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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="">1.8.1.9027</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</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">
@ -312,41 +312,41 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2014-09-28</td>
<td align="center">S6</td>
<td align="center">Hospital A</td>
<td align="center">2014-06-06</td>
<td align="center">A5</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">2014-08-19</td>
<td align="center">N6</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2016-05-24</td>
<td align="center">G7</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">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2013-12-10</td>
<td align="center">H10</td>
<td align="center">2014-02-26</td>
<td align="center">R3</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2011-12-02</td>
<td align="center">H2</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">M</td>
</tr>
<tr class="even">
<td align="center">2011-05-29</td>
<td align="center">C5</td>
<td align="center">Hospital A</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
@ -356,19 +356,8 @@
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2016-04-01</td>
<td align="center">S7</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">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2017-12-01</td>
<td align="center">S1</td>
<td align="center">2017-07-23</td>
<td align="center">U3</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
@ -377,6 +366,17 @@
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2011-11-18</td>
<td align="center">C7</td>
<td align="center">Hospital D</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">M</td>
</tr>
</tbody>
</table>
<p>Now, let’s start the cleaning and the analysis!</p>
@ -409,16 +409,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,499</td>
<td align="right">52.50%</td>
<td align="right">10,499</td>
<td align="right">52.50%</td>
<td align="right">10,514</td>
<td align="right">52.57%</td>
<td align="right">10,514</td>
<td align="right">52.57%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,501</td>
<td align="right">47.51%</td>
<td align="right">9,486</td>
<td align="right">47.43%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -472,9 +472,9 @@ Longest: 1</p>
<span><span class="co"># ℹ Using column 'patient_id' as input for `col_patient_id`.</span></span>
<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"># =&gt; Found 10,615 'phenotype-based' first isolates (53.1% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,709 'phenotype-based' first isolates (53.5% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 53.1% 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 53.5% 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>
@ -482,10 +482,10 @@ Longest: 1</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></code></pre></div>
<p>So we end up with 10,615 isolates for analysis. Now our data looks like:</p>
<p>So we end up with 10,709 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%">
@ -498,7 +498,7 @@ Longest: 1</p>
<col width="3%">
<col width="6%">
<col width="11%">
<col width="12%">
<col width="11%">
<col width="9%">
<col width="5%">
</colgroup>
@ -521,77 +521,29 @@ Longest: 1</p>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2014-09-28</td>
<td align="center">S6</td>
<td align="center">Hospital A</td>
<td align="center">2014-06-06</td>
<td align="center">A5</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">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">2</td>
<td align="center">2014-08-19</td>
<td align="center">N6</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">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">3</td>
<td align="center">2016-05-24</td>
<td align="center">G7</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">I</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-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">6</td>
<td align="center">2017-12-01</td>
<td align="center">S1</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">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="odd">
<td align="left">8</td>
<td align="center">2011-02-09</td>
<td align="center">B9</td>
<td align="center">Hospital C</td>
<tr class="even">
<td align="left">4</td>
<td align="center">2011-05-29</td>
<td align="center">C5</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">M</td>
<td align="center">Gram-positive</td>
@ -599,17 +551,65 @@ Longest: 1</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">7</td>
<td align="center">2010-02-05</td>
<td align="center">B6</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">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">11</td>
<td align="center">2015-02-05</td>
<td align="left">9</td>
<td align="center">2016-10-20</td>
<td align="center">F6</td>
<td align="center">Hospital B</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">R</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="odd">
<td align="left">13</td>
<td align="center">2010-05-11</td>
<td align="center">G7</td>
<td align="center">Hospital D</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">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="even">
<td align="left">14</td>
<td align="center">2010-04-05</td>
<td align="center">T2</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">S</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>
@ -636,8 +636,8 @@ 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: 10,615<br>
Available: 10,615 (100.0%, NA: 0 = 0.0%)<br>
Length: 10,709<br>
