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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="">1.8.2.9073</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9074</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">28 December 2022</h4>
<h4 data-toc-skip class="date">29 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 28 December 2022.</p>
generated on 29 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">2022-12-28</td>
<td align="center">2022-12-29</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">2022-12-28</td>
<td align="center">2022-12-29</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">2022-12-28</td>
<td align="center">2022-12-29</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -380,12 +380,12 @@ data set:</p>
<col width="13%">
<col width="13%">
<col width="13%">
<col width="26%">
<col width="28%">
<col width="5%">
<col width="5%">
<col width="5%">
<col width="5%">
<col width="9%">
<col width="8%">
</colgroup>
<thead><tr class="header">
<th align="center">date</th>
@ -400,21 +400,21 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2012-10-08</td>
<td align="center">Q3</td>
<td align="center">2017-11-28</td>
<td align="center">U1</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2013-07-19</td>
<td align="center">E4</td>
<td align="center">Hospital C</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">2010-08-10</td>
<td align="center">J3</td>
<td align="center">Hospital B</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
@ -422,48 +422,48 @@ data set:</p>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2013-11-07</td>
<td align="center">T6</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">R</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2015-10-03</td>
<td align="center">J10</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">2016-11-06</td>
<td align="center">I10</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2010-05-23</td>
<td align="center">J8</td>
<tr class="even">
<td align="center">2014-03-16</td>
<td align="center">N7</td>
<td align="center">Hospital A</td>
<td align="center">Streptococcus pneumoniae</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>
</tr>
<tr class="odd">
<td align="center">2011-08-16</td>
<td align="center">O4</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2016-04-21</td>
<td align="center">D5</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">2017-11-18</td>
<td align="center">Z3</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</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>
<td align="center">R</td>
<td align="center">F</td>
</tr>
</tbody>
</table>
@ -499,16 +499,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,476</td>
<td align="right">52.38%</td>
<td align="right">10,476</td>
<td align="right">52.38%</td>
<td align="right">10,243</td>
<td align="right">51.22%</td>
<td align="right">10,243</td>
<td align="right">51.22%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,524</td>
<td align="right">47.62%</td>
<td align="right">9,757</td>
<td align="right">48.79%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -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 10,714 'phenotype-based' first isolates (53.6% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,640 '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 53.6% 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">
@ -634,7 +634,7 @@ on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html"
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="co"># Including isolates from ICU.</span></span></code></pre></div>
<p>So we end up with 10,714 isolates for analysis. Now our data looks
<p>So we end up with 10,640 isolates for analysis. Now our data looks
like:</p>
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">data_1st</span><span class="op">)</span></span></code></pre></div>
@ -673,94 +673,30 @@ like:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2012-10-08</td>
<td align="center">Q3</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">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="left">3</td>
<td align="center">2013-11-07</td>
<td align="center">T6</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">2016-11-06</td>
<td align="center">I10</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="center">2010-05-23</td>
<td align="center">J8</td>
<tr class="even">
<td align="left">4</td>
<td align="center">2014-03-16</td>
<td align="center">N7</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">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">6</td>
<td align="center">2016-04-21</td>
<td align="center">D5</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">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="odd">
<td align="left">7</td>
<td align="center">2017-06-14</td>
<td align="center">J3</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="even">
<td align="left">8</td>
<td align="center">2010-04-03</td>
