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<a class="navbar-brand me-2" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9118</small>
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<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</small>
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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="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</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">
@ -178,7 +178,7 @@
<h4 data-toc-skip class="author">Dr. Matthijs
Berends</h4>
<h4 data-toc-skip class="date">11 February 2023</h4>
<h4 data-toc-skip class="date">12 February 2023</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/AMR.Rmd" class="external-link"><code>vignettes/AMR.Rmd</code></a></small>
<div class="d-none name"><code>AMR.Rmd</code></div>
@ -190,7 +190,7 @@ Berends</h4>
website update since they are based on randomly created values and the
page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
Markdown</a>. However, the methodology remains unchanged. This page was
generated on 11 February 2023.</p>
generated on 12 February 2023.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@ -246,21 +246,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2023-02-11</td>
<td align="center">2023-02-12</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="center">2023-02-11</td>
<td align="center">2023-02-12</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<tr class="odd">
<td align="center">2023-02-11</td>
<td align="center">2023-02-12</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -411,68 +411,68 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2012-01-10</td>
<td align="center">X7</td>
<td align="center">2011-02-07</td>
<td align="center">G7</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">M</td>
</tr>
<tr class="even">
<td align="center">2016-04-30</td>
<td align="center">C8</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2017-01-11</td>
<td align="center">D6</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2013-10-15</td>
<td align="center">Y7</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">2013-01-08</td>
<td align="center">R7</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2014-07-13</td>
<td align="center">B3</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">2010-01-11</td>
<td align="center">Z6</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</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">M</td>
<td align="center">R</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2017-10-17</td>
<td align="center">C2</td>
<td align="center">2017-06-16</td>
<td align="center">P4</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2017-06-05</td>
<td align="center">C6</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">M</td>
</tr>
<tr class="even">
<td align="center">2010-11-25</td>
<td align="center">H4</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia 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>
</tr>
@ -510,16 +510,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,273</td>
<td align="right">51.37%</td>
<td align="right">10,273</td>
<td align="right">51.37%</td>
<td align="right">10,413</td>
<td align="right">52.07%</td>
<td align="right">10,413</td>
<td align="right">52.07%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,727</td>
<td align="right">48.64%</td>
<td align="right">9,587</td>
<td align="right">47.94%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -632,9 +632,9 @@ takes into account the antimicrobial susceptibility test results using
<span><span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span></span>
<span><span class="co"># 2</span></span>
<span><span class="co"># Including isolates from ICU.</span></span>
<span><span class="co"># =&gt; Found 12,300 'phenotype-based' first isolates (61.5% of total where a</span></span>
<span><span class="co"># =&gt; Found 12,241 'phenotype-based' first isolates (61.2% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 61.5% is suitable for resistance analysis! We can now filter
<p>So only 61.2% is suitable for resistance analysis! We can now filter
on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the
<code>dplyr</code> package:</p>
<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
@ -644,11 +644,11 @@ on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html"
<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 12 300 isolates for analysis. Now our data looks
<p>So we end up with 12 241 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%">
@ -662,7 +662,7 @@ like:</p>
<col width="6%">
<col width="11%">
<col width="12%">
<col width="9%">
<col width="7%">
<col width="5%">
</colgroup>
<thead><tr class="header">
@ -683,74 +683,58 @@ like:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2011-02-07</td>
<td align="center">G7</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">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="left">2</td>
<td align="center">2017-01-11</td>
<td align="center">D6</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">2016-04-30</td>
<td align="center">C8</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">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">10</td>
<td align="center">2011-03-19</td>
<td align="center">U9</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">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">11</td>
<td align="center">2010-12-27</td>
<td align="center">A2</td>
<td align="left">3</td>
<td align="center">2013-01-08</td>
<td align="center">R7</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">12</td>
<td align="center">2012-12-11</td>
<td align="center">I9</td>
<td align="center">Hospital B</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">13</td>
<td align="center">2015-07-02</td>
<td align="center">Y10</td>
<td align="center">Hospital D</td>
<td align="left">4</td>
<td align="center">2010-01-11</td>
<td align="center">Z6</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">R</td>
@ -762,22 +746,38 @@ like:</p>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">15</td>
<td align="center">2015-08-12</td>
<td align="center">V4</td>
<td align="center">Hospital B</td>
<tr class="odd">
<td align="left">6</td>
<td align="center">2017-06-05</td>
<td align="center">C6</td>
<td align="center">Hospital C</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">F</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-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">7</td>
<td align="center">2015-07-18</td>
<td align="center">F7</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">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>
</tbody>
</table>
<p>Time for the analysis!</p>
@ -811,8 +811,8 @@ readable:</p>
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://msberends.github.io/cleaner/reference/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></span></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 12,300<br>
Available: 12,300 (100%, NA: 0 = 0%)<br>
Length: 12,241<br>
Available: 12,241 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -837,33 +837,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">5,826</td>
<td align="right">47.37%</td>
<td align="right">5,826</td>
<td align="right">47.37%</td>
<td align="right">5,831</td>
<td align="right">47.63%</td>
<td align="right">5,831</td>
<td align="right">47.63%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,233</td>
<td align="right">26.28%</td>
<td align="right">9,059</td>
<td align="right">73.65%</td>
<td align="right">3,241</td>
<td align="right">26.48%</td>
<td align="right">9,072</td>
<td align="right">74.11%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">1,875</td>
<td align="right">15.24%</td>
<td align="right">10,934</td>
<td align="right">88.89%</td>
<td align="right">1,857</td>
<td align="right">15.17%</td>
<td align="right">10,929</td>
<td align="right">89.28%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,366</td>
<td align="right">11.11%</td>
<td align="right">12,300</td>
<td align="right">1,312</td>
<td align="right">10.72%</td>
<td align="right">12,241</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -884,15 +884,15 @@ antibiotic class they are in:</p>
<col width="9%">
<col width="9%">
<col width="9%">
<col width="10%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="6%">
<col width="11%">
<col width="4%">
<col width="4%">
<col width="4%">
<col width="4%">
<col width="6%">
<col width="12%">
<col width="9%">
<col width="12%">
<col width="7%">
<col width="5%">
</colgroup>
<thead><tr class="header">
@ -912,24 +912,24 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2012-12-11</td>
<td align="center">I9</td>
<td align="center">2011-02-07</td>
<td align="center">G7</td>
<td align="center">Hospital B</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">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="center">2015-07-02</td>
<td align="center">Y10</td>
<td align="center">Hospital D</td>
<td align="center">2010-01-11</td>
<td align="center">Z6</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">R</td>
@ -942,13 +942,13 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2012-09-28</td>
<td align="center">N1</td>
<td align="center">Hospital D</td>
<td align="center">2015-07-18</td>
<td align="center">F7</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">I</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
@ -957,28 +957,13 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2011-07-31</td>
<td align="center">K9</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">I</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">2012-06-02</td>
<td align="center">V9</td>
<td align="center">2017-10-11</td>
<td align="center">X3</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">I</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>
@ -986,19 +971,34 @@ antibiotic class they are in:</p>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2012-02-06</td>
<td align="center">M7</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<tr class="odd">
<td align="center">2015-05-07</td>
<td align="center">J3</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</td>
<td align="center">I</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">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">2013-12-05</td>
<td align="center">D10</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">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>
</tbody>
@ -1012,6 +1012,7 @@ different bug/drug combinations, you can use the
<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="op">)</span> <span class="co"># show first 6 rows</span></span></code></pre></div>
<table class="table">
<thead><tr class="header">
<th align="left"></th>
<th align="center">mo</th>
<th align="center">ab</th>
<th align="center">S</th>
@ -1021,52 +1022,58 @@ different bug/drug combinations, you can use the
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">2</td>
<td align="center">E. coli</td>
<td align="center">S</td>
<td align="center">1489</td>
<td align="center">1236</td>
<td align="center">3101</td>
<td align="center">5826</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">S1</td>
<td align="center">2720</td>
<td align="center">AMC</td>
<td align="center">2728</td>
<td align="center">1160</td>
<td align="center">1946</td>
<td align="center">5826</td>
<td align="center">1943</td>
<td align="center">5831</td>
</tr>
<tr class="even">
<td align="left">1</td>
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">1490</td>
<td align="center">1233</td>
<td align="center">3108</td>
<td align="center">5831</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="center">E. coli</td>
<td align="center">S2</td>
<td align="center">1974</td>
<td align="center">1845</td>
<td align="center">CIP</td>
<td align="center">2007</td>
<td align="center">5826</td>
<td align="center">1763</td>
<td align="center">2061</td>
<td align="center">5831</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="center">E. coli</td>
<td align="center">S3</td>
<td align="center">2027</td>
<td align="center">1830</td>
<td align="center">1969</td>
<td align="center">5826</td>
<td align="center">GEN</td>
<td align="center">1949</td>
<td align="center">1853</td>
<td align="center">2029</td>
<td align="center">5831</td>
</tr>
<tr class="odd">
<td align="left">6</td>
<td align="center">K. pneumoniae</td>
<td align="center">S</td>
<td align="center">0</td>
<td align="center">0</td>
<td align="center">1366</td>
<td align="center">1366</td>
<td align="center">AMC</td>
<td align="center">584</td>
<td align="center">249</td>
<td align="center">479</td>
<td align="center">1312</td>
</tr>
<tr class="even">
<td align="left">5</td>
<td align="center">K. pneumoniae</td>
<td align="center">S1</td>
<td align="center">570</td>
<td align="center">310</td>
<td align="center">486</td>
<td align="center">1366</td>
<td align="center">AMX</td>
<td align="center">0</td>
<td align="center">0</td>
<td align="center">1312</td>
<td align="center">1312</td>
</tr>
</tbody>
</table>
@ -1087,35 +1094,35 @@ different bug/drug combinations, you can use the
<tbody>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">S</td>
<td align="center">2027</td>
<td align="center">1830</td>
<td align="center">1969</td>
<td align="center">5826</td>
<td align="center">GEN</td>
<td align="center">1949</td>
<td align="center">1853</td>
<td align="center">2029</td>
<td align="center">5831</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">S</td>
<td align="center">501</td>
<td align="center">402</td>
<td align="center">463</td>
<td align="center">1366</td>
<td align="center">GEN</td>
<td align="center">452</td>
<td align="center">426</td>
<td align="center">434</td>
<td align="center">1312</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">S</td>
<td align="center">1155</td>
<td align="center">992</td>
<td align="center">1086</td>
<td align="center">3233</td>
<td align="center">GEN</td>
<td align="center">1098</td>
<td align="center">1008</td>
<td align="center">1135</td>
<td align="center">3241</td>
</tr>
<tr class="even">
<td align="center">S. pneumoniae</td>
<td align="center">S</td>
<td align="center">GEN</td>
<td align="center">0</td>
<td align="center">0</td>
<td align="center">1875</td>
<td align="center">1875</td>
<td align="center">1857</td>
<td align="center">1857</td>
</tr>
</tbody>
</table>
@ -1147,7 +1154,7 @@ 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] 0.59</span></span></code></pre></div>
<span><span class="co"># [1] 0.5836941</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">
@ -1162,19 +1169,19 @@ own:</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5931973</td>
<td align="center">0.5864297</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5891020</td>
<td align="center">0.5778776</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5969416</td>
<td align="center">0.5783004</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5818110</td>
<td align="center">0.5938144</td>
</tr>
</tbody>
</table>
@ -1199,23 +1206,23 @@ 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">0.5931973</td>
<td align="center">3675</td>
<td align="center">0.5864297</td>
<td align="center">3714</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5891020</td>
<td align="center">4276</td>
<td align="center">0.5778776</td>
<td align="center">4231</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5969416</td>
<td align="center">1831</td>
<td align="center">0.5783004</td>
<td align="center">1871</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5818110</td>
<td align="center">2518</td>
<td align="center">0.5938144</td>
<td align="center">2425</td>
</tr>
</tbody>
</table>
@ -1240,27 +1247,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.6659801</td>
<td align="center">0.6620323</td>
<td align="center">0.8884312</td>
<td align="center">0.6667810</td>
<td align="center">0.6520322</td>
<td align="center">0.8814955</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.6442167</td>
<td align="center">0.6610542</td>
<td align="center">0.8755490</td>
<td align="center">0.6349085</td>
<td align="center">0.6692073</td>
<td align="center">0.8833841</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.6523353</td>
<td align="center">0.6640891</td>
<td align="center">0.8892669</td>
<td align="center">0.6599815</td>
<td align="center">0.6497994</td>
<td align="center">0.8707189</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.4650667</td>
<td align="center">0.4787291</td>
<td align="center">0.0000000</td>
<td align="center">0.4650667</td>
<td align="center">0.4787291</td>
</tr>
</tbody>
</table>
@ -1288,23 +1295,23 @@ classes, use a antibiotic class selector such as
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">59.3%</td>
<td align="right">37.6%</td>
<td align="right">58.6%</td>
<td align="right">36.7%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">58.9%</td>
<td align="right">37.3%</td>
<td align="right">57.8%</td>
<td align="right">36.4%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">59.7%</td>
<td align="right">36.4%</td>
<td align="right">57.8%</td>
<td align="right">37.7%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">58.2%</td>
<td align="right">36.3%</td>
<td align="right">59.4%</td>
<td align="right">36.5%</td>
</tr>
</tbody>
</table>
@ -1420,16 +1427,18 @@ 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 0.5 0.0625 0.25 64 0.025 0.002 128 0.25 16 </span></span>
<span><span class="co"># [11] 0.0625 0.002 32 32 64 &gt;=256 0.005 0.25 32 2 </span></span>
<span><span class="co"># [21] 4 0.002 0.01 128 &gt;=256 0.0625 2 0.002 4 0.001 </span></span>
<span><span class="co"># [31] 4 8 128 0.001 0.0625 32 0.01 0.002 64 16 </span></span>
<span><span class="co"># [41] 8 16 0.25 0.25 0.001 64 128 0.025 0.01 2 </span></span>
<span><span class="co"># [51] 0.01 1 0.0625 8 4 8 0.25 128 0.002 0.001 </span></span>
<span><span class="co"># [61] 1 2 0.25 0.5 128 0.125 0.125 1 0.5 0.001 </span></span>
<span><span class="co"># [71] 0.002 0.002 16 64 0.0625 2 0.0625 0.025 0.5 0.002 </span></span>
<span><span class="co"># [81] 4 &gt;=256 0.01 32 0.025 0.002 0.125 128 8 4 </span></span>
<span><span class="co"># [91] 0.005 4 1 4 128 &gt;=256 0.01 8 128 32</span></span></code></pre></div>
<span><span class="co"># [1] 0.01 &gt;=256 &lt;=0.001 8 0.005 0.005 0.01 1 4 </span></span>
<span><span class="co"># [10] &gt;=256 0.0625 4 16 0.01 32 0.01 &gt;=256 32 </span></span>
<span><span class="co"># [19] 4 0.0625 0.005 64 128 8 &lt;=0.001 0.25 0.005 </span></span>
<span><span class="co"># [28] 0.0625 &lt;=0.001 0.125 0.0625 0.025 0.01 2 32 4 </span></span>
<span><span class="co"># [37] 4 128 0.002 &lt;=0.001 0.025 &gt;=256 0.125 0.5 2 </span></span>
<span><span class="co"># [46] 0.025 0.005 &gt;=256 16 0.5 2 0.25 0.25 0.25 </span></span>
<span><span class="co"># [55] 64 8 &lt;=0.001 8 4 0.0625 &lt;=0.001 0.0625 1 </span></span>
<span><span class="co"># [64] 0.0625 0.01 1 0.002 16 &lt;=0.001 0.125 0.005 0.0625 </span></span>
<span><span class="co"># [73] 16 0.125 128 0.005 16 64 8 16 &lt;=0.001</span></span>
<span><span class="co"># [82] 16 4 2 0.002 64 8 64 0.5 0.025 </span></span>
<span><span class="co"># [91] 1 0.025 1 32 0.002 16 0.125 0.125 16 </span></span>
<span><span class="co"># [100] 0.01</span></span></code></pre></div>
<div class="sourceCode" id="cb36"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">mic_values</span><span class="op">)</span></span></code></pre></div>
@ -1463,10 +1472,10 @@ 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] 31 21 27 24 29 23 31 18 22 25 23 27 28 21 26 20 18 30 29 28 25 25 22 17 27</span></span>
<span><span class="co"># [26] 22 26 30 24 25 27 18 28 20 25 30 28 22 22 31 30 27 25 22 26 21 30 31 20 27</span></span>
<span><span class="co"># [51] 31 21 22 19 21 19 29 29 19 31 30 18 18 19 27 18 18 27 29 28 21 23 18 29 20</span></span>
<span><span class="co"># [76] 17 20 18 22 25 21 20 28 26 27 22 19 30 19 18 29 28 29 23 19 21 18 25 19 17</span></span></code></pre></div>
<span><span class="co"># [1] 20 19 27 26 31 31 29 20 28 29 17 25 20 20 26 30 21 26 28 26 29 28 25 17 19</span></span>
<span><span class="co"># [26] 18 25 25 24 21 21 17 25 17 31 18 21 18 21 30 18 29 20 27 29 29 19 25 21 22</span></span>
<span><span class="co"># [51] 30 25 30 21 22 23 25 22 27 19 17 30 28 25 17 19 21 26 18 22 31 27 21 26 20</span></span>
<span><span class="co"># [76] 21 30 24 26 17 31 23 23 23 19 25 31 17 21 23 24 22 29 23 24 21 22 27 27 23</span></span></code></pre></div>
<div class="sourceCode" id="cb42"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">disk_values</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></code></pre></div>

