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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="">1.8.2.9103</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</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">
@ -71,6 +71,11 @@
Conduct AMR Analysis
</a>
<a class="dropdown-item" href="../reference/antibiogram.html">
<span class="fa fa-file-prescription"></span>
Generate Antibiogram (Trad./Syndromic/WISCA)
</a>
<a class="dropdown-item" href="../articles/resistance_predict.html">
<span class="fa fa-dice"></span>
@ -173,7 +178,7 @@
<h4 data-toc-skip class="author">Dr. Matthijs
Berends</h4>
<h4 data-toc-skip class="date">24 January 2023</h4>
<h4 data-toc-skip class="date">08 February 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>
@ -185,7 +190,7 @@ 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 24 January 2023.</p>
generated on 08 February 2023.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@ -241,21 +246,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2023-01-24</td>
<td align="center">2023-02-08</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">2023-01-24</td>
<td align="center">2023-02-08</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">2023-01-24</td>
<td align="center">2023-02-08</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -406,70 +411,70 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2018-01-01</td>
<td align="center">Y10</td>
<td align="center">Hospital B</td>
<td align="center">2012-11-01</td>
<td align="center">T4</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">I</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">2012-02-22</td>
<td align="center">D10</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">2011-08-07</td>
<td align="center">Q3</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2015-12-24</td>
<td align="center">H3</td>
<td align="center">Hospital C</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2017-07-13</td>
<td align="center">U7</td>
<td align="center">2015-04-08</td>
<td align="center">A9</td>
<td align="center">Hospital D</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2016-02-29</td>
<td align="center">O4</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">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">F</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2016-02-09</td>
<td align="center">S1</td>
<td align="center">Hospital B</td>
<td align="center">2017-07-30</td>
<td align="center">I8</td>
<td align="center">Hospital D</td>
<td align="center">Klebsiella pneumoniae</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">2012-01-05</td>
<td align="center">M5</td>
<td align="center">Hospital B</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2015-02-21</td>
<td align="center">E9</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
</tr>
</tbody>
</table>
@ -505,18 +510,18 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,349</td>
<td align="right">51.75%</td>
<td align="right">10,349</td>
<td align="right">51.75%</td>
<td align="right">10,359</td>
<td align="right">51.80%</td>
<td align="right">10,359</td>
<td align="right">51.8%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,651</td>
<td align="right">48.26%</td>
<td align="right">9,641</td>
<td align="right">48.21%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
<td align="right">100.0%</td>
</tr>
</tbody>
</table>
@ -546,7 +551,7 @@ and <code><a href="https://dplyr.tidyverse.org/reference/across.html" class="ext
<span><span class="co"># [1] "AMX" "AMC" "CIP" "GEN"</span></span>
<span></span>
<span><span class="va">data</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="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="fu">where</span><span class="op">(</span><span class="va">is_sir_eligible</span><span class="op">)</span>, <span class="va">as.sir</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is_sir_eligible</span><span class="op">)</span>, <span class="va">as.sir</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
<p>Finally, we will apply <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">EUCAST
rules</a> on our antimicrobial results. In Europe, most medical
microbiological laboratories already apply these rules. Our package
@ -627,9 +632,9 @@ 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 12,429 'phenotype-based' first isolates (62.1% of total where a</span></span>
<span><span class="co"># =&gt; Found 20,000 'phenotype-based' first isolates (100.0% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 62.1% is suitable for resistance analysis! We can now filter
<p>So only 100% 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">
@ -638,15 +643,13 @@ on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html"
<p>For future use, the above two syntaxes can be shortened:</p>
<div class="sourceCode" id="cb16"><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>
