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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="">1.8.2.9086</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9088</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">06 January 2023</h4>
<h4 data-toc-skip class="date">07 January 2023</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/AMR.Rmd" class="external-link"><code>vignettes/AMR.Rmd</code></a></small>
<div class="d-none name"><code>AMR.Rmd</code></div>
@ -180,7 +180,7 @@ Berends</h4>
website update since they are based on randomly created values and the
page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
Markdown</a>. However, the methodology remains unchanged. This page was
generated on 06 January 2023.</p>
generated on 07 January 2023.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@ -236,21 +236,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2023-01-06</td>
<td align="center">2023-01-07</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="center">2023-01-06</td>
<td align="center">2023-01-07</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<tr class="odd">
<td align="center">2023-01-06</td>
<td align="center">2023-01-07</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>
@ -400,54 +400,32 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2015-04-28</td>
<td align="center">V8</td>
<td align="center">Hospital D</td>
<td align="center">2015-01-23</td>
<td align="center">N4</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2010-06-20</td>
<td align="center">B4</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">2015-06-12</td>
<td align="center">K2</td>
<td align="center">Hospital A</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2015-12-01</td>
<td align="center">S9</td>
<td align="center">Hospital A</td>
<td align="center">2017-03-19</td>
<td align="center">Z7</td>
<td align="center">Hospital C</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">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2014-02-21</td>
<td align="center">D1</td>
<td align="center">2010-04-01</td>
<td align="center">I9</td>
<td align="center">Hospital A</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
@ -455,14 +433,36 @@ data set:</p>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2013-02-17</td>
<td align="center">K6</td>
<td align="center">Hospital D</td>
<td align="center">2015-08-04</td>
<td align="center">X4</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2016-09-21</td>
<td align="center">W8</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2010-01-28</td>
<td align="center">H9</td>
<td align="center">Hospital A</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">M</td>
</tr>
</tbody>
@ -499,16 +499,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,411</td>
<td align="right">52.06%</td>
<td align="right">10,411</td>
<td align="right">52.06%</td>
<td align="right">10,284</td>
<td align="right">51.42%</td>
<td align="right">10,284</td>
<td align="right">51.42%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,589</td>
<td align="right">47.95%</td>
<td align="right">9,716</td>
<td align="right">48.58%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -621,10 +621,10 @@ 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 10,790 'phenotype-based' first isolates (54.0% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,750 'phenotype-based' first isolates (53.8% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 54% 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
<p>So only 53.8% 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">
<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>
@ -634,11 +634,11 @@ it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" cl
<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 10,790 isolates for analysis. Now our data looks
<p>So we end up with 10,750 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 class="table">
<table style="width:100%;" class="table">
<colgroup>
<col width="2%">
<col width="9%">
@ -651,7 +651,7 @@ like:</p>
<col width="3%">
<col width="6%">
<col width="11%">
<col width="11%">
<col width="12%">
<col width="9%">
<col width="5%">
</colgroup>
@ -673,30 +673,30 @@ like:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">3</td>
<td align="center">2015-06-12</td>
<td align="center">K2</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="left">1</td>
<td align="center">2015-01-23</td>
<td align="center">N4</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">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">Streptococcus</td>
<td align="center">pneumoniae</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">4</td>
<td align="center">2015-12-01</td>
<td align="center">S9</td>
<td align="center">Hospital A</td>
<td align="left">2</td>
<td align="center">2017-03-19</td>
<td align="center">Z7</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">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
@ -705,63 +705,63 @@ like:</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">4</td>
<td align="center">2015-08-04</td>
<td align="center">X4</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">5</td>
<td align="center">2014-02-21</td>
<td align="center">D1</td>
<td align="center">2016-09-21</td>
<td align="center">W8</td>
<td align="center">Hospital A</td>
<td align="center">B_KLBSL_PNMN</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="odd">
<td align="left">6</td>
<td align="center">2010-01-28</td>
<td align="center">H9</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">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="even">
