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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="">1.8.2.9046</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9047</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">
@ -163,7 +163,7 @@
<h4 data-toc-skip class="author">Dr. Matthijs
Berends</h4>
<h4 data-toc-skip class="date">10 November 2022</h4>
<h4 data-toc-skip class="date">12 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>
@ -175,7 +175,7 @@ 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 10 November 2022.</p>
generated on 12 November 2022.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@ -231,21 +231,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2022-11-10</td>
<td align="center">2022-11-12</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="center">2022-11-10</td>
<td align="center">2022-11-12</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<tr class="odd">
<td align="center">2022-11-10</td>
<td align="center">2022-11-12</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -375,12 +375,12 @@ 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>
@ -395,66 +395,66 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2014-05-09</td>
<td align="center">P10</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">2012-12-23</td>
<td align="center">H10</td>
<td align="center">Hospital D</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</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">2011-01-22</td>
<td align="center">L6</td>
<td align="center">2017-08-16</td>
<td align="center">S1</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">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">R</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2013-03-14</td>
<td align="center">C1</td>
<td align="center">2014-12-04</td>
<td align="center">J1</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">I</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">2012-07-02</td>
<td align="center">K8</td>
<td align="center">Hospital D</td>
<td align="center">Streptococcus 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">2012-07-21</td>
<td align="center">R6</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">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2011-02-12</td>
<td align="center">U4</td>
<td align="center">Hospital B</td>
<td align="center">2012-11-26</td>
<td align="center">K8</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</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">2011-07-23</td>
<td align="center">Z2</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia 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>
</tr>
<tr class="even">
<td align="center">2016-05-31</td>
<td align="center">S7</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>
@ -494,16 +494,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,478</td>
<td align="right">52.39%</td>
<td align="right">10,478</td>
<td align="right">52.39%</td>
<td align="right">10,563</td>
<td align="right">52.82%</td>
<td align="right">10,563</td>
<td align="right">52.82%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,522</td>
<td align="right">47.61%</td>
<td align="right">9,437</td>
<td align="right">47.19%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -616,9 +616,9 @@ 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 10,664 'phenotype-based' first isolates (53.3% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,633 'phenotype-based' first isolates (53.2% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 53.3% 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">
@ -629,11 +629,11 @@ 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 10,664 isolates for analysis. Now our data looks
<p>So we end up with 10,633 isolates for analysis. Now our data looks
like:</p>
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">data_1st</span><span class="op">)</span></span></code></pre></div>
<table style="width:100%;" class="table">
<table class="table">
<colgroup>
<col width="2%">
<col width="9%">
@ -647,7 +647,7 @@ 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">
@ -668,29 +668,29 @@ like:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">5</td>
<td align="center">2012-07-02</td>
<td align="center">K8</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="left">3</td>
<td align="center">2012-07-21</td>
<td align="center">R6</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">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">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">8</td>
<td align="center">2012-03-12</td>
<td align="center">K1</td>
<td align="center">Hospital B</td>
<td align="left">4</td>
<td align="center">2012-11-26</td>
<td align="center">K8</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
@ -700,15 +700,15 @@ like:</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">9</td>
<td align="center">2012-02-20</td>
<td align="center">U3</td>
<td align="left">5</td>
<td align="center">2011-07-23</td>
