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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="">1.8.2.9060</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9061</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -168,7 +168,7 @@
<h4 data-toc-skip class="author">Dr. Matthijs
Berends</h4>
<h4 data-toc-skip class="date">10 December 2022</h4>
<h4 data-toc-skip class="date">11 December 2022</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/AMR.Rmd" class="external-link"><code>vignettes/AMR.Rmd</code></a></small>
<div class="d-none name"><code>AMR.Rmd</code></div>
@@ -180,7 +180,7 @@ Berends</h4>
website update since they are based on randomly created values and the
page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
Markdown</a>. However, the methodology remains unchanged. This page was
generated on 10 December 2022.</p>
generated on 11 December 2022.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@@ -236,21 +236,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2022-12-10</td>
<td align="center">2022-12-11</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="center">2022-12-10</td>
<td align="center">2022-12-11</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<tr class="odd">
<td align="center">2022-12-10</td>
<td align="center">2022-12-11</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@@ -400,70 +400,70 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2012-03-09</td>
<td align="center">P2</td>
<td align="center">2014-06-10</td>
<td align="center">K4</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">M</td>
</tr>
<tr class="even">
<td align="center">2016-05-04</td>
<td align="center">F6</td>
<td align="center">Hospital A</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2014-07-20</td>
<td align="center">J2</td>
<td align="center">Hospital A</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">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2011-01-23</td>
<td align="center">O1</td>
<td align="center">2010-05-15</td>
<td align="center">N5</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">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2015-12-18</td>
<td align="center">O8</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">Klebsiella pneumoniae</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">F</td>
</tr>
<tr class="even">
<td align="center">2011-12-08</td>
<td align="center">I9</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">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2010-07-15</td>
<td align="center">J5</td>
<td align="center">2016-12-01</td>
<td align="center">T2</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</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">2014-12-28</td>
<td align="center">D6</td>
<td align="center">Hospital C</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">R</td>
<td align="center">2010-05-10</td>
<td align="center">W4</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">M</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
</tbody>
</table>
@@ -499,16 +499,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,307</td>
<td align="right">51.54%</td>
<td align="right">10,307</td>
<td align="right">51.54%</td>
<td align="right">10,335</td>
<td align="right">51.68%</td>
<td align="right">10,335</td>
<td align="right">51.68%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,693</td>
<td align="right">48.47%</td>
<td align="right">9,665</td>
<td align="right">48.33%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@@ -621,7 +621,7 @@ takes into account the antimicrobial susceptibility test results using
<span><span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span></span>
<span><span class="co"># 2</span></span>
<span><span class="co"># Including isolates from ICU.</span></span>
<span><span class="co"># =&gt; Found 10,602 'phenotype-based' first isolates (53.0% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,609 '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% 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
@@ -634,7 +634,7 @@ it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" cl
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="co"># Including isolates from ICU.</span></span></code></pre></div>
<p>So we end up with 10,602 isolates for analysis. Now our data looks
<p>So we end up with 10,609 isolates for analysis. Now our data looks
like:</p>
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">data_1st</span><span class="op">)</span></span></code></pre></div>
@@ -673,61 +673,29 @@ like:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2012-03-09</td>
<td align="center">P2</td>
<td align="left">2</td>
<td align="center">2016-05-04</td>
<td align="center">F6</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">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>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="center">2014-07-20</td>
