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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="">1.8.1.9047</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9049</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">
@ -162,7 +162,7 @@
<img src="../logo.svg" class="logo" alt=""><h1>How to conduct AMR data analysis</h1>
<h4 data-toc-skip class="author">Dr. Matthijs Berends</h4>
<h4 data-toc-skip class="date">30 August 2022</h4>
<h4 data-toc-skip class="date">01 September 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>
@ -170,7 +170,7 @@
<p><strong>Note:</strong> values on this page will change with every 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 30 August 2022.</p>
<p><strong>Note:</strong> values on this page will change with every 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 01 September 2022.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@ -201,21 +201,21 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2022-08-30</td>
<td align="center">2022-09-01</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">2022-08-30</td>
<td align="center">2022-09-01</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">2022-08-30</td>
<td align="center">2022-09-01</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -325,69 +325,69 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2012-12-24</td>
<td align="center">A3</td>
<td align="center">2016-11-10</td>
<td align="center">P6</td>
<td align="center">Hospital C</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">F</td>
</tr>
<tr class="even">
<td align="center">2011-10-29</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">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2011-07-22</td>
<td align="center">G4</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2015-10-11</td>
<td align="center">S9</td>
<td align="center">Hospital C</td>
<td align="center">Streptococcus pneumoniae</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>
</tr>
<tr class="odd">
<td align="center">2013-10-26</td>
<td align="center">Q7</td>
<td align="center">Hospital C</td>
<td align="center">2011-04-20</td>
<td align="center">O10</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">2014-03-21</td>
<td align="center">Y1</td>
<td align="center">Hospital A</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2016-02-25</td>
<td align="center">V4</td>
<td align="center">Hospital B</td>
<td align="center">2012-08-21</td>
<td align="center">I2</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2014-07-02</td>
<td align="center">N6</td>
<td align="center">2017-03-26</td>
<td align="center">T2</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</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">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
</tbody>
@ -422,16 +422,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,470</td>
<td align="right">52.35%</td>
<td align="right">10,470</td>
<td align="right">52.35%</td>
<td align="right">10,422</td>
<td align="right">52.11%</td>
<td align="right">10,422</td>
<td align="right">52.11%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,530</td>
<td align="right">47.65%</td>
<td align="right">9,578</td>
<td align="right">47.89%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -488,9 +488,9 @@ Longest: 1</p>
<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 10,675 'phenotype-based' first isolates (53.4% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,604 'phenotype-based' first isolates (53.0% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 53.4% 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>
<p>So only 53.0% 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>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">first</span> <span class="op">==</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
@ -499,10 +499,10 @@ Longest: 1</p>
<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 10,675 isolates for analysis. Now our data looks like:</p>
<p>So we end up with 10,604 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%">
@ -516,7 +516,7 @@ Longest: 1</p>
<col width="6%">
<col width="11%">
<col width="12%">
<col width="9%">
<col width="7%">
<col width="5%">
</colgroup>
<thead><tr class="header">
@ -537,44 +537,12 @@ Longest: 1</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">4</td>
<td align="center">2014-03-21</td>
<td align="center">Y1</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="even">
<td align="left">5</td>
<td align="center">2016-02-25</td>
<td align="center">V4</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">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">6</td>
<td align="center">2014-07-02</td>
<td align="center">N6</td>
<td align="center">Hospital B</td>
<td align="left">1</td>
<td align="center">2016-11-10</td>
