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<a class="navbar-brand me-2" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9126</small>
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9126</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9131</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -178,7 +178,7 @@
<h4 data-toc-skip class="author">Dr. Matthijs
Berends</h4>
<h4 data-toc-skip class="date">14 February 2023</h4>
<h4 data-toc-skip class="date">15 February 2023</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/AMR.Rmd" class="external-link"><code>vignettes/AMR.Rmd</code></a></small>
<div class="d-none name"><code>AMR.Rmd</code></div>
@ -190,7 +190,7 @@ Berends</h4>
website update since they are based on randomly created values and the
page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
Markdown</a>. However, the methodology remains unchanged. This page was
generated on 14 February 2023.</p>
generated on 15 February 2023.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@ -246,21 +246,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2023-02-14</td>
<td align="center">2023-02-15</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="center">2023-02-14</td>
<td align="center">2023-02-15</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<tr class="odd">
<td align="center">2023-02-14</td>
<td align="center">2023-02-15</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -411,9 +411,42 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2010-12-31</td>
<td align="center">U7</td>
<td align="center">Hospital C</td>
<td align="center">2010-08-08</td>
<td align="center">Y8</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2011-03-02</td>
<td align="center">Q1</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2016-04-28</td>
<td align="center">S9</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2014-08-07</td>
<td align="center">T10</td>
<td align="center">Hospital D</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">R</td>
<td align="center">R</td>
@ -421,59 +454,26 @@ data set:</p>
<td align="center">R</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2012-10-26</td>
<td align="center">C3</td>
<tr class="odd">
<td align="center">2014-04-21</td>
<td align="center">I3</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2015-12-06</td>
<td align="center">A7</td>
<td align="center">Hospital C</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2016-07-03</td>
<td align="center">J4</td>
<td align="center">Hospital A</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2016-04-02</td>
<td align="center">A4</td>
<td align="center">Hospital A</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2016-06-10</td>
<td align="center">F6</td>
<td align="center">2012-08-08</td>
<td align="center">M4</td>
<td align="center">Hospital B</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">M</td>
</tr>
</tbody>
@ -510,16 +510,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,376</td>
<td align="right">51.88%</td>
<td align="right">10,376</td>
<td align="right">51.88%</td>
<td align="right">10,421</td>
<td align="right">52.11%</td>
<td align="right">10,421</td>
<td align="right">52.11%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,624</td>
<td align="right">48.12%</td>
<td align="right">9,579</td>
<td align="right">47.90%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -632,10 +632,10 @@ 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"># 2</span></span>
<span><span class="co"># Including isolates from ICU.</span></span>
<span><span class="co"># =&gt; Found 12,299 'phenotype-based' first isolates (61.5% of total where a</span></span>
<span><span class="co"># =&gt; Found 12,198 'phenotype-based' first isolates (61.0% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 61.5% is suitable for resistance analysis! We can now filter
on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the
<p>So only 61% is suitable for resistance analysis! We can now filter on
it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the
<code>dplyr</code> package:</p>
<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
@ -644,7 +644,7 @@ on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html"
<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<p>So we end up with 12 299 isolates for analysis. Now our data looks
<p>So we end up with 12 198 isolates for analysis. Now our data looks
like:</p>
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">data_1st</span><span class="op">)</span></span></code></pre></div>
@ -683,30 +683,14 @@ like:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">2</td>
<td align="center">2012-10-26</td>
<td align="center">C3</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">7</td>
<td align="center">2013-06-13</td>
<td align="center">Q4</td>
<td align="left">1</td>
<td align="center">2010-08-08</td>
<td align="center">Y8</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
@ -714,70 +698,86 @@ like:</p>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">11</td>
<td align="center">2014-08-27</td>
<td align="center">K9</td>
<td align="center">Hospital B</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">14</td>
<td align="center">2016-03-09</td>
<td align="center">F2</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">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="odd">
<td align="left">15</td>
<td align="center">2011-09-20</td>
<td align="center">C6</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">16</td>
<td align="center">2017-02-27</td>
<td align="center">Y6</td>
<td align="center">Hospital B</td>
<td align="left">2</td>
<td align="center">2011-03-02</td>
<td align="center">Q1</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">4</td>
<td align="center">2014-08-07</td>
<td align="center">T10</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="left">6</td>
<td align="center">2012-08-08</td>
<td align="center">M4</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">I</td>
<td align="center">I</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">7</td>
<td align="center">2017-02-12</td>
<td align="center">O7</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">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">8</td>
<td align="center">2011-02-09</td>
<td align="center">K4</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">I</td>
<td align="center">I</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>
</tbody>
</table>
<p>Time for the analysis!</p>
@ -811,8 +811,8 @@ readable:</p>
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://msberends.github.io/cleaner/reference/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></span></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 12,299<br>
Available: 12,299 (100%, NA: 0 = 0%)<br>
Length: 12,198<br>
Available: 12,198 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -837,33 +837,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">5,867</td>
<td align="right">47.70%</td>
<td align="right">5,867</td>
<td align="right">47.70%</td>
<td align="right">5,861</td>
<td align="right">48.05%</td>
<td align="right">5,861</td>
<td align="right">48.05%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,232</td>
<td align="right">26.28%</td>
<td align="right">9,099</td>
<td align="right">73.98%</td>
<td align="right">3,183</td>
<td align="right">26.09%</td>
<td align="right">9,044</td>
<td align="right">74.14%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">1,853</td>
<td align="right">15.07%</td>
<td align="right">10,952</td>
<td align="right">89.05%</td>
<td align="right">1,850</td>
<td align="right">15.17%</td>
<td align="right">10,894</td>
<td align="right">89.31%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,347</td>
<td align="right">10.95%</td>
<td align="right">12,299</td>
<td align="right">1,304</td>
<td align="right">10.69%</td>
<td align="right">12,198</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -912,73 +912,13 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2016-03-09</td>
<td align="center">F2</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">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">2011-09-20</td>
<td align="center">C6</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2015-05-24</td>
<td align="center">Q4</td>
<td align="center">Hospital A</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">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2014-10-15</td>
<td align="center">N1</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2012-01-21</td>
<td align="center">U5</td>
<td align="center">2011-03-02</td>
<td align="center">Q1</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
@ -987,15 +927,75 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2016-08-02</td>
<td align="center">F4</td>
<td align="center">2014-08-07</td>
<td align="center">T10</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</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="odd">
<td align="center">2011-02-09</td>
<td align="center">K4</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">I</td>
<td align="center">I</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-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2016-05-14</td>
<td align="center">P6</td>
<td align="center">Hospital C</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">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="center">2010-02-23</td>
<td align="center">W6</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">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="even">
<td align="center">2014-05-10</td>
<td align="center">R2</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
@ -1025,46 +1025,46 @@ different bug/drug combinations, you can use the
<td align="left">2</td>
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">2757</td>
<td align="center">1154</td>
<td align="center">1956</td>
<td align="center">5867</td>