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@ -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="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</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">

58
articles/MDR.html
View File

@ -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="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</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">
@ -385,18 +385,18 @@ names or codes, this would have worked exactly the same way:</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span>
<span><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
<span><span class="co"># 1 S R I I S I</span></span>
<span><span class="co"># 2 S S S S I R</span></span>
<span><span class="co"># 3 I S R R I S</span></span>
<span><span class="co"># 4 R S S I S R</span></span>
<span><span class="co"># 5 S I S I S I</span></span>
<span><span class="co"># 6 R S R R R S</span></span>
<span><span class="co"># 1 S I S R I S</span></span>
<span><span class="co"># 2 S R I I R I</span></span>
<span><span class="co"># 3 S S S S R R</span></span>
<span><span class="co"># 4 S R S I I R</span></span>
<span><span class="co"># 5 S I R S R I</span></span>
<span><span class="co"># 6 S R I R R S</span></span>
<span><span class="co"># kanamycin</span></span>
<span><span class="co"># 1 S</span></span>
<span><span class="co"># 1 I</span></span>
<span><span class="co"># 2 S</span></span>
<span><span class="co"># 3 R</span></span>
<span><span class="co"># 4 S</span></span>
<span><span class="co"># 5 S</span></span>
<span><span class="co"># 3 S</span></span>
<span><span class="co"># 4 R</span></span>
<span><span class="co"># 5 I</span></span>
<span><span class="co"># 6 S</span></span></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can
use:</p>
@ -438,40 +438,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3210</td>
<td align="right">64.20%</td>
<td align="right">3210</td>
<td align="right">64.20%</td>
<td align="right">3144</td>
<td align="right">62.88%</td>
<td align="right">3144</td>
<td align="right">62.88%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">1036</td>
<td align="right">20.72%</td>
<td align="right">4246</td>
<td align="right">84.92%</td>
<td align="right">1032</td>
<td align="right">20.64%</td>
<td align="right">4176</td>
<td align="right">83.52%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">418</td>
<td align="right">8.36%</td>
<td align="right">4664</td>
<td align="right">93.28%</td>
<td align="right">465</td>
<td align="right">9.30%</td>
<td align="right">4641</td>
<td align="right">92.82%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">229</td>
<td align="right">4.58%</td>
<td align="right">4893</td>
<td align="right">97.86%</td>
<td align="right">263</td>
<td align="right">5.26%</td>
<td align="right">4904</td>
<td align="right">98.08%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">107</td>
<td align="right">2.14%</td>
<td align="right">96</td>
<td align="right">1.92%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

