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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="">1.8.2.9054</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9057</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">29 November 2022</h4>
<h4 data-toc-skip class="date">09 December 2022</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/AMR.Rmd" class="external-link"><code>vignettes/AMR.Rmd</code></a></small>
<div class="d-none name"><code>AMR.Rmd</code></div>
@ -180,7 +180,7 @@ Berends</h4>
website update since they are based on randomly created values and the
page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
Markdown</a>. However, the methodology remains unchanged. This page was
generated on 29 November 2022.</p>
generated on 09 December 2022.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@ -236,21 +236,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2022-11-29</td>
<td align="center">2022-12-09</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">2022-11-29</td>
<td align="center">2022-12-09</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">2022-11-29</td>
<td align="center">2022-12-09</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="28%">
<col width="26%">
<col width="5%">
<col width="5%">
<col width="5%">
<col width="5%">
<col width="8%">
<col width="9%">
</colgroup>
<thead><tr class="header">
<th align="center">date</th>
@ -400,66 +400,66 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2016-02-08</td>
<td align="center">L4</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">2012-06-16</td>
<td align="center">S5</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2011-06-04</td>
<td align="center">B4</td>
<td align="center">Hospital B</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">M</td>
</tr>
<tr class="odd">
<td align="center">2010-12-27</td>
<td align="center">U10</td>
<td align="center">Hospital B</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2013-08-11</td>
<td align="center">H1</td>
<td align="center">Hospital C</td>
<td align="center">2012-08-31</td>
<td align="center">Q2</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="odd">
<td align="center">2012-08-17</td>
<td align="center">S9</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">R</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2011-04-20</td>
<td align="center">M7</td>
<td align="center">Hospital B</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2011-08-27</td>
<td align="center">M9</td>
<td align="center">Hospital B</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">2016-10-02</td>
<td align="center">Z1</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2015-04-24</td>
<td align="center">L8</td>
<td align="center">Hospital C</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">R</td>
<td align="center">2017-10-05</td>
<td align="center">L10</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>
@ -499,18 +499,18 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,441</td>
<td align="right">52.21%</td>
<td align="right">10,441</td>
<td align="right">52.21%</td>
<td align="right">10,540</td>
<td align="right">52.7%</td>
<td align="right">10,540</td>
<td align="right">52.7%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,559</td>
<td align="right">47.80%</td>
<td align="right">9,460</td>
<td align="right">47.3%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
<td align="right">100.0%</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 10,709 'phenotype-based' first isolates (53.5% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,641 'phenotype-based' first isolates (53.2% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 53.5% is suitable for resistance analysis! We can now filter
<p>So only 53.2% is suitable for resistance analysis! We can now filter
on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the
<code>dplyr</code> package:</p>
<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
@ -634,11 +634,11 @@ on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html"
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="co"># Including isolates from ICU.</span></span></code></pre></div>
<p>So we end up with 10,709 isolates for analysis. Now our data looks
<p>So we end up with 10,641 isolates for analysis. Now our data looks
like:</p>
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">data_1st</span><span class="op">)</span></span></code></pre></div>
<table style="width:100%;" class="table">
<table class="table">
<colgroup>
<col width="2%">
<col width="9%">
@ -652,7 +652,7 @@ like:</p>
<col width="6%">
<col width="11%">
<col width="12%">
<col width="9%">
<col width="7%">
<col width="5%">
</colgroup>
<thead><tr class="header">
@ -673,58 +673,58 @@ like:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">3</td>
<td align="center">2010-12-27</td>
<td align="center">U10</td>
<td align="left">1</td>
<td align="center">2012-06-16</td>
<td align="center">S5</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</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-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="center">2012-08-31</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">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-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="center">2013-08-11</td>
<td align="center">H1</td>
<td align="center">Hospital C</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="center">2016-10-02</td>
<td align="center">Z1</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">7</td>
<td align="center">2013-10-25</td>