<td align="left">7</td>
<td align="center">2010-03-27</td>
<td align="center">W8</td>
<td align="center">Hospital B</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">14</td>
<td align="center">2011-05-28</td>
<td align="center">H3</td>
<td align="center">2015-05-17</td>
<td align="center">Z1</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="left">15</td>
<td align="center">2012-06-23</td>
<td align="center">V2</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</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>
@ -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: 10,790<br>
Available: 10,790 (100%, NA: 0 = 0%)<br>
Length: 10,750<br>
Available: 10,750 (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">4,663</td>
<td align="right">43.22%</td>
<td align="right">4,663</td>
<td align="right">43.22%</td>
<td align="right">4,767</td>
<td align="right">44.34%</td>
<td align="right">4,767</td>
<td align="right">44.34%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,787</td>
<td align="right">25.83%</td>
<td align="right">7,450</td>
<td align="right">69.05%</td>
<td align="right">2,719</td>
<td align="right">25.29%</td>
<td align="right">7,486</td>
<td align="right">69.64%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,172</td>
<td align="right">20.13%</td>
<td align="right">9,622</td>
<td align="right">89.18%</td>
<td align="right">2,078</td>
<td align="right">19.33%</td>
<td align="right">9,564</td>
<td align="right">88.97%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,168</td>
<td align="right">10.82%</td>
<td align="right">10,790</td>
<td align="right">1,186</td>
<td align="right">11.03%</td>
<td align="right">10,750</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -902,8 +902,38 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2015-06-12</td>
<td align="center">K2</td>
<td align="center">2010-01-28</td>
<td align="center">H9</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2016-02-10</td>
<td align="center">X1</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">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">2015-05-27</td>
<td align="center">D10</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
@ -917,58 +947,28 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2011-05-28</td>
<td align="center">H3</td>
<td align="center">2017-09-20</td>
<td align="center">F9</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="odd">
<td align="center">2016-04-12</td>
<td align="center">Z5</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">2012-06-23</td>
<td align="center">V2</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">I</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="even">
<td align="center">2012-05-13</td>
<td align="center">L1</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">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">2016-05-12</td>
<td align="center">W3</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
@ -977,18 +977,18 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2016-04-28</td>
<td align="center">B6</td>
<td align="center">2011-12-20</td>
<td align="center">D3</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
</tbody>
@ -1013,50 +1013,50 @@ different bug/drug combinations, you can use the
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">2186</td>
<td align="center">130</td>
<td align="center">2347</td>
<td align="center">4663</td>
<td align="center">2241</td>
<td align="center">136</td>
<td align="center">2390</td>
<td align="center">4767</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3398</td>
<td align="center">3489</td>
<td align="center">168</td>
<td align="center">1097</td>
<td align="center">4663</td>
<td align="center">1110</td>
<td align="center">4767</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3398</td>
<td align="center">3502</td>
<td align="center">0</td>
<td align="center">1265</td>
<td align="center">4663</td>
<td align="center">4767</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4096</td>
<td align="center">4141</td>
<td align="center">0</td>
<td align="center">567</td>
<td align="center">4663</td>
<td align="center">626</td>
<td align="center">4767</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">1168</td>
<td align="center">1168</td>
<td align="center">1186</td>
<td align="center">1186</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">945</td>
<td align="center">49</td>
<td align="center">174</td>
<td align="center">1168</td>
<td align="center">924</td>
<td align="center">53</td>
<td align="center">209</td>
<td align="center">1186</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">4096</td>
<td align="center">4141</td>
<td align="center">0</td>
<td align="center">567</td>
<td align="center">4663</td>
<td align="center">626</td>
<td align="center">4767</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1032</td>
<td align="center">1072</td>
<td align="center">0</td>
<td align="center">136</td>
<td align="center">1168</td>
<td align="center">114</td>
<td align="center">1186</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2447</td>
<td align="center">2409</td>
<td align="center">0</td>
<td align="center">340</td>
<td align="center">2787</td>
<td align="center">310</td>
<td align="center">2719</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">2172</td>
<td align="center">2172</td>
<td align="center">2078</td>
<td align="center">2078</td>
</tr>
</tbody>
</table>
@ -1137,7 +1137,7 @@ I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equa
