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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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</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">20 December 2022</h4> <h4 data-toc-skip class="date">21 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 20 December 2022.</p> generated on 21 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">2022-12-20</td> <td align="center">2022-12-21</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">2022-12-20</td> <td align="center">2022-12-21</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">2022-12-20</td> <td align="center">2022-12-21</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>
@ -400,54 +400,32 @@ data set:</p>
</tr></thead> </tr></thead>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="center">2012-05-04</td> <td align="center">2016-06-23</td>
<td align="center">H8</td> <td align="center">Y9</td>
<td align="center">Hospital A</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2014-01-27</td>
<td align="center">P2</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2014-09-23</td>
<td align="center">O2</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2015-09-04</td>
<td align="center">E7</td>
<td align="center">Hospital B</td> <td align="center">Hospital B</td>
<td align="center">Escherichia coli</td> <td align="center">Escherichia coli</td>
<td align="center">R</td> <td align="center">R</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2012-11-25</td>
<td align="center">K4</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td> <td align="center">R</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td> <td align="center">M</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">2011-05-16</td> <td align="center">2014-11-07</td>
<td align="center">Z1</td> <td align="center">W7</td>
<td align="center">Hospital A</td> <td align="center">Hospital C</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">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
@ -455,16 +433,38 @@ data set:</p>
<td align="center">F</td> <td align="center">F</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">2015-10-13</td> <td align="center">2013-08-15</td>
<td align="center">R9</td> <td align="center">R1</td>
<td align="center">Hospital A</td> <td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td> <td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">I</td> <td align="center">I</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="odd">
<td align="center">2015-03-28</td>
<td align="center">I6</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2010-01-20</td>
<td align="center">A9</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>
</tbody> </tbody>
</table> </table>
<p>Now, let’s start the cleaning and the analysis!</p> <p>Now, let’s start the cleaning and the analysis!</p>
@ -499,16 +499,16 @@ 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">10,329</td> <td align="right">10,369</td>
<td align="right">51.65%</td> <td align="right">51.85%</td>
<td align="right">10,329</td> <td align="right">10,369</td>
<td align="right">51.65%</td> <td align="right">51.85%</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">9,671</td> <td align="right">9,631</td>
<td align="right">48.36%</td> <td align="right">48.16%</td>
<td align="right">20,000</td> <td align="right">20,000</td>
<td align="right">100.00%</td> <td align="right">100.00%</td>
</tr> </tr>
@ -621,10 +621,10 @@ 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 10,607 'phenotype-based' first isolates (53.0% of total where a</span></span> <span><span class="co"># =&gt; Found 10,556 'phenotype-based' first isolates (52.8% 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% is suitable for resistance analysis! We can now filter on <p>So only 52.8% is suitable for resistance analysis! We can now filter
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">
<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>
@ -634,7 +634,7 @@ it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" cl
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span> <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 10,607 isolates for analysis. Now our data looks <p>So we end up with 10,556 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>
@ -673,14 +673,78 @@ like:</p>
</tr></thead> </tr></thead>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="left">4</td> <td align="left">1</td>
<td align="center">2015-09-04</td> <td align="center">2016-06-23</td>
<td align="center">E7</td> <td align="center">Y9</td>
<td align="center">Hospital B</td> <td align="center">Hospital B</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>
<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">4</td>
<td align="center">2013-08-15</td>
<td align="center">R1</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td> <td align="center">R</td>
<td align="center">I</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="odd">
<td align="left">9</td>
<td align="center">2010-06-10</td>
<td align="center">R1</td>
<td align="center">Hospital A</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">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">12</td>
<td align="center">2013-04-05</td>
<td align="center">R3</td>
<td align="center">Hospital C</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="odd">
<td align="left">14</td>
<td align="center">2016-09-25</td>
<td align="center">C9</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">M</td> <td align="center">M</td>
<td align="center">Gram-negative</td> <td align="center">Gram-negative</td>
@ -689,83 +753,19 @@ like:</p>
<td align="center">TRUE</td> <td align="center">TRUE</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">9</td> <td align="left">15</td>
<td align="center">2010-01-25</td> <td align="center">2016-12-29</td>
<td align="center">M2</td> <td align="center">X9</td>
<td align="center">Hospital A</td> <td align="center">Hospital C</td>
<td align="center">B_KLBSL_PNMN</td> <td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">10</td>
<td align="center">2014-12-16</td>
<td align="center">V4</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">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-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">11</td>
<td align="center">2013-08-07</td>
<td align="center">G2</td>
<td align="center">Hospital A</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">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="odd">
<td align="left">12</td>
<td align="center">2013-01-20</td>
<td align="center">J7</td>
<td align="center">Hospital B</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td> <td align="center">Gram-negative</td>
<td align="center">Klebsiella</td> <td align="center">Escherichia</td>
<td align="center">pneumoniae</td> <td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">13</td>
<td align="center">2016-04-04</td>
<td align="center">Z1</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td> <td align="center">TRUE</td>
</tr> </tr>
</tbody> </tbody>
@ -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: 10,607<br> Length: 10,556<br>
Available: 10,607 (100%, NA: 0 = 0%)<br> Available: 10,556 (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>
@ -827,34 +827,34 @@ 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">4,601</td> <td align="right">4,539</td>
<td align="right">43.38%</td> <td align="right">43.00%</td>
<td align="right">4,601</td> <td align="right">4,539</td>
<td align="right">43.38%</td> <td align="right">43.0%</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">2,687</td> <td align="right">2,724</td>
<td align="right">25.33%</td> <td align="right">25.81%</td>
<td align="right">7,288</td> <td align="right">7,263</td>
<td align="right">68.71%</td> <td align="right">68.8%</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">2,123</td> <td align="right">2,121</td>
<td align="right">20.02%</td> <td align="right">20.09%</td>
<td align="right">9,411</td> <td align="right">9,384</td>
<td align="right">88.72%</td> <td align="right">88.9%</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">1,196</td> <td align="right">1,172</td>
<td align="right">11.28%</td> <td align="right">11.10%</td>
<td align="right">10,607</td> <td align="right">10,556</td>
<td align="right">100.00%</td> <td align="right">100.0%</td>
</tr> </tr>
</tbody> </tbody>
</table> </table>
@ -902,27 +902,57 @@ antibiotic class they are in:</p>
</tr></thead> </tr></thead>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="center">2016-04-04</td> <td align="center">2015-05-30</td>
<td align="center">Z1</td> <td align="center">G4</td>
<td align="center">Hospital A</td> <td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td> <td align="center">B_STRPT_PNMN</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">S</td>
<td align="center">R</td> <td align="center">R</td>
<td align="center">F</td> <td align="center">M</td>
<td align="center">Gram-positive</td> <td align="center">Gram-positive</td>
<td align="center">Streptococcus</td> <td align="center">Streptococcus</td>
<td align="center">pneumoniae</td> <td align="center">pneumoniae</td>
<td align="center">TRUE</td> <td align="center">TRUE</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">2013-11-29</td> <td align="center">2012-09-30</td>
<td align="center">C10</td> <td align="center">R6</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2010-02-01</td>
<td align="center">J9</td>
<td align="center">Hospital A</td> <td align="center">Hospital A</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>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2012-08-14</td>
<td align="center">G4</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td> <td align="center">R</td>
<td align="center">R</td> <td align="center">R</td>
<td align="center">M</td> <td align="center">M</td>
@ -932,63 +962,33 @@ 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">2017-11-10</td> <td align="center">2013-10-07</td>
<td align="center">V8</td> <td align="center">B5</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2011-01-10</td>
<td align="center">U5</td>
<td align="center">Hospital D</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="odd">
<td align="center">2011-11-05</td>
<td align="center">M4</td>
<td align="center">Hospital D</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">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2014-03-24</td>
