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@ -36,7 +36,7 @@
<a class="navbar-brand me-2" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a> <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="">1.8.2.9054</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9057</small>
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a> <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="">1.8.2.9054</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9057</small>
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.2.9054</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9057</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -168,7 +168,7 @@
<h4 data-toc-skip class="author">Dr. Matthijs <h4 data-toc-skip class="author">Dr. Matthijs
Berends</h4> Berends</h4>
<h4 data-toc-skip class="date">29 November 2022</h4> <h4 data-toc-skip class="date">09 December 2022</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/AMR.Rmd" class="external-link"><code>vignettes/AMR.Rmd</code></a></small> <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> <div class="d-none name"><code>AMR.Rmd</code></div>
@ -180,7 +180,7 @@ Berends</h4>
website update since they are based on randomly created values and the 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 page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
Markdown</a>. However, the methodology remains unchanged. This page was Markdown</a>. However, the methodology remains unchanged. This page was
generated on 29 November 2022.</p> generated on 09 December 2022.</p>
<div class="section level2"> <div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a> <h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2> </h2>
@ -236,21 +236,21 @@ make the structure of your data generally look like this:</p>
</tr></thead> </tr></thead>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="center">2022-11-29</td> <td align="center">2022-12-09</td>
<td align="center">abcd</td> <td align="center">abcd</td>
<td align="center">Escherichia coli</td> <td align="center">Escherichia coli</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">2022-11-29</td> <td align="center">2022-12-09</td>
<td align="center">abcd</td> <td align="center">abcd</td>
<td align="center">Escherichia coli</td> <td align="center">Escherichia coli</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">R</td> <td align="center">R</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">2022-11-29</td> <td align="center">2022-12-09</td>
<td align="center">efgh</td> <td align="center">efgh</td>
<td align="center">Escherichia coli</td> <td align="center">Escherichia coli</td>
<td align="center">R</td> <td align="center">R</td>
@ -380,12 +380,12 @@ data set:</p>
<col width="13%"> <col width="13%">
<col width="13%"> <col width="13%">
<col width="13%"> <col width="13%">
<col width="28%"> <col width="26%">
<col width="5%"> <col width="5%">
<col width="5%"> <col width="5%">
<col width="5%"> <col width="5%">
<col width="5%"> <col width="5%">
<col width="8%"> <col width="9%">
</colgroup> </colgroup>
<thead><tr class="header"> <thead><tr class="header">
<th align="center">date</th> <th align="center">date</th>
@ -400,66 +400,66 @@ data set:</p>
</tr></thead> </tr></thead>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="center">2016-02-08</td> <td align="center">2012-06-16</td>
<td align="center">L4</td> <td align="center">S5</td>
<td align="center">Hospital A</td> <td align="center">Hospital D</td>
<td align="center">Escherichia coli</td> <td align="center">Staphylococcus aureus</td>
<td align="center">R</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>
</tr>
<tr class="even">
<td align="center">2011-06-04</td>
<td align="center">B4</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2010-12-27</td>
<td align="center">U10</td>
<td align="center">Hospital B</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">F</td> <td align="center">F</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">2013-08-11</td> <td align="center">2012-08-31</td>
<td align="center">H1</td> <td align="center">Q2</td>
<td align="center">Hospital C</td> <td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td> <td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2012-08-17</td>
<td align="center">S9</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">R</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2011-04-20</td>
<td align="center">M7</td>
<td align="center">Hospital B</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">M</td> <td align="center">M</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">2011-08-27</td> <td align="center">2016-10-02</td>
<td align="center">M9</td> <td align="center">Z1</td>
<td align="center">Hospital B</td> <td align="center">Hospital A</td>
<td align="center">Streptococcus pneumoniae</td> <td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">F</td>
<td align="center">S</td>
<td align="center">M</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">2015-04-24</td> <td align="center">2017-10-05</td>
<td align="center">L8</td> <td align="center">L10</td>
<td align="center">Hospital C</td> <td align="center">Hospital B</td>
<td align="center">Streptococcus pneumoniae</td> <td align="center">Escherichia coli</td>
<td align="center">R</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
@ -499,18 +499,18 @@ Longest: 1</p>
<tr class="odd"> <tr class="odd">
<td align="left">1</td> <td align="left">1</td>
<td align="left">M</td> <td align="left">M</td>
<td align="right">10,441</td> <td align="right">10,540</td>
<td align="right">52.21%</td> <td align="right">52.7%</td>
<td align="right">10,441</td> <td align="right">10,540</td>
<td align="right">52.21%</td> <td align="right">52.7%</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">2</td> <td align="left">2</td>
<td align="left">F</td> <td align="left">F</td>
<td align="right">9,559</td> <td align="right">9,460</td>
<td align="right">47.80%</td> <td align="right">47.3%</td>
<td align="right">20,000</td> <td align="right">20,000</td>
<td align="right">100.00%</td> <td align="right">100.0%</td>
</tr> </tr>
</tbody> </tbody>
</table> </table>
@ -621,9 +621,9 @@ 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"># Basing inclusion on all antimicrobial results, using a points threshold of</span></span>
<span><span class="co"># 2</span></span> <span><span class="co"># 2</span></span>
<span><span class="co"># Including isolates from ICU.</span></span> <span><span class="co"># Including isolates from ICU.</span></span>
<span><span class="co"># =&gt; Found 10,709 'phenotype-based' first isolates (53.5% of total where a</span></span> <span><span class="co"># =&gt; Found 10,641 'phenotype-based' first isolates (53.2% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div> <span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 53.5% is suitable for resistance analysis! We can now filter <p>So only 53.2% 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 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> <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
@ -634,11 +634,11 @@ on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html"
<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> <code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span> <span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="co"># Including isolates from ICU.</span></span></code></pre></div> <span><span class="co"># Including isolates from ICU.</span></span></code></pre></div>
<p>So we end up with 10,709 isolates for analysis. Now our data looks <p>So we end up with 10,641 isolates for analysis. Now our data looks
like:</p> like:</p>
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r"> <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> <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> <colgroup>
<col width="2%"> <col width="2%">
<col width="9%"> <col width="9%">
@ -652,7 +652,7 @@ like:</p>
<col width="6%"> <col width="6%">
<col width="11%"> <col width="11%">
<col width="12%"> <col width="12%">
<col width="9%"> <col width="7%">
<col width="5%"> <col width="5%">
</colgroup> </colgroup>
<thead><tr class="header"> <thead><tr class="header">
@ -673,58 +673,58 @@ like:</p>
</tr></thead> </tr></thead>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="left">3</td> <td align="left">1</td>
<td align="center">2010-12-27</td> <td align="center">2012-06-16</td>
<td align="center">U10</td> <td align="center">S5</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="center">2012-08-31</td>
<td align="center">Q2</td>
<td align="center">Hospital B</td> <td align="center">Hospital B</td>
<td align="center">B_KLBSL_PNMN</td> <td align="center">B_STPHY_AURS</td>
<td align="center">R</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">F</td> <td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="center">2013-08-11</td>
<td align="center">H1</td>
<td align="center">Hospital C</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-positive</td> <td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td> <td align="center">Staphylococcus</td>
<td align="center">aureus</td> <td align="center">aureus</td>
<td align="center">TRUE</td> <td align="center">TRUE</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="left">5</td>
<td align="center">2016-10-02</td>
<td align="center">Z1</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">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">7</td> <td align="left">7</td>
<td align="center">2013-10-25</td> <td align="center">2017-06-29</td>
<td align="center">I3</td> <td align="center">S6</td>
<td align="center">Hospital A</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">R</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">9</td>
<td align="center">2011-08-23</td>
<td align="center">Y10</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</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>
@ -737,28 +737,12 @@ like:</p>
<td align="center">TRUE</td> <td align="center">TRUE</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="left">11</td> <td align="left">8</td>
<td align="center">2012-08-03</td> <td align="center">2014-10-17</td>
<td align="center">U10</td> <td align="center">G10</td>
<td align="center">Hospital A</td> <td align="center">Hospital D</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">12</td>
<td align="center">2013-12-31</td>
<td align="center">L3</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td> <td align="center">B_STPHY_AURS</td>
<td align="center">R</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
@ -768,6 +752,22 @@ like:</p>
<td align="center">aureus</td> <td align="center">aureus</td>
<td align="center">TRUE</td> <td align="center">TRUE</td>
</tr> </tr>
<tr class="even">
<td align="left">10</td>
<td align="center">2011-04-23</td>
<td align="center">V8</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">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
</tbody> </tbody>
</table> </table>
<p>Time for the analysis!</p> <p>Time for the analysis!</p>
@ -801,8 +801,8 @@ readable:</p>
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://msberends.github.io/cleaner/reference/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></span></code></pre></div> <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><strong>Frequency table</strong></p>
<p>Class: character<br> <p>Class: character<br>
Length: 10,709<br> Length: 10,641<br>
Available: 10,709 (100%, NA: 0 = 0%)<br> Available: 10,641 (100%, NA: 0 = 0%)<br>
Unique: 4</p> Unique: 4</p>
<p>Shortest: 16<br> <p>Shortest: 16<br>
Longest: 24</p> Longest: 24</p>
@ -827,33 +827,33 @@ Longest: 24</p>
<tr class="odd"> <tr class="odd">
<td align="left">1</td> <td align="left">1</td>
<td align="left">Escherichia coli</td> <td align="left">Escherichia coli</td>
<td align="right">4,635</td> <td align="right">4,597</td>
<td align="right">43.28%</td> <td align="right">43.20%</td>
<td align="right">4,635</td> <td align="right">4,597</td>
<td align="right">43.28%</td> <td align="right">43.20%</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">2</td> <td align="left">2</td>
<td align="left">Staphylococcus aureus</td> <td align="left">Staphylococcus aureus</td>
<td align="right">2,757</td> <td align="right">2,714</td>
<td align="right">25.74%</td> <td align="right">25.51%</td>
<td align="right">7,392</td> <td align="right">7,311</td>
<td align="right">69.03%</td> <td align="right">68.71%</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="left">3</td> <td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td> <td align="left">Streptococcus pneumoniae</td>
<td align="right">2,115</td> <td align="right">2,148</td>
<td align="right">19.75%</td> <td align="right">20.19%</td>
<td align="right">9,507</td> <td align="right">9,459</td>
<td align="right">88.78%</td> <td align="right">88.89%</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">4</td> <td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td> <td align="left">Klebsiella pneumoniae</td>
<td align="right">1,202</td> <td align="right">1,182</td>
<td align="right">11.22%</td> <td align="right">11.11%</td>
<td align="right">10,709</td> <td align="right">10,641</td>
<td align="right">100.00%</td> <td align="right">100.00%</td>
</tr> </tr>
</tbody> </tbody>
@ -874,14 +874,14 @@ antibiotic class they are in:</p>
<col width="9%"> <col width="9%">
<col width="9%"> <col width="9%">
<col width="9%"> <col width="9%">
<col width="11%"> <col width="10%">
<col width="3%"> <col width="3%">
<col width="3%"> <col width="3%">
<col width="3%"> <col width="3%">
<col width="3%"> <col width="3%">
<col width="6%"> <col width="6%">
<col width="11%"> <col width="11%">
<col width="11%"> <col width="12%">
<col width="9%"> <col width="9%">
<col width="5%"> <col width="5%">
</colgroup> </colgroup>
@ -902,24 +902,9 @@ antibiotic class they are in:</p>
</tr></thead> </tr></thead>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="center">2014-06-23</td> <td align="center">2011-04-23</td>
<td align="center">T5</td> <td align="center">V8</td>
<td align="center">Hospital B</td> <td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2016-09-29</td>
<td align="center">N9</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td> <td align="center">B_ESCHR_COLI</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
@ -931,14 +916,14 @@ antibiotic class they are in:</p>
<td align="center">coli</td> <td align="center">coli</td>
<td align="center">TRUE</td> <td align="center">TRUE</td>
</tr> </tr>
<tr class="odd"> <tr class="even">
<td align="center">2011-01-04</td> <td align="center">2010-11-09</td>
<td align="center">E8</td> <td align="center">A10</td>
<td align="center">Hospital B</td> <td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</td> <td align="center">B_STRPT_PNMN</td>
<td align="center">R</td> <td align="center">R</td>
<td align="center">R</td> <td align="center">R</td>
<td align="center">S</td> <td align="center">R</td>
<td align="center">R</td> <td align="center">R</td>
<td align="center">M</td> <td align="center">M</td>
<td align="center">Gram-positive</td> <td align="center">Gram-positive</td>
@ -946,13 +931,28 @@ antibiotic class they are in:</p>
<td align="center">pneumoniae</td> <td align="center">pneumoniae</td>
<td align="center">TRUE</td> <td align="center">TRUE</td>
</tr> </tr>
<tr class="odd">
<td align="center">2017-01-15</td>
<td align="center">C6</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</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-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even"> <tr class="even">
<td align="center">2017-12-28</td> <td align="center">2014-07-20</td>
<td align="center">Z5</td> <td align="center">X1</td>
<td align="center">Hospital C</td> <td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td> <td align="center">B_STRPT_PNMN</td>
<td align="center">S</td> <td align="center">R</td>
<td align="center">S</td> <td align="center">R</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">R</td> <td align="center">R</td>
<td align="center">F</td> <td align="center">F</td>
@ -962,24 +962,24 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td> <td align="center">TRUE</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">2010-08-11</td> <td align="center">2010-05-23</td>
<td align="center">C6</td> <td align="center">T8</td>
<td align="center">Hospital C</td> <td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</td> <td align="center">B_STPHY_AURS</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">R</td> <td align="center">R</td>
<td align="center">M</td> <td align="center">F</td>
<td align="center">Gram-positive</td> <td align="center">Gram-positive</td>
<td align="center">Streptococcus</td> <td align="center">Staphylococcus</td>
<td align="center">pneumoniae</td> <td align="center">aureus</td>
<td align="center">TRUE</td> <td align="center">TRUE</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">2012-08-24</td> <td align="center">2014-12-22</td>
<td align="center">Z9</td> <td align="center">T5</td>
<td align="center">Hospital A</td> <td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td> <td align="center">B_STRPT_PNMN</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