<td align="center">2766</td>
<td align="center">1144</td>
<td align="center">1951</td>
<td align="center">5861</td>
</tr>
<tr class="even">
<td align="left">1</td>
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">1536</td>
<td align="center">1221</td>
<td align="center">3110</td>
<td align="center">5867</td>
<td align="center">1499</td>
<td align="center">1230</td>
<td align="center">3132</td>
<td align="center">5861</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">2046</td>
<td align="center">1793</td>
<td align="center">2028</td>
<td align="center">5867</td>
<td align="center">2070</td>
<td align="center">1784</td>
<td align="center">2007</td>
<td align="center">5861</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">2007</td>
<td align="center">1817</td>
<td align="center">2043</td>
<td align="center">5867</td>
<td align="center">2005</td>
<td align="center">1804</td>
<td align="center">2052</td>
<td align="center">5861</td>
</tr>
<tr class="odd">
<td align="left">6</td>
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">600</td>
<td align="center">285</td>
<td align="center">462</td>
<td align="center">1347</td>
<td align="center">573</td>
<td align="center">281</td>
<td align="center">450</td>
<td align="center">1304</td>
</tr>
<tr class="even">
<td align="left">5</td>
@ -1072,8 +1072,8 @@ different bug/drug combinations, you can use the
<td align="center">AMX</td>
<td align="center">0</td>
<td align="center">0</td>
<td align="center">1347</td>
<td align="center">1347</td>
<td align="center">1304</td>
<td align="center">1304</td>
</tr>
</tbody>
</table>
@ -1095,34 +1095,34 @@ different bug/drug combinations, you can use the
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">2007</td>
<td align="center">1817</td>
<td align="center">2043</td>
<td align="center">5867</td>
<td align="center">2005</td>
<td align="center">1804</td>
<td align="center">2052</td>
<td align="center">5861</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">462</td>
<td align="center">409</td>
<td align="center">476</td>
<td align="center">1347</td>
<td align="center">411</td>
<td align="center">441</td>
<td align="center">452</td>
<td align="center">1304</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">1091</td>
<td align="center">1034</td>
<td align="center">1107</td>
<td align="center">3232</td>
<td align="center">1092</td>
<td align="center">1014</td>
<td align="center">1077</td>
<td align="center">3183</td>
</tr>
<tr class="even">
<td align="center">S. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">0</td>
<td align="center">0</td>
<td align="center">1853</td>
<td align="center">1853</td>
<td align="center">1850</td>
<td align="center">1850</td>
</tr>
</tbody>
</table>
@ -1154,7 +1154,7 @@ I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equa
own:</p>
<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span></span>
<span><span class="co"># [1] 0.5841125</span></span></code></pre></div>
<span><span class="co"># [1] 0.5823086</span></span></code></pre></div>
<p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and
<code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
@ -1169,19 +1169,19 @@ own:</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5842217</td>
<td align="center">0.5925926</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5908142</td>
<td align="center">0.5784499</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5761879</td>
<td align="center">0.5731311</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5779626</td>
<td align="center">0.5802005</td>
</tr>
</tbody>
</table>
@ -1206,23 +1206,23 @@ all isolates available for every group (i.e. values S, I or R):</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5842217</td>
<td align="center">3752</td>
<td align="center">0.5925926</td>
<td align="center">3726</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5908142</td>
<td align="center">4311</td>
<td align="center">0.5784499</td>
<td align="center">4232</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5761879</td>
<td align="center">1831</td>
<td align="center">0.5731311</td>
<td align="center">1846</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5779626</td>
<td align="center">2405</td>
<td align="center">0.5802005</td>
<td align="center">2394</td>
</tr>
</tbody>
</table>
@ -1247,27 +1247,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.6666099</td>
<td align="center">0.6517811</td>
<td align="center">0.8825635</td>
<td align="center">0.6671217</td>
<td align="center">0.6498891</td>
<td align="center">0.8846613</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.6570156</td>
<td align="center">0.6466221</td>
<td align="center">0.8619154</td>
<td align="center">0.6549080</td>
<td align="center">0.6533742</td>
<td align="center">0.8788344</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.6667698</td>
<td align="center">0.6574876</td>
<td align="center">0.8932550</td>
<td align="center">0.6830035</td>
<td align="center">0.6616400</td>
<td align="center">0.8850141</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.4700486</td>
<td align="center">0.4837838</td>
<td align="center">0.0000000</td>
<td align="center">0.4700486</td>
<td align="center">0.4837838</td>
</tr>
</tbody>
</table>
@ -1295,23 +1295,23 @@ classes, use a antibiotic class selector such as
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">58.4%</td>
<td align="right">37.3%</td>
<td align="right">59.3%</td>
<td align="right">36.3%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">59.1%</td>
<td align="right">37.2%</td>
<td align="right">57.8%</td>
<td align="right">35.5%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">57.6%</td>
<td align="right">35.2%</td>
<td align="right">57.3%</td>
<td align="right">35.6%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">57.8%</td>
<td align="right">34.3%</td>
<td align="right">58.0%</td>
<td align="right">35.6%</td>
</tr>
</tbody>
</table>
@ -1427,18 +1427,18 @@ classes) <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code>:</p>
<code class="sourceCode R"><span><span class="va">mic_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span></span>
<span><span class="va">mic_values</span></span>
<span><span class="co"># Class 'mic'</span></span>
<span><span class="co"># [1] 0.5 0.25 4 0.002 &lt;=0.001 0.005 0.25 0.005 32 </span></span>
<span><span class="co"># [10] 0.025 64 0.025 0.5 0.125 16 0.25 0.01 32 </span></span>
<span><span class="co"># [19] &lt;=0.001 0.125 0.125 64 2 0.125 16 128 0.002 </span></span>
<span><span class="co"># [28] 0.002 1 0.0625 0.125 8 64 128 0.0625 64 </span></span>
<span><span class="co"># [37] 128 0.005 0.125 0.005 32 64 64 32 256 </span></span>
<span><span class="co"># [46] 128 0.0625 &lt;=0.001 &lt;=0.001 256 8 4 2 1 </span></span>
<span><span class="co"># [55] 16 0.002 1 1 &lt;=0.001 1 8 0.5 2 </span></span>
<span><span class="co"># [64] 2 2 1 &lt;=0.001 2 32 16 0.01 0.002 </span></span>
<span><span class="co"># [73] 16 0.025 0.002 0.01 1 0.25 0.25 64 1 </span></span>
<span><span class="co"># [82] 0.125 &lt;=0.001 16 0.25 8 4 0.25 0.002 0.0625 </span></span>
<span><span class="co"># [91] 128 0.005 128 256 64 2 256 0.025 0.25 </span></span>
<span><span class="co"># [100] 4</span></span></code></pre></div>
<span><span class="co"># [1] 0.01 &gt;=256 0.5 64 64 &gt;=256 0.005 1 &gt;=256 </span></span>
<span><span class="co"># [10] 16 4 32 1 2 64 0.0625 0.0625 8 </span></span>
<span><span class="co"># [19] 64 2 0.01 8 1 0.002 0.5 0.5 0.002 </span></span>
<span><span class="co"># [28] 0.0625 0.005 32 2 0.01 1 4 64 8 </span></span>
<span><span class="co"># [37] 0.125 32 0.125 0.002 &gt;=256 0.005 0.002 2 8 </span></span>
<span><span class="co"># [46] &gt;=256 &gt;=256 0.01 32 0.002 64 0.5 8 2 </span></span>
<span><span class="co"># [55] 0.25 4 0.002 0.002 0.125 8 0.25 &lt;=0.001 32 </span></span>
<span><span class="co"># [64] &lt;=0.001 &lt;=0.001 0.002 &gt;=256 0.002 0.5 0.125 0.01 &lt;=0.001</span></span>
<span><span class="co"># [73] 2 8 0.01 0.25 128 0.025 128 0.25 0.005 </span></span>
<span><span class="co"># [82] 0.01 0.002 32 32 1 0.5 &gt;=256 2 0.025 </span></span>
<span><span class="co"># [91] 4 8 4 0.25 0.5 0.5 1 0.01 32 </span></span>
<span><span class="co"># [100] 0.5</span></span></code></pre></div>
<div class="sourceCode" id="cb36"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">mic_values</span><span class="op">)</span></span></code></pre></div>
@ -1472,10 +1472,10 @@ plotting:</p>
<code class="sourceCode R"><span><span class="va">disk_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_disk</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span>
<span><span class="va">disk_values</span></span>
<span><span class="co"># Class 'disk'</span></span>
<span><span class="co"># [1] 18 29 29 26 17 27 24 26 25 24 23 20 19 25 22 24 20 19 24 17 23 21 19 21 20</span></span>
<span><span class="co"># [26] 26 18 17 26 22 25 19 25 26 17 26 19 29 20 27 19 22 31 25 19 28 25 17 29 31</span></span>
<span><span class="co"># [51] 26 31 29 21 19 28 30 30 31 28 30 22 22 22 17 31 22 19 21 17 28 29 17 28 26</span></span>
<span><span class="co"># [76] 20 20 20 19 25 17 28 28 31 24 28 21 28 20 25 21 28 27 23 27 22 31 27 27 18</span></span></code></pre></div>
<span><span class="co"># [1] 24 28 29 21 30 30 22 20 23 25 31 28 24 20 25 18 17 21 28 24 19 31 28 25 17</span></span>
<span><span class="co"># [26] 30 31 25 26 18 29 27 29 24 23 31 18 22 22 31 20 24 27 18 18 29 27 30 25 27</span></span>
<span><span class="co"># [51] 17 29 20 26 24 18 26 28 22 30 29 20 26 28 30 24 19 19 26 17 22 22 17 30 24</span></span>
<span><span class="co"># [76] 17 27 20 23 23 18 30 27 21 24 19 25 23 24 20 18 30 20 23 22 25 18 30 28 21</span></span></code></pre></div>
<div class="sourceCode" id="cb42"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">disk_values</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></code></pre></div>