<td align="center">I3</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</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">9</td>
<td align="center">2011-08-23</td>
<td align="center">Y10</td>
<td align="center">Hospital A</td>
<td align="center">2017-06-29</td>
<td align="center">S6</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
@ -737,28 +737,12 @@ like:</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">11</td>
<td align="center">2012-08-03</td>
<td align="center">U10</td>
<td align="center">Hospital A</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">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">12</td>
<td align="center">2013-12-31</td>
<td align="center">L3</td>
<td align="center">Hospital A</td>
<td align="left">8</td>
<td align="center">2014-10-17</td>
<td align="center">G10</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
@ -768,6 +752,22 @@ like:</p>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">10</td>
<td align="center">2011-04-23</td>
<td align="center">V8</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">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>
</tbody>
</table>
<p>Time for the analysis!</p>
@ -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: 10,709<br>
Available: 10,709 (100%, NA: 0 = 0%)<br>
Length: 10,641<br>
Available: 10,641 (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">4,635</td>
<td align="right">43.28%</td>
<td align="right">4,635</td>
<td align="right">43.28%</td>
<td align="right">4,597</td>
<td align="right">43.20%</td>
<td align="right">4,597</td>
<td align="right">43.20%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,757</td>
<td align="right">25.74%</td>
<td align="right">7,392</td>
<td align="right">69.03%</td>
<td align="right">2,714</td>
<td align="right">25.51%</td>
<td align="right">7,311</td>
<td align="right">68.71%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,115</td>
<td align="right">19.75%</td>
<td align="right">9,507</td>
<td align="right">88.78%</td>
<td align="right">2,148</td>
<td align="right">20.19%</td>
<td align="right">9,459</td>
<td align="right">88.89%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,202</td>
<td align="right">11.22%</td>
<td align="right">10,709</td>
<td align="right">1,182</td>
<td align="right">11.11%</td>
<td align="right">10,641</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="11%">
<col width="10%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="6%">
<col width="11%">
<col width="11%">
<col width="12%">
<col width="9%">
<col width="5%">
</colgroup>
@ -902,24 +902,9 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2014-06-23</td>
<td align="center">T5</td>
<td align="center">2011-04-23</td>
<td align="center">V8</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">2016-09-29</td>
<td align="center">N9</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -931,14 +916,14 @@ antibiotic class they are in:</p>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2011-01-04</td>
<td align="center">E8</td>
<td align="center">Hospital B</td>
<tr class="even">
<td align="center">2010-11-09</td>
<td align="center">A10</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
@ -946,13 +931,28 @@ antibiotic class they are in:</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2017-01-15</td>
<td align="center">C6</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">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">TRUE</td>
</tr>
<tr class="even">
<td align="center">2017-12-28</td>
<td align="center">Z5</td>
<td align="center">Hospital C</td>
<td align="center">2014-07-20</td>
<td align="center">X1</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">F</td>
@ -962,24 +962,24 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2010-08-11</td>
<td align="center">C6</td>
<td align="center">2010-05-23</td>
<td align="center">T8</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</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">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">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2012-08-24</td>
<td align="center">Z9</td>
<td align="center">Hospital A</td>
<td align="center">2014-12-22</td>
<td align="center">T5</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
@ -1013,50 +1013,50 @@ different bug/drug combinations, you can use the
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">2204</td>
<td align="center">121</td>
<td align="center">2310</td>
<td align="center">4635</td>
<td align="center">2172</td>
<td align="center">140</td>
<td align="center">2285</td>
<td align="center">4597</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3389</td>
<td align="center">150</td>
<td align="center">1096</td>
<td align="center">4635</td>
<td align="center">3386</td>
<td align="center">145</td>
<td align="center">1066</td>
<td align="center">4597</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3408</td>
<td align="center">3365</td>
<td align="center">0</td>
<td align="center">1227</td>
<td align="center">4635</td>
<td align="center">1232</td>
<td align="center">4597</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4065</td>
<td align="center">4016</td>
<td align="center">0</td>
<td align="center">570</td>
<td align="center">4635</td>
<td align="center">581</td>
<td align="center">4597</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">1202</td>
<td align="center">1202</td>
<td align="center">1182</td>
<td align="center">1182</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">927</td>
<td align="center">50</td>
<td align="center">225</td>
<td align="center">1202</td>