@ -1013,50 +1013,50 @@ different bug/drug combinations, you can use the
<tr class="odd"> <tr class="odd">
<td align="center">E. coli</td> <td align="center">E. coli</td>
<td align="center">AMX</td> <td align="center">AMX</td>
<td align="center">2204</td> <td align="center">2172</td>
<td align="center">121</td> <td align="center">140</td>
<td align="center">2310</td> <td align="center">2285</td>
<td align="center">4635</td> <td align="center">4597</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">E. coli</td> <td align="center">E. coli</td>
<td align="center">AMC</td> <td align="center">AMC</td>
<td align="center">3389</td> <td align="center">3386</td>
<td align="center">150</td> <td align="center">145</td>
<td align="center">1096</td> <td align="center">1066</td>
<td align="center">4635</td> <td align="center">4597</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">E. coli</td> <td align="center">E. coli</td>
<td align="center">CIP</td> <td align="center">CIP</td>
<td align="center">3408</td> <td align="center">3365</td>
<td align="center">0</td> <td align="center">0</td>
<td align="center">1227</td> <td align="center">1232</td>
<td align="center">4635</td> <td align="center">4597</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">E. coli</td> <td align="center">E. coli</td>
<td align="center">GEN</td> <td align="center">GEN</td>
<td align="center">4065</td> <td align="center">4016</td>
<td align="center">0</td> <td align="center">0</td>
<td align="center">570</td> <td align="center">581</td>
<td align="center">4635</td> <td align="center">4597</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">K. pneumoniae</td> <td align="center">K. pneumoniae</td>
<td align="center">AMX</td> <td align="center">AMX</td>
<td align="center">0</td> <td align="center">0</td>
<td align="center">0</td> <td align="center">0</td>
<td align="center">1202</td> <td align="center">1182</td>
<td align="center">1202</td> <td align="center">1182</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">K. pneumoniae</td> <td align="center">K. pneumoniae</td>
<td align="center">AMC</td> <td align="center">AMC</td>
<td align="center">927</td> <td align="center">952</td>
<td align="center">50</td> <td align="center">45</td>
<td align="center">225</td> <td align="center">185</td>
<td align="center">1202</td> <td align="center">1182</td>
</tr> </tr>
</tbody> </tbody>
</table> </table>
@ -1078,34 +1078,34 @@ different bug/drug combinations, you can use the
<tr class="odd"> <tr class="odd">
<td align="center">E. coli</td> <td align="center">E. coli</td>
<td align="center">GEN</td> <td align="center">GEN</td>
<td align="center">4065</td> <td align="center">4016</td>
<td align="center">0</td> <td align="center">0</td>
<td align="center">570</td> <td align="center">581</td>
<td align="center">4635</td> <td align="center">4597</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">K. pneumoniae</td> <td align="center">K. pneumoniae</td>
<td align="center">GEN</td> <td align="center">GEN</td>
<td align="center">1095</td> <td align="center">1072</td>
<td align="center">0</td> <td align="center">0</td>
<td align="center">107</td> <td align="center">110</td>
<td align="center">1202</td> <td align="center">1182</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">S. aureus</td> <td align="center">S. aureus</td>
<td align="center">GEN</td> <td align="center">GEN</td>
<td align="center">2408</td> <td align="center">2418</td>
<td align="center">0</td> <td align="center">0</td>
<td align="center">349</td> <td align="center">296</td>
<td align="center">2757</td> <td align="center">2714</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">S. pneumoniae</td> <td align="center">S. pneumoniae</td>
<td align="center">GEN</td> <td align="center">GEN</td>
<td align="center">0</td> <td align="center">0</td>
<td align="center">0</td> <td align="center">0</td>
<td align="center">2115</td> <td align="center">2148</td>
<td align="center">2115</td> <td align="center">2148</td>
</tr> </tr>
</tbody> </tbody>
</table> </table>
@ -1137,7 +1137,7 @@ I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equa
own:</p> own:</p>
<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r"> <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> <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] 0.5429078</span></span></code></pre></div> <span><span class="co"># [1] 0.5409266</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 <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> <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"> <div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
@ -1152,19 +1152,19 @@ own:</p>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="center">Hospital A</td> <td align="center">Hospital A</td>
<td align="center">0.5461974</td> <td align="center">0.5447103</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">Hospital B</td> <td align="center">Hospital B</td>
<td align="center">0.5343758</td> <td align="center">0.5458963</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">Hospital C</td> <td align="center">Hospital C</td>
<td align="center">0.5487149</td> <td align="center">0.5324921</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">Hospital D</td> <td align="center">Hospital D</td>
<td align="center">0.5482517</td> <td align="center">0.5330882</td>
</tr> </tr>
</tbody> </tbody>
</table> </table>
@ -1189,23 +1189,23 @@ all isolates available for every group (i.e. values S, I or R):</p>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="center">Hospital A</td> <td align="center">Hospital A</td>
<td align="center">0.5461974</td> <td align="center">0.5447103</td>
<td align="center">3182</td> <td align="center">3176</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">Hospital B</td> <td align="center">Hospital B</td>
<td align="center">0.5343758</td> <td align="center">0.5458963</td>
<td align="center">3709</td> <td align="center">3704</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">Hospital C</td> <td align="center">Hospital C</td>
<td align="center">0.5487149</td> <td align="center">0.5324921</td>
<td align="center">1673</td> <td align="center">1585</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">Hospital D</td> <td align="center">Hospital D</td>
<td align="center">0.5482517</td> <td align="center">0.5330882</td>
<td align="center">2145</td> <td align="center">2176</td>
</tr> </tr>
</tbody> </tbody>
</table> </table>
@ -1230,27 +1230,27 @@ therapies very easily:</p>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="center">Escherichia</td> <td align="center">Escherichia</td>
<td align="center">0.7635383</td> <td align="center">0.7681096</td>
<td align="center">0.8770227</td> <td align="center">0.8736132</td>
<td align="center">0.9766990</td> <td align="center">0.9769415</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">Klebsiella</td> <td align="center">Klebsiella</td>
<td align="center">0.8128120</td> <td align="center">0.8434856</td>
<td align="center">0.9109817</td> <td align="center">0.9069374</td>
<td align="center">0.9833611</td> <td align="center">0.9780034</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">Staphylococcus</td> <td align="center">Staphylococcus</td>
<td align="center">0.7972434</td> <td align="center">0.8043478</td>
<td align="center">0.8734131</td> <td align="center">0.8909359</td>
<td align="center">0.9818643</td> <td align="center">0.9837878</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">Streptococcus</td> <td align="center">Streptococcus</td>
<td align="center">0.5399527</td> <td align="center">0.5474860</td>
<td align="center">0.0000000</td> <td align="center">0.0000000</td>
<td align="center">0.5399527</td> <td align="center">0.5474860</td>
</tr> </tr>
</tbody> </tbody>
</table> </table>
@ -1278,23 +1278,23 @@ classes, use a antibiotic class selector such as
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="left">Hospital A</td> <td align="left">Hospital A</td>
<td align="right">54.6%</td> <td align="right">54.5%</td>
<td align="right">27.7%</td> <td align="right">25.0%</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">Hospital B</td> <td align="left">Hospital B</td>
<td align="right">53.4%</td> <td align="right">54.6%</td>
<td align="right">26.4%</td> <td align="right">26.7%</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="left">Hospital C</td> <td align="left">Hospital C</td>
<td align="right">54.9%</td> <td align="right">53.2%</td>
<td align="right">25.2%</td> <td align="right">26.2%</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">Hospital D</td> <td align="left">Hospital D</td>
<td align="right">54.8%</td> <td align="right">53.3%</td>
<td align="right">26.7%</td> <td align="right">25.5%</td>
</tr> </tr>
</tbody> </tbody>
</table> </table>
@ -1410,16 +1410,18 @@ classes) <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code>:</p>
<code class="sourceCode R"><span><span class="va">mic_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span></span> <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="va">mic_values</span></span>
<span><span class="co"># Class 'mic'</span></span> <span><span class="co"># Class 'mic'</span></span>
<span><span class="co"># [1] 8 64 2 1 0.002 128 0.01 0.25 2 0.125 </span></span> <span><span class="co"># [1] &gt;=256 &lt;=0.001 16 0.25 4 0.025 128 16 &gt;=256 </span></span>
<span><span class="co"># [11] 16 0.01 256 4 64 2 0.002 256 0.01 8 </span></span> <span><span class="co"># [10] 0.005 0.25 1 1 64 8 0.002 0.5 64 </span></span>
<span><span class="co"># [21] 0.025 0.025 16 0.025 8 1 128 0.125 4 0.001 </span></span> <span><span class="co"># [19] &gt;=256 0.25 0.5 0.005 0.025 0.25 8 2 0.01 </span></span>
<span><span class="co"># [31] 4 256 4 1 0.01 0.025 1 0.001 0.002 2 </span></span> <span><span class="co"># [28] 0.002 0.025 0.5 64 4 2 64 2 1 </span></span>
<span><span class="co"># [41] 0.001 2 0.01 128 0.01 1 16 0.5 64 0.0625</span></span> <span><span class="co"># [37] &lt;=0.001 128 0.25 0.0625 64 8 1 64 64 </span></span>
<span><span class="co"># [51] 8 0.005 16 32 128 4 0.01 32 0.025 0.005 </span></span> <span><span class="co"># [46] 0.5 &gt;=256 0.01 2 16 4 0.002 0.005 32 </span></span>
<span><span class="co"># [61] 32 0.01 0.125 256 32 16 8 0.025 4 1 </span></span> <span><span class="co"># [55] 16 32 0.0625 4 8 0.125 8 0.01 64 </span></span>
<span><span class="co"># [71] 16 16 0.125 0.002 16 32 0.5 0.0625 256 2 </span></span> <span><span class="co"># [64] 8 0.005 0.025 0.5 2 16 0.25 1 &lt;=0.001</span></span>
<span><span class="co"># [81] 0.005 0.01 1 0.005 0.125 0.0625 0.001 0.025 4 0.01 </span></span> <span><span class="co"># [73] 0.005 0.0625 0.01 0.0625 0.25 32 0.5 0.005 0.5 </span></span>
<span><span class="co"># [91] 2 1 0.025 256 0.0625 0.001 0.125 0.005 0.0625 0.001</span></span></code></pre></div> <span><span class="co"># [82] 0.005 4 0.002 4 &lt;=0.001 8 &lt;=0.001 0.01 0.125 </span></span>
<span><span class="co"># [91] 0.005 0.25 16 0.01 0.01 &gt;=256 0.01 0.025 0.5 </span></span>
<span><span class="co"># [100] &lt;=0.001</span></span></code></pre></div>
<div class="sourceCode" id="cb36"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb36"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span> <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> <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>
@ -1453,10 +1455,10 @@ plotting:</p>
<code class="sourceCode R"><span><span class="va">disk_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_disk</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span> <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="va">disk_values</span></span>
<span><span class="co"># Class 'disk'</span></span> <span><span class="co"># Class 'disk'</span></span>
<span><span class="co"># [1] 31 26 18 31 23 20 17 17 28 29 27 20 23 19 19 24 23 29 20 17 24 26 31 21 20</span></span> <span><span class="co"># [1] 30 28 18 29 30 23 29 25 25 24 19 22 18 23 27 21 27 21 25 30 23 31 25 27 26</span></span>
<span><span class="co"># [26] 26 19 20 18 31 18 17 31 19 26 20 19 27 20 22 17 25 24 29 19 24 28 25 20 22</span></span> <span><span class="co"># [26] 26 29 23 22 24 18 29 27 24 17 25 23 22 20 28 27 21 31 21 25 25 27 23 23 18</span></span>
<span><span class="co"># [51] 30 23 18 28 29 22 18 23 30 18 18 22 24 29 26 23 31 31 21 20 31 21 26 23 25</span></span> <span><span class="co"># [51] 31 31 31 31 24 27 26 31 26 27 27 26 20 26 26 28 24 26 19 25 21 27 19 31 21</span></span>
<span><span class="co"># [76] 23 26 25 29 22 26 18 23 29 26 31 25 17 30 23 21 28 31 26 30 29 29 25 28 27</span></span></code></pre></div> <span><span class="co"># [76] 18 26 30 23 28 28 27 31 21 17 28 28 22 21 26 23 26 28 27 31 29 30 28 23 28</span></span></code></pre></div>
<div class="sourceCode" id="cb42"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb42"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span> <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> <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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articles/EUCAST.html
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.2.9054</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9057</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"> <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
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.2.9054</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9057</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -375,19 +375,19 @@ names or codes, this would have worked exactly the same way:</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r"> <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> <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"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
<span><span class="co"># 1 R R S I R I</span></span> <span><span class="co"># 1 R R S R I I</span></span>
<span><span class="co"># 2 S I I R I I</span></span> <span><span class="co"># 2 R S S S I S</span></span>
<span><span class="co"># 3 I R S R R I</span></span> <span><span class="co"># 3 R S R I S S</span></span>
<span><span class="co"># 4 R R R R R S</span></span> <span><span class="co"># 4 R S S I I R</span></span>
<span><span class="co"># 5 R I I I I R</span></span> <span><span class="co"># 5 S R R I I I</span></span>
<span><span class="co"># 6 S S S I S S</span></span> <span><span class="co"># 6 S I I R R S</span></span>
<span><span class="co"># kanamycin</span></span> <span><span class="co"># kanamycin</span></span>
<span><span class="co"># 1 R</span></span> <span><span class="co"># 1 S</span></span>
<span><span class="co"># 2 R</span></span> <span><span class="co"># 2 R</span></span>
<span><span class="co"># 3 S</span></span> <span><span class="co"># 3 R</span></span>
<span><span class="co"># 4 S</span></span> <span><span class="co"># 4 R</span></span>
<span><span class="co"># 5 I</span></span> <span><span class="co"># 5 I</span></span>
<span><span class="co"># 6 I</span></span></code></pre></div> <span><span class="co"># 6 R</span></span></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can <p>We can now add the interpretation of MDR-TB to our data set. You can
use:</p> use:</p>
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
@ -428,40 +428,40 @@ Unique: 5</p>
<tr class="odd"> <tr class="odd">
<td align="left">1</td> <td align="left">1</td>
<td align="left">Mono-resistant</td> <td align="left">Mono-resistant</td>
<td align="right">3210</td> <td align="right">3254</td>
<td align="right">64.20%</td> <td align="right">65.08%</td>
<td align="right">3210</td> <td align="right">3254</td>
<td align="right">64.20%</td> <td align="right">65.08%</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">2</td> <td align="left">2</td>
<td align="left">Negative</td> <td align="left">Negative</td>
<td align="right">1010</td> <td align="right">960</td>
<td align="right">20.20%</td> <td align="right">19.20%</td>
<td align="right">4220</td> <td align="right">4214</td>
<td align="right">84.40%</td> <td align="right">84.28%</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="left">3</td> <td align="left">3</td>
<td align="left">Multi-drug-resistant</td> <td align="left">Multi-drug-resistant</td>
<td align="right">451</td> <td align="right">443</td>
<td align="right">9.02%</td> <td align="right">8.86%</td>
<td align="right">4671</td> <td align="right">4657</td>
<td align="right">93.42%</td> <td align="right">93.14%</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">4</td> <td align="left">4</td>
<td align="left">Poly-resistant</td> <td align="left">Poly-resistant</td>
<td align="right">235</td> <td align="right">240</td>
<td align="right">4.70%</td> <td align="right">4.80%</td>
<td align="right">4906</td> <td align="right">4897</td>
<td align="right">98.12%</td> <td align="right">97.94%</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="left">5</td> <td align="left">5</td>
<td align="left">Extensively drug-resistant</td> <td align="left">Extensively drug-resistant</td>
<td align="right">94</td> <td align="right">103</td>
<td align="right">1.88%</td> <td align="right">2.06%</td>
<td align="right">5000</td> <td align="right">5000</td>
<td align="right">100.00%</td> <td align="right">100.00%</td>
</tr> </tr>