4
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</small>
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@ -290,7 +290,7 @@ function:</p>
<span><span class="co"># [1] "Caryophanales" "Enterobacterales" "Lactobacillales" "Pseudomonadales"</span></span>
<span><span class="co"># Importance of components:</span></span>
<span><span class="co"># PC1 PC2 PC3 PC4 PC5 PC6 PC7</span></span>
<span><span class="co"># Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 9.577e-17</span></span>
<span><span class="co"># Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 1.232e-16</span></span>
<span><span class="co"># Proportion of Variance 0.5799 0.3531 0.0471 0.01435 0.00541 0.00012 0.000e+00</span></span>
<span><span class="co"># Cumulative Proportion 0.5799 0.9330 0.9801 0.99446 0.99988 1.00000 1.000e+00</span></span></code></pre></div>
<pre><code><span><span class="co"># Groups (n=4, named as 'order'):</span></span>

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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9118</small>
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@ -178,7 +178,7 @@
<h4 data-toc-skip class="author">Dr. Matthijs
Berends</h4>
<h4 data-toc-skip class="date">11 February 2023</h4>
<h4 data-toc-skip class="date">12 February 2023</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/SPSS.Rmd" class="external-link"><code>vignettes/SPSS.Rmd</code></a></small>
<div class="d-none name"><code>SPSS.Rmd</code></div>

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@ -38,7 +38,7 @@
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</small>
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@ -176,7 +176,7 @@
<main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
<h4 data-toc-skip class="date">11 February 2023</h4>
<h4 data-toc-skip class="date">12 February 2023</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<div class="d-none name"><code>datasets.Rmd</code></div>

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@ -42,7 +42,7 @@
<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="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</small>
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@ -210,7 +210,7 @@
</h5>
<p><a href="./countries_large.png"><img src="./countries.png" target="_blank" align="right" style="max-width: 300px;"></a></p>
<p>Since its first public release in early 2018, this R package has been used in almost all countries in the world. Click the map to enlarge and to see the country names.</p>
<p>With the help of contributors from all corners of the world, the <code>AMR</code> package is available in <img src="lang_en.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> English, <img src="lang_cs.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Czech, <img src="lang_zh.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Chinese, <img src="lang_da.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Danish, <img src="lang_nl.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Dutch, <img src="lang_fi.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Finnish, <img src="lang_fr.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> French, <img src="lang_de.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> German, <img src="lang_el.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Greek, <img src="lang_it.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Italian, <img src="lang_ja.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Japanese, <img src="lang_pl.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Polish, <img src="lang_pt.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Portuguese, <img src="lang_ru.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Russian, <img src="lang_es.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Spanish, <img src="lang_sv.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Swedish, <img src="lang_tr.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Turkish, and <img src="lang_uk.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.</p>
<p>With the help of contributors from all corners of the world, the <code>AMR</code> package is available in <img src="lang_en.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> English, <img src="lang_cs.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Czech, <img src="lang_zh.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Chinese, <img src="lang_da.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Danish, <img src="lang_nl.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Dutch, <img src="lang_fi.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Finnish, <img src="lang_fr.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> French, <img src="lang_de.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> German, <img src="lang_el.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Greek, <img src="lang_it.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Italian, <img src="lang_ja.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Japanese, <img src="lang_no.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Norwegian, <img src="lang_pl.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Polish, <img src="lang_pt.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Portuguese, <img src="lang_ro.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Romanian, <img src="lang_ru.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Russian, <img src="lang_es.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Spanish, <img src="lang_sv.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Swedish, <img src="lang_tr.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Turkish, and <img src="lang_uk.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.</p>
</div>
</div>
<div class="section level3">