<td align="center">Z2</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">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>
@ -716,51 +716,51 @@ like:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">10</td>
<td align="center">2016-05-10</td>
<td align="center">O8</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</td>
<td align="left">6</td>
<td align="center">2016-05-31</td>
<td align="center">S7</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-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">11</td>
<td align="center">2015-12-30</td>
<td align="center">W3</td>
<td align="center">Hospital D</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">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">7</td>
<td align="center">2011-07-29</td>
<td align="center">C9</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">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">13</td>
<td align="center">2010-05-02</td>
<td align="center">L5</td>
<td align="left">14</td>
<td align="center">2016-07-22</td>
<td align="center">N8</td>
<td align="center">Hospital D</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">B_ESCHR_COLI</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">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>
</tbody>
@ -796,8 +796,8 @@ 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: 10,664<br>
Available: 10,664 (100%, NA: 0 = 0%)<br>
Length: 10,633<br>
Available: 10,633 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -822,33 +822,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">4,611</td>
<td align="right">43.24%</td>
<td align="right">4,611</td>
<td align="right">43.24%</td>
<td align="right">4,624</td>
<td align="right">43.49%</td>
<td align="right">4,624</td>
<td align="right">43.49%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,676</td>
<td align="right">25.09%</td>
<td align="right">7,287</td>
<td align="right">68.33%</td>
<td align="right">2,730</td>
<td align="right">25.67%</td>
<td align="right">7,354</td>
<td align="right">69.16%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,152</td>
<td align="right">20.18%</td>
<td align="right">9,439</td>
<td align="right">88.51%</td>
<td align="right">2,082</td>
<td align="right">19.58%</td>
<td align="right">9,436</td>
<td align="right">88.74%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,225</td>
<td align="right">11.49%</td>
<td align="right">10,664</td>
<td align="right">1,197</td>
<td align="right">11.26%</td>
<td align="right">10,633</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -897,83 +897,8 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2012-07-02</td>
<td align="center">K8</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">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">2012-02-20</td>
<td align="center">U3</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>
<tr class="odd">
<td align="center">2016-05-10</td>
<td align="center">O8</td>
<td align="center">Hospital C</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">2010-05-02</td>
<td align="center">L5</td>
<td align="center">Hospital D</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="odd">
<td align="center">2012-09-16</td>
<td align="center">J7</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">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">2017-10-31</td>
<td align="center">U5</td>
<td align="center">2012-12-19</td>
<td align="center">S3</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
@ -986,6 +911,81 @@ antibiotic class they are in:</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2013-04-29</td>
<td align="center">E8</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">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="odd">
<td align="center">2014-11-08</td>
<td align="center">R2</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">2012-09-13</td>
<td align="center">W3</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">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">2017-11-23</td>
<td align="center">F9</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">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">2014-07-26</td>
<td align="center">R5</td>
<td align="center">Hospital C</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">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
<p>If you want to get a quick glance of the number of isolates in
@ -1009,50 +1009,50 @@ 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">2188</td>
<td align="center">122</td>
<td align="center">2301</td>
<td align="center">4611</td>
<td align="center">2175</td>
<td align="center">124</td>
<td align="center">2325</td>
<td align="center">4624</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3364</td>
<td align="center">162</td>
<td align="center">1085</td>
<td align="center">4611</td>
<td align="center">3402</td>
<td align="center">145</td>
<td align="center">1077</td>
<td align="center">4624</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3385</td>