Available: 10,709 (100.0%, NA: 0 = 0.0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -654,33 +654,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">4,629</td>
<td align="right">43.61%</td>
<td align="right">4,629</td>
<td align="right">43.61%</td>
<td align="right">4,602</td>
<td align="right">42.97%</td>
<td align="right">4,602</td>
<td align="right">42.97%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,687</td>
<td align="right">25.31%</td>
<td align="right">7,316</td>
<td align="right">68.92%</td>
<td align="right">2,816</td>
<td align="right">26.30%</td>
<td align="right">7,418</td>
<td align="right">69.27%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,137</td>
<td align="right">20.13%</td>
<td align="right">9,453</td>
<td align="right">89.05%</td>
<td align="right">2,079</td>
<td align="right">19.41%</td>
<td align="right">9,497</td>
<td align="right">88.68%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,162</td>
<td align="right">10.95%</td>
<td align="right">10,615</td>
<td align="right">1,212</td>
<td align="right">11.32%</td>
<td align="right">10,709</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -699,14 +699,14 @@ Longest: 24</p>
<col width="9%">
<col width="9%">
<col width="9%">
<col width="10%">
<col width="11%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="6%">
<col width="11%">
<col width="12%">
<col width="11%">
<col width="9%">
<col width="5%">
</colgroup>
@ -727,13 +727,58 @@ Longest: 24</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2014-08-19</td>
<td align="center">N6</td>
<td align="center">2011-05-29</td>
<td align="center">C5</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-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2016-10-20</td>
<td align="center">F6</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">R</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="odd">
<td align="center">2011-12-15</td>
<td align="center">U7</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="center">2015-06-08</td>
<td align="center">U7</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
@ -741,14 +786,14 @@ Longest: 24</p>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2011-02-09</td>
<td align="center">B9</td>
<td align="center">Hospital C</td>
<tr class="odd">
<td align="center">2011-07-14</td>
<td align="center">J7</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
@ -756,64 +801,19 @@ Longest: 24</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2013-08-26</td>
<td align="center">V10</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2010-09-09</td>
<td align="center">Z10</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2015-09-08</td>
<td align="center">A6</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">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">2016-01-11</td>
<td align="center">T7</td>
<td align="center">2017-10-13</td>
<td align="center">G8</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</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">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">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
</tbody>
@ -837,50 +837,50 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">2208</td>
<td align="center">124</td>
<td align="center">2297</td>
<td align="center">4629</td>
<td align="center">2159</td>
<td align="center">125</td>
<td align="center">2318</td>
<td align="center">4602</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3392</td>
<td align="center">168</td>
<td align="center">1069</td>
<td align="center">4629</td>
<td align="center">3391</td>
<td align="center">140</td>
<td align="center">1071</td>
<td align="center">4602</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3361</td>
<td align="center">3331</td>
<td align="center">0</td>
<td align="center">1268</td>
<td align="center">4629</td>
<td align="center">1271</td>
<td align="center">4602</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4051</td>
<td align="center">4013</td>
<td align="center">0</td>
<td align="center">578</td>
<td align="center">4629</td>
<td align="center">589</td>
<td align="center">4602</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">1162</td>
<td align="center">1162</td>
<td align="center">1212</td>
<td align="center">1212</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">936</td>
<td align="center">31</td>
<td align="center">195</td>
<td align="center">1162</td>
<td align="center">980</td>
<td align="center">30</td>
<td align="center">202</td>
<td align="center">1212</td>
</tr>
</tbody>
</table>
@ -903,34 +903,34 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4051</td>
<td align="center">4013</td>
<td align="center">0</td>
<td align="center">578</td>
<td align="center">4629</td>
<td align="center">589</td>
<td align="center">4602</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1046</td>
<td align="center">1069</td>
<td align="center">0</td>
<td align="center">116</td>
<td align="center">1162</td>
<td align="center">143</td>
<td align="center">1212</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2370</td>
<td align="center">2505</td>
<td align="center">0</td>
<td align="center">317</td>
<td align="center">2687</td>
<td align="center">311</td>
<td align="center">2816</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">2137</td>
<td align="center">2137</td>
<td align="center">2079</td>
<td align="center">2079</td>
</tr>
</tbody>
</table>
@ -944,7 +944,7 @@ 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] 0.5423457</span></span></code></pre></div>
<span><span class="co"># [1] 0.5464563</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>