26
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -142,7 +142,7 @@
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="1.8.2.9118" id="amr-1829118">AMR 1.8.2.9118<a class="anchor" aria-label="anchor" href="#amr-1829118"></a></h2>
<h2 class="pkg-version" data-toc-text="1.8.2.9119" id="amr-1829119">AMR 1.8.2.9119<a class="anchor" aria-label="anchor" href="#amr-1829119"></a></h2>
<p><em>(this beta version will eventually become v2.0! We’re happy to reach a new major milestone soon!)</em></p>
<p>This is a new major release of the AMR package, with great new additions but also some breaking changes for current users. These are all listed below.</p>
<p><strong><a href="https://en.wikipedia.org/wiki/TL;DR" class="external-link">TL;DR</a></strong></p>
@ -156,31 +156,31 @@
<li>Now available in 20 languages</li>
<li>Many small bug fixes</li>
</ul><div class="section level3">
<h3 id="new-1-8-2-9118">New<a class="anchor" aria-label="anchor" href="#new-1-8-2-9118"></a></h3>
<h3 id="new-1-8-2-9119">New<a class="anchor" aria-label="anchor" href="#new-1-8-2-9119"></a></h3>
<div class="section level4">
<h4 id="sir-vs-rsi-1-8-2-9118">SIR vs. RSI<a class="anchor" aria-label="anchor" href="#sir-vs-rsi-1-8-2-9118"></a></h4>
<h4 id="sir-vs-rsi-1-8-2-9119">SIR vs. RSI<a class="anchor" aria-label="anchor" href="#sir-vs-rsi-1-8-2-9119"></a></h4>
<p>For this milestone version, we replaced all mentions of RSI with SIR, to comply with what is actually being commonly used in the field of clinical microbiology when it comes to this tri-form regarding AMR.</p>
<p>While existing functions such as <code><a href="../reference/AMR-deprecated.html">as.rsi()</a></code>, <code><a href="../reference/AMR-deprecated.html">rsi_df()</a></code> and <code><a href="../reference/AMR-deprecated.html">ggplot_rsi()</a></code> still work, their replacements <code><a href="../reference/as.sir.html">as.sir()</a></code>, <code><a href="../reference/proportion.html">sir_df()</a></code>, <code><a href="../reference/ggplot_sir.html">ggplot_sir()</a></code> are now the current functions for AMR data analysis. A warning will be thrown once a session to remind users about this. The data set <code>rsi_translation</code> is now called <code>clinical_breakpoints</code> to better reflect its content.</p>
<p>The ‘RSI functions’ will be removed in a future version, but not before late 2023 / early 2024.</p>
</div>
<div class="section level4">
<h4 id="new-antibiogram-function-1-8-2-9118">New antibiogram function<a class="anchor" aria-label="anchor" href="#new-antibiogram-function-1-8-2-9118"></a></h4>
<h4 id="new-antibiogram-function-1-8-2-9119">New antibiogram function<a class="anchor" aria-label="anchor" href="#new-antibiogram-function-1-8-2-9119"></a></h4>
<p>With the new <code><a href="../reference/antibiogram.html">antibiogram()</a></code> function, users can now generate traditional, combined, syndromic, and even weighted-incidence syndromic combination antibiograms (WISCA). With this, we follow the logic in the previously described work of Klinker <em>et al.</em> (2021, DOI <a href="https://doi.org/10.1177/20499361211011373" class="external-link">10.1177/20499361211011373</a>) and Barbieri <em>et al.</em> (2021, DOI <a href="https://doi.org/10.1186/s13756-021-00939-2" class="external-link">10.1186/s13756-021-00939-2</a>).</p>
<p>The help page for <code><a href="../reference/antibiogram.html">antibiogram()</a></code> extensively elaborates on use cases, and <code><a href="../reference/antibiogram.html">antibiogram()</a></code> also supports printing in R Markdown and Quarto, with support for 20 languages.</p>
<p>Furthermore, different plotting methods were implemented to allow for graphical visualisations as well.</p>
</div>
<div class="section level4">
<h4 id="interpretation-of-mic-and-disk-diffusion-values-1-8-2-9118">Interpretation of MIC and disk diffusion values<a class="anchor" aria-label="anchor" href="#interpretation-of-mic-and-disk-diffusion-values-1-8-2-9118"></a></h4>
<h4 id="interpretation-of-mic-and-disk-diffusion-values-1-8-2-9119">Interpretation of MIC and disk diffusion values<a class="anchor" aria-label="anchor" href="#interpretation-of-mic-and-disk-diffusion-values-1-8-2-9119"></a></h4>
<p>The clinical breakpoints and intrinsic resistance of EUCAST 2022 and CLSI 2022 have been added for <code><a href="../reference/as.sir.html">as.sir()</a></code>. EUCAST 2022 (v12.0) is now the new default guideline for all MIC and disks diffusion interpretations, and for <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> to apply EUCAST Expert Rules. The default guideline (EUCAST) can now be changed with the new <code>AMR_guideline</code> option, such as: <code>options(AMR_guideline = "CLSI 2020")</code>.</p>
<p>Interpretation guidelines older than 10 years were removed, the oldest now included guidelines of EUCAST and CLSI are from 2013.</p>
</div>
<div class="section level4">
<h4 id="supported-languages-1-8-2-9118">Supported languages<a class="anchor" aria-label="anchor" href="#supported-languages-1-8-2-9118"></a></h4>
<h4 id="supported-languages-1-8-2-9119">Supported languages<a class="anchor" aria-label="anchor" href="#supported-languages-1-8-2-9119"></a></h4>
<p>We added support for the following ten languages: Chinese (simplified), Czech, Finnish, Greek, Japanese, Norwegian (bokmål), Polish, Romanian, Turkish and Ukrainian. All antibiotic names are now available in these languages, and the AMR package will automatically determine a supported language based on the user’s system language.</p>
<p>We are very grateful for the valuable input by our colleagues from other countries. The <code>AMR</code> package is now available in 20 languages in total, and according to download stats used in almost all countries in the world!</p>
</div>
<div class="section level4">
<h4 id="microbiological-taxonomy-1-8-2-9118">Microbiological taxonomy<a class="anchor" aria-label="anchor" href="#microbiological-taxonomy-1-8-2-9118"></a></h4>
<h4 id="microbiological-taxonomy-1-8-2-9119">Microbiological taxonomy<a class="anchor" aria-label="anchor" href="#microbiological-taxonomy-1-8-2-9119"></a></h4>
<p>The <code>microorganisms</code> data set no longer relies on the Catalogue of Life, but on the List of Prokaryotic names with Standing in Nomenclature (LPSN) and is supplemented with the ‘backbone taxonomy’ from the Global Biodiversity Information Facility (GBIF). The structure of this data set has changed to include separate LPSN and GBIF identifiers. Almost all previous MO codes were retained. It contains over 1,400 taxonomic names from 2022.</p>
<p>We previously relied on our own experience to categorise species into pathogenic groups, but we were very happy to encounter the very recent work of Bartlett <em>et al.</em> (2022, DOI <a href="https://doi.org/10.1099/mic.0.001269" class="external-link">10.1099/mic.0.001269</a>) who extensively studied medical-scientific literature to categorise all bacterial species into groups. See <code><a href="../reference/mo_matching_score.html">mo_matching_score()</a></code> on how their work was incorporated into the <code>prevalence</code> column of the <code>microorganisms</code> data set. Using their results, the <code><a href="../reference/as.mo.html">as.mo()</a></code> and all <code>mo_*()</code> functions are now much better capable of converting user input to valid taxonomic records.</p>
<p>The new function <code><a href="../reference/add_custom_microorganisms.html">add_custom_microorganisms()</a></code> allows users to add custom microorganisms to the <code>AMR</code> package.</p>
@ -204,7 +204,7 @@
<li>The <code>microorganisms.old</code> data set was removed, and all previously accepted names are now included in the <code>microorganisms</code> data set. A new column <code>status</code> contains <code>"accepted"</code> for currently accepted names and <code>"synonym"</code> for taxonomic synonyms; currently invalid names. All previously accepted names now have a microorganisms ID and - if available - an LPSN, GBIF and SNOMED CT identifier.</li>
</ul></div>
<div class="section level4">
<h4 id="antibiotic-agents-and-selectors-1-8-2-9118">Antibiotic agents and selectors<a class="anchor" aria-label="anchor" href="#antibiotic-agents-and-selectors-1-8-2-9118"></a></h4>
<h4 id="antibiotic-agents-and-selectors-1-8-2-9119">Antibiotic agents and selectors<a class="anchor" aria-label="anchor" href="#antibiotic-agents-and-selectors-1-8-2-9119"></a></h4>
<p>The new function <code><a href="../reference/add_custom_antimicrobials.html">add_custom_antimicrobials()</a></code> allows users to add custom antimicrobial codes and names to the <code>AMR</code> package.</p>
<p>The <code>antibiotics</code> data set was greatly updated:</p>
<ul><li>The following 20 antibiotics have been added (also includes the <a href="https://www.whocc.no/atc_ddd_index/?code=J01RA&amp;showdescription=no" class="external-link">new J01RA ATC group</a>): azithromycin/fluconazole/secnidazole (AFC), cefepime/amikacin (CFA), cefixime/ornidazole (CEO), ceftriaxone/beta-lactamase inhibitor (CEB), ciprofloxacin/metronidazole (CIM), ciprofloxacin/ornidazole (CIO), ciprofloxacin/tinidazole (CIT), furazidin (FUR), isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST), lascufloxacin (LSC), levofloxacin/ornidazole (LEO), nemonoxacin (NEM), norfloxacin/metronidazole (NME), norfloxacin/tinidazole (NTI), ofloxacin/ornidazole (OOR), oteseconazole (OTE), rifampicin/ethambutol/isoniazid (REI), sarecycline (SRC), tetracycline/oleandomycin (TOL), and thioacetazone (TAT)</li>
@ -216,14 +216,14 @@
</ul><p>Also, we added support for using antibiotic selectors in scoped <code>dplyr</code> verbs (with or without using <code><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars()</a></code>), such as in: <code>... %&gt;% summarise_at(aminoglycosides(), resistance)</code>, please see <code><a href="../reference/proportion.html">resistance()</a></code> for examples.</p>
</div>
<div class="section level4">
<h4 id="antiviral-agents-1-8-2-9118">Antiviral agents<a class="anchor" aria-label="anchor" href="#antiviral-agents-1-8-2-9118"></a></h4>
<h4 id="antiviral-agents-1-8-2-9119">Antiviral agents<a class="anchor" aria-label="anchor" href="#antiviral-agents-1-8-2-9119"></a></h4>
<p>We now added extensive support for antiviral agents! For the first time, the <code>AMR</code> package has extensive support for antiviral drugs and to work with their names, codes and other data in any way.</p>
<ul><li>The <code>antivirals</code> data set has been extended with 18 new drugs (also from the <a href="https://www.whocc.no/atc_ddd_index/?code=J05AJ&amp;showdescription=no" class="external-link">new J05AJ ATC group</a>) and now also contains antiviral identifiers and LOINC codes</li>
<li>A new data type <code>av</code> (<em>antivirals</em>) has been added, which is functionally similar to <code>ab</code> for antibiotics</li>
<li>Functions <code><a href="../reference/as.av.html">as.av()</a></code>, <code><a href="../reference/av_property.html">av_name()</a></code>, <code><a href="../reference/av_property.html">av_atc()</a></code>, <code><a href="../reference/av_property.html">av_synonyms()</a></code>, <code><a href="../reference/av_from_text.html">av_from_text()</a></code> have all been added as siblings to their <code>ab_*()</code> equivalents</li>
</ul></div>
<div class="section level4">
<h4 id="other-new-functions-1-8-2-9118">Other new functions<a class="anchor" aria-label="anchor" href="#other-new-functions-1-8-2-9118"></a></h4>
<h4 id="other-new-functions-1-8-2-9119">Other new functions<a class="anchor" aria-label="anchor" href="#other-new-functions-1-8-2-9119"></a></h4>
<ul><li>Function <code><a href="../reference/proportion.html">sir_confidence_interval()</a></code> to add confidence intervals in AMR calculation. This is now also included in <code><a href="../reference/proportion.html">sir_df()</a></code> and <code><a href="../reference/proportion.html">proportion_df()</a></code>.</li>
<li>Function <code><a href="../reference/mean_amr_distance.html">mean_amr_distance()</a></code> to calculate the mean AMR distance. The mean AMR distance is a normalised numeric value to compare AMR test results and can help to identify similar isolates, without comparing antibiograms by hand.</li>
<li>Function <code><a href="../reference/as.sir.html">sir_interpretation_history()</a></code> to view the history of previous runs of <code><a href="../reference/as.sir.html">as.sir()</a></code> (previously <code><a href="../reference/AMR-deprecated.html">as.rsi()</a></code>). This returns a ‘logbook’ with the selected guideline, reference table and specific interpretation of each row in a data set on which <code><a href="../reference/as.sir.html">as.sir()</a></code> was run.</li>
@ -232,7 +232,7 @@
</ul></div>
</div>
<div class="section level3">
<h3 id="changes-1-8-2-9118">Changes<a class="anchor" aria-label="anchor" href="#changes-1-8-2-9118"></a></h3>
<h3 id="changes-1-8-2-9119">Changes<a class="anchor" aria-label="anchor" href="#changes-1-8-2-9119"></a></h3>
<ul><li>Argument <code>combine_IR</code> has been removed from this package (affecting functions <code><a href="../reference/count.html">count_df()</a></code>, <code><a href="../reference/proportion.html">proportion_df()</a></code>, and <code><a href="../reference/proportion.html">sir_df()</a></code> and some plotting functions), since it was replaced with <code>combine_SI</code> three years ago</li>
<li>Using <code>units</code> in <code>ab_ddd(..., units = "...")</code> had been deprecated for some time and is now not supported anymore. Use <code><a href="../reference/ab_property.html">ab_ddd_units()</a></code> instead.</li>
<li>Support for <code>data.frame</code>-enhancing R packages, more specifically: <code><a href="https://Rdatatable.gitlab.io/data.table/reference/data.table.html" class="external-link">data.table::data.table</a></code>, <code><a href="https://sfirke.github.io/janitor/reference/tabyl.html" class="external-link">janitor::tabyl</a></code>, <code><a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble::tibble</a></code>, and <code><a href="https://tsibble.tidyverts.org/reference/tsibble.html" class="external-link">tsibble::tsibble</a></code>. AMR package functions that have a data set as output (such as <code><a href="../reference/proportion.html">sir_df()</a></code> and <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code>), will now return the same data type as the input.</li>
@ -272,7 +272,7 @@
<li>Fix for using <code><a href="../reference/g.test.html">g.test()</a></code> with zeroes in a 2x2 table</li>
</ul></div>
<div class="section level3">
<h3 id="other-1-8-2-9118">Other<a class="anchor" aria-label="anchor" href="#other-1-8-2-9118"></a></h3>
<h3 id="other-1-8-2-9119">Other<a class="anchor" aria-label="anchor" href="#other-1-8-2-9119"></a></h3>
<ul><li>Added Peter Dutey-Magni, Dmytro Mykhailenko, Anton Mymrikov, Andrew Norgan, Jonas Salm, and Anita Williams as contributors, to thank them for their valuable input</li>
<li>New website to make use of the new Bootstrap 5 and pkgdown 2.0. The website now contains results for all examples and will be automatically regenerated with every change to our repository, using GitHub Actions</li>
<li>All R and Rmd files in this project are now styled using the <code>styler</code> package</li>