<td align="center">0</td>
<td align="center">1226</td>
<td align="center">4611</td>
<td align="center">1239</td>
<td align="center">4624</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4060</td>
<td align="center">4046</td>
<td align="center">0</td>
<td align="center">551</td>
<td align="center">4611</td>
<td align="center">578</td>
<td align="center">4624</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">1225</td>
<td align="center">1225</td>
<td align="center">1197</td>
<td align="center">1197</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">916</td>
<td align="center">69</td>
<td align="center">240</td>
<td align="center">1225</td>
<td align="center">922</td>
<td align="center">67</td>
<td align="center">208</td>
<td align="center">1197</td>
</tr>
</tbody>
</table>
@ -1075,34 +1075,34 @@ 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">4060</td>
<td align="center">4046</td>
<td align="center">0</td>
<td align="center">551</td>
<td align="center">4611</td>
<td align="center">578</td>
<td align="center">4624</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1095</td>
<td align="center">1060</td>
<td align="center">0</td>
<td align="center">130</td>
<td align="center">1225</td>
<td align="center">137</td>
<td align="center">1197</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2375</td>
<td align="center">2411</td>
<td align="center">0</td>
<td align="center">301</td>
<td align="center">2676</td>
<td align="center">319</td>
<td align="center">2730</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">2152</td>
<td align="center">2152</td>
<td align="center">2082</td>
<td align="center">2082</td>
</tr>
</tbody>
</table>
@ -1134,7 +1134,7 @@ 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] 0.5425731</span></span></code></pre></div>
<span><span class="co"># [1] 0.5444371</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">
@ -1149,19 +1149,19 @@ own:</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5365469</td>
<td align="center">0.5425466</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5426068</td>
<td align="center">0.5360493</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5511222</td>
<td align="center">0.5492327</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5450684</td>
<td align="center">0.5585458</td>
</tr>
</tbody>
</table>
@ -1186,23 +1186,23 @@ 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">0.5365469</td>
<td align="center">3174</td>
<td align="center">0.5425466</td>
<td align="center">3220</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5426068</td>
<td align="center">3767</td>
<td align="center">0.5360493</td>
<td align="center">3731</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5511222</td>
<td align="center">1604</td>
<td align="center">0.5492327</td>
<td align="center">1564</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5450684</td>
<td align="center">2119</td>
<td align="center">0.5585458</td>
<td align="center">2118</td>
</tr>
</tbody>
</table>
@ -1227,27 +1227,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7646931</td>
<td align="center">0.8805031</td>
<td align="center">0.9750596</td>
<td align="center">0.7670848</td>
<td align="center">0.8750000</td>
<td align="center">0.9764273</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8040816</td>
<td align="center">0.8938776</td>
<td align="center">0.9779592</td>
<td align="center">0.8262322</td>
<td align="center">0.8855472</td>
<td align="center">0.9791145</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7997010</td>
<td align="center">0.8875187</td>
<td align="center">0.9824365</td>
<td align="center">0.7908425</td>
<td align="center">0.8831502</td>
<td align="center">0.9754579</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5473978</td>
<td align="center">0.5317003</td>
<td align="center">0.0000000</td>
<td align="center">0.5473978</td>
<td align="center">0.5317003</td>
</tr>
</tbody>
</table>
@ -1275,23 +1275,23 @@ classes, use a antibiotic class selector such as
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">53.7%</td>
<td align="right">25.7%</td>
<td align="right">54.3%</td>
<td align="right">25.2%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">54.3%</td>
<td align="right">27.0%</td>
<td align="right">53.6%</td>
<td align="right">26.7%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">55.1%</td>
<td align="right">27.6%</td>
<td align="right">54.9%</td>
<td align="right">25.9%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">54.5%</td>
<td align="right">26.4%</td>
<td align="right">55.9%</td>
<td align="right">29.3%</td>
</tr>
</tbody>
</table>
@ -1407,18 +1407,16 @@ 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] 2 &lt;=0.001 4 8 16 0.5 &gt;=256 0.002 2 </span></span>
<span><span class="co"># [10] 0.0625 &lt;=0.001 0.025 0.002 0.002 0.005 0.5 32 2 </span></span>
<span><span class="co"># [19] 4 0.0625 0.5 0.125 32 8 &gt;=256 &lt;=0.001 0.0625 </span></span>
<span><span class="co"># [28] 1 0.025 0.01 0.25 64 4 4 0.01 0.002 </span></span>