<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 12,429 isolates for analysis. Now our data looks
<span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<p>So we end up with 20,000 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%">
<col width="9%">
<col width="9%">
@ -662,7 +665,6 @@ like:</p>
<col width="5%">
</colgroup>
<thead><tr class="header">
<th align="left"></th>
<th align="center">date</th>
<th align="center">patient_id</th>
<th align="center">hospital</th>
@ -679,15 +681,14 @@ like:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2018-01-01</td>
<td align="center">Y10</td>
<td align="center">Hospital B</td>
<td align="center">2012-11-01</td>
<td align="center">T4</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">I</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">Escherichia</td>
@ -695,77 +696,27 @@ like:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="center">2012-02-22</td>
<td align="center">D10</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">I</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="center">2016-02-29</td>
<td align="center">O4</td>
<td align="center">Hospital B</td>
<td align="center">2011-08-07</td>
<td align="center">Q3</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">I</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">6</td>
<td align="center">2016-02-09</td>
<td align="center">S1</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">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>
<tr class="odd">
<td align="left">7</td>
<td align="center">2013-02-22</td>
<td align="center">S5</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">R</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">9</td>
<td align="center">2014-08-17</td>
<td align="center">J7</td>
<td align="center">2015-04-08</td>
<td align="center">A9</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">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
@ -774,6 +725,51 @@ like:</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2017-07-30</td>
<td align="center">I8</td>
<td align="center">Hospital D</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">I</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">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2012-01-05</td>
<td align="center">M5</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">R</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2015-02-21</td>
<td align="center">E9</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</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">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
<p>Time for the analysis!</p>
@ -807,8 +803,8 @@ 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: 12,429<br>
Available: 12,429 (100%, NA: 0 = 0%)<br>
Length: 20,000<br>
Available: 20,000 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -833,33 +829,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">5,950</td>
<td align="right">47.87%</td>
<td align="right">5,950</td>
<td align="right">47.87%</td>
<td align="right">9,956</td>
<td align="right">49.78%</td>
<td align="right">9,956</td>
<td align="right">49.78%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,328</td>
<td align="right">26.78%</td>
<td align="right">9,278</td>
<td align="right">74.65%</td>
<td align="right">4,995</td>
<td align="right">24.98%</td>
<td align="right">14,951</td>
<td align="right">74.76%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">1,809</td>
<td align="right">14.55%</td>
<td align="right">11,087</td>
<td align="right">89.20%</td>
<td align="right">3,001</td>
<td align="right">15.01%</td>
<td align="right">17,952</td>
<td align="right">89.76%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,342</td>
<td align="right">10.80%</td>
<td align="right">12,429</td>
<td align="right">2,048</td>
<td align="right">10.24%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -908,42 +904,12 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2012-02-22</td>
<td align="center">D10</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">I</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2016-02-09</td>
<td align="center">S1</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">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>
<tr class="odd">
<td align="center">2014-08-17</td>
<td align="center">J7</td>
<td align="center">2015-04-08</td>
<td align="center">A9</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">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
@ -953,50 +919,80 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2013-05-07</td>
<td align="center">V6</td>
<td align="center">2012-01-05</td>
<td align="center">M5</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">I</td>
<td align="center">R</td>
<td align="center">F</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">2013-10-28</td>
<td align="center">P9</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">2015-02-21</td>