2
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@ -11,7 +11,7 @@ articles:
datasets: datasets.html
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
last_built: 2023-02-11T21:33Z
last_built: 2023-02-12T10:25Z
urls:
reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles

2
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@ -10,7 +10,7 @@
<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="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</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">

2
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@ -10,7 +10,7 @@
<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="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</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">

2
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@ -18,7 +18,7 @@ The AMR package is available in English, Chinese, Danish, Dutch, French, German,
<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="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</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">

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@ -10,7 +10,7 @@
<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="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</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">

2
reference/WHONET.html
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@ -10,7 +10,7 @@
<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="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</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">

2
reference/ab_from_text.html
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@ -10,7 +10,7 @@
<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="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</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">

2
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@ -10,7 +10,7 @@
<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="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</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">

2
reference/add_custom_antimicrobials.html
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@ -10,7 +10,7 @@
<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="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</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">

2
reference/add_custom_microorganisms.html
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@ -10,7 +10,7 @@
<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="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</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">

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@ -10,7 +10,7 @@
<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="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</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">
@ -205,16 +205,16 @@
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">df</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> birth_date age age_exact age_at_y2k</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1937-01-20 86 86.06027 62</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1954-10-05 68 68.35342 45</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1988-04-16 34 34.82466 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1969-09-13 53 53.41370 30</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1948-10-22 74 74.30685 51</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1981-07-08 41 41.59726 18</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1985-11-10 37 37.25479 14</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1977-10-25 45 45.29863 22</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1966-02-01 57 57.02740 33</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1963-11-17 59 59.23562 36</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1973-02-10 50 50.00548 26</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1996-11-25 26 26.21644 3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1944-11-18 78 78.23562 55</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1953-05-17 69 69.74247 46</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1947-10-24 75 75.30411 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1946-10-16 76 76.32603 53</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1990-07-02 32 32.61644 9</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1967-10-18 55 55.32055 32</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1974-09-23 48 48.38904 25</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1978-11-08 44 44.26301 21</span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>

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@ -10,7 +10,7 @@
<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="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</small>
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@ -14,7 +14,7 @@
<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="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</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">
@ -338,18 +338,18 @@
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ 502 combinations had less than minimum = 30 results and were ignored</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 10 × 7</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> `Pathogen (N min-max)` S S1 S2 S3 S4 S5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> `Pathogen (N min-max)` AMK GEN IPM KAN MEM TOB</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> CoNS (43-309) 86 22 0 0 52 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> E. coli (0-462) 98 97 100 <span style="color: #BB0000;">NA</span> 100 100</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> E. faecalis (0-39) 0 0 0 0 100 <span style="color: #BB0000;">NA</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> K. pneumoniae (0-58) 90 90 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 100 100</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> P. aeruginosa (17-30) 100 100 <span style="color: #BB0000;">NA</span> 0 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> P. mirabilis (0-34) 94 94 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 94 <span style="color: #BB0000;">NA</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> S. aureus (2-233) 99 98 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> S. epidermidis (8-163) 79 51 0 0 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> S. hominis (3-80) 92 85 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> S. pneumoniae (11-117) 0 0 0 0 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> CoNS (43-309) 0 86 52 0 52 22</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> E. coli (0-462) 100 98 100 <span style="color: #BB0000;">NA</span> 100 97</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> E. faecalis (0-39) 0 0 100 0 <span style="color: #BB0000;">NA</span> 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> K. pneumoniae (0-58) <span style="color: #BB0000;">NA</span> 90 100 <span style="color: #BB0000;">NA</span> 100 90</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> P. aeruginosa (17-30) <span style="color: #BB0000;">NA</span> 100 <span style="color: #BB0000;">NA</span> 0 <span style="color: #BB0000;">NA</span> 100</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> P. mirabilis (0-34) <span style="color: #BB0000;">NA</span> 94 94 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 94</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> S. aureus (2-233) <span style="color: #BB0000;">NA</span> 99 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 98</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> S. epidermidis (8-163) 0 79 <span style="color: #BB0000;">NA</span> 0 <span style="color: #BB0000;">NA</span> 51</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> S. hominis (3-80) <span style="color: #BB0000;">NA</span> 92 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 85</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> S. pneumoniae (11-117) 0 0 <span style="color: #BB0000;">NA</span> 0 <span style="color: #BB0000;">NA</span> 0</span>
<span class="r-in"><span> </span></span>
<span class="r-in"><span><span class="fu">antibiogram</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
<span class="r-in"><span> antibiotics <span class="op">=</span> <span class="fu"><a href="antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>,</span></span>
@ -358,29 +358,11 @@
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (tobramycin), 'AMK' (amikacin) and 'KAN' (kanamycin)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ 4 combinations had less than minimum = 30 results and were ignored</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S1".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S2".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S3".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S1".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S2".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S3".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>there are records with missing times, which will be dropped.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>multiple rows match for ab=NA: first taken</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2 × 2</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> `Pathogen (N min-max)` `NA`</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Gram-negative (35-686) 96</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> Gram-positive (436-1170) 63</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> `Pathogen (N min-max)` J01GB01 J01GB03 J01GB04 J01GB06</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Gram-negative (35-686) 96 96 0 98</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> Gram-positive (436-1170) 34 63 0 0</span>
<span class="r-in"><span> </span></span>
<span class="r-in"><span><span class="fu">antibiogram</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
<span class="r-in"><span> antibiotics <span class="op">=</span> <span class="fu"><a href="antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span>,</span></span>
@ -388,32 +370,14 @@
<span class="r-in"><span> mo_transform <span class="op">=</span> <span class="st">"name"</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ 172 combinations had less than minimum = 30 results and were ignored</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S1".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S1".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S1".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>there are records with missing times, which will be dropped.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>multiple rows match for ab=NA: first taken</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 5 × 2</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> `Pathogen (N min-max)` `NA`</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Coagulase-negative Staphylococcus (CoNS) (48-48) 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> Enterococcus faecalis (0-38) 100</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Escherichia coli (418-422) 100</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> Klebsiella pneumoniae (51-53) 100</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">5</span> Proteus mirabilis (27-32) 94</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 5 × 3</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> `Pathogen (N min-max)` Imipenem Meropenem</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Coagulase-negative Staphylococcus (CoNS) (48-48) 52 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> Enterococcus faecalis (0-38) 100 <span style="color: #BB0000;">NA</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Escherichia coli (418-422) 100 100</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> Klebsiella pneumoniae (51-53) 100 100</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">5</span> Proteus mirabilis (27-32) 94 <span style="color: #BB0000;">NA</span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Combined antibiogram -------------------------------------------------</span></span></span>
@ -424,10 +388,10 @@
<span class="r-in"><span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ 3 combinations had less than minimum = 30 results and were ignored</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> `Pathogen (N min-max)` S S1 S2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Gram-negative (641-693) 88 98 99</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> Gram-positive (345-1044) 86 95 98</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> `Pathogen (N min-max)` TZP `TZP + GEN` `TZP + TOB`</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Gram-negative (641-693) 88 99 98</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> Gram-positive (345-1044) 86 98 95</span>
<span class="r-in"><span> </span></span>
<span class="r-in"><span><span class="fu">antibiogram</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
<span class="r-in"><span> antibiotics <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"TZP"</span>, <span class="st">"TZP+TOB"</span><span class="op">)</span>,</span></span>
@ -435,21 +399,12 @@
<span class="r-in"><span> ab_transform <span class="op">=</span> <span class="st">"name"</span>,</span></span>
<span class="r-in"><span> sep <span class="op">=</span> <span class="st">" &amp; "</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ 2 combinations had less than minimum = 30 results and were ignored</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S1".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S1".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>there are records with missing times, which will be dropped.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>multiple rows match for ab=NA: first taken</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2 × 2</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> `Pathogen (N min-max)` `NA`</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Gram-negative (641-693) 88</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> Gram-positive (345-550) 86</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2 × 3</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> `Pathogen (N min-max)` `Piperacillin/tazobactam` Piperacillin/tazobactam &amp; …¹</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Gram-negative (641-693) 88 98</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> Gram-positive (345-550) 86 95</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with abbreviated variable name ¹​`Piperacillin/tazobactam &amp; Tobramycin`</span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Syndromic antibiogram ------------------------------------------------</span></span></span>
@ -463,22 +418,22 @@
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ 1581 combinations had less than minimum = 30 results and were ignored</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 14 × 8</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> `Syndromic Group` `Pathogen (N min-max)` S S1 S2 S3 S4 S5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> `Syndromic Group` `Pathogen (N min-max)` AMK GEN IPM KAN MEM TOB</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical CoNS (23-205) 89 26 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 57 57</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> ICU CoNS (10-73) 79 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Outpatient CoNS (3-31) 84 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical E. coli (0-299) 98 98 100 <span style="color: #BB0000;">NA</span> 100 100</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> ICU E. coli (0-137) 99 96 100 <span style="color: #BB0000;">NA</span> 100 100</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Clinical K. pneumoniae (0-51) 92 92 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 100 100</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Clinical P. mirabilis (0-30) 100 100 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical S. aureus (2-150) 99 97 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> ICU S. aureus (0-66) 100 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical S. epidermidis (4-79) 82 55 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">11</span> ICU S. epidermidis (4-75) 72 41 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">12</span> Clinical S. hominis (1-45) 96 94 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">13</span> Clinical S. pneumoniae (5-78) 0 0 0 0 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">14</span> ICU S. pneumoniae (5-30) 0 0 0 0 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical CoNS (23-205) <span style="color: #BB0000;">NA</span> 89 57 <span style="color: #BB0000;">NA</span> 57 26</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> ICU CoNS (10-73) <span style="color: #BB0000;">NA</span> 79 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Outpatient CoNS (3-31) <span style="color: #BB0000;">NA</span> 84 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical E. coli (0-299) 100 98 100 <span style="color: #BB0000;">NA</span> 100 98</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> ICU E. coli (0-137) 100 99 100 <span style="color: #BB0000;">NA</span> 100 96</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Clinical K. pneumoniae (0-51) <span style="color: #BB0000;">NA</span> 92 100 <span style="color: #BB0000;">NA</span> 100 92</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Clinical P. mirabilis (0-30) <span style="color: #BB0000;">NA</span> 100 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 100</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical S. aureus (2-150) <span style="color: #BB0000;">NA</span> 99 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 97</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> ICU S. aureus (0-66) <span style="color: #BB0000;">NA</span> 100 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical S. epidermidis (4-79) <span style="color: #BB0000;">NA</span> 82 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 55</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">11</span> ICU S. epidermidis (4-75) <span style="color: #BB0000;">NA</span> 72 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 41</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">12</span> Clinical S. hominis (1-45) <span style="color: #BB0000;">NA</span> 96 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 94</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">13</span> Clinical S. pneumoniae (5-78) 0 0 <span style="color: #BB0000;">NA</span> 0 <span style="color: #BB0000;">NA</span> 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">14</span> ICU S. pneumoniae (5-30) 0 0 <span style="color: #BB0000;">NA</span> 0 <span style="color: #BB0000;">NA</span> 0</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># now define a data set with only E. coli</span></span></span>
<span class="r-in"><span><span class="va">ex1</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu"><a href="mo_property.html">mo_genus</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"Escherichia"</span><span class="op">)</span>, <span class="op">]</span></span></span>
@ -495,27 +450,11 @@
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (tobramycin), 'AMK' (amikacin) and 'KAN' (kanamycin)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ 2 combinations had less than minimum = 30 results and were ignored</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S1".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S2".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S1".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S2".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>there are records with missing times, which will be dropped.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>multiple rows match for ab=NA: first taken</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>there are records with missing times, which will be dropped.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>multiple rows match for ab=NA: first taken</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2 × 3</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> `Grupo sindrómico` `Patógeno (N min-max)` `NA`</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> No UCI E. coli (0-325) 98</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> UCI E. coli (0-137) 99</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> `Grupo sindrómico` `Patógeno (N min-max)` Amikacina Gentamicina Tobramicina</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> No UCI E. coli (0-325) 100 98 98</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> UCI E. coli (0-137) 100 99 96</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Weighted-incidence syndromic combination antibiogram (WISCA) ---------</span></span></span>
@ -530,12 +469,12 @@
<span class="r-in"><span> <span class="st">"WISCA Group 1"</span>, <span class="st">"WISCA Group 2"</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ 8 combinations had less than minimum = 10 results and were ignored</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4 × 6</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> `Syndromic Group` `Pathogen (N min-max)` S S1 S2 S3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> WISCA Group 1 Gram-negative (261-285) 76 95 89 99</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> WISCA Group 2 Gram-negative (380-442) 76 98 88 98</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> WISCA Group 1 Gram-positive (123-406) 76 89 81 95</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> WISCA Group 2 Gram-positive (222-732) 76 89 88 95</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> `Syndromic Group` `Pathogen (N min-max)` AMC `AMC + CIP` TZP `TZP + TOB`</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> WISCA Group 1 Gram-negative (261-285) 76 95 89 99</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> WISCA Group 2 Gram-negative (380-442) 76 98 88 98</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> WISCA Group 1 Gram-positive (123-406) 76 89 81 95</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> WISCA Group 2 Gram-positive (222-732) 76 89 88 95</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Generate plots with ggplot2 or base R --------------------------------</span></span></span>