<td align="center">952</td>
<td align="center">45</td>
<td align="center">185</td>
<td align="center">1182</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">4065</td>
<td align="center">4016</td>
<td align="center">0</td>
<td align="center">570</td>
<td align="center">4635</td>
<td align="center">581</td>
<td align="center">4597</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1095</td>
<td align="center">1072</td>
<td align="center">0</td>
<td align="center">107</td>
<td align="center">1202</td>
<td align="center">110</td>
<td align="center">1182</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2408</td>
<td align="center">2418</td>
<td align="center">0</td>
<td align="center">349</td>
<td align="center">2757</td>
<td align="center">296</td>
<td align="center">2714</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">2115</td>
<td align="center">2115</td>
<td align="center">2148</td>
<td align="center">2148</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] 0.5429078</span></span></code></pre></div>
<span><span class="co"># [1] 0.5409266</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">0.5461974</td>
<td align="center">0.5447103</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5343758</td>
<td align="center">0.5458963</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5487149</td>
<td align="center">0.5324921</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5482517</td>
<td align="center">0.5330882</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">0.5461974</td>
<td align="center">3182</td>
<td align="center">0.5447103</td>
<td align="center">3176</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5343758</td>
<td align="center">3709</td>
<td align="center">0.5458963</td>
<td align="center">3704</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5487149</td>
<td align="center">1673</td>
<td align="center">0.5324921</td>
<td align="center">1585</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5482517</td>
<td align="center">2145</td>
<td align="center">0.5330882</td>
<td align="center">2176</td>
</tr>
</tbody>
</table>
@ -1230,27 +1230,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7635383</td>
<td align="center">0.8770227</td>
<td align="center">0.9766990</td>
<td align="center">0.7681096</td>
<td align="center">0.8736132</td>
<td align="center">0.9769415</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8128120</td>
<td align="center">0.9109817</td>
<td align="center">0.9833611</td>
<td align="center">0.8434856</td>
<td align="center">0.9069374</td>
<td align="center">0.9780034</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7972434</td>
<td align="center">0.8734131</td>
<td align="center">0.9818643</td>
<td align="center">0.8043478</td>
<td align="center">0.8909359</td>
<td align="center">0.9837878</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5399527</td>
<td align="center">0.5474860</td>
<td align="center">0.0000000</td>
<td align="center">0.5399527</td>
<td align="center">0.5474860</td>
</tr>
</tbody>
</table>
@ -1278,23 +1278,23 @@ classes, use a antibiotic class selector such as
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">54.6%</td>
<td align="right">27.7%</td>
<td align="right">54.5%</td>
<td align="right">25.0%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">53.4%</td>
<td align="right">26.4%</td>
<td align="right">54.6%</td>
<td align="right">26.7%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">54.9%</td>
<td align="right">25.2%</td>
<td align="right">53.2%</td>
<td align="right">26.2%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">54.8%</td>
<td align="right">26.7%</td>
<td align="right">53.3%</td>
<td align="right">25.5%</td>
</tr>
</tbody>
</table>
@ -1410,16 +1410,18 @@ classes) <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code>:</p>
<code class="sourceCode R"><span><span class="va">mic_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span></span>
<span><span class="va">mic_values</span></span>
<span><span class="co"># Class 'mic'</span></span>
<span><span class="co"># [1] 8 64 2 1 0.002 128 0.01 0.25 2 0.125 </span></span>
<span><span class="co"># [11] 16 0.01 256 4 64 2 0.002 256 0.01 8 </span></span>
<span><span class="co"># [21] 0.025 0.025 16 0.025 8 1 128 0.125 4 0.001 </span></span>
<span><span class="co"># [31] 4 256 4 1 0.01 0.025 1 0.001 0.002 2 </span></span>
<span><span class="co"># [41] 0.001 2 0.01 128 0.01 1 16 0.5 64 0.0625</span></span>
<span><span class="co"># [51] 8 0.005 16 32 128 4 0.01 32 0.025 0.005 </span></span>
<span><span class="co"># [61] 32 0.01 0.125 256 32 16 8 0.025 4 1 </span></span>
<span><span class="co"># [71] 16 16 0.125 0.002 16 32 0.5 0.0625 256 2 </span></span>
<span><span class="co"># [81] 0.005 0.01 1 0.005 0.125 0.0625 0.001 0.025 4 0.01 </span></span>
<span><span class="co"># [91] 2 1 0.025 256 0.0625 0.001 0.125 0.005 0.0625 0.001</span></span></code></pre></div>
<span><span class="co"># [1] &gt;=256 &lt;=0.001 16 0.25 4 0.025 128 16 &gt;=256 </span></span>
<span><span class="co"># [10] 0.005 0.25 1 1 64 8 0.002 0.5 64 </span></span>
<span><span class="co"># [19] &gt;=256 0.25 0.5 0.005 0.025 0.25 8 2 0.01 </span></span>
<span><span class="co"># [28] 0.002 0.025 0.5 64 4 2 64 2 1 </span></span>
<span><span class="co"># [37] &lt;=0.001 128 0.25 0.0625 64 8 1 64 64 </span></span>
<span><span class="co"># [46] 0.5 &gt;=256 0.01 2 16 4 0.002 0.005 32 </span></span>
<span><span class="co"># [55] 16 32 0.0625 4 8 0.125 8 0.01 64 </span></span>
<span><span class="co"># [64] 8 0.005 0.025 0.5 2 16 0.25 1 &lt;=0.001</span></span>