<td align="center">E9</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2017-04-15</td>
<td align="center">V10</td>
<td align="center">Hospital B</td>
<td align="center">2017-04-27</td>
<td align="center">C9</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2012-06-09</td>
<td align="center">C6</td>
<td align="center">Hospital A</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">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2011-12-09</td>
<td align="center">W4</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">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>
</tbody>
</table>
<p>If you want to get a quick glance of the number of isolates in
@ -1018,51 +1014,51 @@ different bug/drug combinations, you can use the
<tbody>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">1484</td>
<td align="center">1261</td>
<td align="center">3205</td>
<td align="center">5950</td>
<td align="center">AMC</td>
<td align="center">4463</td>
<td align="center">2199</td>
<td align="center">3294</td>
<td align="center">9956</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">2726</td>
<td align="center">1214</td>
<td align="center">2010</td>
<td align="center">5950</td>
<td align="center">AMX</td>
<td align="center">2238</td>
<td align="center">2141</td>
<td align="center">5577</td>
<td align="center">9956</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">2026</td>
<td align="center">1824</td>
<td align="center">2100</td>
<td align="center">5950</td>
<td align="center">3359</td>
<td align="center">3299</td>
<td align="center">3298</td>
<td align="center">9956</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">2016</td>
<td align="center">1853</td>
<td align="center">2081</td>
<td align="center">5950</td>
<td align="center">3360</td>
<td align="center">3332</td>
<td align="center">3264</td>
<td align="center">9956</td>
</tr>
<tr class="odd">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">886</td>
<td align="center">446</td>
<td align="center">716</td>
<td align="center">2048</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMX</td>
<td align="center">0</td>
<td align="center">0</td>
<td align="center">1342</td>
<td align="center">1342</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">599</td>
<td align="center">262</td>
<td align="center">481</td>
<td align="center">1342</td>
<td align="center">2048</td>
<td align="center">2048</td>
</tr>
</tbody>
</table>
@ -1084,34 +1080,34 @@ different bug/drug combinations, you can use the
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">2016</td>
<td align="center">1853</td>
<td align="center">2081</td>
<td align="center">5950</td>
<td align="center">3360</td>
<td align="center">3332</td>
<td align="center">3264</td>
<td align="center">9956</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">468</td>
<td align="center">429</td>
<td align="center">445</td>
<td align="center">1342</td>
<td align="center">682</td>
<td align="center">656</td>
<td align="center">710</td>
<td align="center">2048</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">1083</td>
<td align="center">1090</td>
<td align="center">1155</td>
<td align="center">3328</td>
<td align="center">1668</td>
<td align="center">1653</td>
<td align="center">1674</td>
<td align="center">4995</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">1809</td>
<td align="center">1809</td>
<td align="center">3001</td>
<td align="center">3001</td>
</tr>
</tbody>
</table>
@ -1143,7 +1139,7 @@ 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] 0.5882211</span></span></code></pre></div>
<span><span class="co"># [1] 0.60575</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">
@ -1158,19 +1154,19 @@ own:</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5883152</td>
<td align="center">0.6017567</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5836154</td>
<td align="center">0.6139130</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5717427</td>
<td align="center">0.6064538</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.6082433</td>
<td align="center">0.5972906</td>
</tr>
</tbody>
</table>
@ -1195,23 +1191,23 @@ all isolates available for every group (i.e. values S, I or R):</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5883152</td>
<td align="center">3680</td>
<td align="center">0.6017567</td>
<td align="center">6034</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5836154</td>
<td align="center">4431</td>
<td align="center">0.6139130</td>
<td align="center">6900</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5717427</td>
<td align="center">1819</td>
<td align="center">0.6064538</td>
<td align="center">3006</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.6082433</td>
<td align="center">2499</td>
<td align="center">0.5972906</td>
<td align="center">4060</td>
</tr>
</tbody>
</table>
@ -1236,27 +1232,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.6621849</td>