<span><span class="co"># [37] 0.025 0.25 128 8 2 0.005 64 1 &gt;=256 </span></span>
<span><span class="co"># [46] 0.002 0.25 0.25 16 0.005 0.0625 64 128 1 </span></span>
<span><span class="co"># [55] 0.002 2 8 &gt;=256 0.5 8 0.005 4 32 </span></span>
<span><span class="co"># [64] 0.025 0.25 4 2 4 0.125 0.025 32 0.005 </span></span>
<span><span class="co"># [73] 8 0.25 &gt;=256 4 128 1 8 64 2 </span></span>
<span><span class="co"># [82] 64 128 8 0.5 0.0625 0.025 0.01 0.01 64 </span></span>
<span><span class="co"># [91] 1 0.01 8 32 1 2 64 0.0625 0.125 </span></span>
<span><span class="co"># [100] 64</span></span></code></pre></div>
<span><span class="co"># [1] 0.001 0.5 0.002 4 0.025 8 4 32 0.025 32 </span></span>
<span><span class="co"># [11] &gt;=256 0.001 0.5 0.5 0.002 0.002 0.025 16 1 0.025 </span></span>
<span><span class="co"># [21] &gt;=256 0.0625 0.002 0.5 0.0625 4 1 0.001 16 &gt;=256 </span></span>
<span><span class="co"># [31] 0.005 0.002 0.002 &gt;=256 0.005 0.025 0.5 8 0.125 0.125 </span></span>
<span><span class="co"># [41] 0.005 0.005 &gt;=256 4 0.005 0.001 0.025 0.01 0.01 128 </span></span>
<span><span class="co"># [51] 0.001 0.5 0.005 32 64 8 0.005 8 0.001 32 </span></span>
<span><span class="co"># [61] 0.5 128 0.001 2 32 0.125 16 16 8 0.002 </span></span>
<span><span class="co"># [71] 0.25 4 0.25 128 0.002 0.5 0.25 0.025 0.025 4 </span></span>
<span><span class="co"># [81] &gt;=256 8 0.002 1 0.001 64 0.25 0.5 0.005 16 </span></span>
<span><span class="co"># [91] 0.025 0.25 0.025 1 2 2 &gt;=256 1 0.5 0.125</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>
@ -1452,10 +1450,10 @@ 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] 29 17 24 23 25 21 17 17 25 27 20 28 25 24 27 31 24 26 22 17 30 31 28 17 31</span></span>
<span><span class="co"># [26] 17 31 30 26 27 27 25 26 20 27 26 22 23 27 25 25 29 17 23 21 28 25 19 27 26</span></span>
<span><span class="co"># [51] 17 22 30 31 17 18 29 31 30 25 17 18 27 18 26 28 19 30 30 18 26 31 19 29 23</span></span>
<span><span class="co"># [76] 27 17 23 19 21 29 17 24 19 31 22 21 28 18 20 24 30 26 28 20 23 17 30 19 22</span></span></code></pre></div>
<span><span class="co"># [1] 30 31 30 24 26 25 23 24 17 22 30 27 20 19 24 21 21 20 21 26 22 24 18 30 17</span></span>
<span><span class="co"># [26] 28 30 22 27 27 31 19 24 27 23 18 30 21 20 18 19 21 26 18 18 20 17 27 30 25</span></span>
<span><span class="co"># [51] 31 21 23 23 27 19 24 30 25 22 31 19 26 26 24 27 19 17 25 20 28 28 26 24 19</span></span>
<span><span class="co"># [76] 22 18 30 23 27 27 21 28 21 24 23 17 23 20 24 31 17 21 17 19 26 18 29 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="">1.8.2.9046</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9047</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="">1.8.2.9046</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9047</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">
@ -370,18 +370,18 @@ names or codes, this would have worked exactly the same way:</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span>
<span><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
<span><span class="co"># 1 S R I S I R</span></span>
<span><span class="co"># 2 I I R R I R</span></span>
<span><span class="co"># 3 S R S I I R</span></span>
<span><span class="co"># 4 R S S R S R</span></span>
<span><span class="co"># 5 R S S S S I</span></span>
<span><span class="co"># 6 S R R I S I</span></span>
<span><span class="co"># 1 R S R S R R</span></span>
<span><span class="co"># 2 R I R R R I</span></span>
<span><span class="co"># 3 I R S I S R</span></span>
<span><span class="co"># 4 I I I R I S</span></span>
<span><span class="co"># 5 R R S R I S</span></span>
<span><span class="co"># 6 S S R R R I</span></span>
<span><span class="co"># kanamycin</span></span>
<span><span class="co"># 1 I</span></span>
<span><span class="co"># 2 S</span></span>
<span><span class="co"># 3 R</span></span>
<span><span class="co"># 4 I</span></span>
<span><span class="co"># 5 R</span></span>
<span><span class="co"># 3 S</span></span>
<span><span class="co"># 4 S</span></span>
<span><span class="co"># 5 S</span></span>
<span><span class="co"># 6 R</span></span></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can
use:</p>
@ -423,40 +423,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3247</td>
<td align="right">64.94%</td>
<td align="right">3247</td>
<td align="right">64.94%</td>
<td align="right">3231</td>
<td align="right">64.62%</td>
<td align="right">3231</td>
<td align="right">64.62%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">946</td>
<td align="right">18.92%</td>
<td align="right">4193</td>
<td align="right">83.86%</td>
<td align="right">961</td>
<td align="right">19.22%</td>
<td align="right">4192</td>
<td align="right">83.84%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">434</td>
<td align="right">8.68%</td>
<td align="right">4627</td>
<td align="right">92.54%</td>
<td align="right">445</td>
<td align="right">8.90%</td>
<td align="right">4637</td>
