td>
</tr>
<tr class="odd">
<td align="center">2016-01-14</td>
<td align="center">Q3</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2013-02-21</td>
<td align="center">X1</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">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
</tbody>
</table>
<p>Now, let’s start the cleaning and the analysis!</p>
@ -499,18 +499,18 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,420</td>
<td align="right">52.1%</td>
<td align="right">10,420</td>
<td align="right">52.1%</td>
<td align="right">10,496</td>
<td align="right">52.48%</td>
<td align="right">10,496</td>
<td align="right">52.48%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,580</td>
<td align="right">47.9%</td>
<td align="right">9,504</td>
<td align="right">47.52%</td>
<td align="right">20,000</td>
<td align="right">100.0%</td>
<td align="right">100.00%</td>
</tr>
</tbody>
</table>
@ -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 10,650 'phenotype-based' first isolates (53.3% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,612 'phenotype-based' first isolates (53.1% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 53.3% is suitable for resistance analysis! We can now filter
<p>So only 53.1% is suitable for resistance analysis! We can now filter
on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the
<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 10,650 isolates for analysis. Now our data looks
<p>So we end up with 10,612 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>
@ -674,8 +674,24 @@ like:</p>
<tbody>
<tr class="odd">
<td align="left">2</td>
<td align="center">2013-01-09</td>
<td align="center">A10</td>
<td align="center">2014-07-14</td>
<td align="center">M7</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">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">3</td>
<td align="center">2010-06-02</td>
<td align="center">F6</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
@ -688,84 +704,68 @@ like:</p>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">3</td>
<td align="center">2010-03-15</td>
<td align="center">W2</td>
<tr class="odd">
<td align="left">7</td>
<td align="center">2013-01-21</td>
<td align="center">Z7</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">R</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">4</td>
<td align="center">2010-01-24</td>
<td align="center">W4</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>
<tr class="even">
<td align="left">8</td>
<td align="center">2013-05-01</td>
<td align="center">S2</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">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">5</td>
<td align="center">2012-08-18</td>
<td align="center">P7</td>
<td align="center">Hospital B</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">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="odd">
<td align="left">8</td>
<td align="center">2012-07-26</td>
<td align="center">J5</td>
<td align="left">12</td>
<td align="center">2016-06-06</td>
<td align="center">Q6</td>
<td align="center">Hospital D</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">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">9</td>
<td align="center">2015-03-14</td>
<td align="center">I4</td>
<td align="center">Hospital C</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="left">14</td>
<td align="center">2016-01-03</td>
<td align="center">N4</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">S</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
</tbody>
@ -801,8 +801,8 @@ readable:</p>
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://msberends.github.io/cleaner/reference/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></span></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 10,650<br>
Available: 10,650 (100%, NA: 0 = 0%)<br>
Length: 10,612<br>
Available: 10,612 (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">4,668</td>
<td align="right">43.83%</td>
<td align="right">4,668</td>
<td align="right">43.83%</td>
<td align="right">4,601</td>
<td align="right">43.36%</td>
<td align="right">4,601</td>
<td align="right">43.36%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,688</td>
<td align="right">25.24%</td>
<td align="right">7,356</td>
<td align="right">69.07%</td>
<td align="right">2,686</td>
<td align="right">25.31%</td>
<td align="right">7,287</td>
<td align="right">68.67%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,093</td>
<td align="right">19.65%</td>
<td align="right">9,449</td>
<td align="right">88.72%</td>
<td align="right">2,115</td>
<td align="right">19.93%</td>
<td align="right">9,402</td>
<td align="right">88.60%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,201</td>
<td align="right">11.28%</td>
<td align="right">10,650</td>