<td align="center">K7</td>
<td align="center">Hospital A</td> <td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</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">R</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2011-06-29</td>
<td align="center">K10</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">R</td> <td align="center">R</td>
<td align="center">R</td> <td align="center">R</td>
<td align="center">M</td> <td align="center">M</td>
<td align="center">Gram-positive</td> <td align="center">Gram-negative</td>
<td align="center">Streptococcus</td> <td align="center">Escherichia</td>
<td align="center">pneumoniae</td> <td align="center">coli</td>
<td align="center">TRUE</td> <td align="center">TRUE</td>
</tr> </tr>
</tbody> </tbody>
@ -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">2191</td> <td align="center">2172</td>
<td align="center">122</td> <td align="center">112</td>
<td align="center">2288</td> <td align="center">2255</td>
<td align="center">4601</td> <td align="center">4539</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">3385</td> <td align="center">3374</td>
<td align="center">179</td> <td align="center">137</td>
<td align="center">1037</td> <td align="center">1028</td>
<td align="center">4601</td> <td align="center">4539</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">3387</td> <td align="center">3321</td>
<td align="center">0</td> <td align="center">0</td>
<td align="center">1214</td> <td align="center">1218</td>
<td align="center">4601</td> <td align="center">4539</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">4036</td> <td align="center">3979</td>
<td align="center">0</td> <td align="center">0</td>
<td align="center">565</td> <td align="center">560</td>
<td align="center">4601</td> <td align="center">4539</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">1196</td> <td align="center">1172</td>
<td align="center">1196</td> <td align="center">1172</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">939</td> <td align="center">913</td>
<td align="center">45</td> <td align="center">54</td>
<td align="center">212</td> <td align="center">205</td>
<td align="center">1196</td> <td align="center">1172</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">4036</td> <td align="center">3979</td>
<td align="center">0</td> <td align="center">0</td>
<td align="center">565</td> <td align="center">560</td>
<td align="center">4601</td> <td align="center">4539</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">1072</td> <td align="center">1061</td>
<td align="center">0</td> <td align="center">0</td>
<td align="center">124</td> <td align="center">111</td>
<td align="center">1196</td> <td align="center">1172</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">2428</td> <td align="center">2420</td>
<td align="center">0</td> <td align="center">0</td>
<td align="center">259</td> <td align="center">304</td>
<td align="center">2687</td> <td align="center">2724</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">2123</td> <td align="center">2121</td>
<td align="center">2123</td> <td align="center">2121</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] 0.5453946</span></span></code></pre></div> <span><span class="co"># [1] 0.5442402</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">0.5539478</td> <td align="center">0.5429724</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">Hospital B</td> <td align="center">Hospital B</td>
<td align="center">0.5484475</td> <td align="center">0.5454295</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">Hospital C</td> <td align="center">Hospital C</td>
<td align="center">0.5440806</td> <td align="center">0.5458488</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">Hospital D</td> <td align="center">Hospital D</td>
<td align="center">0.5280418</td> <td align="center">0.5428845</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">0.5539478</td> <td align="center">0.5429724</td>
<td align="center">3179</td> <td align="center">3223</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">Hospital B</td> <td align="center">Hospital B</td>
<td align="center">0.5484475</td> <td align="center">0.5454295</td>
<td align="center">3736</td> <td align="center">3632</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">Hospital C</td> <td align="center">Hospital C</td>
<td align="center">0.5440806</td> <td align="center">0.5458488</td>
<td align="center">1588</td> <td align="center">1614</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">Hospital D</td> <td align="center">Hospital D</td>
<td align="center">0.5280418</td> <td align="center">0.5428845</td>
<td align="center">2104</td> <td align="center">2087</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">0.7746142</td> <td align="center">0.7735184</td>
<td align="center">0.8772006</td> <td align="center">0.8766248</td>
<td align="center">0.9780483</td> <td align="center">0.9806125</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">Klebsiella</td> <td align="center">Klebsiella</td>
<td align="center">0.8227425</td> <td align="center">0.8250853</td>
<td align="center">0.8963211</td> <td align="center">0.9052901</td>
<td align="center">0.9790970</td> <td align="center">0.9880546</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">Staphylococcus</td> <td align="center">Staphylococcus</td>
<td align="center">0.7789356</td> <td align="center">0.7991924</td>
<td align="center">0.9036100</td> <td align="center">0.8883994</td>
<td align="center">0.9810197</td> <td align="center">0.9801762</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">Streptococcus</td> <td align="center">Streptococcus</td>
<td align="center">0.5336788</td> <td align="center">0.5299387</td>
<td align="center">0.0000000</td> <td align="center">0.0000000</td>
<td align="center">0.5336788</td> <td align="center">0.5299387</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">55.4%</td> <td align="right">54.3%</td>
<td align="right">27.0%</td> <td align="right">25.1%</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">Hospital B</td> <td align="left">Hospital B</td>
<td align="right">54.8%</td> <td align="right">54.5%</td>
<td align="right">26.5%</td> <td align="right">26.6%</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="left">Hospital C</td> <td align="left">Hospital C</td>
<td align="right">54.4%</td> <td align="right">54.6%</td>
<td align="right">26.2%</td> <td align="right">26.7%</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">Hospital D</td> <td align="left">Hospital D</td>
<td align="right">52.8%</td> <td align="right">54.3%</td>
<td align="right">27.1%</td> <td align="right">27.4%</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 16 16 0.01 8 0.01 0.001 0.01 0.125 32 </span></span> <span><span class="co"># [1] 0.25 &gt;=256 128 0.125 16 1 0.025 32 0.0625 </span></span>
<span><span class="co"># [11] 2 4 0.002 0.002 0.002 16 0.0625 0.005 0.005 8 </span></span> <span><span class="co"># [10] 0.125 1 0.5 32 4 128 0.125 8 8 </span></span>
<span><span class="co"># [21] 0.001 64 2 0.125 16 &gt;=256 0.005 0.001 4 0.005 </span></span> <span><span class="co"># [19] 128 0.01 0.125 0.01 0.01 0.25 0.005 32 32 </span></span>
<span><span class="co"># [31] 2 0.005 2 32 2 4 16 1 0.01 0.025 </span></span> <span><span class="co"># [28] 0.025 0.25 &lt;=0.001 0.5 0.25 2 4 64 0.002 </span></span>
<span><span class="co"># [41] 0.0625 0.01 8 128 0.25 0.01 0.01 128 0.0625 0.25 </span></span> <span><span class="co"># [37] 2 0.5 0.002 8 &gt;=256 16 128 0.0625 4 </span></span>
<span><span class="co"># [51] 2 8 0.0625 32 0.01 32 32 0.01 8 0.002 </span></span> <span><span class="co"># [46] 0.01 0.5 &gt;=256 1 32 1 32 32 0.25 </span></span>
<span><span class="co"># [61] 0.25 4 2 0.25 16 64 4 &gt;=256 64 64 </span></span> <span><span class="co"># [55] 0.01 &lt;=0.001 0.25 128 2 0.25 0.5 128 0.005 </span></span>
<span><span class="co"># [71] 64 32 32 0.25 &gt;=256 0.125 0.01 0.0625 128 4 </span></span> <span><span class="co"># [64] &gt;=256 32 128 &gt;=256 16 &lt;=0.001 0.002 32 32 </span></span>
<span><span class="co"># [81] 0.01 0.25 0.001 2 16 0.002 0.01 0.002 &gt;=256 0.025 </span></span> <span><span class="co"># [73] 0.005 32 0.025 0.005 0.01 0.25 0.5 32 128 </span></span>
<span><span class="co"># [91] 8 &gt;=256 16 0.002 2 0.125 0.0625 0.002 &gt;=256 0.025</span></span></code></pre></div> <span><span class="co"># [82] &lt;=0.001 0.125 0.025 1 &lt;=0.001 32 0.5 4 1 </span></span>
<span><span class="co"># [91] 2 32 16 0.0625 0.01 0.125 16 &gt;=256 2 </span></span>
<span><span class="co"># [100] 0.01</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] 17 22 17 18 28 30 30 31 20 20 17 23 18 30 27 28 18 27 25 25 25 25 17 19 20</span></span> <span><span class="co"># [1] 19 18 19 27 29 19 23 21 19 20 17 24 29 25 24 29 19 21 25 21 23 27 28 28 25</span></span>
<span><span class="co"># [26] 24 19 25 20 23 30 25 23 18 20 23 24 29 19 27 29 21 17 21 25 25 17 29 24 20</span></span> <span><span class="co"># [26] 31 31 26 27 26 29 29 20 25 31 22 25 25 18 29 17 22 21 26 23 24 18 17 28 21</span></span>
<span><span class="co"># [51] 24 20 17 30 23 22 25 17 17 21 19 20 27 29 26 25 22 21 29 31 19 21 29 24 29</span></span> <span><span class="co"># [51] 26 19 28 22 20 26 24 19 24 23 31 27 23 24 25 20 30 25 25 22 30 28 22 29 26</span></span>
<span><span class="co"># [76] 31 24 22 20 22 28 18 28 28 17 20 23 31 19 23 26 31 19 30 29 17 26 28 29 30</span></span></code></pre></div> <span><span class="co"># [76] 28 26 25 28 27 30 21 19 22 25 30 29 28 31 30 21 26 20 31 28 26 17 19 26 22</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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</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">

60
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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</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 S R R S I S</span></span> <span><span class="co"># 1 R I I S S S</span></span>
<span><span class="co"># 2 I R S S S S</span></span> <span><span class="co"># 2 R R I R S R</span></span>
<span><span class="co"># 3 I R S R S S</span></span> <span><span class="co"># 3 R R I R R I</span></span>
<span><span class="co"># 4 R R S I I R</span></span> <span><span class="co"># 4 R R R R S S</span></span>
<span><span class="co"># 5 S I R I S R</span></span> <span><span class="co"># 5 S I R I I I</span></span>