<td align="center">Z10</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">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
@ -768,6 +704,70 @@ like:</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">6</td>
<td align="center">2017-11-18</td>
<td align="center">Z3</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">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">7</td>
<td align="center">2017-06-30</td>
<td align="center">E1</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<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="odd">
<td align="left">13</td>
<td align="center">2014-08-26</td>
<td align="center">E5</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">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">14</td>
<td align="center">2017-08-09</td>
<td align="center">N2</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">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: 10,714<br>
Available: 10,714 (100%, NA: 0 = 0%)<br>
Length: 10,640<br>
Available: 10,640 (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">4,648</td>
<td align="right">43.38%</td>
<td align="right">4,648</td>
<td align="right">43.38%</td>
<td align="right">4,559</td>
<td align="right">42.85%</td>
<td align="right">4,559</td>
<td align="right">42.85%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,764</td>
<td align="right">25.80%</td>
<td align="right">7,412</td>
<td align="right">69.18%</td>
<td align="right">2,780</td>
<td align="right">26.13%</td>
<td align="right">7,339</td>
<td align="right">68.98%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,103</td>
<td align="right">19.63%</td>
<td align="right">9,515</td>
<td align="right">88.81%</td>
<td align="right">2,122</td>
<td align="right">19.94%</td>
<td align="right">9,461</td>
<td align="right">88.92%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,199</td>
<td align="right">11.19%</td>
<td align="right">10,714</td>
<td align="right">1,179</td>
<td align="right">11.08%</td>
<td align="right">10,640</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -902,24 +902,24 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2012-10-08</td>
<td align="center">Q3</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">2014-03-16</td>
<td align="center">N7</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">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">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2013-11-07</td>
<td align="center">T6</td>
<td align="center">Hospital B</td>
<td align="center">2017-11-18</td>
<td align="center">Z3</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
@ -932,58 +932,58 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2010-04-03</td>
<td align="center">Z10</td>
<td align="center">2012-10-06</td>
<td align="center">U6</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">2013-06-09</td>
<td align="center">O7</td>
<td align="center">Hospital B</td>
<td align="center">B_KLBSL_PNMN</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">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">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2017-04-03</td>
<td align="center">H8</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<tr class="even">
<td align="center">2014-12-18</td>
<td align="center">T1</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2015-05-29</td>
<td align="center">X6</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">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">2010-10-05</td>
<td align="center">R6</td>
<td align="center">2011-09-05</td>
<td align="center">T9</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</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">2179</td>
<td align="center">143</td>
<td align="center">2326</td>
<td align="center">4648</td>
<td align="center">2174</td>
<td align="center">118</td>
<td align="center">2267</td>
<td align="center">4559</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3402</td>
<td align="center">164</td>
<td align="center">1082</td>
<td align="center">4648</td>
<td align="center">3334</td>
<td align="center">183</td>
<td align="center">1042</td>
<td align="center">4559</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3405</td>
<td align="center">3360</td>
<td align="center">0</td>
<td align="center">1243</td>
<td align="center">4648</td>
<td align="center">1199</td>
<td align="center">4559</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4065</td>
<td align="center">3972</td>
<td align="center">0</td>
<td align="center">583</td>
<td align="center">4648</td>
<td align="center">587</td>
<td align="center">4559</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">1199</td>
<td align="center">1199</td>
<td align="center">1179</td>
<td align="center">1179</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">953</td>
<td align="center">38</td>
<td align="center">208</td>
<td align="center">1199</td>
<td align="center">931</td>
<td align="center">49</td>
<td align="center">199</td>