138
reference/antibiotic_class_selectors.html
View File

@ -10,7 +10,7 @@
<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="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</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">
@ -851,135 +851,13 @@
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Using column 'mo' as input for mo_is_gram_positive()</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For glycopeptides() using columns 'VAN' (vancomycin) and 'TEC'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (teicoplanin)</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S" and "S1".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S1".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S1".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S1".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S1".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S1".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S1".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S1".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S1".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S1".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S1".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S1".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S1".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S1".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S1".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S1".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S1".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S1".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S1".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S1".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S1".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S1".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in (function (..., na.last = TRUE, decreasing = FALSE, method = c("auto", "shell", "radix")) { z &lt;- list(...) decreasing &lt;- as.logical(decreasing) if (length(z) == 1L &amp;&amp; is.numeric(x &lt;- z[[1L]]) &amp;&amp; !is.object(x) &amp;&amp; length(x) &gt; 0) { if (.Internal(sorted_fpass(x, decreasing, na.last))) return(seq_along(x)) } method &lt;- match.arg(method) if (any(vapply(z, is.object, logical(1L)))) { z &lt;- lapply(z, function(x) if (is.object(x)) as.vector(xtfrm(x)) else x) return(do.call("order", c(z, list(na.last = na.last, decreasing = decreasing, method = method)))) } if (method == "auto") { useRadix &lt;- all(vapply(z, function(x) { (is.numeric(x) || is.factor(x) || is.logical(x)) &amp;&amp; is.integer(length(x)) }, logical(1L))) method &lt;- if (useRadix) "radix" else "shell" } if (method != "radix" &amp;&amp; !is.na(na.last)) { if (length(decreasing) &gt; 1L) stop("'decreasing' of length &gt; 1 is only for method = \"radix\"") return(.Internal(order(na.last, decreasing, ...))) } if (method == "radix") { decreasing &lt;- rep_len(as.logical(decreasing), length(z)) return(.Internal(radixsort(na.last, decreasing, FALSE, TRUE, ...))) } if (any(diff((l.z &lt;- lengths(z)) != 0L))) stop("argument lengths differ") na &lt;- vapply(z, is.na, rep.int(NA, l.z[1L])) ok &lt;- if (is.matrix(na)) rowSums(na) == 0L else !any(na) if (all(!ok)) return(integer()) z[[1L]][!ok] &lt;- NA ans &lt;- do.call("order", c(z, list(decreasing = decreasing))) ans[ok[ans]]})(NULL, NULL, NULL):</span> argument 1 is not a vector</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2 × 8</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Group Drug CoNS E. fa…¹ S. au…² S. ep…³ S. ho…⁴ S. pn…⁵</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> <span style="color: #949494;">"</span>Glycopeptides<span style="color: #949494;">"</span> Teicoplanin (TE… <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> <span style="color: #949494;">"</span> 0.0%… <span style="color: #949494;">"</span>64.1%… <span style="color: #949494;">"</span> 6.8%… <span style="color: #949494;">""</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> <span style="color: #949494;">""</span> Vancomycin (VAN… <span style="color: #949494;">"</span> 0.… <span style="color: #949494;">"</span> 0.0%… <span style="color: #949494;">"</span> 0.0%… <span style="color: #949494;">"</span> 0.0%… <span style="color: #949494;">"</span> 0.0%… <span style="color: #949494;">"</span> 0.0%…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with abbreviated variable names ¹​`E. faecalis`, ²​`S. aureus`,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ³​`S. epidermidis`, ⁴​`S. hominis`, ⁵​`S. pneumoniae`</span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
<span class="r-in"><span> some_column <span class="op">=</span> <span class="st">"some_value"</span>,</span></span>

2
reference/antibiotics.html
View File

@ -10,7 +10,7 @@
<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="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</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">

2
reference/as.ab.html
View File

@ -10,7 +10,7 @@
<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="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</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">

2
reference/as.av.html
View File

@ -10,7 +10,7 @@
<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="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</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">

2
reference/as.disk.html
View File

@ -10,7 +10,7 @@
<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="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</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">

2
reference/as.mic.html
View File

@ -10,7 +10,7 @@
<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="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</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">

2
reference/as.mo.html
View File

@ -10,7 +10,7 @@
<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="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</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">