<span><span class="co"># 6 S I I I I R</span></span> <span><span class="co"># 6 S R R S I 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 S</span></span> <span><span class="co"># 2 I</span></span>
<span><span class="co"># 3 I</span></span> <span><span class="co"># 3 I</span></span>
<span><span class="co"># 4 S</span></span> <span><span class="co"># 4 I</span></span>
<span><span class="co"># 5 R</span></span> <span><span class="co"># 5 S</span></span>
<span><span class="co"># 6 S</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">3211</td> <td align="right">3215</td>
<td align="right">64.22%</td> <td align="right">64.30%</td>
<td align="right">3211</td> <td align="right">3215</td>
<td align="right">64.22%</td> <td align="right">64.30%</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">1047</td> <td align="right">997</td>
<td align="right">20.94%</td> <td align="right">19.94%</td>
<td align="right">4258</td> <td align="right">4212</td>
<td align="right">85.16%</td> <td align="right">84.24%</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">410</td> <td align="right">445</td>
<td align="right">8.20%</td> <td align="right">8.90%</td>
<td align="right">4668</td> <td align="right">4657</td>
<td align="right">93.36%</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">248</td> <td align="right">242</td>
<td align="right">4.96%</td> <td align="right">4.84%</td>
<td align="right">4916</td> <td align="right">4899</td>
<td align="right">98.32%</td> <td align="right">97.98%</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">84</td> <td align="right">101</td>
<td align="right">1.68%</td> <td align="right">2.02%</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>

2
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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</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/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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</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">20 December 2022</h4> <h4 data-toc-skip class="date">21 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>

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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</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">20 December 2022</h4> <h4 data-toc-skip class="date">21 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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</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/welcome_to_AMR.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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</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
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@ -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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</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">
@ -176,7 +176,7 @@
<li>Corrects for duplicate isolates, <strong>calculates and predicts AMR</strong> per antibiotic class</li> <li>Corrects for duplicate isolates, <strong>calculates and predicts AMR</strong> per antibiotic class</li>
<li>Integrates with <strong>WHONET</strong>, ATC, <strong>EARS-Net</strong>, PubChem, <strong>LOINC</strong> and <strong>SNOMED CT</strong> <li>Integrates with <strong>WHONET</strong>, ATC, <strong>EARS-Net</strong>, PubChem, <strong>LOINC</strong> and <strong>SNOMED CT</strong>
</li> </li>
<li>Works on Windows, macOS and Linux with <strong>all versions of R</strong> since R-3.0 and is ompletely <strong>dependency-free</strong>, highly suitable for places with <strong>limited resources</strong> <li>Works on Windows, macOS and Linux with <strong>all versions of R</strong> since R-3.0 and is completely <strong>dependency-free</strong>, highly suitable for places with <strong>limited resources</strong>
</li> </li>
</ul> </ul>
<div style="display: flex;"> <div style="display: flex;">

37
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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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</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">
@ -132,7 +132,7 @@
</div> </div>
<div class="section level2"> <div class="section level2">
<h2 class="pkg-version" data-toc-text="1.8.2.9068" id="amr-1829068">AMR 1.8.2.9068<a class="anchor" aria-label="anchor" href="#amr-1829068"></a></h2> <h2 class="pkg-version" data-toc-text="1.8.2.9069" id="amr-1829069">AMR 1.8.2.9069<a class="anchor" aria-label="anchor" href="#amr-1829069"></a></h2>
<p><em>(this beta version will eventually become v2.0! We’re happy to reach a new major milestone soon!)</em></p> <p><em>(this beta version will eventually become v2.0! We’re happy to reach a new major milestone soon!)</em></p>
<p>This is a new major release of the AMR package, with great new additions but also some breaking changes for current users. These are all listed below.</p> <p>This is a new major release of the AMR package, with great new additions but also some breaking changes for current users. These are all listed below.</p>
<p><strong><a href="https://en.wikipedia.org/wiki/TL;DR" class="external-link">TL;DR</a></strong></p> <p><strong><a href="https://en.wikipedia.org/wiki/TL;DR" class="external-link">TL;DR</a></strong></p>
@ -146,19 +146,19 @@
</li> </li>
<li>Many small bug fixes</li> <li>Many small bug fixes</li>
</ul><div class="section level3"> </ul><div class="section level3">
<h3 id="new-1-8-2-9068">New<a class="anchor" aria-label="anchor" href="#new-1-8-2-9068"></a></h3> <h3 id="new-1-8-2-9069">New<a class="anchor" aria-label="anchor" href="#new-1-8-2-9069"></a></h3>
<div class="section level5"> <div class="section level4">
<h5 id="interpretation-of-mic-and-disk-diffusion-values-1-8-2-9068">Interpretation of MIC and disk diffusion values<a class="anchor" aria-label="anchor" href="#interpretation-of-mic-and-disk-diffusion-values-1-8-2-9068"></a></h5> <h4 id="interpretation-of-mic-and-disk-diffusion-values-1-8-2-9069">Interpretation of MIC and disk diffusion values<a class="anchor" aria-label="anchor" href="#interpretation-of-mic-and-disk-diffusion-values-1-8-2-9069"></a></h4>
<p>EUCAST 2022 and CLSI 2022 guidelines 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. The default guideline (EUCAST) can now be changed with the new <code>AMR_guideline</code> option, such as: <code>options(AMR_guideline = "CLSI 2020")</code>.</p> <p>EUCAST 2022 and CLSI 2022 guidelines 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. The default guideline (EUCAST) can now be changed with the new <code>AMR_guideline</code> option, such as: <code>options(AMR_guideline = "CLSI 2020")</code>.</p>
<p>Interpretation guidelines older than 10 years were removed, the oldest now included guidelines of EUCAST and CLSI are from 2013.</p> <p>Interpretation guidelines older than 10 years were removed, the oldest now included guidelines of EUCAST and CLSI are from 2013.</p>
</div> </div>
<div class="section level5"> <div class="section level4">
<h5 id="supported-languages-1-8-2-9068">Supported languages<a class="anchor" aria-label="anchor" href="#supported-languages-1-8-2-9068"></a></h5> <h4 id="supported-languages-1-8-2-9069">Supported languages<a class="anchor" aria-label="anchor" href="#supported-languages-1-8-2-9069"></a></h4>
<p>We added support for the following languages: Chinese, Greek, Japanese, Polish, Turkish and Ukrainian. All antibiotic names are now available in these languages, and the AMR package will automatically determine a supported language based on the user system language.</p> <p>We added support for the following languages: Chinese, Greek, Japanese, Polish, Turkish and Ukrainian. All antibiotic names are now available in these languages, and the AMR package will automatically determine a supported language based on the user system language.</p>
<p>We are very grateful for the valuable input by our colleagues from other countries. The <code>AMR</code> package is now available in 16 languages and according to download stats used in almost all countries in the world!</p> <p>We are very grateful for the valuable input by our colleagues from other countries. The <code>AMR</code> package is now available in 16 languages and according to download stats used in almost all countries in the world!</p>
</div> </div>
<div class="section level5"> <div class="section level4">
<h5 id="microbiological-taxonomy-1-8-2-9068">Microbiological taxonomy<a class="anchor" aria-label="anchor" href="#microbiological-taxonomy-1-8-2-9068"></a></h5> <h4 id="microbiological-taxonomy-1-8-2-9069">Microbiological taxonomy<a class="anchor" aria-label="anchor" href="#microbiological-taxonomy-1-8-2-9069"></a></h4>
<p>The <code>microorganisms</code> no longer relies on the Catalogue of Life, but on the List of Prokaryotic names with Standing in Nomenclature (LPSN) and is supplemented with the ‘backbone taxonomy’ from the Global Biodiversity Information Facility (GBIF). The structure of this data set has changed to include separate LPSN and GBIF identifiers. Almost all previous MO codes were retained. It contains over 1,400 taxonomic names from 2022.</p> <p>The <code>microorganisms</code> no longer relies on the Catalogue of Life, but on the List of Prokaryotic names with Standing in Nomenclature (LPSN) and is supplemented with the ‘backbone taxonomy’ from the Global Biodiversity Information Facility (GBIF). The structure of this data set has changed to include separate LPSN and GBIF identifiers. Almost all previous MO codes were retained. It contains over 1,400 taxonomic names from 2022.</p>
<p>We previously relied on our own experience to categorise species into pathogenic groups, but we were very happy to encounter the very recent work of Bartlett <em>et al.</em> (2022, DOI <a href="https://doi.org/10.1099/mic.0.001269" class="external-link">10.1099/mic.0.001269</a>) who extensively studied medical-scientific literature to categorise all bacterial species into groups. See <code><a href="../reference/mo_matching_score.html">mo_matching_score()</a></code> on how their work was incorporated into the <code>prevalence</code> column of the <code>microorganisms</code> data set. Using their results, the <code><a href="../reference/as.mo.html">as.mo()</a></code> and all <code>mo_*()</code> functions are now much better capable of converting user input to valid taxonomic records.</p> <p>We previously relied on our own experience to categorise species into pathogenic groups, but we were very happy to encounter the very recent work of Bartlett <em>et al.</em> (2022, DOI <a href="https://doi.org/10.1099/mic.0.001269" class="external-link">10.1099/mic.0.001269</a>) who extensively studied medical-scientific literature to categorise all bacterial species into groups. See <code><a href="../reference/mo_matching_score.html">mo_matching_score()</a></code> on how their work was incorporated into the <code>prevalence</code> column of the <code>microorganisms</code> data set. Using their results, the <code><a href="../reference/as.mo.html">as.mo()</a></code> and all <code>mo_*()</code> functions are now much better capable of converting user input to valid taxonomic records.</p>