<td align="right">1,210</td>
<td align="right">11.40%</td>
<td align="right">10,612</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>
@ -902,55 +902,85 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2010-03-15</td>
<td align="center">W2</td>
<td align="center">2013-05-01</td>
<td align="center">S2</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">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2016-06-06</td>
<td align="center">Q6</td>
<td align="center">Hospital D</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">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">2014-10-11</td>
<td align="center">K4</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2016-09-23</td>
<td align="center">P4</td>
<td align="center">Hospital D</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">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">2012-11-13</td>
<td align="center">A1</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">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">2013-02-15</td>
<td align="center">F3</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">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="even">
<td align="center">2010-01-24</td>
<td align="center">W4</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">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="center">2012-07-26</td>
<td align="center">J5</td>
<td align="center">Hospital D</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">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2010-02-12</td>
<td align="center">E10</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">S</td>
@ -961,36 +991,6 @@ antibiotic class they are in:</p>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2011-12-23</td>
<td align="center">R5</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="even">
<td align="center">2017-05-04</td>
<td align="center">X9</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>
</tbody>
</table>
<p>If you want to get a quick glance of the number of isolates in
@ -1014,50 +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">2216</td>
<td align="center">123</td>
<td align="center">2329</td>
<td align="center">4668</td>
<td align="center">2181</td>
<td align="center">142</td>
<td align="center">2278</td>
<td align="center">4601</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3459</td>
<td align="center">138</td>
<td align="center">1071</td>
<td align="center">4668</td>
<td align="center">3411</td>
<td align="center">174</td>
<td align="center">1016</td>
<td align="center">4601</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3368</td>
<td align="center">3377</td>
<td align="center">0</td>
<td align="center">1300</td>
<td align="center">4668</td>
<td align="center">1224</td>
<td align="center">4601</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4117</td>
<td align="center">4021</td>
<td align="center">0</td>
<td align="center">551</td>
<td align="center">4668</td>
<td align="center">580</td>
<td align="center">4601</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">1201</td>
<td align="center">1201</td>
<td align="center">1210</td>
<td align="center">1210</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">952</td>
<td align="center">36</td>
<td align="center">213</td>
<td align="center">1201</td>
<td align="center">934</td>
<td align="center">38</td>
<td align="center">238</td>
<td align="center">1210</td>
</tr>
</tbody>
</table>
@ -1080,34 +1080,34 @@ 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">4117</td>
<td align="center">4021</td>
<td align="center">0</td>
<td align="center">551</td>
<td align="center">4668</td>
<td align="center">580</td>
<td align="center">4601</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1100</td>
<td align="center">1098</td>
<td align="center">0</td>
<td align="center">101</td>
<td align="center">1201</td>
<td align="center">112</td>
<td align="center">1210</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2397</td>
<td align="center">2365</td>
<td align="center">0</td>
<td align="center">291</td>
<td align="center">2688</td>
<td align="center">321</td>
<td align="center">2686</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">2093</td>
<td align="center">2093</td>
<td align="center">2115</td>
<td align="center">2115</td>
</tr>
</tbody>
</table>
@ -1139,7 +1139,7 @@ I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equa
own:</p>
<div class="sourceCode" id="cb26"><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] 0.5415962</span></span></code></pre></div>
<span><span class="co"># [1] 0.5434414</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="cb27"><pre class="downlit sourceCode r">
@ -1154,19 +1154,19 @@ own:</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5346793</td>