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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9126</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9131</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

58
articles/MDR.html
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9126</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9131</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -385,19 +385,19 @@ names or codes, this would have worked exactly the same way:</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span>
<span><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
<span><span class="co"># 1 R S S R I S</span></span>
<span><span class="co"># 2 S I I S I I</span></span>
<span><span class="co"># 3 R I S R R R</span></span>
<span><span class="co"># 4 S R S I S R</span></span>
<span><span class="co"># 5 R S R S S R</span></span>
<span><span class="co"># 6 I I S S S I</span></span>
<span><span class="co"># 1 R R R I S I</span></span>
<span><span class="co"># 2 S I R S I I</span></span>
<span><span class="co"># 3 R S R I R R</span></span>
<span><span class="co"># 4 I I I I R R</span></span>
<span><span class="co"># 5 I R I R S R</span></span>
<span><span class="co"># 6 S R S I I I</span></span>
<span><span class="co"># kanamycin</span></span>
<span><span class="co"># 1 I</span></span>
<span><span class="co"># 1 S</span></span>
<span><span class="co"># 2 R</span></span>
<span><span class="co"># 3 R</span></span>
<span><span class="co"># 3 S</span></span>
<span><span class="co"># 4 I</span></span>
<span><span class="co"># 5 I</span></span>
<span><span class="co"># 6 R</span></span></code></pre></div>
<span><span class="co"># 5 S</span></span>
<span><span class="co"># 6 S</span></span></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can
use:</p>
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
@ -438,40 +438,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3263</td>
<td align="right">65.26%</td>
<td align="right">3263</td>
<td align="right">65.26%</td>
<td align="right">3198</td>
<td align="right">63.96%</td>
<td align="right">3198</td>
<td align="right">63.96%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">970</td>
<td align="right">19.40%</td>
<td align="right">4233</td>
<td align="right">84.66%</td>
<td align="right">997</td>
<td align="right">19.94%</td>
<td align="right">4195</td>
<td align="right">83.90%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">433</td>
<td align="right">8.66%</td>
<td align="right">4666</td>
<td align="right">93.32%</td>
<td align="right">438</td>
<td align="right">8.76%</td>
<td align="right">4633</td>
<td align="right">92.66%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">229</td>
<td align="right">4.58%</td>
<td align="right">4895</td>
<td align="right">97.90%</td>
<td align="right">257</td>
<td align="right">5.14%</td>
<td align="right">4890</td>
<td align="right">97.80%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">105</td>
<td align="right">2.10%</td>
<td align="right">110</td>
<td align="right">2.20%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

2
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9126</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9131</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">

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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9126</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9131</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -178,7 +178,7 @@
<h4 data-toc-skip class="author">Dr. Matthijs
Berends</h4>
<h4 data-toc-skip class="date">14 February 2023</h4>
<h4 data-toc-skip class="date">15 February 2023</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/SPSS.Rmd" class="external-link"><code>vignettes/SPSS.Rmd</code></a></small>
<div class="d-none name"><code>SPSS.Rmd</code></div>

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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9126</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9131</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">

4
articles/datasets.html
View File

@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9126</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9131</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">
@ -176,7 +176,7 @@
<main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
<h4 data-toc-skip class="date">14 February 2023</h4>
<h4 data-toc-skip class="date">15 February 2023</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<div class="d-none name"><code>datasets.Rmd</code></div>

2
articles/index.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9126</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9131</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9126</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9131</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
articles/welcome_to_AMR.html
View File

@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9126</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9131</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
authors.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9126</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9131</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">

5
extra.css
View File

@ -54,10 +54,13 @@ mark, .mark {
background: rgba(17, 143, 118, 0.25) !important;
}
/* smaller tables */
.table {
font-size: 0.9em !important;
}
/* SYNTAX */
/* These are simple changes for the syntax highlighting */
pre {
font-size: 0.8em !important;
}

2
extra.js
View File

@ -52,7 +52,7 @@ $(document).ready(function() {
// add doctoral titles to authors
function doct_tit(x) {
if (typeof(x) != "undefined") {
x = x.replace(/Author, maintainer/g, "Principle developer");
x = x.replace(/Author, maintainer/g, "Principle maintainer");
x = x.replace(/Author, contributor/g, "Contributing maintainer");
x = x.replace(/Thesis advisor/g, "(former) Doctoral advisor");
// contributors