<td align="center">J2</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">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="center">2011-01-23</td>
<td align="center">O1</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">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">9</td>
<td align="center">2015-07-08</td>
<td align="center">F4</td>
<td align="center">2010-05-15</td>
<td align="center">N5</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">S</td>
<td align="center">R</td>
<td align="center">M</td>
@@ -737,13 +705,13 @@ like:</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">12</td>
<td align="center">2017-05-31</td>
<td align="center">R4</td>
<td align="center">Hospital A</td>
<td align="left">4</td>
<td align="center">2015-12-18</td>
<td align="center">O8</td>
<td align="center">Hospital D</td>
<td align="center">B_KLBSL_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">S</td>
<td align="center">F</td>
@@ -753,21 +721,53 @@ like:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">13</td>
<td align="center">2010-09-11</td>
<td align="center">A3</td>
<td align="left">5</td>
<td align="center">2016-12-01</td>
<td align="center">T2</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">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">7</td>
<td align="center">2012-12-26</td>
<td align="center">U7</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">9</td>
<td align="center">2010-11-22</td>
<td align="center">R6</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">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>Time for the analysis!</p>
@@ -801,8 +801,8 @@ readable:</p>
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://msberends.github.io/cleaner/reference/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></span></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 10,602<br>
Available: 10,602 (100%, NA: 0 = 0%)<br>
Length: 10,609<br>
Available: 10,609 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@@ -827,33 +827,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">4,643</td>
<td align="right">43.79%</td>
<td align="right">4,643</td>
<td align="right">43.79%</td>
<td align="right">4,637</td>
<td align="right">43.71%</td>
<td align="right">4,637</td>
<td align="right">43.71%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,690</td>
<td align="right">25.37%</td>
<td align="right">7,333</td>
<td align="right">69.17%</td>
<td align="right">2,731</td>
<td align="right">25.74%</td>
<td align="right">7,368</td>
<td align="right">69.45%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,056</td>
<td align="right">19.39%</td>
<td align="right">9,389</td>
<td align="right">88.56%</td>
<td align="right">2,078</td>
<td align="right">19.59%</td>
<td align="right">9,446</td>
<td align="right">89.04%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,213</td>
<td align="right">11.44%</td>
<td align="right">10,602</td>
<td align="right">1,163</td>
<td align="right">10.96%</td>
<td align="right">10,609</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@@ -902,27 +902,27 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2012-03-09</td>
<td align="center">P2</td>
<td align="center">2016-05-04</td>
<td align="center">F6</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">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>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2015-07-08</td>
<td align="center">F4</td>
<td align="center">2010-05-15</td>
<td align="center">N5</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">S</td>
<td align="center">R</td>
<td align="center">M</td>
@@ -932,12 +932,12 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2016-01-05</td>
<td align="center">X1</td>
<td align="center">Hospital A</td>
<td align="center">2012-12-26</td>
<td align="center">U7</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">S</td>
<td align="center">R</td>
<td align="center">F</td>
@@ -947,9 +947,9 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2012-02-13</td>
<td align="center">U8</td>
<td align="center">Hospital B</td>
<td align="center">2010-11-22</td>
<td align="center">R6</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
@@ -962,35 +962,35 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2014-07-06</td>
<td align="center">P9</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">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="even">
<td align="center">2016-03-03</td>
<td align="center">B8</td>
<td align="center">Hospital B</td>
<td align="center">2015-02-05</td>
<td align="center">U1</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">R</td>
<td align="center">M</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2017-05-10</td>