<td align="center">1179</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">3972</td>
<td align="center">0</td>
<td align="center">583</td>
<td align="center">4648</td>
<td align="center">587</td>
<td align="center">4559</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1067</td>
<td align="center">1056</td>
<td align="center">0</td>
<td align="center">132</td>
<td align="center">1199</td>
<td align="center">123</td>
<td align="center">1179</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2469</td>
<td align="center">2441</td>
<td align="center">0</td>
<td align="center">295</td>
<td align="center">2764</td>
<td align="center">339</td>
<td align="center">2780</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">2103</td>
<td align="center">2103</td>
<td align="center">2122</td>
<td align="center">2122</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] 0.5460146</span></span></code></pre></div>
<span><span class="co"># [1] 0.5412594</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">0.5537216</td>
<td align="center">0.5416017</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5401750</td>
<td align="center">0.5477551</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5323097</td>
<td align="center">0.5425532</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5546335</td>
<td align="center">0.5287303</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">0.5537216</td>
<td align="center">3211</td>
<td align="center">0.5416017</td>
<td align="center">3209</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5401750</td>
<td align="center">3771</td>
<td align="center">0.5477551</td>
<td align="center">3675</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5323097</td>
<td align="center">1563</td>
<td align="center">0.5425532</td>
<td align="center">1598</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5546335</td>
<td align="center">2169</td>
<td align="center">0.5287303</td>
<td align="center">2158</td>
</tr>
</tbody>
</table>
@ -1230,27 +1230,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7672117</td>
<td align="center">0.8745697</td>
<td align="center">0.9776248</td>
<td align="center">0.7714411</td>
<td align="center">0.8712437</td>
<td align="center">0.9749945</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8265221</td>
<td align="center">0.8899083</td>
<td align="center">0.9799833</td>
<td align="center">0.8312129</td>
<td align="center">0.8956743</td>
<td align="center">0.9847328</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7735166</td>
<td align="center">0.8932706</td>
<td align="center">0.9804631</td>
<td align="center">0.7827338</td>
<td align="center">0.8780576</td>
<td align="center">0.9748201</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5344746</td>
<td align="center">0.5494816</td>
<td align="center">0.0000000</td>
<td align="center">0.5344746</td>
<td align="center">0.5494816</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">55.4%</td>
<td align="right">27.3%</td>
<td align="right">54.2%</td>
<td align="right">26.5%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">54.0%</td>
<td align="right">26.6%</td>
<td align="right">54.8%</td>
<td align="right">26.7%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">53.2%</td>
<td align="right">26.2%</td>
<td align="right">54.3%</td>
<td align="right">25.7%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">55.5%</td>
<td align="right">27.9%</td>
<td align="right">52.9%</td>
<td align="right">25.9%</td>
</tr>
</tbody>
</table>
@ -1410,18 +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] 8 0.025 2 128 2 0.125 64 2 0.005 </span></span>
<span><span class="co"># [10] 0.01 32 16 128 1 8 0.5 &lt;=0.001 0.025 </span></span>
<span><span class="co"># [19] 0.0625 4 4 0.25 8 0.5 2 0.005 0.005 </span></span>
<span><span class="co"># [28] 64 8 0.0625 64 0.025 0.5 &lt;=0.001 0.0625 0.25 </span></span>
<span><span class="co"># [37] 0.0625 0.002 0.01 0.25 256 0.01 2 2 1 </span></span>
<span><span class="co"># [46] 32 64 0.125 128 256 &lt;=0.001 &lt;=0.001 64 0.25 </span></span>
<span><span class="co"># [55] 1 &lt;=0.001 0.005 4 32 1 0.002 16 8 </span></span>
<span><span class="co"># [64] &lt;=0.001 0.005 64 0.25 8 0.0625 0.01 16 1 </span></span>
<span><span class="co"># [73] 1 0.0625 0.25 0.5 0.25 8 0.125 0.002 0.25 </span></span>
<span><span class="co"># [82] 0.005 0.5 8 64 0.01 0.002 0.125 8 0.0625 </span></span>
<span><span class="co"># [91] 0.005 0.002 0.002 0.005 0.025 &lt;=0.001 &lt;=0.001 0.025 2 </span></span>
<span><span class="co"># [100] 128</span></span></code></pre></div>
<span><span class="co"># [1] 32 0.01 4 2 0.25 32 0.025 0.001 0.0625 4 </span></span>
<span><span class="co"># [11] 128 64 0.005 0.01 0.025 0.25 0.025 0.125 256 0.0625</span></span>
<span><span class="co"># [21] 0.001 0.125 0.25 0.01 8 0.0625 1 0.125 16 0.5 </span></span>
<span><span class="co"># [31] 0.125 16 0.25 128 0.25 2 256 32 0.005 0.002 </span></span>
<span><span class="co"># [41] 16 0.005 0.001 256 0.025 4 128 256 0.005 32 </span></span>