45
index.html
View File

@ -42,7 +42,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9126</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9131</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">
@ -347,7 +347,7 @@
<h4 id="generating-antibiograms">Generating antibiograms<a class="anchor" aria-label="anchor" href="#generating-antibiograms"></a>
</h4>
<p>The <code>AMR</code> package supports generating traditional, combined, syndromic, and even weighted-incidence syndromic combination antibiograms (WISCA).</p>
<p>If used inside R Markdown or Quarto, the table will be printed in the right output format automatically (such as markdown, LaTeX, HTML, etc.).</p>
<p>If used inside R Markdown or Quarto, the table will be printed in the right output format automatically (such as markdown, LaTeX, HTML, etc.) when using <code><a href="https://rdrr.io/r/base/print.html" class="external-link">print()</a></code> on an antibiogram object.</p>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
<span> antibiotics <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
@ -481,11 +481,40 @@
</tr>
</tbody>
</table>
<p>Like many other functions in this package, <code>antibiograms()</code> comes with support for 20 languages that are often detected automatically based on system language:</p>
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
<span> antibiotics <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"CIP"</span>, <span class="st">"TOB"</span>, <span class="st">"GEN"</span><span class="op">)</span>,</span>
<span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span>,</span>
<span> ab_transform <span class="op">=</span> <span class="st">"name"</span>,</span>
<span> language <span class="op">=</span> <span class="st">"uk"</span><span class="op">)</span> <span class="co"># Ukrainian</span></span></code></pre></div>
<table class="table">
<thead><tr class="header">
<th align="left">Збудник (N min-max)</th>
<th align="right">Гентаміцин</th>
<th align="right">Тобраміцин</th>
<th align="right">Ципрофлоксацин</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">Грамнегативні (684-686)</td>
<td align="right">96</td>
<td align="right">96</td>
<td align="right">91</td>
</tr>
<tr class="even">
<td align="left">Грампозитивні (665-1170)</td>
<td align="right">63</td>
<td align="right">34</td>
<td align="right">77</td>
</tr>
</tbody>
</table>
</div>
<div class="section level4">
<h4 id="calculating-resistance-per-group">Calculating resistance per group<a class="anchor" aria-label="anchor" href="#calculating-resistance-per-group"></a>
</h4>
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span></span>
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span>
<span></span>
@ -533,7 +562,7 @@
</tr>
</tbody>
</table>
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># transform the antibiotic columns to names:</span></span>
<span><span class="va">out</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/ab_property.html">set_ab_names</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<table class="table">
@ -580,7 +609,7 @@
</tr>
</tbody>
</table>
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># transform the antibiotic column to ATC codes:</span></span>
<span><span class="va">out</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/ab_property.html">set_ab_names</a></span><span class="op">(</span>property <span class="op">=</span> <span class="st">"atc"</span><span class="op">)</span></span></code></pre></div>
<table class="table">
@ -660,7 +689,7 @@
</h4>
<p><a href="https://cran.r-project.org/package=AMR" class="external-link"><img src="https://www.r-pkg.org/badges/version-ago/AMR" alt="CRAN"></a> <a href="https://cran.r-project.org/package=AMR" class="external-link"><img src="https://cranlogs.r-pkg.org/badges/grand-total/AMR" alt="CRANlogs"></a></p>
<p>This package is available <a href="https://cran.r-project.org/package=AMR" class="external-link">here on the official R network (CRAN)</a>. Install this package in R from CRAN by using the command:</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"AMR"</span><span class="op">)</span></span></code></pre></div>
<p>It will be downloaded and installed automatically. For RStudio, click on the menu <em>Tools</em> &gt; <em>Install Packages…</em> and then type in “AMR” and press <kbd>Install</kbd>.</p>
<p><strong>Note:</strong> Not all functions on this website may be available in this latest release. To use all functions and data sets mentioned on this website, install the latest development version.</p>
@ -674,13 +703,13 @@
<ol style="list-style-type: decimal">
<li>
<p>Manually, using:</p>
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"remotes"</span><span class="op">)</span> <span class="co"># if you haven't already</span></span>
<span><span class="fu">remotes</span><span class="fu">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html" class="external-link">install_github</a></span><span class="op">(</span><span class="st">"msberends/AMR"</span><span class="op">)</span></span></code></pre></div>
</li>
<li>
<p>Automatically, using the <a href="https://ropensci.org/r-universe/" class="external-link">rOpenSci R-universe platform</a>, by adding <a href="https://msberends.r-universe.dev" class="external-link">our R-universe address</a> to your list of repositories (‘repos’):</p>
<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">options</a></span><span class="op">(</span>repos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"repos"</span><span class="op">)</span>,</span>
<span> msberends <span class="op">=</span> <span class="st">"https://msberends.r-universe.dev"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
<p>After this, you can install and update this <code>AMR</code> package like any official release (e.g., using <code>install.packages("AMR")</code> or in RStudio via <em>Tools</em> &gt; <em>Check for Package Updates…</em>).</p>