<p>We also made the following changes regarding the included taxonomy or microorganisms functions:</p> <p>We also made the following changes regarding the included taxonomy or microorganisms functions:</p>
@ -180,8 +180,8 @@
</ul></li> </ul></li>
<li>The <code>microorganisms.old</code> data set was removed, and all previously accepted names are now included in the <code>microorganisms</code> data set. A new column <code>status</code> contains <code>"accepted"</code> for currently accepted names and <code>"synonym"</code> for taxonomic synonyms; currently invalid names. All previously accepted names now have a microorganisms ID and - if available - an LPSN, GBIF and SNOMED CT identifier.</li> <li>The <code>microorganisms.old</code> data set was removed, and all previously accepted names are now included in the <code>microorganisms</code> data set. A new column <code>status</code> contains <code>"accepted"</code> for currently accepted names and <code>"synonym"</code> for taxonomic synonyms; currently invalid names. All previously accepted names now have a microorganisms ID and - if available - an LPSN, GBIF and SNOMED CT identifier.</li>
</ul></div> </ul></div>
<div class="section level5"> <div class="section level4">
<h5 id="antibiotic-agents-and-selectors-1-8-2-9068">Antibiotic agents and selectors<a class="anchor" aria-label="anchor" href="#antibiotic-agents-and-selectors-1-8-2-9068"></a></h5> <h4 id="antibiotic-agents-and-selectors-1-8-2-9069">Antibiotic agents and selectors<a class="anchor" aria-label="anchor" href="#antibiotic-agents-and-selectors-1-8-2-9069"></a></h4>
<p>The new function <code><a href="../reference/add_custom_antimicrobials.html">add_custom_antimicrobials()</a></code> allows users to add custom antimicrobial codes and names to the <code>AMR</code> package.</p> <p>The new function <code><a href="../reference/add_custom_antimicrobials.html">add_custom_antimicrobials()</a></code> allows users to add custom antimicrobial codes and names to the <code>AMR</code> package.</p>
<p>The <code>antibiotics</code> data set was greatly updated:</p> <p>The <code>antibiotics</code> data set was greatly updated:</p>
<ul><li>The following 20 antibiotics have been added (also includes the <a href="https://www.whocc.no/atc_ddd_index/?code=J01RA&amp;showdescription=no" class="external-link">new J01RA ATC group</a>): azithromycin/fluconazole/secnidazole (AFC), cefepime/amikacin (CFA), cefixime/ornidazole (CEO), ceftriaxone/beta-lactamase inhibitor (CEB), ciprofloxacin/metronidazole (CIM), ciprofloxacin/ornidazole (CIO), ciprofloxacin/tinidazole (CIT), furazidin (FUR), isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST), lascufloxacin (LSC), levofloxacin/ornidazole (LEO), nemonoxacin (NEM), norfloxacin/metronidazole (NME), norfloxacin/tinidazole (NTI), ofloxacin/ornidazole (OOR), oteseconazole (OTE), rifampicin/ethambutol/isoniazid (REI), sarecycline (SRC), tetracycline/oleandomycin (TOL), and thioacetazone (TAT)</li> <ul><li>The following 20 antibiotics have been added (also includes the <a href="https://www.whocc.no/atc_ddd_index/?code=J01RA&amp;showdescription=no" class="external-link">new J01RA ATC group</a>): azithromycin/fluconazole/secnidazole (AFC), cefepime/amikacin (CFA), cefixime/ornidazole (CEO), ceftriaxone/beta-lactamase inhibitor (CEB), ciprofloxacin/metronidazole (CIM), ciprofloxacin/ornidazole (CIO), ciprofloxacin/tinidazole (CIT), furazidin (FUR), isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST), lascufloxacin (LSC), levofloxacin/ornidazole (LEO), nemonoxacin (NEM), norfloxacin/metronidazole (NME), norfloxacin/tinidazole (NTI), ofloxacin/ornidazole (OOR), oteseconazole (OTE), rifampicin/ethambutol/isoniazid (REI), sarecycline (SRC), tetracycline/oleandomycin (TOL), and thioacetazone (TAT)</li>
@ -192,15 +192,15 @@
<li>Support for antimicrobial interpretation of anaerobic bacteria, by adding a ‘placeholder’ code <code>B_ANAER</code> to the <code>microorganisms</code> data set and adding the breakpoints of anaerobics to the <code>rsi_interpretation</code> data set, which is used by <code><a href="../reference/as.rsi.html">as.rsi()</a></code> for interpretion of MIC and disk diffusion values</li> <li>Support for antimicrobial interpretation of anaerobic bacteria, by adding a ‘placeholder’ code <code>B_ANAER</code> to the <code>microorganisms</code> data set and adding the breakpoints of anaerobics to the <code>rsi_interpretation</code> data set, which is used by <code><a href="../reference/as.rsi.html">as.rsi()</a></code> for interpretion of MIC and disk diffusion values</li>
</ul><p>Also, we added support for using antibiotic selectors in scoped <code>dplyr</code> verbs (with or without using <code><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars()</a></code>), such as in: <code>... %&gt;% summarise_at(aminoglycosides(), resistance)</code>, please see <code><a href="../reference/proportion.html">resistance()</a></code> for examples.</p> </ul><p>Also, we added support for using antibiotic selectors in scoped <code>dplyr</code> verbs (with or without using <code><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars()</a></code>), such as in: <code>... %&gt;% summarise_at(aminoglycosides(), resistance)</code>, please see <code><a href="../reference/proportion.html">resistance()</a></code> for examples.</p>
</div> </div>
<div class="section level5"> <div class="section level4">
<h5 id="antiviral-agents-1-8-2-9068">Antiviral agents<a class="anchor" aria-label="anchor" href="#antiviral-agents-1-8-2-9068"></a></h5> <h4 id="antiviral-agents-1-8-2-9069">Antiviral agents<a class="anchor" aria-label="anchor" href="#antiviral-agents-1-8-2-9069"></a></h4>
<p>We now added extensive support for antiviral agents! For the first time, the <code>AMR</code> package has extensive support for antiviral drugs and to work with their names, codes and other data in any way.</p> <p>We now added extensive support for antiviral agents! For the first time, the <code>AMR</code> package has extensive support for antiviral drugs and to work with their names, codes and other data in any way.</p>
<ul><li>The <code>antivirals</code> data set has been extended with 18 new drugs (also from the <a href="https://www.whocc.no/atc_ddd_index/?code=J05AJ&amp;showdescription=no" class="external-link">new J05AJ ATC group</a>) and now also contains antiviral identifiers and LOINC codes</li> <ul><li>The <code>antivirals</code> data set has been extended with 18 new drugs (also from the <a href="https://www.whocc.no/atc_ddd_index/?code=J05AJ&amp;showdescription=no" class="external-link">new J05AJ ATC group</a>) and now also contains antiviral identifiers and LOINC codes</li>
<li>A new data type <code>av</code> (<em>antivirals</em>) has been added, which is functionally similar to <code>ab</code> for antibiotics</li> <li>A new data type <code>av</code> (<em>antivirals</em>) has been added, which is functionally similar to <code>ab</code> for antibiotics</li>
<li>Functions <code><a href="../reference/as.av.html">as.av()</a></code>, <code><a href="../reference/av_property.html">av_name()</a></code>, <code><a href="../reference/av_property.html">av_atc()</a></code>, <code><a href="../reference/av_property.html">av_synonyms()</a></code>, <code><a href="../reference/av_from_text.html">av_from_text()</a></code> have all been added as siblings to their <code>ab_*()</code> equivalents</li> <li>Functions <code><a href="../reference/as.av.html">as.av()</a></code>, <code><a href="../reference/av_property.html">av_name()</a></code>, <code><a href="../reference/av_property.html">av_atc()</a></code>, <code><a href="../reference/av_property.html">av_synonyms()</a></code>, <code><a href="../reference/av_from_text.html">av_from_text()</a></code> have all been added as siblings to their <code>ab_*()</code> equivalents</li>
</ul></div> </ul></div>
<div class="section level5"> <div class="section level4">
<h5 id="other-new-functions-1-8-2-9068">Other new functions<a class="anchor" aria-label="anchor" href="#other-new-functions-1-8-2-9068"></a></h5> <h4 id="other-new-functions-1-8-2-9069">Other new functions<a class="anchor" aria-label="anchor" href="#other-new-functions-1-8-2-9069"></a></h4>
<ul><li>Function <code><a href="../reference/proportion.html">rsi_confidence_interval()</a></code> to add confidence intervals in AMR calculation. This is now also included in <code><a href="../reference/proportion.html">rsi_df()</a></code> and <code><a href="../reference/proportion.html">proportion_df()</a></code>.</li> <ul><li>Function <code><a href="../reference/proportion.html">rsi_confidence_interval()</a></code> to add confidence intervals in AMR calculation. This is now also included in <code><a href="../reference/proportion.html">rsi_df()</a></code> and <code><a href="../reference/proportion.html">proportion_df()</a></code>.</li>
<li>Function <code><a href="../reference/mean_amr_distance.html">mean_amr_distance()</a></code> to calculate the mean AMR distance. The mean AMR distance is a normalised numeric value to compare AMR test results and can help to identify similar isolates, without comparing antibiograms by hand.</li> <li>Function <code><a href="../reference/mean_amr_distance.html">mean_amr_distance()</a></code> to calculate the mean AMR distance. The mean AMR distance is a normalised numeric value to compare AMR test results and can help to identify similar isolates, without comparing antibiograms by hand.</li>