<td align="right">92.74%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">270</td>
<td align="right">5.40%</td>
<td align="right">4897</td>
<td align="right">97.94%</td>
<td align="right">250</td>
<td align="right">5.00%</td>
<td align="right">4887</td>
<td align="right">97.74%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">103</td>
<td align="right">2.06%</td>
<td align="right">113</td>
<td align="right">2.26%</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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@ -38,7 +38,7 @@
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@ -163,7 +163,7 @@
<h4 data-toc-skip class="author">Dr. Matthijs
Berends</h4>
<h4 data-toc-skip class="date">10 November 2022</h4>
<h4 data-toc-skip class="date">12 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>
<div class="d-none name"><code>SPSS.Rmd</code></div>

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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9046</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">10 November 2022</h4>
<h4 data-toc-skip class="date">12 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>
<div class="d-none name"><code>datasets.Rmd</code></div>
@ -191,7 +191,7 @@ column names:<br><em>mo</em>, <em>fullname</em>, <em>status</em>, <em>kingdom</e
<em>gbif_renamed_to</em>, <em>prevalence</em> and <em>snomed</em>.</p>
<p>This data set is in R available as <code>microorganisms</code>, after
you load the <code>AMR</code> package.</p>
<p>It was last updated on 10 November 2022 21:10:16 UTC. Find more info
<p>It was last updated on 12 November 2022 08:46:26 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
@ -490,7 +490,7 @@ column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>a
<em>iv_ddd</em>, <em>iv_units</em> and <em>loinc</em>.</p>
<p>This data set is in R available as <code>antibiotics</code>, after
you load the <code>AMR</code> package.</p>
<p>It was last updated on 10 November 2022 21:10:16 UTC. Find more info
<p>It was last updated on 12 November 2022 08:46:26 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
@ -687,7 +687,7 @@ column names:<br><em>atc</em>, <em>cid</em>, <em>name</em>, <em>atc_group</em>,
<em>iv_ddd</em> and <em>iv_units</em>.</p>
<p>This data set is in R available as <code>antivirals</code>, after you
load the <code>AMR</code> package.</p>
<p>It was last updated on 10 November 2022 21:10:16 UTC. Find more info
<p>It was last updated on 12 November 2022 08:46:26 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
@ -847,7 +847,7 @@ column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>
<em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
<p>This data set is in R available as <code>rsi_translation</code>,
after you load the <code>AMR</code> package.</p>
<p>It was last updated on 10 November 2022 21:10:16 UTC. Find more info
<p>It was last updated on 12 November 2022 08:46:26 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
@ -1020,7 +1020,7 @@ Resistance<a class="anchor" aria-label="anchor" href="#intrinsic_resistant-intri
column names:<br><em>mo</em> and <em>ab</em>.</p>
<p>This data set is in R available as <code>intrinsic_resistant</code>,
after you load the <code>AMR</code> package.</p>
<p>It was last updated on 10 November 2022 21:10:16 UTC. Find more info
<p>It was last updated on 12 November 2022 08:46:26 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
@ -1308,7 +1308,7 @@ column names:<br><em>ab</em>, <em>name</em>, <em>type</em>, <em>dose</em>,
<em>original_txt</em> and <em>eucast_version</em>.</p>
<p>This data set is in R available as <code>dosage</code>, after you
load the <code>AMR</code> package.</p>
<p>It was last updated on 10 November 2022 21:10:16 UTC. Find more info
<p>It was last updated on 12 November 2022 08:46:26 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
@ -1458,7 +1458,7 @@ column names:<br><em>date</em>, <em>patient</em>, <em>age</em>, <em>gender</em>,
<em>MUP</em> and <em>RIF</em>.</p>
<p>This data set is in R available as <code>example_isolates</code>,
after you load the <code>AMR</code> package.</p>
<p>It was last updated on 10 November 2022 21:10:16 UTC. Find more info
<p>It was last updated on 12 November 2022 08:46:26 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates.html">here</a>.</p>
<div class="section level3">
<h3 id="source-6">Source<a class="anchor" aria-label="anchor" href="#source-6"></a>
@ -1871,7 +1871,7 @@ column names:<br><em>patient_id</em>, <em>hospital</em>, <em>date</em>,
<p>This data set is in R available as
<code>example_isolates_unclean</code>, after you load the
<code>AMR</code> package.</p>
<p>It was last updated on 10 November 2022 21:10:16 UTC. Find more info
<p>It was last updated on 12 November 2022 08:46:26 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates_unclean.html">here</a>.</p>
<div class="section level3">
<h3 id="source-7">Source<a class="anchor" aria-label="anchor" href="#source-7"></a>

2
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