26
news/index.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9126</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9131</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">
@ -142,7 +142,7 @@
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="1.8.2.9126" id="amr-1829126">AMR 1.8.2.9126<a class="anchor" aria-label="anchor" href="#amr-1829126"></a></h2>
<h2 class="pkg-version" data-toc-text="1.8.2.9131" id="amr-1829131">AMR 1.8.2.9131<a class="anchor" aria-label="anchor" href="#amr-1829131"></a></h2>
<p><em>(this beta version will eventually become v2.0! We’re happy to reach a new major milestone soon!)</em></p>
<p>This is a new major release of the AMR package, with great new additions but also some breaking changes for current users. These are all listed below.</p>
<p><strong><a href="https://en.wikipedia.org/wiki/TL;DR" class="external-link">TL;DR</a></strong></p>
@ -156,32 +156,32 @@
<li>Now available in 20 languages</li>
<li>Many small bug fixes</li>
</ul><div class="section level3">
<h3 id="new-1-8-2-9126">New<a class="anchor" aria-label="anchor" href="#new-1-8-2-9126"></a></h3>
<h3 id="new-1-8-2-9131">New<a class="anchor" aria-label="anchor" href="#new-1-8-2-9131"></a></h3>
<div class="section level4">
<h4 id="sir-vs-rsi-1-8-2-9126">SIR vs. RSI<a class="anchor" aria-label="anchor" href="#sir-vs-rsi-1-8-2-9126"></a></h4>
<h4 id="sir-vs-rsi-1-8-2-9131">SIR vs. RSI<a class="anchor" aria-label="anchor" href="#sir-vs-rsi-1-8-2-9131"></a></h4>
<p>For this milestone version, we replaced all mentions of RSI with SIR, to comply with what is actually being commonly used in the field of clinical microbiology when it comes to this tri-form regarding AMR.</p>
<p>While existing functions such as <code><a href="../reference/AMR-deprecated.html">as.rsi()</a></code>, <code><a href="../reference/AMR-deprecated.html">rsi_df()</a></code> and <code><a href="../reference/AMR-deprecated.html">ggplot_rsi()</a></code> still work, their replacements <code><a href="../reference/as.sir.html">as.sir()</a></code>, <code><a href="../reference/proportion.html">sir_df()</a></code>, <code><a href="../reference/ggplot_sir.html">ggplot_sir()</a></code> are now the current functions for AMR data analysis. A warning will be thrown once a session to remind users about this. The data set <code>rsi_translation</code> is now called <code>clinical_breakpoints</code> to better reflect its content.</p>
<p>The ‘RSI functions’ will be removed in a future version, but not before late 2023 / early 2024.</p>
</div>
<div class="section level4">
<h4 id="new-antibiogram-function-1-8-2-9126">New antibiogram function<a class="anchor" aria-label="anchor" href="#new-antibiogram-function-1-8-2-9126"></a></h4>
<h4 id="new-antibiogram-function-1-8-2-9131">New antibiogram function<a class="anchor" aria-label="anchor" href="#new-antibiogram-function-1-8-2-9131"></a></h4>
<p>With the new <code><a href="../reference/antibiogram.html">antibiogram()</a></code> function, users can now generate traditional, combined, syndromic, and even weighted-incidence syndromic combination antibiograms (WISCA). With this, we follow the logic in the previously described work of Klinker <em>et al.</em> (2021, DOI <a href="https://doi.org/10.1177/20499361211011373" class="external-link">10.1177/20499361211011373</a>) and Barbieri <em>et al.</em> (2021, DOI <a href="https://doi.org/10.1186/s13756-021-00939-2" class="external-link">10.1186/s13756-021-00939-2</a>).</p>
<p>The help page for <code><a href="../reference/antibiogram.html">antibiogram()</a></code> extensively elaborates on use cases, and <code><a href="../reference/antibiogram.html">antibiogram()</a></code> also supports printing in R Markdown and Quarto, with support for 20 languages.</p>
<p>Furthermore, different plotting methods were implemented to allow for graphical visualisations as well.</p>
</div>
<div class="section level4">
<h4 id="interpretation-of-mic-and-disk-diffusion-values-1-8-2-9126">Interpretation of MIC and disk diffusion values<a class="anchor" aria-label="anchor" href="#interpretation-of-mic-and-disk-diffusion-values-1-8-2-9126"></a></h4>
<h4 id="interpretation-of-mic-and-disk-diffusion-values-1-8-2-9131">Interpretation of MIC and disk diffusion values<a class="anchor" aria-label="anchor" href="#interpretation-of-mic-and-disk-diffusion-values-1-8-2-9131"></a></h4>
<p>The clinical breakpoints and intrinsic resistance of EUCAST 2022 and CLSI 2022 have been added for <code><a href="../reference/as.sir.html">as.sir()</a></code>. EUCAST 2022 (v12.0) is now the new default guideline for all MIC and disks diffusion interpretations, and for <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> to apply EUCAST Expert Rules. The default guideline (EUCAST) can now be changed with the new <code>AMR_guideline</code> option, such as: <code>options(AMR_guideline = "CLSI 2020")</code>.</p>
<p>With the new arguments <code>include_PKPD</code> (default: <code>TRUE</code>) and <code>include_screening</code> (default: <code>FALSE</code>), users can now specify whether breakpoints for screening and from the PK/PD table should be included when interpreting MICs and disks diffusion values. These options can be set globally, which can be read in <a href="https://msberends.github.io/AMR/reference/AMR-options.html">our new manual</a>.</p>
<p>Interpretation guidelines older than 10 years were removed, the oldest now included guidelines of EUCAST and CLSI are from 2013.</p>
</div>
<div class="section level4">
<h4 id="supported-languages-1-8-2-9126">Supported languages<a class="anchor" aria-label="anchor" href="#supported-languages-1-8-2-9126"></a></h4>
<h4 id="supported-languages-1-8-2-9131">Supported languages<a class="anchor" aria-label="anchor" href="#supported-languages-1-8-2-9131"></a></h4>
<p>We added support for the following ten languages: Chinese (simplified), Czech, Finnish, Greek, Japanese, Norwegian (bokmål), Polish, Romanian, Turkish and Ukrainian. All antibiotic names are now available in these languages, and the AMR package will automatically determine a supported language based on the user’s system language.</p>
<p>We are very grateful for the valuable input by our colleagues from other countries. The <code>AMR</code> package is now available in 20 languages in total, and according to download stats used in almost all countries in the world!</p>
</div>
<div class="section level4">
<h4 id="microbiological-taxonomy-1-8-2-9126">Microbiological taxonomy<a class="anchor" aria-label="anchor" href="#microbiological-taxonomy-1-8-2-9126"></a></h4>
<h4 id="microbiological-taxonomy-1-8-2-9131">Microbiological taxonomy<a class="anchor" aria-label="anchor" href="#microbiological-taxonomy-1-8-2-9131"></a></h4>
<p>The <code>microorganisms</code> data set no longer relies on the Catalogue of Life, but on the List of Prokaryotic names with Standing in Nomenclature (LPSN) and is supplemented with the ‘backbone taxonomy’ from the Global Biodiversity Information Facility (GBIF). The structure of this data set has changed to include separate LPSN and GBIF identifiers. Almost all previous MO codes were retained. It contains over 1,400 taxonomic names from 2022.</p>
<p>We previously relied on our own experience to categorise species into pathogenic groups, but we were very happy to encounter the very recent work of Bartlett <em>et al.</em> (2022, DOI <a href="https://doi.org/10.1099/mic.0.001269" class="external-link">10.1099/mic.0.001269</a>) who extensively studied medical-scientific literature to categorise all bacterial species into groups. See <code><a href="../reference/mo_matching_score.html">mo_matching_score()</a></code> on how their work was incorporated into the <code>prevalence</code> column of the <code>microorganisms</code> data set. Using their results, the <code><a href="../reference/as.mo.html">as.mo()</a></code> and all <code>mo_*()</code> functions are now much better capable of converting user input to valid taxonomic records.</p>
<p>The new function <code><a href="../reference/add_custom_microorganisms.html">add_custom_microorganisms()</a></code> allows users to add custom microorganisms to the <code>AMR</code> package.</p>
@ -205,7 +205,7 @@
<li>The <code>microorganisms.old</code> data set was removed, and all previously accepted names are now included in the <code>microorganisms</code> data set. A new column <code>status</code> contains <code>"accepted"</code> for currently accepted names and <code>"synonym"</code> for taxonomic synonyms; currently invalid names. All previously accepted names now have a microorganisms ID and - if available - an LPSN, GBIF and SNOMED CT identifier.</li>
</ul></div>
<div class="section level4">
<h4 id="antibiotic-agents-and-selectors-1-8-2-9126">Antibiotic agents and selectors<a class="anchor" aria-label="anchor" href="#antibiotic-agents-and-selectors-1-8-2-9126"></a></h4>
<h4 id="antibiotic-agents-and-selectors-1-8-2-9131">Antibiotic agents and selectors<a class="anchor" aria-label="anchor" href="#antibiotic-agents-and-selectors-1-8-2-9131"></a></h4>
<p>The new function <code><a href="../reference/add_custom_antimicrobials.html">add_custom_antimicrobials()</a></code> allows users to add custom antimicrobial codes and names to the <code>AMR</code> package.</p>
<p>The <code>antibiotics</code> data set was greatly updated:</p>
<ul><li>The following 20 antibiotics have been added (also includes the <a href="https://www.whocc.no/atc_ddd_index/?code=J01RA&amp;showdescription=no" class="external-link">new J01RA ATC group</a>): azithromycin/fluconazole/secnidazole (AFC), cefepime/amikacin (CFA), cefixime/ornidazole (CEO), ceftriaxone/beta-lactamase inhibitor (CEB), ciprofloxacin/metronidazole (CIM), ciprofloxacin/ornidazole (CIO), ciprofloxacin/tinidazole (CIT), furazidin (FUR), isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST), lascufloxacin (LSC), levofloxacin/ornidazole (LEO), nemonoxacin (NEM), norfloxacin/metronidazole (NME), norfloxacin/tinidazole (NTI), ofloxacin/ornidazole (OOR), oteseconazole (OTE), rifampicin/ethambutol/isoniazid (REI), sarecycline (SRC), tetracycline/oleandomycin (TOL), and thioacetazone (TAT)</li>
@ -217,14 +217,14 @@
</ul><p>Also, we added support for using antibiotic selectors in scoped <code>dplyr</code> verbs (with or without using <code><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars()</a></code>), such as in: <code>... %&gt;% summarise_at(aminoglycosides(), resistance)</code>, please see <code><a href="../reference/proportion.html">resistance()</a></code> for examples.</p>
</div>
<div class="section level4">
<h4 id="antiviral-agents-1-8-2-9126">Antiviral agents<a class="anchor" aria-label="anchor" href="#antiviral-agents-1-8-2-9126"></a></h4>
<h4 id="antiviral-agents-1-8-2-9131">Antiviral agents<a class="anchor" aria-label="anchor" href="#antiviral-agents-1-8-2-9131"></a></h4>
<p>We now added extensive support for antiviral agents! For the first time, the <code>AMR</code> package has extensive support for antiviral drugs and to work with their names, codes and other data in any way.</p>
<ul><li>The <code>antivirals</code> data set has been extended with 18 new drugs (also from the <a href="https://www.whocc.no/atc_ddd_index/?code=J05AJ&amp;showdescription=no" class="external-link">new J05AJ ATC group</a>) and now also contains antiviral identifiers and LOINC codes</li>
<li>A new data type <code>av</code> (<em>antivirals</em>) has been added, which is functionally similar to <code>ab</code> for antibiotics</li>
<li>Functions <code><a href="../reference/as.av.html">as.av()</a></code>, <code><a href="../reference/av_property.html">av_name()</a></code>, <code><a href="../reference/av_property.html">av_atc()</a></code>, <code><a href="../reference/av_property.html">av_synonyms()</a></code>, <code><a href="../reference/av_from_text.html">av_from_text()</a></code> have all been added as siblings to their <code>ab_*()</code> equivalents</li>
</ul></div>
<div class="section level4">
<h4 id="other-new-functions-1-8-2-9126">Other new functions<a class="anchor" aria-label="anchor" href="#other-new-functions-1-8-2-9126"></a></h4>
<h4 id="other-new-functions-1-8-2-9131">Other new functions<a class="anchor" aria-label="anchor" href="#other-new-functions-1-8-2-9131"></a></h4>
<ul><li>Function <code><a href="../reference/proportion.html">sir_confidence_interval()</a></code> to add confidence intervals in AMR calculation. This is now also included in <code><a href="../reference/proportion.html">sir_df()</a></code> and <code><a href="../reference/proportion.html">proportion_df()</a></code>.</li>
<li>Function <code><a href="../reference/mean_amr_distance.html">mean_amr_distance()</a></code> to calculate the mean AMR distance. The mean AMR distance is a normalised numeric value to compare AMR test results and can help to identify similar isolates, without comparing antibiograms by hand.</li>
<li>Function <code><a href="../reference/as.sir.html">sir_interpretation_history()</a></code> to view the history of previous runs of <code><a href="../reference/as.sir.html">as.sir()</a></code> (previously <code><a href="../reference/AMR-deprecated.html">as.rsi()</a></code>). This returns a ‘logbook’ with the selected guideline, reference table and specific interpretation of each row in a data set on which <code><a href="../reference/as.sir.html">as.sir()</a></code> was run.</li>
@ -233,7 +233,7 @@
</ul></div>
</div>
<div class="section level3">
<h3 id="changes-1-8-2-9126">Changes<a class="anchor" aria-label="anchor" href="#changes-1-8-2-9126"></a></h3>
<h3 id="changes-1-8-2-9131">Changes<a class="anchor" aria-label="anchor" href="#changes-1-8-2-9131"></a></h3>
<ul><li>Argument <code>combine_IR</code> has been removed from this package (affecting functions <code><a href="../reference/count.html">count_df()</a></code>, <code><a href="../reference/proportion.html">proportion_df()</a></code>, and <code><a href="../reference/proportion.html">sir_df()</a></code> and some plotting functions), since it was replaced with <code>combine_SI</code> three years ago</li>
<li>Using <code>units</code> in <code>ab_ddd(..., units = "...")</code> had been deprecated for some time and is now not supported anymore. Use <code><a href="../reference/ab_property.html">ab_ddd_units()</a></code> instead.</li>
<li>Support for <code>data.frame</code>-enhancing R packages, more specifically: <code><a href="https://Rdatatable.gitlab.io/data.table/reference/data.table.html" class="external-link">data.table::data.table</a></code>, <code><a href="https://sfirke.github.io/janitor/reference/tabyl.html" class="external-link">janitor::tabyl</a></code>, <code><a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble::tibble</a></code>, and <code><a href="https://tsibble.tidyverts.org/reference/tsibble.html" class="external-link">tsibble::tsibble</a></code>. AMR package functions that have a data set as output (such as <code><a href="../reference/proportion.html">sir_df()</a></code> and <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code>), will now return the same data type as the input.</li>
@ -275,7 +275,7 @@
<code><a href="../reference/get_episode.html">get_episode()</a></code> now returns class <code>integer</code> instead of <code>numeric</code> since they are always whole numbers</li>
</ul></div>
<div class="section level3">
<h3 id="other-1-8-2-9126">Other<a class="anchor" aria-label="anchor" href="#other-1-8-2-9126"></a></h3>
<h3 id="other-1-8-2-9131">Other<a class="anchor" aria-label="anchor" href="#other-1-8-2-9131"></a></h3>
<ul><li>Added Peter Dutey-Magni, Dmytro Mykhailenko, Anton Mymrikov, Andrew Norgan, Jonas Salm, and Anita Williams as contributors, to thank them for their valuable input</li>
<li>New website to make use of the new Bootstrap 5 and pkgdown 2.0. The website now contains results for all examples and will be automatically regenerated with every change to our repository, using GitHub Actions</li>
<li>All R and Rmd files in this project are now styled using the <code>styler</code> package</li>