<li>Function <code><a href="../reference/as.rsi.html">rsi_interpretation_history()</a></code> to view the history of previous runs of <code><a href="../reference/as.rsi.html">as.rsi()</a></code>. This returns a ‘logbook’ with the selected guideline, reference table and specific interpretation of each row in a data set on which <code><a href="../reference/as.rsi.html">as.rsi()</a></code> was run.</li> <li>Function <code><a href="../reference/as.rsi.html">rsi_interpretation_history()</a></code> to view the history of previous runs of <code><a href="../reference/as.rsi.html">as.rsi()</a></code>. This returns a ‘logbook’ with the selected guideline, reference table and specific interpretation of each row in a data set on which <code><a href="../reference/as.rsi.html">as.rsi()</a></code> was run.</li>
@ -209,7 +209,7 @@
</ul></div> </ul></div>
</div> </div>
<div class="section level3"> <div class="section level3">
<h3 id="changes-1-8-2-9068">Changes<a class="anchor" aria-label="anchor" href="#changes-1-8-2-9068"></a></h3> <h3 id="changes-1-8-2-9069">Changes<a class="anchor" aria-label="anchor" href="#changes-1-8-2-9069"></a></h3>
<ul><li>Argument <code>combine_IR</code> has been removed from this package (affecting functions <code><a href="../reference/count.html">count_df()</a></code>, <code><a href="../reference/proportion.html">proportion_df()</a></code>, and <code><a href="../reference/proportion.html">rsi_df()</a></code> and some plotting functions), since it was replaced with <code>combine_SI</code> three years ago</li> <ul><li>Argument <code>combine_IR</code> has been removed from this package (affecting functions <code><a href="../reference/count.html">count_df()</a></code>, <code><a href="../reference/proportion.html">proportion_df()</a></code>, and <code><a href="../reference/proportion.html">rsi_df()</a></code> and some plotting functions), since it was replaced with <code>combine_SI</code> three years ago</li>
<li>Using <code>units</code> in <code>ab_ddd(..., units = "...")</code> had been deprecated for some time and is now not supported anymore. Use <code><a href="../reference/ab_property.html">ab_ddd_units()</a></code> instead.</li> <li>Using <code>units</code> in <code>ab_ddd(..., units = "...")</code> had been deprecated for some time and is now not supported anymore. Use <code><a href="../reference/ab_property.html">ab_ddd_units()</a></code> instead.</li>
<li>Support for <code>data.frame</code>-enhancing R packages, more specifically: <code><a href="https://Rdatatable.gitlab.io/data.table/reference/data.table.html" class="external-link">data.table::data.table</a></code>, <code><a href="https://rdrr.io/pkg/janitor/man/tabyl.html" class="external-link">janitor::tabyl</a></code>, <code><a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble::tibble</a></code>, and <code><a href="https://tsibble.tidyverts.org/reference/tsibble.html" class="external-link">tsibble::tsibble</a></code>. AMR package functions that have a data set as output (such as <code><a href="../reference/proportion.html">rsi_df()</a></code> and <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code>), will now return the same data type as the input.</li> <li>Support for <code>data.frame</code>-enhancing R packages, more specifically: <code><a href="https://Rdatatable.gitlab.io/data.table/reference/data.table.html" class="external-link">data.table::data.table</a></code>, <code><a href="https://rdrr.io/pkg/janitor/man/tabyl.html" class="external-link">janitor::tabyl</a></code>, <code><a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble::tibble</a></code>, and <code><a href="https://tsibble.tidyverts.org/reference/tsibble.html" class="external-link">tsibble::tsibble</a></code>. AMR package functions that have a data set as output (such as <code><a href="../reference/proportion.html">rsi_df()</a></code> and <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code>), will now return the same data type as the input.</li>
@ -248,13 +248,14 @@
<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 level3"> <div class="section level3">
<h3 id="other-1-8-2-9068">Other<a class="anchor" aria-label="anchor" href="#other-1-8-2-9068"></a></h3> <h3 id="other-1-8-2-9069">Other<a class="anchor" aria-label="anchor" href="#other-1-8-2-9069"></a></h3>
<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>
<li>Set scalar conditional expressions (<code>&amp;&amp;</code> and <code>||</code>) where possible to comply with the upcoming R 4.3</li> <li>Set scalar conditional expressions (<code>&amp;&amp;</code> and <code>||</code>) where possible to comply with the upcoming R 4.3</li>
<li>An enormous lot of code cleaning, fixing some small bugs on the way</li> <li>An enormous lot of code cleaning, fixing some small bugs on the way</li>
</ul></div> </ul><hr><p>This changelog only contains changes from AMR v2.0 and later. For prior versions, please see <a href="https://github.com/msberends/AMR/blob/v1.8.2/NEWS.md" class="external-link">our archive</a>.</p>
</div>
</div> </div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
</nav></aside></div> </nav></aside></div>

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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: 2022-12-20T21:45Z last_built: 2022-12-21T08:18Z
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

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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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</small>
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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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</small>
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reference/WHOCC.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>
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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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</small>
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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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</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 1999-08-14 23 23.35068 0</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 1 1970-07-07 52 52.45753 29</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1939-01-30 83 83.88767 60</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 2 1997-08-06 25 25.37534 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1974-06-28 48 48.47945 25</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 3 1933-06-01 89 89.55616 66</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1976-03-17 46 46.76164 23</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 4 1956-01-20 66 66.91781 43</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1985-12-22 36 36.99452 14</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 5 1937-05-20 85 85.58904 62</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1960-12-10 62 62.02740 39</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 6 1967-08-29 55 55.31233 32</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1996-02-09 26 26.86027 3</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 7 1989-05-15 33 33.60274 10</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1969-05-20 53 53.58630 30</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 8 1988-11-01 34 34.13699 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1950-09-14 72 72.26575 49</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 9 1931-08-12 91 91.35890 68</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1962-08-23 60 60.32603 37</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 10 1936-08-10 86 86.36438 63</span>
</code></pre></div> </code></pre></div>
</div> </div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>

2
reference/age_groups.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>
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reference/antibiotic_class_selectors.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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</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/antibiotics.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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</small>
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2
reference/as.ab.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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</small>
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2
reference/as.av.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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</small>
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2
reference/as.disk.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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</small>
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2
reference/as.mic.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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</small>
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2
reference/as.mo.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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</small>
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reference/as.rsi.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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</small>
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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> 2022-12-20 <span style="color: #949494;">21:45:50</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> 2022-12-21 <span style="color: #949494;">08:18:35</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> 2022-12-20 <span style="color: #949494;">21:45:51</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> 2022-12-21 <span style="color: #949494;">08:18:36</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> 2022-12-20 <span style="color: #949494;">21:45:51</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> 2022-12-21 <span style="color: #949494;">08:18:36</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> 2022-12-20 <span style="color: #949494;">21:45:51</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> 2022-12-21 <span style="color: #949494;">08:18:37</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> 2022-12-20 <span style="color: #949494;">21:45:52</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> 2022-12-21 <span style="color: #949494;">08:18:37</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> 2022-12-20 <span style="color: #949494;">21:45:52</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> 2022-12-21 <span style="color: #949494;">08:18:38</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> 2022-12-20 <span style="color: #949494;">21:45:53</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> 2022-12-21 <span style="color: #949494;">08:18:38</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> 2022-12-20 <span style="color: #949494;">21:45:53</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> 2022-12-21 <span style="color: #949494;">08:18:38</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> 2022-12-20 <span style="color: #949494;">21:45:53</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> 2022-12-21 <span style="color: #949494;">08:18:38</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> 2022-12-20 <span style="color: #949494;">21:45:53</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> 2022-12-21 <span style="color: #949494;">08:18:38</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