4
articles/PCA.html
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.2.9054</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9057</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -280,7 +280,7 @@ function:</p>
<span><span class="co"># [1] "Caryophanales" "Enterobacterales" "Lactobacillales" "Pseudomonadales"</span></span> <span><span class="co"># [1] "Caryophanales" "Enterobacterales" "Lactobacillales" "Pseudomonadales"</span></span>
<span><span class="co"># Importance of components:</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"># 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 5.121e-17</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"># Proportion of Variance 0.5799 0.3531 0.0471 0.01435 0.00541 0.00012 0.000e+00</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> <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> <pre><code><span><span class="co"># Groups (n=4, named as 'order'):</span></span>

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articles/SPSS.html
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.2.9054</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9057</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -168,7 +168,7 @@
<h4 data-toc-skip class="author">Dr. Matthijs <h4 data-toc-skip class="author">Dr. Matthijs
Berends</h4> Berends</h4>
<h4 data-toc-skip class="date">29 November 2022</h4> <h4 data-toc-skip class="date">09 December 2022</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> <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> <div class="d-none name"><code>SPSS.Rmd</code></div>
@ -247,7 +247,7 @@ data using a custom made website. The webdesign knowledge needed
<li> <li>
<p><strong>R has a huge community.</strong></p> <p><strong>R has a huge community.</strong></p>
<p>Many R users just ask questions on websites like <a href="https://stackoverflow.com" class="external-link">StackOverflow.com</a>, the largest <p>Many R users just ask questions on websites like <a href="https://stackoverflow.com" class="external-link">StackOverflow.com</a>, the largest
online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">472,394 online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">473,435
R-related questions</a> have already been asked on this platform (that R-related questions</a> have already been asked on this platform (that
covers questions and answers for any programming language). In my own covers questions and answers for any programming language). In my own
experience, most questions are answered within a couple of experience, most questions are answered within a couple of