22
reference/as.sir.html
View File

@ -10,7 +10,7 @@
<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="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</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">
@ -524,16 +524,16 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 50 × 17</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index ab_input ab_guid…¹ mo_in…² mo_guideline guide…³</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2023-02-11 <span style="color: #949494;">21:34:34</span> 1 TOB TOB Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2023-02-11 <span style="color: #949494;">21:34:34</span> 1 GEN GEN Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2023-02-11 <span style="color: #949494;">21:34:34</span> 1 CIP CIP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2023-02-11 <span style="color: #949494;">21:34:33</span> 1 AMP AMP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2023-02-11 <span style="color: #949494;">21:34:27</span> 1 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2023-02-11 <span style="color: #949494;">21:34:27</span> 2 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2023-02-11 <span style="color: #949494;">21:34:27</span> 3 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2023-02-11 <span style="color: #949494;">21:34:27</span> 4 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2023-02-11 <span style="color: #949494;">21:34:27</span> 5 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2023-02-11 <span style="color: #949494;">21:34:27</span> 6 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2023-02-12 <span style="color: #949494;">10:26:44</span> 1 TOB TOB Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2023-02-12 <span style="color: #949494;">10:26:43</span> 1 GEN GEN Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2023-02-12 <span style="color: #949494;">10:26:43</span> 1 CIP CIP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2023-02-12 <span style="color: #949494;">10:26:42</span> 1 AMP AMP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2023-02-12 <span style="color: #949494;">10:26:36</span> 1 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2023-02-12 <span style="color: #949494;">10:26:36</span> 2 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2023-02-12 <span style="color: #949494;">10:26:36</span> 3 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2023-02-12 <span style="color: #949494;">10:26:36</span> 4 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2023-02-12 <span style="color: #949494;">10:26:36</span> 5 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2023-02-12 <span style="color: #949494;">10:26:36</span> 6 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 40 more rows, 10 more variables: ref_table &lt;chr&gt;, method &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># input &lt;dbl&gt;, outcome &lt;sir&gt;, breakpoint_S_R &lt;chr&gt;, ab_considered &lt;lgl&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># mo_considered &lt;lgl&gt;, breakpoint_S &lt;lgl&gt;, breakpoint_R &lt;lgl&gt;,</span></span>

2
reference/atc_online.html
View File

@ -10,7 +10,7 @@
<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="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</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">

2
reference/av_from_text.html
View File

@ -10,7 +10,7 @@
<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="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</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">

2
reference/av_property.html
View File

@ -10,7 +10,7 @@
<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="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</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">

2
reference/availability.html
View File

@ -10,7 +10,7 @@
<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="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</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">

3759
reference/bug_drug_combinations.html
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File diff suppressed because it is too large Load Diff

2
reference/clinical_breakpoints.html
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@ -10,7 +10,7 @@
<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="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</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">

2
reference/count.html
View File

@ -12,7 +12,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<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="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</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">

2
reference/custom_eucast_rules.html
View File

@ -10,7 +10,7 @@
<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="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</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">

2
reference/dosage.html
View File

@ -10,7 +10,7 @@
<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="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</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">

2
reference/eucast_rules.html
View File

@ -12,7 +12,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
<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="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</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">

2
reference/example_isolates.html
View File

@ -10,7 +10,7 @@
<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="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</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">

2
reference/example_isolates_unclean.html
View File

@ -10,7 +10,7 @@
<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="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</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">

2
reference/first_isolate.html
View File

@ -12,7 +12,7 @@
<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="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</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">

2
reference/g.test.html
View File

@ -10,7 +10,7 @@
<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="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</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">

89
reference/get_episode.html
View File

@ -10,7 +10,7 @@
<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="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</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">
@ -192,28 +192,27 @@
<span class="r-in"><span><span class="va">df</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq_len</a></span><span class="op">(</span><span class="fl">2000</span><span class="op">)</span>, size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># indices</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 18 31 37 38 34 17 23 19 11 33 12 38 17 4 37 6 47 45 1 31 32 41 23 21 30</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 7 45 43 44 42 6 45 11 42 21 40 9 31 4 26 11 21 19 18 1 36 37 23 41 43</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 39 31 28 18 9 14 20 9 26 2 5 35 45 24 38 15 15 5 33 13 35 25 27 29 16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 13 47 15 10 45 27 21 32 34 39 18 48 20 3 22 44 17 19 41 40 8 28 7 46 3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 8 20 30 31 41 14 26 24 14 7 41 41 5 19 44 29 34 15 40 42 43 16 45 8 6</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 10 37 42 32 9 36 18 19 42 28 19 29 20 46 27 1 2 42 39 11 4 12 36 13 18</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 17 6 31 8 1 38 46 8 25 17 27 31 3 27 10 18 29 29 24 16 44 17 33 10 25</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 36 2 23 7 44 42 12 46 45 44 34 2 17 38 21 22 35 22 25 32 39 43 30 35 11</span>
<span class="r-in"><span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># TRUE/FALSE</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] FALSE TRUE FALSE TRUE TRUE TRUE TRUE FALSE TRUE TRUE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] TRUE TRUE FALSE TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] FALSE FALSE TRUE FALSE TRUE FALSE FALSE TRUE TRUE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] TRUE TRUE FALSE TRUE FALSE TRUE FALSE FALSE FALSE TRUE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] TRUE TRUE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] FALSE FALSE TRUE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] TRUE TRUE TRUE FALSE TRUE TRUE TRUE TRUE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] FALSE FALSE TRUE TRUE TRUE TRUE FALSE TRUE TRUE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] TRUE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] FALSE FALSE FALSE FALSE FALSE TRUE TRUE TRUE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] FALSE FALSE FALSE FALSE</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># filter on results from the third 60-day episode only, using base R</span></span></span>
<span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, <span class="fl">60</span><span class="op">)</span> <span class="op">==</span> <span class="fl">3</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2003-01-25 088256 73 F ICU B_STPHY_CONS R NA R R </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2003-03-18 889500 61 M Clinical B_STPHY_CONS R NA R R </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 1 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-10-20 F35553 51 M ICU B_STPHY_AURS S NA S NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># FEP &lt;sir&gt;, CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># GEN &lt;sir&gt;, TOB &lt;sir&gt;, AMK &lt;sir&gt;, KAN &lt;sir&gt;, TMP &lt;sir&gt;, SXT &lt;sir&gt;,</span></span>
@ -258,19 +257,19 @@
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">patient</span>, <span class="va">ward</span>, <span class="va">date</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 100 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: ward, patient [95]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: ward, patient [94]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward date patient new_index new_logical</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical 2007-08-22 005088 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical 2009-07-24 006827 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Clinical 2012-11-24 023456 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical 2013-10-30 066601 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> ICU 2014-06-28 078381 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> ICU 2002-06-04 082413 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> ICU 2014-02-08 082622 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> ICU 2003-01-25 088256 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Clinical 2008-07-22 0E2483 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> ICU 2007-08-10 0E2483 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> ICU 2004-05-04 022060 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical 2006-07-21 059414 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Clinical 2002-05-14 077552 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical 2003-10-01 0DBB93 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> ICU 2009-05-08 0DBB93 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> ICU 2007-06-21 0E2483 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Clinical 2012-09-03 107DD1 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical 2010-11-01 119392 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Clinical 2007-08-10 122506 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical 2009-08-14 146F70 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 90 more rows</span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
@ -286,9 +285,9 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward n_patients n_episodes_365 n_episodes_60 n_episodes_30</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 54 13 34 44</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 34 9 24 28</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 7 5 7 7</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 65 13 38 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 25 10 18 25</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 4 3 4 4</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># grouping on patients and microorganisms leads to the same</span></span></span>
<span class="r-in"><span><span class="co"># results as first_isolate() when using 'episode-based':</span></span></span>
@ -306,7 +305,7 @@
<span class="r-in"><span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/identical.html" class="external-link">identical</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">y</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] FALSE</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># but is_new_episode() has a lot more flexibility than first_isolate(),</span></span></span>
<span class="r-in"><span><span class="co"># since you can now group on anything that seems relevant:</span></span></span>
@ -318,19 +317,19 @@
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_data.html" class="external-link">group_vars</a></span><span class="op">(</span><span class="va">.</span><span class="op">)</span>, <span class="va">flag_episode</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 100 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, mo, ward [97]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, mo, ward [95]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> patient mo ward flag_episode</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> A66134 B_STPHY_AURS Outpatient TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 824233 B_STPHY_AURS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 078381 B_STPHY_EPDR ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 483195 B_STPHY_HMNS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> B33776 B_ACNTB Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 851259 B_STRPT_PNMN Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 6F0804 B_STRPT_PNMN Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 122506 B_STPHY_AURS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 904485 B_STRPT ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 695956 B_STRPT_PNMN Outpatient TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 955371 B_STPHY_AURS ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 0E2483 B_ESCHR_COLI ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 119392 B_STPHY_CONS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> A26106 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 557266 B_STPHY_HMLY Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 5DF436 B_STPHY_AURS ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 501361 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 195736 B_STPHY_AURS Outpatient TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 904485 B_STRPT_ANGN ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 842593 B_STPHY_CONS ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 90 more rows</span></span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>

2
reference/ggplot_pca.html
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@ -10,7 +10,7 @@
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2
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@ -10,7 +10,7 @@
<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="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</small>
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2
reference/guess_ab_col.html
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@ -10,7 +10,7 @@
<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="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</small>
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2
reference/index.html
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@ -10,7 +10,7 @@
<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="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</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">

2
reference/intrinsic_resistant.html
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@ -10,7 +10,7 @@
<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="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</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">