<span><span class="co"># [51] 1 0.125 16 0.25 0.01 0.5 0.5 0.125 0.0625 64 </span></span>
<span><span class="co"># [61] 0.005 128 0.001 0.005 16 0.0625 32 0.01 8 256 </span></span>
<span><span class="co"># [71] 0.001 0.0625 1 0.01 32 128 0.01 16 2 0.001 </span></span>
<span><span class="co"># [81] 0.01 0.0625 0.0625 16 2 0.001 0.125 0.001 4 0.0625</span></span>
<span><span class="co"># [91] 0.5 1 0.125 0.005 8 4 1 0.025 0.5 32</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>
@ -1455,10 +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] 28 24 19 18 21 30 31 20 21 17 24 27 21 18 28 29 28 19 25 18 18 21 17 18 28</span></span>
<span><span class="co"># [26] 28 27 18 28 20 30 25 17 23 21 18 17 19 19 17 28 26 25 18 31 19 31 23 29 20</span></span>
<span><span class="co"># [51] 29 26 18 18 26 24 23 17 17 25 23 21 23 28 22 22 24 30 18 19 20 24 31 27 27</span></span>
<span><span class="co"># [76] 27 27 26 18 18 30 23 22 26 17 27 19 25 31 30 25 20 18 30 19 20 19 19 22 21</span></span></code></pre></div>
<span><span class="co"># [1] 29 23 28 30 26 21 27 30 21 31 23 25 22 30 18 24 24 24 29 28 31 28 25 31 27</span></span>
<span><span class="co"># [26] 26 30 21 25 30 31 24 24 30 17 30 27 20 31 26 20 23 17 31 31 28 28 26 20 19</span></span>
<span><span class="co"># [51] 24 30 26 24 18 18 17 24 28 24 19 27 31 20 18 23 27 31 19 19 17 27 23 25 19</span></span>
<span><span class="co"># [76] 18 20 26 18 19 26 21 17 28 22 26 24 28 27 22 17 22 28 20 19 17 17 20 19 24</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="">1.8.2.9073</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9074</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="">1.8.2.9073</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9074</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 I S R I R I</span></span>
<span><span class="co"># 2 I R R I S R</span></span>
<span><span class="co"># 3 S R S I S S</span></span>
<span><span class="co"># 4 S R S I I I</span></span>
<span><span class="co"># 5 R R S I S S</span></span>
<span><span class="co"># 6 S S S R I I</span></span>
<span><span class="co"># 1 S R S S R R</span></span>
<span><span class="co"># 2 I S I S S R</span></span>
<span><span class="co"># 3 S I I R R S</span></span>
<span><span class="co"># 4 S R I R S R</span></span>
<span><span class="co"># 5 I R S S S I</span></span>
<span><span class="co"># 6 R R S I I I</span></span>
<span><span class="co"># kanamycin</span></span>
<span><span class="co"># 1 R</span></span>
<span><span class="co"># 2 S</span></span>
<span><span class="co"># 3 S</span></span>
<span><span class="co"># 3 I</span></span>
<span><span class="co"># 4 R</span></span>
<span><span class="co"># 5 R</span></span>
<span><span class="co"># 6 I</span></span></code></pre></div>
<span><span class="co"># 5 S</span></span>
<span><span class="co"># 6 S</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">3237</td>
<td align="right">64.74%</td>
<td align="right">3237</td>
<td align="right">64.74%</td>
<td align="right">3249</td>
<td align="right">64.98%</td>
<td align="right">3249</td>
<td align="right">64.98%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">1000</td>
<td align="right">20.00%</td>
<td align="right">4237</td>
<td align="right">84.74%</td>
<td align="right">977</td>
<td align="right">19.54%</td>
<td align="right">4226</td>
<td align="right">84.52%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">410</td>
<td align="right">8.20%</td>
<td align="right">4647</td>
<td align="right">92.94%</td>
<td align="right">420</td>
<td align="right">8.40%</td>
<td align="right">4646</td>
<td align="right">92.92%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">261</td>
<td align="right">5.22%</td>
<td align="right">4908</td>
<td align="right">98.16%</td>
<td align="right">249</td>
<td align="right">4.98%</td>
<td align="right">4895</td>
<td align="right">97.90%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">92</td>
<td align="right">1.84%</td>
<td align="right">105</td>
<td align="right">2.10%</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="">1.8.2.9073</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9074</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="">1.8.2.9073</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">28 December 2022</h4>
<h4 data-toc-skip class="date">29 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>

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="">1.8.2.9073</small>
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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="">1.8.2.9073</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9074</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">28 December 2022</h4>
<h4 data-toc-skip class="date">29 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>
<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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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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