reference/atc_online.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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</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/av_from_text.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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</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/av_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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</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/availability.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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</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/bug_drug_combinations.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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</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/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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</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/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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</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/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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</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/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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</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">

133
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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</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">
@ -182,39 +182,42 @@
<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] 4 47 50 30 20 54 24 18 16 33 25 50 23 32 37 61 20 11 27 36 17 55 13 59 4</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 56 28 13 12 36 4 6 15 40 7 48 3 31 55 4 54 20 43 1 32 38 34 9 36 53</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 12 30 60 46 17 2 39 24 3 7 60 11 58 43 43 13 16 62 47 56 16 61 5 21 46</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [26] 16 54 27 44 54 62 3 8 36 1 19 6 9 54 27 4 18 47 9 13 31 11 32 16 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 54 14 8 6 10 40 6 32 46 23 58 4 21 24 13 52 11 23 22 11 32 14 34 57 27</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [51] 48 7 37 36 24 37 36 10 40 52 51 21 34 47 59 27 56 23 59 58 59 34 4 11 38</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 19 59 28 39 36 30 2 33 15 25 56 19 1 20 60 40 60 17 17 8 21 44 42 10 15</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [76] 3 57 61 15 32 3 13 12 44 26 62 62 22 60 21 62 43 47 49 59 55 13 8 46 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [101] 8 36 20 19 52 4 60 19 30 41 37 2 47 10 15 35 40 45 12 37 11 9 60 1 34</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [101] 5 10 55 28 12 20 26 16 56 24 34 13 39 40 41 50 35 50 11 56 51 22 19 54 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [126] 46 7 48 1 9 6 6 13 15 26 48 45 38 23 31 23 46 5 8 11 17 12 16 55 60</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [126] 37 56 32 4 13 45 9 30 38 27 13 20 41 35 43 55 59 59 17 15 40 23 20 25 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [151] 32 7 12 59 15 26 56 28 40 57 11 42 40 6 20 13 7 15 53 29 45 49 14 33 23</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [151] 22 44 1 14 13 52 32 60 13 14 29 33 55 17 46 51 57 28 17 30 1 43 31 26 38</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [176] 52 51 19 54 10 16 58 50 54 8 37 48 16 51 49 20 31 53 52 60 22 44 29 32 57</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [176] 2 17 13 56 51 34 10 31 58 2 56 46 58 1 9 59 27 42 33 61 26 20 58 19 33</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 TRUE TRUE TRUE FALSE TRUE FALSE TRUE TRUE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] FALSE FALSE TRUE TRUE FALSE FALSE TRUE TRUE FALSE FALSE FALSE TRUE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [13] TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE TRUE FALSE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [25] TRUE FALSE TRUE FALSE TRUE FALSE FALSE TRUE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [37] FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [49] FALSE FALSE TRUE TRUE TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] FALSE FALSE TRUE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [61] TRUE TRUE FALSE TRUE TRUE TRUE FALSE TRUE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [73] FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [85] FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [97] TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [109] FALSE TRUE FALSE FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [109] FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [121] FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE TRUE FALSE TRUE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [121] FALSE TRUE TRUE FALSE FALSE FALSE TRUE TRUE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [133] TRUE FALSE TRUE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [133] FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [145] FALSE FALSE FALSE TRUE TRUE TRUE FALSE TRUE TRUE FALSE FALSE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [145] FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [157] FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [157] FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [169] TRUE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [169] FALSE TRUE FALSE TRUE FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [181] FALSE TRUE TRUE FALSE FALSE FALSE TRUE FALSE TRUE TRUE FALSE TRUE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [181] FALSE TRUE FALSE FALSE TRUE FALSE TRUE FALSE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [193] FALSE FALSE FALSE TRUE FALSE TRUE TRUE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [193] TRUE FALSE TRUE FALSE FALSE FALSE FALSE TRUE</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: 1 × 46</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4 × 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> 2002-07-30 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: #BCBCBC;">1</span> 2002-07-21 955940 82 F Clinical B_PSDMN_AERG R NA NA R </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2002-06-04 082413 78 M ICU B_STRPT_PNMN S NA NA S </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2002-07-28 F54261 69 M Clinical B_STPHY_CONS R NA S NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2002-06-05 24D393 20 F Clinical 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>
@ -250,16 +253,16 @@
<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> 304347 2002-11-04 B FALSE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 784436 2016-05-28 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 919B60 2013-12-31 A TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 533225 2008-10-01 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 715822 2015-01-10 B TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> B95551 2004-12-17 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 501361 2008-10-31 A TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> D65308 2004-11-03 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> E19253 2006-08-23 B TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> BF4515 2010-12-29 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> D36589 2016-02-18 C FALSE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> F35553 2002-10-20 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> ED4982 2007-07-13 C FALSE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> D97054 2003-04-13 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> E59875 2006-03-25 C FALSE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 452212 2005-04-22 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 240662 2005-10-26 B FALSE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 083080 2012-04-16 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> EC9741 2009-06-18 B FALSE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 914520 2003-07-31 B FALSE </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>
@ -271,19 +274,19 @@
<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="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 × 5</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 200 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: ward, patient [178]</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: ward, patient [173]</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> Clinical 2002-11-04 304347 1 TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> ICU 2016-05-28 784436 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical 2013-12-31 919B60 1 TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical 2008-10-01 533225 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Clinical 2015-01-10 715822 1 TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Outpatient 2004-12-17 B95551 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical 2008-10-31 501361 1 TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> ICU 2004-11-03 D65308 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Clinical 2006-08-23 E19253 1 TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Clinical 2010-12-29 BF4515 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> ICU 2016-02-18 D36589 1 TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> ICU 2002-10-20 F35553 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> ICU 2007-07-13 ED4982 1 TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Clinical 2003-04-13 D97054 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> ICU 2006-03-25 E59875 1 TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> ICU 2005-04-22 452212 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Clinical 2005-10-26 240662 1 TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Clinical 2012-04-16 083080 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Outpatient 2009-06-18 EC9741 1 TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical 2003-07-31 914520 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>