2
articles/WHONET.html
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.2.9054</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9057</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

4
articles/datasets.html
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.2.9054</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9057</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -166,7 +166,7 @@
<main id="main" class="col-md-9"><div class="page-header"> <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> <img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
<h4 data-toc-skip class="date">29 November 2022</h4> <h4 data-toc-skip class="date">09 December 2022</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> <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> <div class="d-none name"><code>datasets.Rmd</code></div>

2
articles/index.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.2.9054</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9057</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"> <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
articles/resistance_predict.html
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.2.9054</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9057</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"> <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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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.2.9054</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9057</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"> <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
authors.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a> <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="">1.8.2.9054</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9057</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

4
index.html
View File

@ -42,7 +42,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a> <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="">1.8.2.9054</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9057</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -527,7 +527,7 @@
<p>Manually, using:</p> <p>Manually, using:</p>
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"remotes"</span><span class="op">)</span> <span class="co"># if you haven't already</span></span> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"remotes"</span><span class="op">)</span> <span class="co"># if you haven't already</span></span>
<span><span class="fu">remotes</span><span class="fu">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html" class="external-link">install_github</a></span><span class="op">(</span><span class="st">"msberends/AMR"</span><span class="op">)</span></span></code></pre></div> <span><span class="fu">remotes</span><span class="fu">::</span><span class="fu">install_github</span><span class="op">(</span><span class="st">"msberends/AMR"</span><span class="op">)</span></span></code></pre></div>
</li> </li>
<li> <li>
<p>Automatically, using the <a href="https://ropensci.org/r-universe/" class="external-link">rOpenSci R-universe platform</a>, by adding <a href="https://msberends.r-universe.dev" class="external-link">our R-universe address</a> to your list of repositories (‘repos’):</p> <p>Automatically, using the <a href="https://ropensci.org/r-universe/" class="external-link">rOpenSci R-universe platform</a>, by adding <a href="https://msberends.r-universe.dev" class="external-link">our R-universe address</a> to your list of repositories (‘repos’):</p>