<td align="center">P6</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">S</td>
@ -585,13 +553,13 @@ Longest: 1</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">9</td>
<td align="center">2011-11-29</td>
<td align="center">Q4</td>
<td align="center">Hospital B</td>
<td align="left">2</td>
<td align="center">2011-10-29</td>
<td align="center">T4</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">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
@ -601,14 +569,30 @@ Longest: 1</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">14</td>
<td align="center">2013-03-07</td>
<td align="center">A2</td>
<td align="left">7</td>
<td align="center">2015-01-09</td>
<td align="center">J10</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="even">
<td align="left">9</td>
<td align="center">2016-05-25</td>
<td align="center">F8</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
@ -616,20 +600,36 @@ Longest: 1</p>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">15</td>
<td align="center">2010-02-05</td>
<td align="center">X6</td>
<td align="center">Hospital D</td>
<td align="center">B_KLBSL_PNMN</td>
<tr class="odd">
<td align="left">10</td>
<td align="center">2010-01-21</td>
<td align="center">Z8</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">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">11</td>
<td align="center">2012-10-12</td>
<td align="center">B5</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">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>
</tbody>
@ -653,8 +653,8 @@ Longest: 1</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://rdrr.io/pkg/cleaner/man/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: 10,675<br>
Available: 10,675 (100.0%, NA: 0 = 0.0%)<br>
Length: 10,604<br>
Available: 10,604 (100.0%, NA: 0 = 0.0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -671,33 +671,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">4,591</td>
<td align="right">43.01%</td>
<td align="right">4,591</td>
<td align="right">43.01%</td>
<td align="right">4,672</td>
<td align="right">44.06%</td>
<td align="right">4,672</td>
<td align="right">44.06%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,738</td>
<td align="right">25.65%</td>
<td align="right">7,329</td>
<td align="right">68.66%</td>
<td align="right">2,714</td>
<td align="right">25.59%</td>
<td align="right">7,386</td>
<td align="right">69.65%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,156</td>
<td align="right">20.20%</td>
<td align="right">9,485</td>
<td align="right">88.85%</td>
<td align="right">2,051</td>
<td align="right">19.34%</td>
<td align="right">9,437</td>
<td align="right">88.99%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,190</td>
<td align="right">11.15%</td>
<td align="right">10,675</td>
<td align="right">1,167</td>
<td align="right">11.01%</td>
<td align="right">10,604</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -716,14 +716,14 @@ Longest: 24</p>
<col width="9%">
<col width="9%">
<col width="9%">
<col width="11%">
<col width="10%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="6%">
<col width="11%">
<col width="11%">
<col width="12%">
<col width="9%">
<col width="5%">
</colgroup>
@ -744,13 +744,43 @@ Longest: 24</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2014-03-21</td>
<td align="center">Y1</td>
<td align="center">Hospital A</td>
<td align="center">2012-10-12</td>
<td align="center">B5</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">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">2017-11-10</td>
<td align="center">A8</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">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">2010-08-21</td>
<td align="center">Y3</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
@ -759,75 +789,45 @@ Longest: 24</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2016-02-25</td>
<td align="center">V4</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">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2011-06-30</td>
<td align="center">I1</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">2015-12-30</td>
<td align="center">B1</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">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">2017-06-02</td>
<td align="center">D10</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">M</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</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">2012-11-07</td>
<td align="center">W10</td>
<td align="center">Hospital A</td>
<td align="center">2014-10-15</td>
<td align="center">N2</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</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="even">
<td align="center">2017-09-12</td>
<td align="center">O7</td>
<td align="center">Hospital D</td>