2
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@ -11,7 +11,7 @@ articles:
datasets: datasets.html
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
last_built: 2023-02-14T16:11Z
last_built: 2023-02-15T18:52Z
urls:
reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles

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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9126</small>
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -18,7 +18,7 @@ The AMR package is available in English, Chinese, Danish, Dutch, French, German,
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9126</small>
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9126</small>
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reference/add_custom_antimicrobials.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9126</small>
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reference/add_custom_microorganisms.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9126</small>
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9126</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9131</small>
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@ -205,16 +205,16 @@
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">df</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> birth_date age age_exact age_at_y2k</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1968-10-11 54 54.34521 31</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1940-04-02 82 82.87123 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1986-08-02 36 36.53699 13</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1990-05-20 32 32.73973 9</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1952-02-05 71 71.02466 47</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1989-05-03 33 33.78630 10</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1966-03-27 56 56.88767 33</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1985-10-11 37 37.34521 14</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1952-11-23 70 70.22740 47</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1972-05-17 50 50.74795 27</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1999-05-08 23 23.77534 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1956-01-15 67 67.08493 43</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1938-07-04 84 84.61918 61</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1986-09-26 36 36.38904 13</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1951-07-28 71 71.55342 48</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1988-10-29 34 34.29863 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1980-10-10 42 42.35068 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1964-01-25 59 59.05753 35</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1947-04-26 75 75.80822 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1991-06-27 31 31.63836 8</span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>

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@ -10,7 +10,7 @@
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@ -10,7 +10,7 @@
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@ -279,7 +279,7 @@
<span> <span class="va">.</span><span class="op">$</span><span class="va">gender</span> <span class="op">==</span> <span class="st">"Male"</span> <span class="op">&amp;</span></span>
<span> <span class="va">.</span><span class="op">$</span><span class="va">condition</span> <span class="op">==</span> <span class="st">"Heart Disease"</span>,</span>
<span> <span class="st">"Study Group"</span>, <span class="st">"Control Group"</span><span class="op">)</span><span class="op">)</span></span></code></pre><p></p></div></li>
</ol><p>All types of antibiograms can be generated with the functions as described on this page, and can be plotted (using <code><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">ggplot2::autoplot()</a></code> or base <span style="R">R</span> <code><a href="plot.html">plot()</a></code>/<code><a href="https://rdrr.io/r/graphics/barplot.html" class="external-link">barplot()</a></code>) or printed into R Markdown / Quarto formats for reports. Use functions from specific 'table reporting' packages to transform the output of <code>antibiogram()</code> to your needs, e.g. <code>flextable::as_flextable()</code> or <code>gt::gt()</code>.</p>
</ol><p>All types of antibiograms can be generated with the functions as described on this page, and can be plotted (using <code><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">ggplot2::autoplot()</a></code> or base <span style="R">R</span> <code><a href="plot.html">plot()</a></code>/<code><a href="https://rdrr.io/r/graphics/barplot.html" class="external-link">barplot()</a></code>) or printed into R Markdown / Quarto formats for reports using <code><a href="https://rdrr.io/r/base/print.html" class="external-link">print()</a></code>. Use functions from specific 'table reporting' packages to transform the output of <code>antibiogram()</code> to your needs, e.g. <code>flextable::as_flextable()</code> or <code>gt::gt()</code>.</p>
<p>Note that for combination antibiograms, it is important to realise that susceptibility can be calculated in two ways, which can be set with the <code>only_all_tested</code> argument (defaults to <code>FALSE</code>). See this example for two antibiotics, Drug A and Drug B, about how <code>antibiogram()</code> works to calculate the %SI:</p>
<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="sc">--------------------------------------------------------------------</span></span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a> only_all_tested <span class="ot">=</span> <span class="cn">FALSE</span> only_all_tested <span class="ot">=</span> <span class="cn">TRUE</span></span>