21
news/index.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.2.9054</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9057</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -132,10 +132,10 @@
</div> </div>
<div class="section level2"> <div class="section level2">
<h2 class="pkg-version" data-toc-text="1.8.2.9054" id="amr-1829054">AMR 1.8.2.9054<a class="anchor" aria-label="anchor" href="#amr-1829054"></a></h2> <h2 class="pkg-version" data-toc-text="1.8.2.9057" id="amr-1829057">AMR 1.8.2.9057<a class="anchor" aria-label="anchor" href="#amr-1829057"></a></h2>
<p>This version will eventually become v2.0! We’re happy to reach a new major milestone soon!</p> <p>This version will eventually become v2.0! We’re happy to reach a new major milestone soon!</p>
<div class="section level4"> <div class="section level4">
<h4 id="breaking-1-8-2-9054">Breaking<a class="anchor" aria-label="anchor" href="#breaking-1-8-2-9054"></a></h4> <h4 id="breaking-1-8-2-9057">Breaking<a class="anchor" aria-label="anchor" href="#breaking-1-8-2-9057"></a></h4>
<ul><li>Removed all species of the taxonomic kingdom Chromista from the package. This was done for multiple reasons: <ul><li>Removed all species of the taxonomic kingdom Chromista from the package. This was done for multiple reasons:
<ul><li>CRAN allows packages to be around 5 MB maximum, some packages are exempted but this package is not one of them</li> <ul><li>CRAN allows packages to be around 5 MB maximum, some packages are exempted but this package is not one of them</li>
<li>Chromista are not relevant when it comes to antimicrobial resistance, thus lacking the primary scope of this package</li> <li>Chromista are not relevant when it comes to antimicrobial resistance, thus lacking the primary scope of this package</li>
@ -151,7 +151,7 @@
<li>Using <code>units</code> in <code>ab_ddd(..., units = "...")</code> had been deprecated and is now not supported anymore. Use <code><a href="../reference/ab_property.html">ab_ddd_units()</a></code> instead.</li> <li>Using <code>units</code> in <code>ab_ddd(..., units = "...")</code> had been deprecated and is now not supported anymore. Use <code><a href="../reference/ab_property.html">ab_ddd_units()</a></code> instead.</li>
</ul></div> </ul></div>
<div class="section level4"> <div class="section level4">
<h4 id="new-1-8-2-9054">New<a class="anchor" aria-label="anchor" href="#new-1-8-2-9054"></a></h4> <h4 id="new-1-8-2-9057">New<a class="anchor" aria-label="anchor" href="#new-1-8-2-9057"></a></h4>
<ul><li> <ul><li>
<strong>EUCAST 2022 and CLSI 2022 guidelines</strong> have been added for <code><a href="../reference/as.rsi.html">as.rsi()</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.</li> <strong>EUCAST 2022 and CLSI 2022 guidelines</strong> have been added for <code><a href="../reference/as.rsi.html">as.rsi()</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.</li>
<li>Support for the following languages: Chinese, Greek, Japanese, Polish, Turkish and Ukrainian. We are very grateful for the valuable input by our colleagues from other countries. The <code>AMR</code> package is now available in 16 languages. The automatic language determination will give a note at start-up on systems in supported languages.</li> <li>Support for the following languages: Chinese, Greek, Japanese, Polish, Turkish and Ukrainian. We are very grateful for the valuable input by our colleagues from other countries. The <code>AMR</code> package is now available in 16 languages. The automatic language determination will give a note at start-up on systems in supported languages.</li>
@ -193,16 +193,17 @@
</li> </li>
</ul></div> </ul></div>
<div class="section level4"> <div class="section level4">
<h4 id="changed-1-8-2-9054">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-2-9054"></a></h4> <h4 id="changes-1-8-2-9057">Changes<a class="anchor" aria-label="anchor" href="#changes-1-8-2-9057"></a></h4>
<ul><li>Fixes and changes for using <code><a href="../reference/as.rsi.html">as.rsi()</a></code>: <ul><li>For <code><a href="../reference/as.rsi.html">as.rsi()</a></code>:
<ul><li>On certain EUCAST breakpoints for MIC values</li> <ul><li>Fixed certain EUCAST breakpoints for MIC values</li>
<li>On <code>NA</code> values (e.g. <code>as.rsi(as.disk(NA), ...)</code>)</li> <li>Allow <code>NA</code> values (e.g. <code>as.rsi(as.disk(NA), ...)</code>)</li>
<li>On bug-drug combinations with multiple breakpoints for different body sites</li> <li>Fix for bug-drug combinations with multiple breakpoints for different body sites</li>
<li>Interpretation from MIC and disk zones is now more informative about availability of breakpoints and more robust</li> <li>Interpretation from MIC and disk zones is now more informative about availability of breakpoints and more robust</li>
<li>The default guideline (EUCAST) can now be changed with <code>options(AMR_guideline = "...")</code> <li>The default guideline (EUCAST) can now be changed with <code>options(AMR_guideline = "...")</code>
</li> </li>
</ul></li> </ul></li>
<li>Removed the <code><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer()</a></code> method for MIC values, since MIC are not integer values and running <code><a href="https://rdrr.io/r/base/table.html" class="external-link">table()</a></code> on MIC values consequently failed for not being able to retrieve the level position (as that’s how normally <code><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer()</a></code> on <code>factor</code>s work)</li> <li>Removed the <code><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer()</a></code> method for MIC values, since MIC are not integer values and running <code><a href="https://rdrr.io/r/base/table.html" class="external-link">table()</a></code> on MIC values consequently failed for not being able to retrieve the level position (as that’s how normally <code><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer()</a></code> on <code>factor</code>s work)</li>
<li>Fixed determination of Gram stains (<code><a href="../reference/mo_property.html">mo_gramstain()</a></code>), since the taxonomic phyla Actinobacteria, Chloroflexi, Firmicutes, and Tenericutes have been renamed to respectively Actinomycetota, Chloroflexota, Bacillota, and Mycoplasmatota in 2021</li>
<li> <li>
<code><a href="https://rdrr.io/r/base/droplevels.html" class="external-link">droplevels()</a></code> on MIC will now return a common <code>factor</code> at default and will lose the <code>mic</code> class. Use <code>droplevels(..., as.mic = TRUE)</code> to keep the <code>mic</code> class.</li> <code><a href="https://rdrr.io/r/base/droplevels.html" class="external-link">droplevels()</a></code> on MIC will now return a common <code>factor</code> at default and will lose the <code>mic</code> class. Use <code>droplevels(..., as.mic = TRUE)</code> to keep the <code>mic</code> class.</li>
<li>Small fix for using <code><a href="../reference/ab_from_text.html">ab_from_text()</a></code> <li>Small fix for using <code><a href="../reference/ab_from_text.html">ab_from_text()</a></code>
@ -231,7 +232,7 @@
<li>Cleaning columns with <code><a href="../reference/as.rsi.html">as.rsi()</a></code>, <code><a href="../reference/as.mic.html">as.mic()</a></code>, or <code><a href="../reference/as.disk.html">as.disk()</a></code> will now show the column name in the warning for invalid results</li> <li>Cleaning columns with <code><a href="../reference/as.rsi.html">as.rsi()</a></code>, <code><a href="../reference/as.mic.html">as.mic()</a></code>, or <code><a href="../reference/as.disk.html">as.disk()</a></code> will now show the column name in the warning for invalid results</li>
</ul></div> </ul></div>
<div class="section level4"> <div class="section level4">
<h4 id="other-1-8-2-9054">Other<a class="anchor" aria-label="anchor" href="#other-1-8-2-9054"></a></h4> <h4 id="other-1-8-2-9057">Other<a class="anchor" aria-label="anchor" href="#other-1-8-2-9057"></a></h4>
<ul><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> <ul><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>Added Peter Dutey-Magni, Dmytro Mykhailenko, Anton Mymrikov, and Jonas Salm as contributors, to thank them for their valuable input</li> <li>Added Peter Dutey-Magni, Dmytro Mykhailenko, Anton Mymrikov, and Jonas Salm as contributors, to thank them for their valuable input</li>
<li>All R and Rmd files in this project are now styled using the <code>styler</code> package</li> <li>All R and Rmd files in this project are now styled using the <code>styler</code> package</li>

2
pkgdown.yml
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@ -11,7 +11,7 @@ articles:
datasets: datasets.html datasets: datasets.html
resistance_predict: resistance_predict.html resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html welcome_to_AMR: welcome_to_AMR.html
last_built: 2022-11-29T18:41Z last_built: 2022-12-09T10:24Z
urls: urls:
reference: https://msberends.github.io/AMR/reference reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles article: https://msberends.github.io/AMR/articles

2
reference/AMR-deprecated.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.2.9054</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9057</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"> <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/AMR.html
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@ -62,7 +62,7 @@ Principal component analysis for AMR
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.2.9054</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9057</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"> <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> <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="">1.8.2.9054</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9057</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"> <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> <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="">1.8.2.9054</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9057</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"> <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> <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="">1.8.2.9054</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9057</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"> <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_property.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.2.9054</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9057</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"> <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> <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="">1.8.2.9054</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9057</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"> <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/age.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.2.9054</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9057</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -195,16 +195,16 @@
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">df</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> birth_date age age_exact age_at_y2k</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1944-12-30 77 77.91507 55</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 1 1982-05-17 40 40.56438 17</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1946-04-06 76 76.64932 53</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 2 1992-09-06 30 30.25753 7</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1933-09-07 89 89.22740 66</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 3 1996-06-28 26 26.44932 3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1992-05-18 30 30.53425 7</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 4 1999-03-07 23 23.75890 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1970-02-25 52 52.75890 29</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 5 1965-11-27 57 57.03288 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1944-11-05 78 78.06575 55</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 6 1939-11-24 83 83.04110 60</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1950-02-10 72 72.80000 49</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 7 1955-12-24 66 66.95890 44</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1995-05-07 27 27.56438 4</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 8 1948-04-02 74 74.68767 51</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1998-09-17 24 24.20000 1</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 9 1950-10-19 72 72.13973 49</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1969-01-26 53 53.84110 30</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 10 1978-01-02 44 44.93425 21</span>
</code></pre></div> </code></pre></div>
</div> </div>
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@ -506,16 +506,16 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 50 × 12</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 50 × 12</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index ab_input ab_gu…¹ mo_in…² mo_guideline guide…³</span> <span class="r-out co"><span class="r-pr">#&gt;</span> datetime index ab_input ab_gu…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: #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> 2022-11-29 <span style="color: #949494;">18:42:02</span> 1 ampicillin AMP Strep … B_STRPT_PNMN EUCAST…</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2022-12-09 <span style="color: #949494;">10:24:24</span> 1 ampicillin AMP Strep … B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2022-11-29 <span style="color: #949494;">18:42:03</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;"> 2</span> 2022-12-09 <span style="color: #949494;">10:24:24</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;"> 3</span> 2022-11-29 <span style="color: #949494;">18:42:03</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;"> 3</span> 2022-12-09 <span style="color: #949494;">10:24:25</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> 2022-11-29 <span style="color: #949494;">18:42:03</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;"> 4</span> 2022-12-09 <span style="color: #949494;">10:24:25</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;"> 5</span> 2022-11-29 <span style="color: #949494;">18:42:04</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;"> 5</span> 2022-12-09 <span style="color: #949494;">10:24:25</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;"> 6</span> 2022-11-29 <span style="color: #949494;">18:42:05</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2022-12-09 <span style="color: #949494;">10:24:26</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2022-11-29 <span style="color: #949494;">18:42:05</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2022-12-09 <span style="color: #949494;">10:24:26</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2022-11-29 <span style="color: #949494;">18:42:05</span> 2 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2022-12-09 <span style="color: #949494;">10:24:26</span> 2 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2022-11-29 <span style="color: #949494;">18:42:05</span> 3 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2022-12-09 <span style="color: #949494;">10:24:26</span> 3 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2022-11-29 <span style="color: #949494;">18:42:05</span> 4 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2022-12-09 <span style="color: #949494;">10:24:26</span> 4 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 40 more rows, 5 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;"># … with 40 more rows, 5 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;rsi&gt;, breakpoint_S_R &lt;chr&gt;, and abbreviated variable</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># input &lt;dbl&gt;, outcome &lt;rsi&gt;, breakpoint_S_R &lt;chr&gt;, and abbreviated variable</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># names ¹​ab_guideline, ²​mo_input, ³​guideline</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># names ¹​ab_guideline, ²​mo_input, ³​guideline</span></span>