<td align="center">T3</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">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
@@ -1013,50 +1013,50 @@ different bug/drug combinations, you can use the
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">2167</td>
<td align="center">142</td>
<td align="center">2169</td>
<td align="center">134</td>
<td align="center">2334</td>
<td align="center">4643</td>
<td align="center">4637</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3405</td>
<td align="center">3403</td>
<td align="center">162</td>
<td align="center">1076</td>
<td align="center">4643</td>
<td align="center">1072</td>
<td align="center">4637</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3364</td>
<td align="center">3398</td>
<td align="center">0</td>
<td align="center">1279</td>
<td align="center">4643</td>
<td align="center">1239</td>
<td align="center">4637</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4053</td>
<td align="center">4041</td>
<td align="center">0</td>
<td align="center">590</td>
<td align="center">4643</td>
<td align="center">596</td>
<td align="center">4637</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">1213</td>
<td align="center">1213</td>
<td align="center">1163</td>
<td align="center">1163</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">935</td>
<td align="center">36</td>
<td align="center">242</td>
<td align="center">1213</td>
<td align="center">906</td>
<td align="center">45</td>
<td align="center">212</td>
<td align="center">1163</td>
</tr>
</tbody>
</table>
@@ -1078,34 +1078,34 @@ different bug/drug combinations, you can use the
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4053</td>
<td align="center">4041</td>
<td align="center">0</td>
<td align="center">590</td>
<td align="center">4643</td>
<td align="center">596</td>
<td align="center">4637</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1087</td>
<td align="center">1041</td>
<td align="center">0</td>
<td align="center">126</td>
<td align="center">1213</td>
<td align="center">122</td>
<td align="center">1163</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2392</td>
<td align="center">2436</td>
<td align="center">0</td>
<td align="center">298</td>
<td align="center">2690</td>
<td align="center">295</td>
<td align="center">2731</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">2056</td>
<td align="center">2056</td>
<td align="center">2078</td>
<td align="center">2078</td>
</tr>
</tbody>
</table>
@@ -1137,7 +1137,7 @@ I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equa
own:</p>
<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span></span>
<span><span class="co"># [1] 0.5470666</span></span></code></pre></div>
<span><span class="co"># [1] 0.5435951</span></span></code></pre></div>
<p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and
<code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
@@ -1152,19 +1152,19 @@ own:</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5567929</td>
<td align="center">0.5376442</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5470541</td>
<td align="center">0.5473011</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5369212</td>
<td align="center">0.5522855</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5402844</td>
<td align="center">0.5400188</td>
</tr>
</tbody>
</table>
@@ -1189,23 +1189,23 @@ all isolates available for every group (i.e. values S, I or R):</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5567929</td>
<td align="center">3143</td>
<td align="center">0.5376442</td>
<td align="center">3294</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5470541</td>
<td align="center">3751</td>
<td align="center">0.5473011</td>
<td align="center">3594</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5369212</td>
<td align="center">1598</td>
<td align="center">0.5522855</td>
<td align="center">1597</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5402844</td>
<td align="center">2110</td>
<td align="center">0.5400188</td>
<td align="center">2124</td>
</tr>
</tbody>
</table>
@@ -1230,27 +1230,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7682533</td>
<td align="center">0.8729270</td>
<td align="center">0.9763084</td>
<td align="center">0.7688160</td>
<td align="center">0.8714686</td>
<td align="center">0.9775717</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8004946</td>
<td align="center">0.8961253</td>
<td align="center">0.9777411</td>
<td align="center">0.8177128</td>
<td align="center">0.8950989</td>
<td align="center">0.9819433</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7955390</td>
<td align="center">0.8892193</td>
<td align="center">0.9795539</td>
<td align="center">0.8033687</td>
<td align="center">0.8919810</td>
<td align="center">0.9794947</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5330739</td>