@ -298,9 +301,9 @@
<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 111 14 49 69</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 107 14 49 69</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;">2</span> ICU 55 13 34 44</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 10 7 10 10</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 11 7 11 11</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>
@ -330,19 +333,19 @@
<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 [187]</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, mo, ward [186]</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> 304347 B_STRPT_PNMN Clinical TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 784436 B_STPHY_HMNS ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 919B60 B_STPHY_AURS Clinical TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 533225 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 715822 B_STPHY_EPDR Clinical TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> B95551 B_STPHY_CONS Outpatient TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 501361 B_ESCHR_COLI Clinical TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> D65308 B_STPHY_EPDR ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> E19253 B_STPHY_CONS Clinical TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> BF4515 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> D36589 B_STPHY_EPDR ICU TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> F35553 B_STPHY_AURS ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> ED4982 B_ESCHR_COLI ICU TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> D97054 B_STPHY_AURS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> E59875 B_STPHY_EPDR ICU TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 452212 B_ENTRC ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 240662 B_STRPT_PNMN Clinical TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 083080 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> EC9741 B_ESCHR_COLI Outpatient TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 914520 B_STPHY_AURS Clinical 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>

2
reference/ggplot_pca.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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</small>
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2
reference/ggplot_rsi.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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</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/guess_ab_col.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</small>
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2
reference/index.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</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/intrinsic_resistant.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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</small>
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2
reference/italicise_taxonomy.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</small>
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2
reference/join.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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</small>
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2
reference/key_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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</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/kurtosis.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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</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] 2.979785</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2.940008</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] -0.01457832</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.03402398</span>
</code></pre></div> </code></pre></div>
</div> </div>
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2
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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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</small>
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2
reference/mdro.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</small>
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78
reference/mean_amr_distance.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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</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] 1 128 0.025 0.002 2 8 0.025 2 128 0.5 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.005 256 0.5 128 32 32 128 128 0.5 0.025</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] 0.03073988 1.36755493 -0.98560777 -1.68148803 0.22171346 0.60366062</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] -1.7639563 0.9825666 -0.5975237 0.8070010 0.4558698 0.4558698</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.98560777 0.22171346 1.36755493 -0.16023370</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.8070010 0.8070010 -0.5975237 -1.3563056</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>
@ -213,38 +213,38 @@
<span class="r-in"><span> tobr <span class="op">=</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span>, ab <span class="op">=</span> <span class="st">"tobr"</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span><span class="op">)</span></span></span> <span class="r-in"><span> tobr <span class="op">=</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span>, ab <span class="op">=</span> <span class="st">"tobr"</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</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-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 &gt;=4 1 4</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 1 A &gt;=64 4 0.5 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 16 &gt;=4 2 4</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 32 2 0.5 &lt;=0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 16 0.5 2 2</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 3 C &lt;=4 2 &gt;=4 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 16 &gt;=4 4 &lt;=0.5</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 4 D &lt;=4 &lt;=0.125 1 &lt;=0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 16 0.125 1 1</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 16 1 0.25 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 32 0.25 4 4</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 16 &lt;=0.125 &gt;=4 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 4 &lt;=0.0625 1 2</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 7 G &gt;=64 0.5 0.5 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 64 0.5 4 4</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 16 0.25 1 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 32 2 4 &lt;=0.5</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 9 I &lt;=4 &lt;=0.125 2 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J &lt;=2 0.5 4 2</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 10 J &gt;=64 0.25 2 1</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] -0.08036866 0.51076165 -0.04318986 0.15636345 -0.75415022 0.48217462</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.57566233 -0.17235135 0.62175861 -0.97114505 -0.17254362 0.15946520</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.97945442 0.75675773 0.20085706 -0.24975135</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.05465037 -0.07283047 -0.09101057 0.17764530</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> 7 G 4 &lt;=0.0625 1 2 -0.97945442</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 4 D &lt;=4 &lt;=0.125 1 &lt;=0.5 -0.97114505</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 16 0.125 1 1 -0.75415022</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 16 1 0.25 2 -0.17254362</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J &lt;=2 0.5 4 2 -0.24975135</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 32 2 0.5 &lt;=0.5 -0.17235135</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A 4 &gt;=4 1 4 -0.08036866</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 9 I &lt;=4 &lt;=0.125 2 4 -0.09101057</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 16 0.5 2 2 -0.04318986</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 16 0.25 1 2 -0.07283047</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 16 &gt;=4 4 &lt;=0.5 0.15636345</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 7 G &gt;=64 0.5 0.5 1 -0.05465037</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 32 2 4 &lt;=0.5 0.20085706</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 16 &lt;=0.125 &gt;=4 2 0.15946520</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 32 0.25 4 4 0.48217462</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 10 J &gt;=64 0.25 2 1 0.17764530</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 16 &gt;=4 2 4 0.51076165</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 1 A &gt;=64 4 0.5 2 0.57566233</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 64 0.5 4 4 0.75675773</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 3 C &lt;=4 2 &gt;=4 4 0.62175861</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>
@ -256,17 +256,17 @@