2
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@ -260,16 +260,16 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 80 × 6</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 80 × 6</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo ab S I R total</span> <span class="r-out co"><span class="r-pr">#&gt;</span> mo ab S I R total</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;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;">*</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;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> Gram-negative PEN 17 1 726 744</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Gram-negative PEN 8 0 717 725</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Gram-negative OXA 9 0 1 10</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Gram-negative OXA 6 0 0 6</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Gram-negative FLC 11 0 1 12</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Gram-negative FLC 6 0 0 6</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Gram-negative AMX 231 1 407 639</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Gram-negative AMX 226 0 405 631</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Gram-negative AMC 473 89 175 737</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Gram-negative AMC 463 89 174 726</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Gram-negative AMP 231 1 407 639</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Gram-negative AMP 226 0 405 631</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Gram-negative TZP 556 11 76 643</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Gram-negative TZP 554 11 76 641</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Gram-negative CZO 94 2 110 206</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Gram-negative CZO 94 2 110 206</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Gram-negative FEP 470 1 14 485</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Gram-negative FEP 470 1 14 485</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Gram-negative CXM 546 22 144 712</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Gram-negative CXM 539 22 142 703</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 70 more rows</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 70 more rows</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Use 'format()' on this result to get a publishable/printable format.</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> Use 'format()' on this result to get a publishable/printable format.</span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>

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> <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="">1.8.2.9054</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9057</small>
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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> <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="">1.8.2.9054</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9057</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"> <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> <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="">1.8.2.9054</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9057</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"> <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> <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="">1.8.2.9054</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9057</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"> <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> <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="">1.8.2.9054</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9057</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"> <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> <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="">1.8.2.9054</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9057</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"> <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/first_isolate.html
View File

@ -12,7 +12,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.2.9054</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9057</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -354,7 +354,7 @@
<span class="r-in"><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">first_isolate</span><span class="op">(</span>info <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span> <span class="op">&amp;</span> <span class="fu"><a href="mo_property.html">mo_is_gram_negative</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>, <span class="op">]</span></span></span> <span class="r-in"><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">first_isolate</span><span class="op">(</span>info <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span> <span class="op">&amp;</span> <span class="fu"><a href="mo_property.html">mo_is_gram_negative</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Including isolates from ICU.</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> Including isolates from ICU.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Using column 'mo' as input for mo_is_gram_negative()</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Using column 'mo' as input for mo_is_gram_negative()</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 460 × 46</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 437 × 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> 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;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span></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;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA </span>
@ -367,7 +367,7 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2002-03-16 4FC193 69 M Clinical B_PSDMN_AERG R NA NA R </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2002-03-16 4FC193 69 M Clinical B_PSDMN_AERG R NA NA R </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2002-04-01 496896 46 F ICU B_ESCHR_COLI R NA NA NA </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2002-04-01 496896 46 F ICU B_ESCHR_COLI R NA NA NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2002-04-23 EE2510 69 F ICU B_ESCHR_COLI R NA NA NA </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2002-04-23 EE2510 69 F ICU B_ESCHR_COLI R NA NA NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 450 more rows, and 36 more variables: AMC &lt;rsi&gt;, AMP &lt;rsi&gt;, TZP &lt;rsi&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 427 more rows, and 36 more variables: AMC &lt;rsi&gt;, AMP &lt;rsi&gt;, TZP &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># CZO &lt;rsi&gt;, FEP &lt;rsi&gt;, CXM &lt;rsi&gt;, FOX &lt;rsi&gt;, CTX &lt;rsi&gt;, CAZ &lt;rsi&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># CZO &lt;rsi&gt;, FEP &lt;rsi&gt;, CXM &lt;rsi&gt;, FOX &lt;rsi&gt;, CTX &lt;rsi&gt;, CAZ &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># CRO &lt;rsi&gt;, GEN &lt;rsi&gt;, TOB &lt;rsi&gt;, AMK &lt;rsi&gt;, KAN &lt;rsi&gt;, TMP &lt;rsi&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># CRO &lt;rsi&gt;, GEN &lt;rsi&gt;, TOB &lt;rsi&gt;, AMK &lt;rsi&gt;, KAN &lt;rsi&gt;, TMP &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># SXT &lt;rsi&gt;, NIT &lt;rsi&gt;, FOS &lt;rsi&gt;, LNZ &lt;rsi&gt;, CIP &lt;rsi&gt;, MFX &lt;rsi&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># SXT &lt;rsi&gt;, NIT &lt;rsi&gt;, FOS &lt;rsi&gt;, LNZ &lt;rsi&gt;, CIP &lt;rsi&gt;, MFX &lt;rsi&gt;,</span></span>

2
reference/g.test.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.2.9054</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9057</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

124
reference/get_episode.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.2.9054</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9057</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -182,40 +182,40 @@
<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">200</span><span class="op">)</span>, <span class="op">]</span></span></span> <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">200</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-in"><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">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># indices</span></span></span> <span class="r-in"><span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</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] 53 62 32 61 13 24 5 35 42 38 15 9 6 4 24 17 13 61 29 35 46 18 27 5 29</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 49 11 47 52 11 50 54 53 64 23 65 64 4 33 34 43 52 35 16 4 9 27 38 10 37</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 15 43 28 19 12 13 32 59 8 32 6 20 2 5 23 21 32 43 45 32 56 37 48 38 29</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [26] 34 39 43 60 8 7 12 47 22 19 22 19 16 6 8 58 4 17 15 21 4 55 3 7 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 13 18 53 7 48 52 24 7 36 52 60 6 32 29 31 5 21 12 58 15 44 31 25 8 41</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [51] 65 45 66 40 62 50 22 18 26 38 17 32 27 49 35 36 30 47 34 24 58 61 36 45 17</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 29 8 44 32 56 11 44 9 32 39 31 13 60 30 33 17 49 10 47 8 19 19 11 7 46</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [76] 48 23 34 28 55 21 53 13 59 30 23 17 60 1 29 48 26 21 8 1 61 29 43 16 29</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [101] 31 15 47 3 25 30 61 36 1 22 55 23 20 60 60 44 63 36 46 58 58 26 51 12 41</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [101] 31 31 12 15 46 31 13 35 39 14 8 64 52 36 60 32 4 48 28 33 30 45 10 25 17</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [126] 13 11 7 2 63 12 23 18 45 26 51 46 54 32 21 11 1 59 9 53 59 62 59 47 8</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [126] 25 42 8 61 60 54 2 20 38 18 63 3 63 10 14 5 26 52 15 57 65 30 22 64 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [151] 54 10 15 56 39 36 50 38 40 57 42 22 31 34 14 49 34 4 26 29 63 59 62 31 8</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [151] 23 61 41 64 58 36 20 15 44 51 57 20 27 41 26 37 29 37 47 18 18 30 28 62 13</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [176] 4 63 33 28 40 40 3 32 4 58 13 11 16 5 58 29 1 46 38 61 59 7 51 34 27</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [176] 38 43 20 31 21 18 35 15 48 14 39 26 44 49 56 64 30 34 22 46 20 1 18 49 12</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">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># TRUE/FALSE</span></span></span> <span class="r-in"><span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</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] FALSE TRUE FALSE FALSE FALSE FALSE TRUE TRUE FALSE TRUE FALSE TRUE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] FALSE FALSE TRUE FALSE TRUE FALSE TRUE FALSE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] FALSE FALSE TRUE TRUE TRUE TRUE FALSE FALSE FALSE FALSE TRUE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [13] FALSE TRUE TRUE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [25] FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] FALSE TRUE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE TRUE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [37] TRUE TRUE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [49] TRUE FALSE TRUE TRUE TRUE TRUE FALSE FALSE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE TRUE TRUE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [61] TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [73] FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE TRUE TRUE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] TRUE FALSE FALSE FALSE TRUE TRUE FALSE FALSE TRUE FALSE TRUE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [85] TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [97] FALSE FALSE FALSE TRUE FALSE TRUE TRUE FALSE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [109] TRUE FALSE TRUE TRUE TRUE FALSE TRUE FALSE FALSE FALSE TRUE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [109] FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [121] FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [121] FALSE FALSE TRUE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [133] TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [133] FALSE TRUE FALSE FALSE TRUE TRUE FALSE FALSE TRUE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [145] TRUE FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE TRUE FALSE TRUE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [145] TRUE FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [157] TRUE FALSE FALSE TRUE TRUE TRUE FALSE FALSE TRUE TRUE TRUE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [157] FALSE FALSE TRUE TRUE FALSE TRUE TRUE TRUE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [169] TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [169] FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [181] TRUE TRUE TRUE TRUE TRUE FALSE FALSE TRUE FALSE FALSE TRUE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [181] FALSE TRUE FALSE FALSE TRUE FALSE TRUE FALSE TRUE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [193] FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [193] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-in"><span></span></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="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">$</span><span class="va">date</span>, <span class="fl">60</span><span class="op">)</span> <span class="op">==</span> <span class="fl">3</span><span class="op">)</span>, <span class="op">]</span></span></span> <span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</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> <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> 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;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span></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;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-06-22 FD8039 75 F ICU B_ESCHR_COLI R NA NA NA </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-08-19 A49852 70 M Clinical B_ESCHR_COLI R NA NA NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2002-06-18 012595 30 M ICU B_CRYNB I NA NA NA </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2002-07-30 218912 76 F ICU B_ESCHR_COLI R NA NA NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 36 more variables: AMC &lt;rsi&gt;, AMP &lt;rsi&gt;, TZP &lt;rsi&gt;, CZO &lt;rsi&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 36 more variables: AMC &lt;rsi&gt;, AMP &lt;rsi&gt;, TZP &lt;rsi&gt;, CZO &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># FEP &lt;rsi&gt;, CXM &lt;rsi&gt;, FOX &lt;rsi&gt;, CTX &lt;rsi&gt;, CAZ &lt;rsi&gt;, CRO &lt;rsi&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># FEP &lt;rsi&gt;, CXM &lt;rsi&gt;, FOX &lt;rsi&gt;, CTX &lt;rsi&gt;, CAZ &lt;rsi&gt;, CRO &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># GEN &lt;rsi&gt;, TOB &lt;rsi&gt;, AMK &lt;rsi&gt;, KAN &lt;rsi&gt;, TMP &lt;rsi&gt;, SXT &lt;rsi&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># GEN &lt;rsi&gt;, TOB &lt;rsi&gt;, AMK &lt;rsi&gt;, KAN &lt;rsi&gt;, TMP &lt;rsi&gt;, SXT &lt;rsi&gt;,</span></span>
@ -251,16 +251,16 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: condition [3]</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: condition [3]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> patient date condition new_episode</span> <span class="r-out co"><span class="r-pr">#&gt;</span> patient date condition new_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;date&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: #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;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> F76601 2015-09-20 A FALSE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 245525 2013-11-02 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> D20588 2017-08-17 A FALSE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 765860 2004-04-07 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 48BB05 2010-03-15 B TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 702351 2013-01-26 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 871020 2017-07-20 B FALSE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 188588 2014-08-19 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 554965 2005-08-29 B FALSE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 28F906 2004-04-05 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 451990 2008-03-22 B FALSE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 62B634 2014-01-16 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> E44854 2003-03-22 C FALSE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> B61087 2015-03-17 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> D91230 2010-12-06 A TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 4F9406 2015-01-23 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 743093 2012-09-14 C FALSE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> D39422 2017-05-17 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> BC9909 2011-07-08 A FALSE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 5B78D5 2007-01-01 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 190 more rows</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 190 more rows</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="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="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span> <span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@ -275,16 +275,16 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: ward, patient [182]</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: ward, patient [182]</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> 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: #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> ICU 2015-09-20 F76601 1 TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> ICU 2013-11-02 245525 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> ICU 2017-08-17 D20588 1 TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical 2004-04-07 765860 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Clinical 2010-03-15 48BB05 1 TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> ICU 2013-01-26 702351 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical 2017-07-20 871020 1 TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical 2014-08-19 188588 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Clinical 2005-08-29 554965 1 TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> ICU 2004-04-05 28F906 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Clinical 2008-03-22 451990 1 TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Clinical 2014-01-16 62B634 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> ICU 2003-03-22 E44854 1 TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> ICU 2015-03-17 B61087 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical 2010-12-06 D91230 1 TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical 2015-01-23 4F9406 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Outpatient 2012-09-14 743093 1 TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Clinical 2017-05-17 D39422 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical 2011-07-08 BC9909 1 TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Outpatient 2007-01-01 5B78D5 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 190 more rows</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 190 more rows</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="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="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span> <span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@ -299,9 +299,9 @@
<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> <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> 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: #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 112 15 51 70</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 116 14 54 75</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 61 13 37 43</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 57 12 39 46</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 9 6 9 9</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 9 6 7 7</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="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></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"># grouping on patients and microorganisms leads to the same</span></span></span>
@ -331,19 +331,19 @@
<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="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-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: 200 × 4</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 200 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, mo, ward [188]</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, mo, ward [190]</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> 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: #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> F76601 B_ESCHR_COLI ICU TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 245525 B_PROTS_MRBL ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> D20588 B_STPHY_HMNS ICU TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 765860 B_STRPT_GRPA Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 48BB05 B_STPHY_CONS Clinical TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 702351 B_ESCHR_COLI ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 871020 B_STPHY_EPDR Clinical TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 188588 B_CTRBC_KOSR Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 554965 B_STPHY_AURS Clinical TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 28F906 B_STPHY_CONS ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 451990 B_ESCHR_COLI Clinical TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 62B634 B_STRPT_PNMN Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> E44854 B_STRPT_PNMN ICU TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> B61087 B_STPHY_EPDR ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> D91230 B_STPHY_EPDR Clinical TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 4F9406 B_KLBSL_PNMN Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 743093 B_ENTRBC_CLOC Outpatient TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> D39422 B_KLBSL_PNMN Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> BC9909 B_ENTRBC_CLOC Clinical TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 5B78D5 B_STPHY_AURS Outpatient TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 190 more rows</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 190 more rows</span></span>
<span class="r-in"><span><span class="co"># }</span></span></span> <span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div> </code></pre></div>