<td align="center">0.5427245</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5482421</td>
<td align="center">0.5589124</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5480192</td>
<td align="center">0.5351942</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5347418</td>
<td align="center">0.5241280</td>
</tr>
</tbody>
</table>
@ -1191,23 +1191,23 @@ 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">0.5346793</td>
<td align="center">3071</td>
<td align="center">0.5427245</td>
<td align="center">3230</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5482421</td>
<td align="center">3783</td>
<td align="center">0.5589124</td>
<td align="center">3641</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5480192</td>
<td align="center">1666</td>
<td align="center">0.5351942</td>
<td align="center">1648</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5347418</td>
<td align="center">2130</td>
<td align="center">0.5241280</td>
<td align="center">2093</td>
</tr>
</tbody>
</table>
@ -1232,27 +1232,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7705656</td>
<td align="center">0.8819623</td>
<td align="center">0.9777207</td>
<td align="center">0.7791784</td>
<td align="center">0.8739404</td>
<td align="center">0.9819604</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8226478</td>
<td align="center">0.9159034</td>
<td align="center">0.9866778</td>
<td align="center">0.8033058</td>
<td align="center">0.9074380</td>
<td align="center">0.9826446</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7979911</td>
<td align="center">0.8917411</td>
<td align="center">0.9769345</td>
<td align="center">0.7915115</td>
<td align="center">0.8804914</td>
<td align="center">0.9791512</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5470616</td>
<td align="center">0.5295508</td>
<td align="center">0.0000000</td>
<td align="center">0.5470616</td>
<td align="center">0.5295508</td>
</tr>
</tbody>
</table>
@ -1280,23 +1280,23 @@ classes, use a antibiotic class selector such as
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">53.5%</td>
<td align="right">25.9%</td>
<td align="right">54.3%</td>
<td align="right">26.9%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">54.8%</td>
<td align="right">26.6%</td>
<td align="right">55.9%</td>
<td align="right">26.8%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">54.8%</td>
<td align="right">26.8%</td>
<td align="right">53.5%</td>
<td align="right">25.5%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">53.5%</td>
<td align="right">24.8%</td>
<td align="right">52.4%</td>
<td align="right">25.9%</td>
</tr>
</tbody>
</table>
@ -1412,18 +1412,16 @@ 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] 0.125 2 0.01 &lt;=0.002 &gt;=256 16 16 1 0.01 </span></span>
<span><span class="co"># [10] 0.25 0.01 64 &lt;=0.002 16 128 0.125 0.125 0.0625 </span></span>
<span><span class="co"># [19] 0.005 1 0.125 &gt;=256 16 0.01 0.125 2 0.25 </span></span>
<span><span class="co"># [28] 0.025 &gt;=256 0.01 0.0625 0.125 0.025 64 0.125 4 </span></span>
<span><span class="co"># [37] 32 64 &gt;=256 32 128 32 64 32 0.01 </span></span>
<span><span class="co"># [46] 0.005 0.0625 16 32 4 4 0.0625 0.01 2 </span></span>
<span><span class="co"># [55] 8 64 4 &gt;=256 4 &gt;=256 1 0.005 &lt;=0.002</span></span>
<span><span class="co"># [64] 0.25 4 0.125 1 128 0.125 128 0.25 1 </span></span>
<span><span class="co"># [73] &gt;=256 8 0.025 64 4 2 16 16 32 </span></span>
<span><span class="co"># [82] 0.25 8 4 16 0.005 64 0.0625 0.25 0.125 </span></span>
<span><span class="co"># [91] 0.25 0.0625 0.01 0.125 0.125 0.01 64 0.125 0.005 </span></span>
<span><span class="co"># [100] 32</span></span></code></pre></div>
<span><span class="co"># [1] 0.001 &gt;=256 &gt;=256 0.25 0.25 0.25 0.0625 &gt;=256 0.025 0.25 </span></span>
<span><span class="co"># [11] 64 0.001 4 &gt;=256 0.005 128 0.5 0.005 &gt;=256 64 </span></span>
<span><span class="co"># [21] 0.025 &gt;=256 0.01 &gt;=256 64 8 &gt;=256 4 0.01 4 </span></span>
<span><span class="co"># [31] 0.001 64 0.125 2 0.002 0.002 2 0.125 128 0.5 </span></span>
<span><span class="co"># [41] 16 0.001 1 32 0.125 0.25 0.025 0.025 0.005 128 </span></span>
<span><span class="co"># [51] 0.01 0.125 0.01 128 2 &gt;=256 0.001 &gt;=256 0.25 0.125 </span></span>
<span><span class="co"># [61] 0.125 32 0.25 0.5 8 0.01 4 0.001 1 0.002 </span></span>
<span><span class="co"># [71] 0.002 0.025 0.025 1 4 0.5 0.5 2 64 0.025 </span></span>
<span><span class="co"># [81] 0.025 0.005 0.005 0.5 &gt;=256 64 0.0625 0.5 0.005 1 </span></span>
<span><span class="co"># [91] 4 0.002 0.5 0.01 0.001 0.5 4 16 32 128</span></span></code></pre></div>
<div class="sourceCode" id="cb37"><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>