<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 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 16 0.5 2 2 -0.04318986 0.0000000</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 1 C &lt;=4 2 &gt;=4 4 0.62175861 0.00000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 A 4 &gt;=4 1 4 -0.08036866 0.0371788</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 2 A &gt;=64 4 0.5 2 0.57566233 0.04609628</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 D 16 &gt;=4 4 &lt;=0.5 0.15636345 0.1995533</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 3 J &gt;=64 0.25 2 1 0.17764530 0.44411330</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 J &lt;=2 0.5 4 2 -0.24975135 0.2065615</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 4 F 16 &lt;=0.125 &gt;=4 2 0.15946520 0.46229341</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 I 32 2 4 &lt;=0.5 0.20085706 0.2440469</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 5 G &gt;=64 0.5 0.5 1 -0.05465037 0.67640897</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 32 0.25 4 4 0.48217462 0.5253645</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 6 H 16 0.25 1 2 -0.07283047 0.69458908</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 B 16 &gt;=4 2 4 0.51076165 0.5539515</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 7 I &lt;=4 &lt;=0.125 2 4 -0.09101057 0.71276918</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 E 16 0.125 1 1 -0.75415022 0.7109604</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 8 B 32 2 0.5 &lt;=0.5 -0.17235135 0.79410996</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 H 64 0.5 4 4 0.75675773 0.7999476</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 9 E 16 1 0.25 2 -0.17254362 0.79430223</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 G 4 &lt;=0.0625 1 2 -0.97945442 0.9362646</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 10 D &lt;=4 &lt;=0.125 1 &lt;=0.5 -0.97114505 1.59290366</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
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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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</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
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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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</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_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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</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_source.html
View File

@ -12,7 +12,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</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/pca.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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</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">

BIN
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2
reference/plot.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</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/proportion.html
View File

@ -12,7 +12,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</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">

36
reference/random.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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</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">
@ -183,43 +183,43 @@
<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">random_mic</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span> <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 256 4 128 0.005 32 128 64 256 1 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 16 0.025 &gt;=256 &gt;=256 4 64 0.25 1 0.01 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 32 0.005 0.025 &lt;=0.001 4 0.005 0.005 64 0.5 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.005 0.5 0.0625 &lt;=0.001 &gt;=256 0.0625 4 16 &gt;=256 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 0.0625 0.01 1 0.01 4 16 2 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> [19] 16 &lt;=0.001 32 32 0.005 32 0.025 </span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span> <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 44 35 48 44 48 6 18 34 9 13 42 45 41 28 24 21 40 41 41 46 44 42 11 39 38</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 21 47 36 47 30 34 46 18 26 41 27 14 21 44 41 44 24 47 27 46 49 43 21 6 15</span>
<span class="r-in"><span><span class="fu">random_rsi</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu">random_rsi</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'rsi'</span> <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'rsi'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] I R I S R I S I R I I R R I S I I R R I R S S R R</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] R S R R S I R I R R S I R R S R R S S S S I S I R</span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># \donttest{</span></span></span> <span class="r-in"><span><span class="co"># \donttest{</span></span></span>
<span class="r-in"><span><span class="co"># make the random generation more realistic by setting a bug and/or drug:</span></span></span> <span class="r-in"><span><span class="co"># make the random generation more realistic by setting a bug and/or drug:</span></span></span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 0.0625-64</span></span></span> <span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 0.0625-64</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span> <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 4 0.025 0.5 0.025 0.01 &lt;=0.001 &gt;=64 0.002 2 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 16 8 0.125 0.01 2 32 &lt;=0.002 0.5 &gt;=64 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.025 1 2 16 0.01 0.025 &gt;=64 0.0625 &gt;=64 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> [10] 32 8 0.01 16 8 0.5 0.025 0.01 0.0625 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 16 0.0625 0.125 32 &gt;=64 0.0625 8 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> [19] 0.5 0.005 0.125 32 16 8 0.125 </span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-16</span></span></span> <span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-16</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span> <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] &gt;=64 2 8 4 8 8 16 2 2 1 2 &lt;=0.5</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] &gt;=64 4 2 &gt;=64 1 32 8 &lt;=0.5 4 16 8 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] 1 8 4 1 32 2 &gt;=64 1 &lt;=0.5 32 1 2 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> [13] &gt;=64 1 32 32 1 2 1 1 2 16 8 &lt;=0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] &gt;=64 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> [25] &lt;=0.5</span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-4</span></span></span> <span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-4</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span> <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.5 1 0.25 0.25 &lt;=0.125 8 4 0.5 &lt;=0.125</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.5 2 2 0.5 0.25 8 2 2 0.5 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] &lt;=0.125 0.25 0.25 2 0.5 0.5 4 0.25 4 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.25 0.25 4 2 2 8 1 8 &lt;=0.125</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 4 &lt;=0.125 &lt;=0.125 1 &lt;=0.125 0.5 0.25 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> [19] 0.25 8 8 8 8 4 2 </span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 8-50</span></span></span> <span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 8-50</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span> <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 50 28 14 47 14 30 24 47 44 16 45 32 21 40 9 34 29 32 21 26 49 47 40 23 43</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 30 21 9 8 48 42 24 21 48 40 39 23 25 47 27 33 48 11 28 13 48 48 12 15 19</span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 11-17</span></span></span> <span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 11-17</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span> <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 13 11 14 12 16 11 13 16 13 17 14 15 12 13 16 11 17 13 15 14 15 15 16 12 15</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 12 13 16 13 17 11 11 17 16 16 17 13 13 11 17 16 17 14 16 12 11 16 12 17 11</span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 12-27</span></span></span> <span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 12-27</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span> <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 24 27 25 18 26 24 24 15 15 16 24 20 24 16 17 27 23 20 24 18 24 23 20 26 24</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 17 27 18 21 19 18 23 20 27 27 16 18 23 26 23 16 22 27 16 22 16 23 24 17 16</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>
</div> </div>

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reference/resistance_predict.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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</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/rsi_translation.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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</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
reference/skewness.html
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@ -12,7 +12,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
<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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</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">
@ -171,7 +171,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
<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">skewness</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Uniform.html" class="external-link">runif</a></span><span class="op">(</span><span class="fl">1000</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">skewness</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Uniform.html" class="external-link">runif</a></span><span class="op">(</span><span class="fl">1000</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.04696702</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.008873477</span>
</code></pre></div> </code></pre></div>
</div> </div>
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reference/translate.html
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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="">1.8.2.9068</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</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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