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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.2.9054</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9057</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"> <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> <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="">1.8.2.9054</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9057</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"> <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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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.2.9054</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9057</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"> <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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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.2.9054</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9057</small>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.2.9054</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9057</small>
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.2.9054</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9057</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"> <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> <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="">1.8.2.9054</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9057</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"> <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
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.2.9054</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9057</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -172,9 +172,9 @@
<div class="section level2"> <div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <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> <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] 3.060168</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2.942494</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-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] 0.01364338</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.008191898</span>
</code></pre></div> </code></pre></div>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.2.9054</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9057</small>
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.2.9054</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9057</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -200,10 +200,10 @@
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">x</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> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">x</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">x</span></span></span> <span class="r-in"><span><span class="va">x</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> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.5 32 1 4 256 64 4 0.002 0.025 0.5 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.125 16 128 0.5 4 0.5 0.0625 0.01 0.025 32 </span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.3241709 0.8396588 -0.1301993 0.2577439 1.4215736 1.0336304</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.5844196 0.9288246 1.5773579 -0.1520641 0.4964691 -0.1520641</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.2577439 -1.8693070 -1.1625023 -0.3241709</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.8005973 -1.3721402 -1.0863687 1.1450024</span>
<span class="r-in"><span></span></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><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> <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>
@ -214,37 +214,37 @@
<span class="r-in"><span><span class="op">)</span></span></span> <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-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> id amox cipr gent tobr</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A 4 &lt;=0.125 &lt;=0.5 4</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 1 A 16 &gt;=4 1 &gt;=8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 4 0.25 1 4</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 8 1 1 &gt;=8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 32 0.25 1 8</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 8 2 4 &lt;=0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 2 &lt;=0.125 &lt;=0.5 1</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 8 0.25 16 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 8 &lt;=0.125 8 1</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 4 &lt;=0.0625 4 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 32 0.25 2 2</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 16 1 2 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 8 0.5 1 2</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 8 2 4 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 2 &gt;=1 8 2</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 4 1 4 &gt;=8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 32 &lt;=0.125 4 4</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 4 0.5 4 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 16 0.25 2 2</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 16 0.125 1 &lt;=0.5</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-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",</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "id" and "tobr"</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> "id" and "tobr"</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>NAs introduced by coercion</span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>NAs introduced by coercion</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.51912782 -0.09831951 0.63538430 -1.20290099 -0.21181627 0.27774576</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.58580073 0.01609138 -0.12243892 0.37435404 -0.58927461 0.35318445</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.04628481 0.49245479 0.45927606 0.12101887</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.37571945 0.10382446 -0.36004270 -0.73721828</span>
<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op">&lt;-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu">where</span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="va">y</span><span class="op">$</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">where</span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</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> 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-msg co"><span class="r-pr">#&gt;</span> "tobr"</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">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span> <span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance</span> <span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 2 &lt;=0.125 &lt;=0.5 1 -1.20290099</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 16 0.125 1 &lt;=0.5 -0.73721828</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A 4 &lt;=0.125 &lt;=0.5 4 -0.51912782</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 4 &lt;=0.0625 4 4 -0.58927461</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 8 &lt;=0.125 8 1 -0.21181627</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 4 0.5 4 2 -0.36004270</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 4 0.25 1 4 -0.09831951</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 8 2 4 &lt;=0.5 -0.12243892</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 8 0.5 1 2 0.04628481</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 8 1 1 &gt;=8 0.01609138</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 16 0.25 2 2 0.12101887</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 4 1 4 &gt;=8 0.10382446</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 32 0.25 2 2 0.27774576</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 16 1 2 4 0.35318445</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 32 &lt;=0.125 4 4 0.45927606</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 8 0.25 16 4 0.37435404</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 2 &gt;=1 8 2 0.49245479</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 8 2 4 4 0.37571945</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 32 0.25 1 8 0.63538430</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 1 A 16 &gt;=4 1 &gt;=8 0.58580073</span>
<span class="r-in"><span></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> <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="va">y</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span> <span class="r-in"><span> <span class="va">y</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@ -257,16 +257,16 @@
<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> 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-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> id amox cipr gent tobr amr_distance check_id_C</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 C 32 0.25 1 8 0.63538430 0.0000000</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 1 C 8 2 4 &lt;=0.5 -0.12243892 0.0000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 H 2 &gt;=1 8 2 0.49245479 0.1429295</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 8 1 1 &gt;=8 0.01609138 0.1385303</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 I 32 &lt;=0.125 4 4 0.45927606 0.1761082</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 3 H 4 1 4 &gt;=8 0.10382446 0.2262634</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 F 32 0.25 2 2 0.27774576 0.3576385</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 4 I 4 0.5 4 2 -0.36004270 0.2376038</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 J 16 0.25 2 2 0.12101887 0.5143654</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 4 &lt;=0.0625 4 4 -0.58927461 0.4668357</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 G 8 0.5 1 2 0.04628481 0.5890995</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 16 1 2 4 0.35318445 0.4756234</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 B 4 0.25 1 4 -0.09831951 0.7337038</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 7 D 8 0.25 16 4 0.37435404 0.4967930</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 E 8 &lt;=0.125 8 1 -0.21181627 0.8472006</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 8 G 8 2 4 4 0.37571945 0.4981584</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 A 4 &lt;=0.125 &lt;=0.5 4 -0.51912782 1.1545121</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 9 J 16 0.125 1 &lt;=0.5 -0.73721828 0.6147794</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 D 2 &lt;=0.125 &lt;=0.5 1 -1.20290099 1.8382853</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 10 A 16 &gt;=4 1 &gt;=8 0.58580073 0.7082397</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="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="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> <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
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.2.9054</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9057</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"> <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> <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="">1.8.2.9054</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9057</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"> <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> <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="">1.8.2.9054</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9057</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