@ -958,19 +958,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5395931</td>
<td align="center">0.5425565</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5418251</td>
<td align="center">0.5403611</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5406250</td>
<td align="center">0.5634772</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5486436</td>
<td align="center">0.5504023</td>
</tr>
</tbody>
</table>
@ -989,23 +989,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5395931</td>
<td align="center">3195</td>
<td align="center">0.5425565</td>
<td align="center">3231</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5418251</td>
<td align="center">3682</td>
<td align="center">0.5403611</td>
<td align="center">3766</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5406250</td>
<td align="center">1600</td>
<td align="center">0.5634772</td>
<td align="center">1599</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5486436</td>
<td align="center">2138</td>
<td align="center">0.5504023</td>
<td align="center">2113</td>
</tr>
</tbody>
</table>
@ -1026,27 +1026,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7690646</td>
<td align="center">0.8751350</td>
<td align="center">0.9775329</td>
<td align="center">0.7672751</td>
<td align="center">0.8720122</td>
<td align="center">0.9778357</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8321859</td>
<td align="center">0.9001721</td>
<td align="center">0.9870912</td>
<td align="center">0.8333333</td>
<td align="center">0.8820132</td>
<td align="center">0.9768977</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7908448</td>
<td align="center">0.8820246</td>
<td align="center">0.9795311</td>
<td align="center">0.8004261</td>
<td align="center">0.8895597</td>
<td align="center">0.9808239</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5395414</td>
<td align="center">0.5430495</td>
<td align="center">0.0000000</td>
<td align="center">0.5395414</td>
<td align="center">0.5430495</td>
</tr>
</tbody>
</table>
@ -1071,23 +1071,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">54.0%</td>
<td align="right">26.6%</td>
<td align="right">54.3%</td>
<td align="right">26.3%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">54.2%</td>
<td align="right">25.7%</td>
<td align="right">54.0%</td>
<td align="right">25.3%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">54.1%</td>
<td align="right">28.1%</td>
<td align="right">56.3%</td>
<td align="right">27.4%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">54.9%</td>
<td align="right">26.4%</td>
<td align="right">55.0%</td>
<td align="right">25.8%</td>
</tr>
</tbody>
</table>
@ -1171,16 +1171,16 @@ 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 0.125 16 0.0625 2 0.001 0.0625 1 32 0.005 </span></span>
<span><span class="co"># [11] 8 0.0625 0.001 0.002 128 32 4 2 0.002 32 </span></span>
<span><span class="co"># [21] 128 16 1 4 256 16 128 64 0.5 8 </span></span>
<span><span class="co"># [31] 0.5 0.25 1 4 16 0.025 0.125 1 1 4 </span></span>
<span><span class="co"># [41] 0.002 16 4 16 128 0.002 8 0.001 0.001 0.005 </span></span>
<span><span class="co"># [51] 0.25 1 0.125 64 0.001 1 8 1 0.005 8 </span></span>
<span><span class="co"># [61] 2 0.025 0.001 0.125 0.025 0.001 256 0.01 2 0.002 </span></span>
<span><span class="co"># [71] 128 0.25 32 8 32 0.001 256 2 4 32 </span></span>
<span><span class="co"># [81] 64 0.002 0.25 4 8 32 0.25 0.5 0.0625 256 </span></span>
<span><span class="co"># [91] 0.25 0.025 0.002 1 0.005 0.025 1 2 0.002 64</span></span></code></pre></div>
<span><span class="co"># [1] 0.5 0.025 0.025 2 0.005 64 0.001 0.025 &gt;=256 0.025 </span></span>
<span><span class="co"># [11] 4 1 32 0.002 0.01 64 16 0.001 4 0.005 </span></span>
<span><span class="co"># [21] 0.125 2 &gt;=256 8 &gt;=256 64 0.5 64 0.0625 2 </span></span>
<span><span class="co"># [31] 128 1 4 8 &gt;=256 4 0.5 0.025 0.0625 &gt;=256 </span></span>
<span><span class="co"># [41] 0.125 64 1 &gt;=256 1 0.001 0.01 2 0.005 0.025 </span></span>
<span><span class="co"># [51] 16 0.001 8 32 0.025 1 0.025 0.25 64 0.125 </span></span>
<span><span class="co"># [61] 0.0625 0.01 128 0.5 0.025 0.001 32 0.001 0.01 0.0625</span></span>
<span><span class="co"># [71] 8 2 0.25 0.002 2 0.01 0.025 0.025 128 128 </span></span>
<span><span class="co"># [81] 0.002 1 0.25 &gt;=256 128 &gt;=256 0.5 0.0625 4 0.01 </span></span>
<span><span class="co"># [91] 0.002 0.002 0.0625 2 0.01 8 0.0625 0.01 0.025 0.25</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>
@ -1209,10 +1209,10 @@ 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] 24 28 17 23 27 26 28 29 30 17 27 18 20 30 28 22 29 28 21 21 27 19 20 25 19</span></span>
<span><span class="co"># [26] 24 26 24 24 31 18 24 31 24 27 20 25 22 20 24 18 27 29 29 28 20 28 17 31 31</span></span>
<span><span class="co"># [51] 24 19 22 24 26 29 18 29 27 22 28 26 29 23 23 23 30 19 31 28 31 24 26 23 29</span></span>
<span><span class="co"># [76] 22 17 23 29 26 24 22 20 27 20 23 31 23 25 23 31 23 28 23 31 25 20 23 22 27</span></span></code></pre></div>
<span><span class="co"># [1] 21 29 21 29 23 20 17 18 24 18 26 30 24 31 18 20 19 21 19 27 28 31 17 30 25</span></span>
<span><span class="co"># [26] 20 17 21 17 23 25 29 29 30 19 31 18 29 22 28 29 28 30 25 31 20 26 22 29 22</span></span>
<span><span class="co"># [51] 23 29 20 31 30 31 28 28 19 27 28 29 17 26 29 30 27 18 17 30 24 25 30 22 26</span></span>
<span><span class="co"># [76] 31 28 26 29 20 23 20 23 27 29 21 24 17 21 29 22 29 28 27 24 23 17 22 22 30</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>