<span><span class="co"># [73] 0.005 0.0625 0.01 0.0625 0.25 32 0.5 0.005 0.5 </span></span>
<span><span class="co"># [82] 0.005 4 0.002 4 &lt;=0.001 8 &lt;=0.001 0.01 0.125 </span></span>
<span><span class="co"># [91] 0.005 0.25 16 0.01 0.01 &gt;=256 0.01 0.025 0.5 </span></span>
<span><span class="co"># [100] &lt;=0.001</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 +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] 31 26 18 31 23 20 17 17 28 29 27 20 23 19 19 24 23 29 20 17 24 26 31 21 20</span></span>
<span><span class="co"># [26] 26 19 20 18 31 18 17 31 19 26 20 19 27 20 22 17 25 24 29 19 24 28 25 20 22</span></span>
<span><span class="co"># [51] 30 23 18 28 29 22 18 23 30 18 18 22 24 29 26 23 31 31 21 20 31 21 26 23 25</span></span>
<span><span class="co"># [76] 23 26 25 29 22 26 18 23 29 26 31 25 17 30 23 21 28 31 26 30 29 29 25 28 27</span></span></code></pre></div>
<span><span class="co"># [1] 30 28 18 29 30 23 29 25 25 24 19 22 18 23 27 21 27 21 25 30 23 31 25 27 26</span></span>
<span><span class="co"># [26] 26 29 23 22 24 18 29 27 24 17 25 23 22 20 28 27 21 31 21 25 25 27 23 23 18</span></span>
<span><span class="co"># [51] 31 31 31 31 24 27 26 31 26 27 27 26 20 26 26 28 24 26 19 25 21 27 19 31 21</span></span>
<span><span class="co"># [76] 18 26 30 23 28 28 27 31 21 17 28 28 22 21 26 23 26 28 27 31 29 30 28 23 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="">1.8.2.9054</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9057</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="">1.8.2.9054</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9057</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 R R S I R I</span></span>
<span><span class="co"># 2 S I I R I I</span></span>
<span><span class="co"># 3 I R S R R I</span></span>
<span><span class="co"># 4 R R R R R S</span></span>
<span><span class="co"># 5 R I I I I R</span></span>
<span><span class="co"># 6 S S S I S S</span></span>
<span><span class="co"># 1 R R S R I I</span></span>
<span><span class="co"># 2 R S S S I S</span></span>
<span><span class="co"># 3 R S R I S S</span></span>
<span><span class="co"># 4 R S S I I R</span></span>
<span><span class="co"># 5 S R R I I I</span></span>
<span><span class="co"># 6 S I I R R S</span></span>
<span><span class="co"># kanamycin</span></span>
<span><span class="co"># 1 R</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 S</span></span>
<span><span class="co"># 3 R</span></span>
<span><span class="co"># 4 R</span></span>
<span><span class="co"># 5 I</span></span>
<span><span class="co"># 6 I</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">3210</td>
<td align="right">64.20%</td>
<td align="right">3210</td>
<td align="right">64.20%</td>
<td align="right">3254</td>
<td align="right">65.08%</td>
<td align="right">3254</td>
<td align="right">65.08%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">1010</td>
<td align="right">20.20%</td>
<td align="right">4220</td>
<td align="right">84.40%</td>
<td align="right">960</td>
<td align="right">19.20%</td>
<td align="right">4214</td>
<td align="right">84.28%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">451</td>
<td align="right">9.02%</td>
<td align="right">4671</td>
<td align="right">93.42%</td>
<td align="right">443</td>
<td align="right">8.86%</td>
<td align="right">4657</td>
<td align="right">93.14%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">235</td>
<td align="right">4.70%</td>
<td align="right">4906</td>
<td align="right">98.12%</td>
<td align="right">240</td>
<td align="right">4.80%</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">94</td>
<td align="right">1.88%</td>
<td align="right">103</td>
<td align="right">2.06%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

4
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="">1.8.2.9054</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9057</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">
@ -280,7 +280,7 @@ function:</p>
<span><span class="co"># [1] "Caryophanales" "Enterobacterales" "Lactobacillales" "Pseudomonadales"</span></span>
<span><span class="co"># Importance of components:</span></span>
<span><span class="co"># PC1 PC2 PC3 PC4 PC5 PC6 PC7</span></span>
<span><span class="co"># Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 5.121e-17</span></span>
<span><span class="co"># Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 9.577e-17</span></span>
<span><span class="co"># Proportion of Variance 0.5799 0.3531 0.0471 0.01435 0.00541 0.00012 0.000e+00</span></span>
<span><span class="co"># Cumulative Proportion 0.5799 0.9330 0.9801 0.99446 0.99988 1.00000 1.000e+00</span></span></code></pre></div>
<pre><code><span><span class="co"># Groups (n=4, named as 'order'):</span></span>

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<h4 data-toc-skip class="author">Dr. Matthijs
Berends</h4>
<h4 data-toc-skip class="date">29 November 2022</h4>
<h4 data-toc-skip class="date">09 December 2022</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/SPSS.Rmd" class="external-link"><code>vignettes/SPSS.Rmd</code></a></small>
<div class="d-none name"><code>SPSS.Rmd</code></div>
@ -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">472,394
online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">473,435
R-related questions</a> have already been asked on this platform (that
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<h4 data-toc-skip class="date">29 November 2022</h4>
<h4 data-toc-skip class="date">09 December 2022</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
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