2
reference/italicise_taxonomy.html
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@ -10,7 +10,7 @@
<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="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</small>
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2
reference/join.html
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@ -10,7 +10,7 @@
<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="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</small>
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2
reference/key_antimicrobials.html
View File

@ -10,7 +10,7 @@
<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="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</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">

6
reference/kurtosis.html
View File

@ -10,7 +10,7 @@
<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="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</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">
@ -182,9 +182,9 @@
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2.985188</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2.983574</span>
<span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span>, excess <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.01268259</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.07041612</span>
</code></pre></div>
</div>
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2
reference/like.html
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9118</small>
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2
reference/mdro.html
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@ -10,7 +10,7 @@
<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="">1.8.2.9118</small>
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69
reference/mean_amr_distance.html
View File

@ -10,7 +10,7 @@
<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="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</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">
@ -201,30 +201,31 @@
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">sir</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_sir</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">sir</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] S R S S I I I S I S</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] I R R R R I S R S R</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">sir</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.3162278 2.8460499 -0.3162278 -0.3162278 -0.3162278 -0.3162278</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.3162278 -0.3162278 -0.3162278 -0.3162278</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -1.1618950 0.7745967 0.7745967 0.7745967 0.7745967 -1.1618950</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -1.1618950 0.7745967 -1.1618950 0.7745967</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">mic</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">mic</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 16 0.125 8 128 4 0.002 &gt;=256 4 128 0.002</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 16 0.01 32 128 4 0.5 &lt;=0.005 &lt;=0.005 0.125 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.125 </span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">mic</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.4477699 -0.6743974 0.2874603 0.9286987 0.1271507 -1.6307699</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 1.0890083 0.1271507 0.9286987 -1.6307699</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.94388242 -1.02867586 1.12920607 1.49985337 0.57323512 0.01726417</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -1.21399951 -1.21399951 -0.35338313 -0.35338313</span>
<span class="r-in"><span><span class="co"># equal to the Z-score of their log2:</span></span></span>
<span class="r-in"><span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span> <span class="op">-</span> <span class="fu"><a href="https://rdrr.io/r/base/mean.html" class="external-link">mean</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="fu"><a href="https://rdrr.io/r/stats/sd.html" class="external-link">sd</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.4477699 -0.6743974 0.2874603 0.9286987 0.1271507 -1.6307699</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 1.0890083 0.1271507 0.9286987 -1.6307699</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.94388242 -1.02867586 1.12920607 1.49985337 0.57323512 0.01726417</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -1.21399951 -1.21399951 -0.35338313 -0.35338313</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">disk</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_disk</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">disk</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 50 46 14 43 29 18 29 15 11 14</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 24 40 44 31 40 34 22 41 49 40</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">disk</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1.5602015 1.2900368 -0.8712814 1.0874132 0.1418365 -0.6011166</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.1418365 -0.8037402 -1.0739049 -0.8712814</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -1.4460560 0.4048957 0.8676336 -0.6362647 0.4048957 -0.2892112</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -1.6774250 0.5205802 1.4460560 0.4048957</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">y</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
<span class="r-in"><span> id <span class="op">=</span> <span class="va">LETTERS</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span></span>
@ -235,21 +236,21 @@
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">y</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A R 31 0.25 &lt;=1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B I 25 8 &gt;=8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C I 17 4 &lt;=1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D R 23 0.5 &lt;=1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E I 17 4 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F S 27 16 &gt;=8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G R 31 0.5 &lt;=1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H S 24 2 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I S 19 16 &gt;=8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J R 30 0.5 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A R 21 2 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B R 20 2 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C S 22 1 16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D S 28 2 16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E I 22 1 0.25</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F R 18 2 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G R 23 2 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H S 25 1 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I I 21 2 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J I 18 2 8</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "tobr"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.01890714 0.38838380 -0.66081724 -0.23677233 -0.47092861 0.59221346</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.13083498 -0.26120004 0.22460615 0.27477269</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.14721958 0.32396692 -0.25487609 0.75483654 -1.03119985 0.15991243</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.69943595 -0.52634353 -0.07812875 -0.19482320</span>
<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op">&lt;-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in .subset(x, j):</span> invalid subscript type 'list'</span>
<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
@ -266,16 +267,16 @@
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "tobr"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance check_id_C</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 C I 17 4 &lt;=1 -0.66081724 0.0000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 E I 17 4 2 -0.47092861 0.1898886</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 H S 24 2 2 -0.26120004 0.3996172</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D R 23 0.5 &lt;=1 -0.23677233 0.4240449</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 A R 31 0.25 &lt;=1 0.01890714 0.6797244</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 G R 31 0.5 &lt;=1 0.13083498 0.7916522</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 I S 19 16 &gt;=8 0.22460615 0.8854234</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 J R 30 0.5 2 0.27477269 0.9355899</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 B I 25 8 &gt;=8 0.38838380 1.0492010</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 F S 27 16 &gt;=8 0.59221346 1.2530307</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 C S 22 1 16 -0.25487609 0.0000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 J I 18 2 8 -0.19482320 0.0600529</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 I I 21 2 4 -0.07812875 0.1767473</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 H S 25 1 1 -0.52634353 0.2714674</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 A R 21 2 1 0.14721958 0.4020957</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F R 18 2 4 0.15991243 0.4147885</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 B R 20 2 4 0.32396692 0.5788430</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 E I 22 1 0.25 -1.03119985 0.7763238</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 G R 23 2 8 0.69943595 0.9543120</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 D S 28 2 16 0.75483654 1.0097126</span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="co"># support for groups</span></span></span>
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>

2
reference/microorganisms.codes.html
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@ -10,7 +10,7 @@
<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="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</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">

2
reference/microorganisms.html
View File

@ -10,7 +10,7 @@
<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="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</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">

2
reference/mo_matching_score.html
View File

@ -10,7 +10,7 @@
<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="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</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">

2
reference/mo_property.html
View File

@ -10,7 +10,7 @@
<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="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</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">

2
reference/mo_source.html
View File

@ -12,7 +12,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<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="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</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">

2
reference/pca.html
View File

@ -10,7 +10,7 @@
<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="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</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">

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2
reference/plot.html
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@ -10,7 +10,7 @@
<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="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</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">

2
reference/proportion.html
View File

@ -12,7 +12,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<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="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</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">

35
reference/random.html
View File

@ -10,7 +10,7 @@
<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="">1.8.2.9118</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9119</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">
@ -193,43 +193,42 @@
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 4 0.125 0.25 0.0625 0.125 8 4 0.125 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 128 0.002 0.25 16 64 4 128 32 0.002 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] &lt;=0.001 0.125 0.125 0.005 64 0.0625 &lt;=0.001</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2 4 64 0.5 2 0.025 0.25 8 0.0625 0.001 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 0.5 32 1 0.25 0.25 0.125 0.025 &gt;=128 32 0.0625</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 0.125 32 16 8 &gt;=128 </span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 7 22 23 44 40 29 7 32 41 7 34 43 37 46 44 49 48 6 13 49 42 12 49 47 46</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 9 12 29 26 27 48 37 36 32 47 34 44 20 36 38 12 50 48 16 34 50 34 42 44 29</span>
<span class="r-in"><span><span class="fu">random_sir</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] S S S S R I S I R I I R S R I I S S I I I S I I R</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] R R R I S I R I S I R I S I I S I S S R R S I R R</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
<span class="r-in"><span><span class="co"># make the random generation more realistic by setting a bug and/or drug:</span></span></span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 0.0625-64</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.0625 0.025 0.01 16 4 0.025 64 128 128 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 0.25 0.125 16 0.125 0.5 0.005 0.25 16 16 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 0.125 64 0.002 1 0.01 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.5 256 32 0.5 0.125 4 0.25 0.002 0.01 0.005 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 1 0.005 16 32 0.0625 0.0625 0.125 1 4 128 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 8 128 4 2 4 </span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-16</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.5 8 2 16 &gt;=32 2 0.5 &gt;=32 8 16 0.25 4 4 16 0.5 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [16] &gt;=32 1 1 0.25 &gt;=32 1 2 1 16 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 16 16 8 4 32 32 4 2 16 32 8 4 4 2 4 16 2 4 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [20] 4 4 32 &lt;=1 16 &lt;=1</span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-4</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 8 0.5 2 0.125 0.25 &gt;=16 &gt;=16 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [9] 8 0.25 8 1 0.25 0.5 &lt;=0.0625 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [17] 8 0.125 4 8 8 &gt;=16 1 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1 4 0.25 0.0625 4 0.125 0.125 1 0.25 0.125 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 0.125 1 0.0625 0.125 8 4 0.5 2 0.5 0.125 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 4 0.25 0.5 0.5 4 </span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 8-50</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 17 25 45 40 20 17 33 24 9 28 19 49 44 12 50 27 12 48 29 49 9 41 45 23 41</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 10 48 23 44 36 40 20 21 39 13 43 50 24 24 41 18 22 37 40 22 45 29 13 44 13</span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 11-17</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 17 12 12 16 11 11 15 17 14 17 14 11 12 14 15 14 16 11 14 15 11 12 16 13 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 15 15 12 16 13 15 12 13 16 17 14 14 14 12 15 13 14 12 17 13 13 16 11 11 17</span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 12-27</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 22 18 25 24 18 19 15 21 25 20 15 17 21 22 26 19 16 26 19 19 19 19 26 27 17</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 16 27 21 20 16 17 19 26 25 25 18 21 18 16 24 27 24 23 24 16 15 22 24 24 15</span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
</div>

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