2
reference/antibiotic_class_selectors.html
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@ -10,7 +10,7 @@
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reference/antibiotics.html
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@ -10,7 +10,7 @@
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@ -10,7 +10,7 @@
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reference/as.mic.html
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@ -10,7 +10,7 @@
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reference/as.mo.html
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@ -10,7 +10,7 @@
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22
reference/as.sir.html
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@ -12,7 +12,7 @@ All breakpoints used for interpretation are publicly available in the clinical_b
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@ -534,16 +534,16 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 50 × 17</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index ab_input ab_guid…¹ mo_in…² mo_guideline guide…³</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2023-02-14 <span style="color: #949494;">16:12:35</span> 1 TOB TOB Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2023-02-14 <span style="color: #949494;">16:12:35</span> 1 GEN GEN Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2023-02-14 <span style="color: #949494;">16:12:34</span> 1 CIP CIP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2023-02-14 <span style="color: #949494;">16:12:34</span> 1 AMP AMP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2023-02-14 <span style="color: #949494;">16:12:28</span> 1 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2023-02-14 <span style="color: #949494;">16:12:28</span> 2 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2023-02-14 <span style="color: #949494;">16:12:28</span> 3 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2023-02-14 <span style="color: #949494;">16:12:28</span> 4 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2023-02-14 <span style="color: #949494;">16:12:28</span> 5 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2023-02-14 <span style="color: #949494;">16:12:28</span> 6 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2023-02-15 <span style="color: #949494;">18:53:27</span> 1 TOB TOB Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2023-02-15 <span style="color: #949494;">18:53:27</span> 1 GEN GEN Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2023-02-15 <span style="color: #949494;">18:53:27</span> 1 CIP CIP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2023-02-15 <span style="color: #949494;">18:53:26</span> 1 AMP AMP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2023-02-15 <span style="color: #949494;">18:53:22</span> 1 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2023-02-15 <span style="color: #949494;">18:53:22</span> 2 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2023-02-15 <span style="color: #949494;">18:53:22</span> 3 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2023-02-15 <span style="color: #949494;">18:53:22</span> 4 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2023-02-15 <span style="color: #949494;">18:53:22</span> 5 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2023-02-15 <span style="color: #949494;">18:53:22</span> 6 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 40 more rows, 10 more variables: ref_table &lt;chr&gt;, method &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># input &lt;dbl&gt;, outcome &lt;sir&gt;, breakpoint_S_R &lt;chr&gt;, ab_considered &lt;lgl&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># mo_considered &lt;lgl&gt;, breakpoint_S &lt;lgl&gt;, breakpoint_R &lt;lgl&gt;,</span></span>

2
reference/atc_online.html
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@ -10,7 +10,7 @@
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reference/av_from_text.html
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@ -10,7 +10,7 @@
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reference/av_property.html
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@ -10,7 +10,7 @@
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reference/availability.html
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@ -10,7 +10,7 @@
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reference/bug_drug_combinations.html
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@ -10,7 +10,7 @@
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reference/clinical_breakpoints.html
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@ -12,7 +12,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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reference/custom_eucast_rules.html
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@ -10,7 +10,7 @@
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@ -10,7 +10,7 @@
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reference/eucast_rules.html
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@ -12,7 +12,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
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reference/example_isolates.html
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@ -12,7 +12,7 @@
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reference/get_episode.html
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@ -10,7 +10,7 @@
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@ -192,29 +192,29 @@
<span class="r-in"><span><span class="va">df</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq_len</a></span><span class="op">(</span><span class="fl">2000</span><span class="op">)</span>, size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># indices</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 19 48 11 15 48 11 47 3 30 22 41 43 43 19 18 37 11 23 5 27 23 36 43 38 20</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 11 31 39 20 46 45 9 32 6 10 47 3 28 42 14 8 22 21 6 47 31 17 35 12 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 20 5 2 42 12 9 40 4 24 32 23 25 15 8 38 22 7 2 46 6 13 8 16 2 24</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 3 8 24 44 34 7 1 33 19 41 10 8 29 26 42 22 28 1 26 45 16 2 5 39 9</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 36 31 10 45 37 31 22 44 49 1 15 11 16 26 19 18 9 45 47 35 6 2 3 44 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 13 2 40 10 1 19 14 32 3 46 22 48 44 47 7 34 34 48 39 27 12 29 17 1 6</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 12 33 35 49 37 39 44 3 30 49 38 37 39 43 6 29 6 5 7 20 22 46 14 6 48</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 6 43 34 45 1 20 10 50 4 15 4 31 20 42 25 24 41 5 7 34 28 47 23 15 21</span>
<span class="r-in"><span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># TRUE/FALSE</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE TRUE TRUE TRUE FALSE FALSE TRUE TRUE TRUE TRUE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] FALSE FALSE TRUE TRUE FALSE TRUE TRUE TRUE FALSE TRUE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] TRUE FALSE TRUE TRUE FALSE TRUE TRUE TRUE TRUE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] FALSE TRUE TRUE TRUE TRUE FALSE TRUE FALSE FALSE FALSE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] TRUE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE TRUE TRUE TRUE TRUE FALSE TRUE TRUE TRUE TRUE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] TRUE TRUE TRUE TRUE TRUE FALSE TRUE TRUE TRUE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] TRUE TRUE FALSE TRUE FALSE FALSE FALSE TRUE TRUE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] TRUE FALSE FALSE TRUE TRUE FALSE FALSE TRUE TRUE TRUE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] TRUE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] FALSE FALSE FALSE FALSE TRUE TRUE TRUE TRUE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] FALSE TRUE FALSE TRUE</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># filter on results from the third 60-day episode only, using base R</span></span></span>
<span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, <span class="fl">60</span><span class="op">)</span> <span class="op">==</span> <span class="fl">3</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-06-23 798871 82 M Clinical B_ENTRC_FCLS NA NA NA NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2002-07-16 241328 78 M Outpatie… B_STPHY_CONS R NA S R </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2002-07-15 C42193 84 M ICU B_STPHY_HMNS R NA R R </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-11-11 D80753 74 F Outpatie… B_STPHY_CONS R NA S NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2002-11-18 956065 89 F Clinical B_ESCHR_COLI R NA NA NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2002-11-16 762305 87 F Clinical B_PROTS_MRBL 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;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># FEP &lt;sir&gt;, CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># GEN &lt;sir&gt;, TOB &lt;sir&gt;, AMK &lt;sir&gt;, KAN &lt;sir&gt;, TMP &lt;sir&gt;, SXT &lt;sir&gt;,</span></span>
@ -249,19 +249,19 @@
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">patient</span>, <span class="va">condition</span>, <span class="va">date</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 100 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, condition [99]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, condition [97]</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> <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> 015240 2007-11-15 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 07545C 2010-02-08 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 088256 2003-01-25 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 092034 2016-08-07 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 0E2483 2007-08-10 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 12CB58 2017-09-23 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 141061 2014-10-22 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 141061 2014-10-22 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 151041 2003-01-31 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 15D386 2004-08-01 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 022060 2004-05-04 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 022060 2004-05-04 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 067927 2002-01-29 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 071099 2005-01-11 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 0F9638 2014-09-22 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 174209 2011-10-03 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 183220 2008-11-14 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 189363 2004-03-16 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 218912 2007-02-24 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 218912 2002-07-30 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 90 more rows</span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
@ -275,19 +275,19 @@
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">patient</span>, <span class="va">ward</span>, <span class="va">date</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 100 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: ward, patient [95]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 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;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical 2007-11-15 015240 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical 2010-02-08 07545C 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> ICU 2003-01-25 088256 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical 2016-08-07 092034 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> ICU 2007-08-10 0E2483 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> ICU 2017-09-23 12CB58 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Clinical 2014-10-22 141061 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical 2014-10-22 141061 1 FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Clinical 2003-01-31 151041 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> ICU 2004-08-01 15D386 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: ward, patient [94]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward date patient new_index new_logical</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> ICU 2004-05-04 022060 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> ICU 2004-05-04 022060 1 FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> ICU 2002-01-29 067927 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical 2005-01-11 071099 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Clinical 2014-09-22 0F9638 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Outpatient 2011-10-03 174209 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Clinical 2008-11-14 183220 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical 2004-03-16 189363 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> ICU 2002-07-30 218912 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> ICU 2007-02-24 218912 2 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 90 more rows</span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
@ -303,9 +303,9 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward n_patients n_episodes_365 n_episodes_60 n_episodes_30</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 61 14 36 45</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 26 8 20 24</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 8 5 8 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 60 12 37 43</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 28 11 23 26</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 6 4 6 6</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># grouping on patients and microorganisms leads to the same</span></span></span>
<span class="r-in"><span><span class="co"># results as first_isolate() when using 'episode-based':</span></span></span>
@ -323,7 +323,7 @@
<span class="r-in"><span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/identical.html" class="external-link">identical</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">y</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># but is_new_episode() has a lot more flexibility than first_isolate(),</span></span></span>
<span class="r-in"><span><span class="co"># since you can now group on anything that seems relevant:</span></span></span>
@ -334,19 +334,19 @@
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_data.html" class="external-link">group_vars</a></span><span class="op">(</span><span class="va">.</span><span class="op">)</span>, <span class="va">flag_episode</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 100 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, mo, ward [99]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> patient mo ward flag_episode</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 744BB5 B_STPHY_AURS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 12CB58 B_STPHY_EPDR ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> F58364 B_STPHY_CONS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> FD439C B_STPHY_CONS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> F67215 B_STPHY_EPDR Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> B95551 B_STPHY_CONS Outpatient TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 6FC260 B_STPHY_HMNS ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 798871 B_ENTRC_FCLS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 451867 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 180928 B_STRPT_AGLC Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, mo, ward [98]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> patient mo ward flag_episode</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> FC0C51 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> D58366 B_ENTRC_FCLS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> E15167 B_ENTRC_FCLS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 964129 B_SERRT_MRCS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 0F9638 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> A66134 B_STPHY_AURS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 183220 B_STPHY_CONS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 960787 B_ENTRC_FACM Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> BF4515 B_ENTRC_FACM ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 495616 B_STPHY_EPDR Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 90 more rows</span></span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>