<td align="center">0.5413859</td>
<td align="center">0.0000000</td>
<td align="center">0.5330739</td>
<td align="center">0.5413859</td>
</tr>
</tbody>
</table>
@@ -1278,23 +1278,23 @@ classes, use a antibiotic class selector such as
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">55.7%</td>
<td align="right">26.3%</td>
<td align="right">53.8%</td>
<td align="right">26.2%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">54.7%</td>
<td align="right">27.3%</td>
<td align="right">26.7%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">53.7%</td>
<td align="right">26.7%</td>
<td align="right">55.2%</td>
<td align="right">25.7%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">54.0%</td>
<td align="right">26.0%</td>
<td align="right">25.4%</td>
</tr>
</tbody>
</table>
@@ -1410,18 +1410,18 @@ 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] 4 &gt;=256 0.25 &lt;=0.001 1 0.002 8 0.025 8 </span></span>
<span><span class="co"># [10] 1 64 0.0625 0.025 16 0.002 1 8 0.01 </span></span>
<span><span class="co"># [19] 0.025 0.01 4 &lt;=0.001 &gt;=256 0.25 0.125 32 4 </span></span>
<span><span class="co"># [28] 64 &lt;=0.001 64 &lt;=0.001 8 4 4 0.0625 0.125 </span></span>
<span><span class="co"># [37] 0.25 4 32 0.5 64 0.002 0.25 0.5 1 </span></span>
<span><span class="co"># [46] 4 0.005 1 32 0.005 0.005 0.125 16 0.025 </span></span>
<span><span class="co"># [55] 32 0.5 32 0.002 8 64 0.5 0.025 2 </span></span>
<span><span class="co"># [64] 32 0.5 4 0.0625 0.002 0.002 0.01 0.005 2 </span></span>
<span><span class="co"># [73] 4 0.002 0.5 64 0.125 32 0.01 4 &lt;=0.001</span></span>
<span><span class="co"># [82] 0.025 1 &lt;=0.001 0.25 0.0625 0.002 4 8 0.5 </span></span>
<span><span class="co"># [91] 0.25 128 32 0.025 0.125 32 32 32 0.5 </span></span>
<span><span class="co"># [100] 0.002</span></span></code></pre></div>
<span><span class="co"># [1] 0.005 0.0625 &lt;=0.001 8 0.025 0.01 8 0.0625 128 </span></span>
<span><span class="co"># [10] 2 0.025 32 1 128 32 2 0.002 &lt;=0.001</span></span>
<span><span class="co"># [19] 8 8 64 64 0.25 0.005 0.0625 8 0.5 </span></span>
<span><span class="co"># [28] 0.0625 0.25 1 64 1 32 16 16 1 </span></span>
<span><span class="co"># [37] 16 0.005 0.25 64 &gt;=256 0.01 2 0.025 0.01 </span></span>
<span><span class="co"># [46] 64 0.5 16 0.01 &gt;=256 0.025 32 0.025 0.5 </span></span>
<span><span class="co"># [55] 0.025 16 &gt;=256 0.01 32 0.125 4 1 8 </span></span>
<span><span class="co"># [64] 128 128 0.0625 2 &gt;=256 64 0.005 0.0625 0.25 </span></span>
<span><span class="co"># [73] 0.002 0.025 2 32 0.005 0.25 64 0.5 4 </span></span>
<span><span class="co"># [82] 128 4 1 16 0.01 8 2 64 0.0625 </span></span>
<span><span class="co"># [91] 64 32 1 4 16 &gt;=256 32 0.25 2 </span></span>
<span><span class="co"># [100] 0.005</span></span></code></pre></div>
<div class="sourceCode" id="cb36"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">mic_values</span><span class="op">)</span></span></code></pre></div>
@@ -1455,10 +1455,10 @@ 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] 24 24 29 30 27 19 20 20 20 19 24 26 19 21 24 28 30 25 25 22 30 29 18 30 18</span></span>
<span><span class="co"># [26] 25 21 23 31 30 26 17 23 21 27 27 24 28 25 22 18 25 29 25 30 30 23 30 23 26</span></span>
<span><span class="co"># [51] 26 20 31 20 18 27 26 22 22 20 30 23 20 26 22 31 21 22 23 25 24 23 23 18 18</span></span>
<span><span class="co"># [76] 17 19 25 17 27 25 17 26 21 24 30 31 30 18 19 30 23 17 27 30 18 21 26 28 24</span></span></code></pre></div>
<span><span class="co"># [1] 21 23 25 27 17 22 21 27 27 22 29 31 31 29 17 18 20 26 27 29 24 26 30 25 23</span></span>
<span><span class="co"># [26] 22 22 19 29 21 31 29 22 29 21 17 26 21 20 28 26 24 21 25 23 25 28 28 29 21</span></span>
<span><span class="co"># [51] 28 20 17 18 27 25 30 28 30 18 22 23 26 31 26 28 27 18 19 22 22 27 28 28 30</span></span>
<span><span class="co"># [76] 29 26 20 20 26 28 19 27 23 20 21 17 30 24 26 25 30 26 28 20 20 27 31 31 18</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>
@@ -1536,12 +1536,12 @@ different.</p>
<footer><div class="pkgdown-footer-left">
<p></p>
<p><code>AMR</code> (for R). Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> in collaboration with non-profit organisations<br><a target="_blank" href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p>
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p>
</div>
<div class="pkgdown-footer-right">
<p></p>
<p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_rug.svg" style="max-width: 150px;"></a></p>
<p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_rug.svg" style="max-width: 150px;"></a><a target="_blank" href="https://www.umcg.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_umcg.svg" style="max-width: 150px;"></a></p>
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</footer>