@ -1457,10 +1455,10 @@ plotting:</p>
<code class="sourceCode R"><span><span class="va">disk_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_disk</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span>
<span><span class="va">disk_values</span></span>
<span><span class="co"># Class 'disk'</span></span>
<span><span class="co"># [1] 22 22 17 17 30 20 21 18 30 22 28 21 18 25 28 19 30 22 22 19 22 29 27 18 31</span></span>
<span><span class="co"># [26] 17 17 27 26 30 23 21 17 23 31 22 27 31 20 18 20 22 23 17 18 20 24 26 21 29</span></span>
<span><span class="co"># [51] 28 31 21 31 23 24 28 31 28 28 23 27 31 18 31 23 22 21 19 21 21 19 31 27 29</span></span>
<span><span class="co"># [76] 20 22 31 17 24 23 27 21 28 21 28 17 31 23 17 25 25 21 31 23 31 18 23 18 19</span></span></code></pre></div>
<span><span class="co"># [1] 30 31 31 26 17 19 19 22 23 25 19 21 29 29 19 19 23 22 28 28 22 28 25 22 21</span></span>
<span><span class="co"># [26] 22 25 24 29 24 19 29 21 25 27 28 20 31 19 21 25 30 22 30 29 23 19 26 23 20</span></span>
<span><span class="co"># [51] 28 24 31 31 22 22 30 30 29 25 24 29 27 24 29 21 17 18 30 19 26 21 18 30 19</span></span>
<span><span class="co"># [76] 28 29 21 25 30 28 31 22 22 27 31 23 30 20 29 23 29 28 31 28 20 26 20 20 25</span></span></code></pre></div>
<div class="sourceCode" id="cb43"><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="">1.8.2.9051</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9052</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

56
articles/MDR.html
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="">1.8.2.9051</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9052</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -375,19 +375,19 @@ names or codes, this would have worked exactly the same way:</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span>
<span><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
<span><span class="co"># 1 S S S I R R</span></span>
<span><span class="co"># 2 I S S S R I</span></span>
<span><span class="co"># 3 S R R I I R</span></span>
<span><span class="co"># 4 I I R I I S</span></span>
<span><span class="co"># 5 R I S S R I</span></span>
<span><span class="co"># 6 I S S S R R</span></span>
<span><span class="co"># 1 S R S I S R</span></span>
<span><span class="co"># 2 R I R S R I</span></span>
<span><span class="co"># 3 S I S R S I</span></span>
<span><span class="co"># 4 I I I I R R</span></span>
<span><span class="co"># 5 S I R S I I</span></span>
<span><span class="co"># 6 R R 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 I</span></span>
<span><span class="co"># 3 S</span></span>
<span><span class="co"># 3 R</span></span>
<span><span class="co"># 4 S</span></span>
<span><span class="co"># 5 S</span></span>
<span><span class="co"># 6 I</span></span></code></pre></div>
<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>
<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">3195</td>
<td align="right">63.90%</td>
<td align="right">3195</td>
<td align="right">63.90%</td>
<td align="right">3220</td>
<td align="right">64.40%</td>
<td align="right">3220</td>
<td align="right">64.40%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">1015</td>
<td align="right">20.30%</td>
<td align="right">4210</td>
<td align="right">84.20%</td>
<td align="right">1018</td>
<td align="right">20.36%</td>
<td align="right">4238</td>
<td align="right">84.76%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">437</td>
<td align="right">8.74%</td>
<td align="right">4647</td>
<td align="right">92.94%</td>
<td align="right">403</td>
<td align="right">8.06%</td>
<td align="right">4641</td>
<td align="right">92.82%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">254</td>
<td align="right">5.08%</td>
<td align="right">4901</td>
<td align="right">98.02%</td>
<td align="right">258</td>
<td align="right">5.16%</td>
<td align="right">4899</td>
<td align="right">97.98%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">99</td>
<td align="right">1.98%</td>
<td align="right">101</td>
<td align="right">2.02%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

2
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<h4 data-toc-skip class="author">Dr. Matthijs
Berends</h4>
<h4 data-toc-skip class="date">14 November 2022</h4>
<h4 data-toc-skip class="date">17 November 2022</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/SPSS.Rmd" class="external-link"><code>vignettes/SPSS.Rmd</code></a></small>
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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">14 November 2022</h4>
<h4 data-toc-skip class="date">17 November 2022</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
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