own:</p>
<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span></span>
<span><span class="co"># [1] 0.5407785</span></span></code></pre></div>
<span><span class="co"># [1] 0.543814</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">0.5431988</td>
<td align="center">0.5540994</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5308912</td>
<td align="center">0.5473965</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5421020</td>
<td align="center">0.5031606</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5527778</td>
<td align="center">0.5518207</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">0.5431988</td>
<td align="center">3345</td>
<td align="center">0.5540994</td>
<td align="center">3281</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5308912</td>
<td align="center">3658</td>
<td align="center">0.5473965</td>
<td align="center">3745</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5421020</td>
<td align="center">1627</td>
<td align="center">0.5031606</td>
<td align="center">1582</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5527778</td>
<td align="center">2160</td>
<td align="center">0.5518207</td>
<td align="center">2142</td>
</tr>
</tbody>
</table>
@ -1230,27 +1230,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7647437</td>
<td align="center">0.8784045</td>
<td align="center">0.9791979</td>
<td align="center">0.7671492</td>
<td align="center">0.8686805</td>
<td align="center">0.9758758</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8510274</td>
<td align="center">0.8835616</td>
<td align="center">0.9837329</td>
<td align="center">0.8237774</td>
<td align="center">0.9038786</td>
<td align="center">0.9806071</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7918909</td>
<td align="center">0.8780050</td>
<td align="center">0.9763186</td>
<td align="center">0.7899963</td>
<td align="center">0.8859875</td>
<td align="center">0.9834498</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5478821</td>
<td align="center">0.5303176</td>
<td align="center">0.0000000</td>
<td align="center">0.5478821</td>
<td align="center">0.5303176</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">54.3%</td>
<td align="right">26.2%</td>
<td align="right">55.4%</td>
<td align="right">26.9%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">53.1%</td>
<td align="right">26.2%</td>
<td align="right">54.7%</td>
<td align="right">27.3%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">54.2%</td>
<td align="right">26.2%</td>
<td align="right">50.3%</td>
<td align="right">25.5%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">55.3%</td>
<td align="right">26.5%</td>
<td align="right">55.2%</td>
<td align="right">25.9%</td>
</tr>
</tbody>
</table>
@ -1410,16 +1410,16 @@ classes) <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code>:</p>
<code class="sourceCode R"><span><span class="va">mic_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span></span>
<span><span class="va">mic_values</span></span>
<span><span class="co"># Class 'mic'</span></span>
<span><span class="co"># [1] 0.25 32 4 0.01 0.005 4 0.01 2 0.01 0.002 </span></span>
<span><span class="co"># [11] 32 32 0.001 32 0.001 1 0.002 64 64 1 </span></span>
<span><span class="co"># [21] 0.125 4 0.25 32 0.025 &gt;=256 64 &gt;=256 0.002 128 </span></span>
<span><span class="co"># [31] 0.125 0.001 8 4 0.25 0.25 0.25 0.002 0.002 128 </span></span>
<span><span class="co"># [41] 0.125 32 0.002 32 0.125 128 0.005 &gt;=256 0.002 0.025 </span></span>
<span><span class="co"># [51] &gt;=256 0.125 0.002 0.5 128 0.005 32 0.001 1 0.025 </span></span>
<span><span class="co"># [61] 0.5 0.125 1 16 0.0625 16 0.002 4 0.001 16 </span></span>
<span><span class="co"># [71] 128 0.125 32 0.25 0.001 0.025 8 64 0.01 8 </span></span>
<span><span class="co"># [81] 0.01 &gt;=256 0.001 0.125 0.005 0.125 &gt;=256 0.25 64 8 </span></span>
<span><span class="co"># [91] 32 &gt;=256 0.0625 128 64 32 0.125 0.125 1 0.0625</span></span></code></pre></div>
<span><span class="co"># [1] 8 0.01 0.01 0.025 128 64 2 0.025 0.0625 0.005 </span></span>
<span><span class="co"># [11] 0.001 0.0625 1 0.002 0.5 0.25 64 0.025 256 128 </span></span>
<span><span class="co"># [21] 0.001 0.005 1 0.125 256 8 0.001 0.25 0.0625 1 </span></span>
<span><span class="co"># [31] 4 0.005 0.5 0.0625 0.002 2 0.0625 0.005 0.005 0.25 </span></span>
<span><span class="co"># [41] 32 0.01 0.01 2 128 16 0.25 8 4 0.025 </span></span>
<span><span class="co"># [51] 32 256 0.0625 128 128 0.001 0.5 0.5 0.125 64 </span></span>
<span><span class="co"># [61] 0.25 8 0.0625 0.001 1 2 256 0.005 4 16 </span></span>
<span><span class="co"># [71] 0.125 0.002 256 64 0.01 8 0.5 0.5 64 1 </span></span>
<span><span class="co"># [81] 0.5 32 4 1 2 0.025 0.0625 0.25 0.005 16 </span></span>
<span><span class="co"># [91] 0.0625 0.002 8 0.001 0.125 0.125 128 64 0.125 64</span></span></code></pre></div>
<div class="sourceCode" id="cb36"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">mic_values</span><span class="op">)</span></span></code></pre></div>
@ -1453,10 +1453,10 @@ plotting:</p>
<code class="sourceCode R"><span><span class="va">disk_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_disk</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span>
<span><span class="va">disk_values</span></span>
<span><span class="co"># Class 'disk'</span></span>
<span><span class="co"># [1] 25 30 29 20 31 19 25 23 27 29 29 31 22 26 20 20 23 17 25 31 19 31 25 26 29</span></span>