<td align="center">2016-04-25</td>
<td align="center">H4</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">S</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">Streptococcus</td>
<td align="center">pneumoniae</td>
@ -854,50 +854,50 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">2171</td>
<td align="center">122</td>
<td align="center">2298</td>
<td align="center">4591</td>
<td align="center">2216</td>
<td align="center">117</td>
<td align="center">2339</td>
<td align="center">4672</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3395</td>
<td align="center">143</td>
<td align="center">1053</td>
<td align="center">4591</td>
<td align="center">3414</td>
<td align="center">156</td>
<td align="center">1102</td>
<td align="center">4672</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3378</td>
<td align="center">3392</td>
<td align="center">0</td>
<td align="center">1213</td>
<td align="center">4591</td>
<td align="center">1280</td>
<td align="center">4672</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4022</td>
<td align="center">4084</td>
<td align="center">0</td>
<td align="center">569</td>
<td align="center">4591</td>
<td align="center">588</td>
<td align="center">4672</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">1190</td>
<td align="center">1190</td>
<td align="center">1167</td>
<td align="center">1167</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">931</td>
<td align="center">47</td>
<td align="center">212</td>
<td align="center">1190</td>
<td align="center">912</td>
<td align="center">53</td>
<td align="center">202</td>
<td align="center">1167</td>
</tr>
</tbody>
</table>
@ -920,34 +920,34 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4022</td>
<td align="center">4084</td>
<td align="center">0</td>
<td align="center">569</td>
<td align="center">4591</td>
<td align="center">588</td>
<td align="center">4672</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1066</td>
<td align="center">1054</td>
<td align="center">0</td>
<td align="center">124</td>
<td align="center">1190</td>
<td align="center">113</td>
<td align="center">1167</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2420</td>
<td align="center">2439</td>
<td align="center">0</td>
<td align="center">318</td>
<td align="center">2738</td>
<td align="center">275</td>
<td align="center">2714</td>
</tr>
<tr class="even">
<td align="center">S. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">0</td>
<td align="center">0</td>
<td align="center">2156</td>
<td align="center">2156</td>
<td align="center">2051</td>
<td align="center">2051</td>
</tr>
</tbody>
</table>
@ -961,7 +961,7 @@ Longest: 24</p>
<p>As per the EUCAST guideline of 2019, we calculate resistance as the proportion of R (<code><a href="../reference/proportion.html">proportion_R()</a></code>, equal to <code><a href="../reference/proportion.html">resistance()</a></code>) and susceptibility as the proportion of S and I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equal to <code><a href="../reference/proportion.html">susceptibility()</a></code>). These functions can be used on their own:</p>
<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span></span>
<span><span class="co"># [1] 0.5525995</span></span></code></pre></div>
<span><span class="co"># [1] 0.5453602</span></span></code></pre></div>
<p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r">
<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>
@ -975,19 +975,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5429191</td>
<td align="center">0.5524672</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5560949</td>
<td align="center">0.5320304</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5516169</td>
<td align="center">0.5509434</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5619137</td>
<td align="center">0.5535714</td>
</tr>
</tbody>
</table>
@ -1008,23 +1008,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5429191</td>
<td align="center">3227</td>
<td align="center">0.5524672</td>
<td align="center">3202</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5560949</td>
<td align="center">3708</td>
<td align="center">0.5320304</td>
<td align="center">3684</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5516169</td>
<td align="center">1608</td>
<td align="center">0.5509434</td>
<td align="center">1590</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5619137</td>
<td align="center">2132</td>
<td align="center">0.5535714</td>
<td align="center">2128</td>
</tr>
</tbody>
</table>
@ -1047,27 +1047,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7706382</td>
<td align="center">0.8760619</td>
<td align="center">0.9797430</td>
<td align="center">0.7641267</td>
<td align="center">0.8741438</td>
<td align="center">0.9762414</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8218487</td>