32
reference/mo_property.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.2.9054</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9057</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -408,8 +408,8 @@
<li><p><code>mo_ref("Shimwellia blattae", keep_synonyms = FALSE)</code> will return <code>"Priest et al., 2010"</code> (without a message)</p></li> <li><p><code>mo_ref("Shimwellia blattae", keep_synonyms = FALSE)</code> will return <code>"Priest et al., 2010"</code> (without a message)</p></li>
</ul><p>The short name - <code>mo_shortname()</code> - almost always returns the first character of the genus and the full species, like <code>"E. coli"</code>. Exceptions are abbreviations of staphylococci (such as <em>"CoNS"</em>, Coagulase-Negative Staphylococci) and beta-haemolytic streptococci (such as <em>"GBS"</em>, Group B Streptococci). Please bear in mind that e.g. <em>E. coli</em> could mean <em>Escherichia coli</em> (kingdom of Bacteria) as well as <em>Entamoeba coli</em> (kingdom of Protozoa). Returning to the full name will be done using <code><a href="as.mo.html">as.mo()</a></code> internally, giving priority to bacteria and human pathogens, i.e. <code>"E. coli"</code> will be considered <em>Escherichia coli</em>. In other words, <code>mo_fullname(mo_shortname("Entamoeba coli"))</code> returns <code>"Escherichia coli"</code>.</p> </ul><p>The short name - <code>mo_shortname()</code> - almost always returns the first character of the genus and the full species, like <code>"E. coli"</code>. Exceptions are abbreviations of staphylococci (such as <em>"CoNS"</em>, Coagulase-Negative Staphylococci) and beta-haemolytic streptococci (such as <em>"GBS"</em>, Group B Streptococci). Please bear in mind that e.g. <em>E. coli</em> could mean <em>Escherichia coli</em> (kingdom of Bacteria) as well as <em>Entamoeba coli</em> (kingdom of Protozoa). Returning to the full name will be done using <code><a href="as.mo.html">as.mo()</a></code> internally, giving priority to bacteria and human pathogens, i.e. <code>"E. coli"</code> will be considered <em>Escherichia coli</em>. In other words, <code>mo_fullname(mo_shortname("Entamoeba coli"))</code> returns <code>"Escherichia coli"</code>.</p>
<p>Since the top-level of the taxonomy is sometimes referred to as 'kingdom' and sometimes as 'domain', the functions <code>mo_kingdom()</code> and <code>mo_domain()</code> return the exact same results.</p> <p>Since the top-level of the taxonomy is sometimes referred to as 'kingdom' and sometimes as 'domain', the functions <code>mo_kingdom()</code> and <code>mo_domain()</code> return the exact same results.</p>
<p>The Gram stain - <code>mo_gramstain()</code> - will be determined based on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002, <a href="https://pubmed.ncbi.nlm.nih.gov/11837318" class="external-link">PMID 11837318</a>), who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes. These bacteria are considered Gram-positive, except for members of the class Negativicutes which are Gram-negative. Members of other bacterial phyla are all considered Gram-negative. Species outside the kingdom of Bacteria will return a value <code>NA</code>. Functions <code>mo_is_gram_negative()</code> and <code>mo_is_gram_positive()</code> always return <code>TRUE</code> or <code>FALSE</code> (except when the input is <code>NA</code> or the MO code is <code>UNKNOWN</code>), thus always return <code>FALSE</code> for species outside the taxonomic kingdom of Bacteria.</p> <p>The Gram stain - <code>mo_gramstain()</code> - will be determined based on the taxonomic kingdom and phylum. Originally, Cavalier-Smith defined the so-called subkingdoms Negibacteria and Posibacteria (2002, <a href="https://pubmed.ncbi.nlm.nih.gov/11837318/" class="external-link">PMID 11837318</a>), and only considered these phyla as Posibacteria: Actinobacteria, Chloroflexi, Firmicutes, and Tenericutes. All of these phyla were renamed to Actinomycetota, Chloroflexota, Bacillota, and Mycoplasmatota (2021, <a href="https://pubmed.ncbi.nlm.nih.gov/34694987/" class="external-link">PMID 34694987</a>). Bacteria in these phyla are considered Gram-positive in this <code>AMR</code> package, except for members of the class Negativicutes (within phylum Bacillota) which are Gram-negative. All other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value <code>NA</code>. Functions <code>mo_is_gram_negative()</code> and <code>mo_is_gram_positive()</code> always return <code>TRUE</code> or <code>FALSE</code> (or <code>NA</code> when the input is <code>NA</code> or the MO code is <code>UNKNOWN</code>), thus always return <code>FALSE</code> for species outside the taxonomic kingdom of Bacteria.</p>
<p>Determination of yeasts - <code>mo_is_yeast()</code> - will be based on the taxonomic kingdom and class. <em>Budding yeasts</em> are fungi of the phylum Ascomycetes, class Saccharomycetes (also called Hemiascomycetes). <em>True yeasts</em> are aggregated into the underlying order Saccharomycetales. Thus, for all microorganisms that are fungi and member of the taxonomic class Saccharomycetes, the function will return <code>TRUE</code>. It returns <code>FALSE</code> otherwise (except when the input is <code>NA</code> or the MO code is <code>UNKNOWN</code>).</p> <p>Determination of yeasts - <code>mo_is_yeast()</code> - will be based on the taxonomic kingdom and class. <em>Budding yeasts</em> are fungi of the phylum Ascomycota, class Saccharomycetes (also called Hemiascomycetes). <em>True yeasts</em> are aggregated into the underlying order Saccharomycetales. Thus, for all microorganisms that are member of the taxonomic class Saccharomycetes, the function will return <code>TRUE</code>. It returns <code>FALSE</code> otherwise (or <code>NA</code> when the input is <code>NA</code> or the MO code is <code>UNKNOWN</code>).</p>
<p>Intrinsic resistance - <code>mo_is_intrinsic_resistant()</code> - will be determined based on the <a href="intrinsic_resistant.html">intrinsic_resistant</a> data set, which is based on <a href="https://www.eucast.org/expert_rules_and_expected_phenotypes/" class="external-link">'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3</a> (2021). The <code>mo_is_intrinsic_resistant()</code> functions can be vectorised over arguments <code>x</code> (input for microorganisms) and over <code>ab</code> (input for antibiotics).</p> <p>Intrinsic resistance - <code>mo_is_intrinsic_resistant()</code> - will be determined based on the <a href="intrinsic_resistant.html">intrinsic_resistant</a> data set, which is based on <a href="https://www.eucast.org/expert_rules_and_expected_phenotypes/" class="external-link">'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3</a> (2021). The <code>mo_is_intrinsic_resistant()</code> functions can be vectorised over arguments <code>x</code> (input for microorganisms) and over <code>ab</code> (input for antibiotics).</p>
<p>All output <a href="translate.html">will be translated</a> where possible.</p> <p>All output <a href="translate.html">will be translated</a> where possible.</p>
<p>The function <code>mo_url()</code> will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species.</p> <p>The function <code>mo_url()</code> will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species.</p>
@ -602,21 +602,27 @@
<span class="r-in"><span><span class="op">}</span></span></span> <span class="r-in"><span><span class="op">}</span></span></span>
<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 Using column 'mo' as input for mo_is_gram_positive()</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Using column 'mo' as input for mo_genus()</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Using column 'mo' as input for mo_genus()</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 12 × 2</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 18 × 2</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> `mo_genus()` n</span> <span class="r-out co"><span class="r-pr">#&gt;</span> `mo_genus()` n</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> <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>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Staphylococcus 840</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Staphylococcus 840</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Streptococcus 275</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Streptococcus 275</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Enterococcus 83</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Enterococcus 83</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Gemella 3</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Corynebacterium 17</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Aerococcus 2</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Micrococcus 6</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Fusibacter 1</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Gemella 3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Globicatella 1</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Aerococcus 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Granulicatella 1</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Cutibacterium 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Lactobacillus 1</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Dermabacter 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Leuconostoc 1</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Fusibacter 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">11</span> Listeria 1</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">11</span> Globicatella 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">12</span> Paenibacillus 1</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">12</span> Granulicatella 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">13</span> Lactobacillus 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">14</span> Leuconostoc 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">15</span> Listeria 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">16</span> Paenibacillus 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">17</span> Rothia 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">18</span> Schaalia 1</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="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="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></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>
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu">mo_is_intrinsic_resistant</span><span class="op">(</span>ab <span class="op">=</span> <span class="st">"vanco"</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span> <span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu">mo_is_intrinsic_resistant</span><span class="op">(</span>ab <span class="op">=</span> <span class="st">"vanco"</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>

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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.2.9054</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9057</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"> <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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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.2.9054</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9057</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"> <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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