<span><span class="co"># [26] 25 24 20 28 22 25 20 22 19 23 28 20 29 22 31 18 30 26 23 31 25 27 24 19 23</span></span>
<span><span class="co"># [51] 29 20 19 22 26 17 17 19 27 27 26 31 17 28 19 22 29 21 31 17 19 19 30 17 21</span></span>
<span><span class="co"># [76] 23 17 31 21 19 27 26 26 22 26 22 21 24 27 18 21 23 27 29 21 23 27 27 29 18</span></span></code></pre></div>
<span><span class="co"># [1] 26 30 22 29 29 24 23 31 22 19 29 24 22 30 20 18 26 25 18 23 23 25 31 24 25</span></span>
<span><span class="co"># [26] 18 30 22 31 24 22 22 25 22 17 22 24 25 28 19 21 21 21 22 18 31 25 22 25 30</span></span>
<span><span class="co"># [51] 25 31 23 21 17 19 31 23 19 20 28 22 26 25 25 24 20 24 25 19 27 28 21 26 23</span></span>
<span><span class="co"># [76] 17 22 23 30 20 20 18 18 22 19 29 31 18 26 20 28 27 24 27 21 17 25 30 22 22</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="">1.8.2.9086</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9088</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
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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="">1.8.2.9086</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9088</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">
@ -375,16 +375,16 @@ 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 I S R I R I</span></span>
<span><span class="co"># 2 S R S R S R</span></span>
<span><span class="co"># 3 I R R S I I</span></span>
<span><span class="co"># 4 R S S S I S</span></span>
<span><span class="co"># 5 I I I S S R</span></span>
<span><span class="co"># 6 S S S S I S</span></span>
<span><span class="co"># 1 S I S S R S</span></span>
<span><span class="co"># 2 S S R I S S</span></span>
<span><span class="co"># 3 I S I S I I</span></span>
<span><span class="co"># 4 R R I S S S</span></span>
<span><span class="co"># 5 I I S I S S</span></span>
<span><span class="co"># 6 S S R S S R</span></span>
<span><span class="co"># kanamycin</span></span>
<span><span class="co"># 1 S</span></span>
<span><span class="co"># 2 I</span></span>
<span><span class="co"># 3 S</span></span>
<span><span class="co"># 1 I</span></span>
<span><span class="co"># 2 S</span></span>
<span><span class="co"># 3 I</span></span>
<span><span class="co"># 4 I</span></span>
<span><span class="co"># 5 I</span></span>
<span><span class="co"># 6 I</span></span></code></pre></div>
@ -428,40 +428,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3214</td>
<td align="right">64.28%</td>
<td align="right">3214</td>
<td align="right">64.28%</td>
<td align="right">3236</td>
<td align="right">64.72%</td>
<td align="right">3236</td>
<td align="right">64.72%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">1024</td>
<td align="right">20.48%</td>
<td align="right">4238</td>
<td align="right">84.76%</td>
<td align="right">965</td>
<td align="right">19.30%</td>
<td align="right">4201</td>
<td align="right">84.02%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">403</td>
<td align="right">8.06%</td>
<td align="right">4641</td>
<td align="right">92.82%</td>
<td align="right">459</td>
<td align="right">9.18%</td>
<td align="right">4660</td>
<td align="right">93.20%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">256</td>
<td align="right">5.12%</td>
<td align="right">4897</td>
<td align="right">97.94%</td>
<td align="right">242</td>
<td align="right">4.84%</td>
<td align="right">4902</td>
<td align="right">98.04%</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">98</td>
<td align="right">1.96%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

2
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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="">1.8.2.9086</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9088</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">

4
articles/SPSS.html
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9086</small>
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@ -168,7 +168,7 @@
<h4 data-toc-skip class="author">Dr. Matthijs
Berends</h4>
<h4 data-toc-skip class="date">06 January 2023</h4>
<h4 data-toc-skip class="date">07 January 2023</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/SPSS.Rmd" class="external-link"><code>vignettes/SPSS.Rmd</code></a></small>
<div class="d-none name"><code>SPSS.Rmd</code></div>

2
articles/WHONET.html
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<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="">1.8.2.9086</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9088</small>
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4
articles/datasets.html
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<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="">1.8.2.9086</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9088</small>
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@ -166,7 +166,7 @@
<main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
<h4 data-toc-skip class="date">06 January 2023</h4>
<h4 data-toc-skip class="date">07 January 2023</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<div class="d-none name"><code>datasets.Rmd</code></div>

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articles/index.html
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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articles/resistance_predict.html
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<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="">1.8.2.9086</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9088</small>
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