<td align="center">0.6502521</td>
<td align="center">0.8878992</td>
<td align="center">0.6691442</td>
<td align="center">0.6721575</td>
<td align="center">0.8938329</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.6415797</td>
<td align="center">0.6684054</td>
<td align="center">0.8941878</td>
<td align="center">0.6503906</td>
<td align="center">0.6533203</td>
<td align="center">0.8803711</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.6676683</td>
<td align="center">0.6529447</td>
<td align="center">0.8846154</td>
<td align="center">0.6654655</td>
<td align="center">0.6648649</td>
<td align="center">0.8852853</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.4693201</td>
<td align="center">0.4325225</td>
<td align="center">0.0000000</td>
<td align="center">0.4693201</td>
<td align="center">0.4325225</td>
</tr>
</tbody>
</table>
@ -1284,23 +1280,23 @@ classes, use a antibiotic class selector such as
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">58.8%</td>
<td align="right">36.2%</td>
<td align="right">60.2%</td>
<td align="right">36.8%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">58.4%</td>
<td align="right">36.9%</td>
<td align="right">61.4%</td>
<td align="right">37.8%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">57.2%</td>
<td align="right">36.3%</td>
<td align="right">60.6%</td>
<td align="right">36.6%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">60.8%</td>
<td align="right">37.1%</td>
<td align="right">59.7%</td>
<td align="right">35.9%</td>
</tr>
</tbody>
</table>
@ -1416,16 +1412,18 @@ classes) <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code>:</p>
<code class="sourceCode R"><span><span class="va">mic_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span></span>
<span><span class="va">mic_values</span></span>
<span><span class="co"># Class 'mic'</span></span>
<span><span class="co"># [1] 256 64 0.001 0.01 8 8 1 0.5 0.5 16 </span></span>
<span><span class="co"># [11] 0.125 256 0.5 0.002 2 0.005 1 1 256 0.002 </span></span>
<span><span class="co"># [21] 0.002 0.01 0.25 2 256 64 0.125 128 0.001 4 </span></span>
<span><span class="co"># [31] 0.125 0.0625 1 64 256 0.25 128 0.5 0.5 32 </span></span>
<span><span class="co"># [41] 16 2 0.125 0.005 8 0.0625 0.01 0.25 0.125 0.025 </span></span>
<span><span class="co"># [51] 0.0625 4 0.125 8 0.002 0.5 0.01 0.025 0.125 0.025 </span></span>
<span><span class="co"># [61] 0.001 16 1 0.25 0.5 2 8 0.01 8 0.0625</span></span>
<span><span class="co"># [71] 2 0.025 8 0.005 0.025 8 0.002 0.002 256 2 </span></span>
<span><span class="co"># [81] 0.01 0.002 16 0.0625 64 8 0.005 32 0.125 0.001 </span></span>
<span><span class="co"># [91] 0.002 2 0.125 8 1 128 0.01 1 0.001 0.025</span></span></code></pre></div>
<span><span class="co"># [1] 0.025 8 0.25 32 0.005 4 32 128 &lt;=0.001</span></span>
<span><span class="co"># [10] 16 0.002 0.002 0.5 2 0.025 0.002 8 128 </span></span>
<span><span class="co"># [19] 0.0625 1 0.125 128 0.5 2 1 8 0.025 </span></span>
<span><span class="co"># [28] 0.01 0.5 0.0625 64 0.25 0.025 64 0.005 128 </span></span>
<span><span class="co"># [37] &lt;=0.001 &lt;=0.001 0.25 2 16 0.125 0.125 0.002 0.125 </span></span>
<span><span class="co"># [46] 32 16 0.005 0.0625 0.0625 32 16 16 8 </span></span>
<span><span class="co"># [55] 0.025 2 0.125 64 16 &lt;=0.001 64 &gt;=256 0.0625 </span></span>
<span><span class="co"># [64] &gt;=256 0.002 &gt;=256 0.125 &gt;=256 0.0625 1 0.0625 0.002 </span></span>
<span><span class="co"># [73] &lt;=0.001 0.005 32 0.25 128 64 32 0.25 0.125 </span></span>
<span><span class="co"># [82] &lt;=0.001 0.5 16 8 0.5 0.5 0.125 0.5 64 </span></span>
<span><span class="co"># [91] 1 0.0625 &gt;=256 0.005 128 &gt;=256 0.025 128 128 </span></span>
<span><span class="co"># [100] 0.01</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>
@ -1459,10 +1457,10 @@ 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 20 25 25 26 18 20 24 23 28 30 18 27 27 25 20 28 21 19 23 27 28 28 24 28</span></span>
<span><span class="co"># [26] 17 25 19 23 30 22 17 31 23 31 24 28 25 28 28 27 31 20 24 18 18 24 29 17 31</span></span>
<span><span class="co"># [51] 17 28 23 26 19 25 18 22 24 18 17 27 26 26 25 18 23 21 21 28 17 25 30 29 29</span></span>
<span><span class="co"># [76] 18 31 20 22 28 23 26 24 27 28 20 25 19 19 17 24 24 17 18 17 30 24 21 29 27</span></span></code></pre></div>
<span><span class="co"># [1] 24 18 24 25 18 27 25 21 28 26 18 23 21 30 27 21 20 30 29 20 29 27 17 31 25</span></span>
<span><span class="co"># [26] 25 20 29 24 30 18 31 31 20 17 30 22 29 27 19 31 25 23 21 26 25 30 28 30 21</span></span>
<span><span class="co"># [51] 24 24 21 27 24 17 19 27 21 21 21 26 30 24 27 24 24 27 28 18 29 17 26 19 21</span></span>
<span><span class="co"># [76] 29 29 31 29 24 20 29 18 21 18 23 22 28 18 19 28 27 18 22 19 20 31 30 22 30</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>