<td align="center">0.8957983</td>
<td align="center">0.9840336</td>
<td align="center">0.8269066</td>
<td align="center">0.9031705</td>
<td align="center">0.9837189</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7797663</td>
<td align="center">0.8838568</td>
<td align="center">0.9762600</td>
<td align="center">0.7940310</td>
<td align="center">0.8986735</td>
<td align="center">0.9812085</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5245826</td>
<td align="center">0.5324232</td>
<td align="center">0.0000000</td>
<td align="center">0.5245826</td>
<td align="center">0.5324232</td>
</tr>
</tbody>
</table>
@ -1092,23 +1092,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">54.3%</td>
<td align="right">27.1%</td>
<td align="right">55.2%</td>
<td align="right">26.6%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">55.6%</td>
<td align="right">26.6%</td>
<td align="right">53.2%</td>
<td align="right">26.1%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">55.2%</td>
<td align="right">27.8%</td>
<td align="right">55.1%</td>
<td align="right">27.3%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">56.2%</td>
<td align="right">27.5%</td>
<td align="right">55.4%</td>
<td align="right">27.0%</td>
</tr>
</tbody>
</table>
@ -1206,16 +1206,18 @@ Longest: 24</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 &lt;mic&gt;</span></span>
<span><span class="co"># [1] 2 0.5 0.5 &gt;=256 0.5 1 0.002 0.025 64 0.25 </span></span>
<span><span class="co"># [11] 0.5 0.0625 0.002 0.025 16 32 8 32 0.125 4 </span></span>
<span><span class="co"># [21] 64 0.002 0.5 &gt;=256 0.001 0.001 0.01 8 0.002 128 </span></span>
<span><span class="co"># [31] 16 0.0625 0.125 0.01 2 0.25 128 2 16 0.01 </span></span>
<span><span class="co"># [41] 4 0.002 16 1 2 0.005 32 0.0625 &gt;=256 4 </span></span>
<span><span class="co"># [51] 0.01 0.01 128 0.5 0.01 0.25 0.25 0.005 2 8 </span></span>
<span><span class="co"># [61] 0.025 64 0.002 1 4 0.01 1 1 16 0.5 </span></span>
<span><span class="co"># [71] 0.005 32 &gt;=256 0.25 0.0625 16 0.125 1 0.125 128 </span></span>
<span><span class="co"># [81] 0.005 0.125 0.001 0.25 1 0.01 32 32 2 64 </span></span>
<span><span class="co"># [91] &gt;=256 0.25 0.025 4 32 16 0.0625 4 0.002 0.002</span></span></code></pre></div>
<span><span class="co"># [1] 0.0625 128 32 32 0.125 2 0.0625 8 0.002 </span></span>
<span><span class="co"># [10] 2 0.0625 64 2 128 0.025 0.125 0.002 64 </span></span>
<span><span class="co"># [19] 0.025 4 0.002 &lt;=0.001 0.0625 0.125 8 16 0.0625 </span></span>
<span><span class="co"># [28] 128 128 256 8 8 16 0.0625 &lt;=0.001 &lt;=0.001</span></span>
<span><span class="co"># [37] 8 256 0.025 &lt;=0.001 32 0.125 128 0.125 1 </span></span>
<span><span class="co"># [46] 0.01 64 0.125 4 2 0.005 128 0.25 32 </span></span>
<span><span class="co"># [55] 1 0.01 0.25 0.0625 0.01 0.25 0.25 8 0.125 </span></span>
<span><span class="co"># [64] 0.25 0.025 &lt;=0.001 8 1 4 1 32 64 </span></span>
<span><span class="co"># [73] 0.5 32 2 2 0.125 0.01 32 64 &lt;=0.001</span></span>
<span><span class="co"># [82] 4 0.5 0.5 4 0.25 4 &lt;=0.001 256 1 </span></span>
<span><span class="co"># [91] 4 4 0.002 0.125 0.125 2 0.002 8 16 </span></span>
<span><span class="co"># [100] 1</span></span></code></pre></div>
<div class="sourceCode" id="cb37"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">mic_values</span><span class="op">)</span></span></code></pre></div>
@ -1244,10 +1246,10 @@ Longest: 24</p>
<span><span class="co"># coli). Run `mo_uncertainties()` to review this.</span></span>
<span><span class="va">disk_values</span></span>
<span><span class="co"># Class &lt;disk&gt;</span></span>
<span><span class="co"># [1] 23 31 24 27 29 20 24 22 27 17 21 28 25 18 29 24 28 17 24 19 22 30 29 17 27</span></span>
<span><span class="co"># [26] 18 20 29 23 23 20 24 20 24 24 18 31 31 29 17 27 19 25 21 18 26 29 18 17 30</span></span>
<span><span class="co"># [51] 27 26 31 18 26 31 30 18 25 25 27 18 30 19 19 25 30 28 19 26 30 21 20 24 22</span></span>
<span><span class="co"># [76] 25 31 17 18 23 27 23 29 24 27 28 25 29 30 27 24 27 28 25 23 27 24 22 27 18</span></span></code></pre></div>
<span><span class="co"># [1] 28 26 29 24 22 28 18 17 22 24 17 18 20 25 23 22 30 21 24 30 26 18 23 28 19</span></span>
<span><span class="co"># [26] 25 24 25 17 25 21 25 20 30 20 29 20 22 25 19 17 29 21 28 28 18 24 26 25 28</span></span>
<span><span class="co"># [51] 20 26 24 19 24 27 19 22 18 28 29 30 31 30 30 30 17 18 20 26 27 27 28 24 23</span></span>
<span><span class="co"># [76] 25 30 29 20 20 20 20 30 24 28 20 30 31 17 17 23 25 27 26 18 23 21 18 22 21</span></span></code></pre></div>
<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">disk_values</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></code></pre></div>