2
reference/ggplot_pca.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9126</small>
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2
reference/ggplot_sir.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9126</small>
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reference/guess_ab_col.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9126</small>
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2
reference/index.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9126</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9131</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/intrinsic_resistant.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9126</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9131</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/italicise_taxonomy.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9126</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9131</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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9126</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9131</small>
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2
reference/key_antimicrobials.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9126</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9131</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

6
reference/kurtosis.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9126</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9131</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -182,9 +182,9 @@
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2.864962</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 3.02291</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] 0.039068</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.06230735</span>
</code></pre></div>
</div>
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2
reference/like.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9126</small>
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2
reference/mdro.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9126</small>
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73
reference/mean_amr_distance.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9126</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9131</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -201,31 +201,30 @@
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">sir</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_sir</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">sir</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] S S S R S I S R S S</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] R R I I I I R S S S</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">sir</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.4743416 -0.4743416 -0.4743416 1.8973666 -0.4743416 -0.4743416</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.4743416 1.8973666 -0.4743416 -0.4743416</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1.449138 1.449138 -0.621059 -0.621059 -0.621059 -0.621059 1.449138</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [8] -0.621059 -0.621059 -0.621059</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">mic</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">mic</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1 0.025 0.25 16 0.0625 &lt;=0.001 0.5 0.01 32 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 128 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] &gt;=128 32 0.25 2 0.5 0.002 0.025 64 8 64 </span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">mic</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.23783965 -0.74097859 -0.13000382 0.97352658 -0.49784728 -1.59508466</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.05391792 -0.98410989 1.15744831 1.52529178</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1.10682807 0.73345287 -0.57336033 -0.01329753 -0.38667273 -1.87378587</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -1.19352311 0.92014047 0.36007767 0.92014047</span>
<span class="r-in"><span><span class="co"># equal to the Z-score of their log2:</span></span></span>
<span class="r-in"><span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span> <span class="op">-</span> <span class="fu"><a href="https://rdrr.io/r/base/mean.html" class="external-link">mean</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="fu"><a href="https://rdrr.io/r/stats/sd.html" class="external-link">sd</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.23783965 -0.74097859 -0.13000382 0.97352658 -0.49784728 -1.59508466</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.05391792 -0.98410989 1.15744831 1.52529178</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1.10682807 0.73345287 -0.57336033 -0.01329753 -0.38667273 -1.87378587</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -1.19352311 0.92014047 0.36007767 0.92014047</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">disk</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_disk</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">disk</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 14 25 22 37 32 46 42 49 34 49</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 40 43 7 33 17 6 43 34 8 46</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">disk</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -1.75679087 -0.83656708 -1.08753720 0.16731342 -0.25097012 0.92022379</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.58559696 1.17119391 -0.08365671 1.17119391</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.7494646 0.9322608 -1.2612940 0.3229400 -0.6519732 -1.3222261</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.9322608 0.3838721 -1.2003619 1.1150570</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">y</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
<span class="r-in"><span> id <span class="op">=</span> <span class="va">LETTERS</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span></span>
@ -235,22 +234,22 @@
<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="va">y</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A S 20 &lt;=0.25 16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B S 19 1 16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C S 28 1 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D I 19 &lt;=0.25 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E S 29 2 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F S 27 1 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G I 28 8 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H R 25 0.5 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I I 19 4 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J S 22 2 8</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 I 29 &lt;=2 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B R 21 &gt;=8 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C R 31 4 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D S 19 4 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E I 21 4 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F R 31 &lt;=2 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G S 20 4 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H R 25 4 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I R 24 &gt;=8 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J S 20 &gt;=8 2</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "tobr"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.29224437 -0.04269298 -0.12726465 -0.81461826 0.24072419 -0.18648338</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.33589052 0.64003364 0.11169208 0.13496321</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.2859019 0.4406350 0.3166812 -0.7958139 -0.6894550 0.6117315</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.7426344 0.3145374 0.9171062 -0.0868861</span>
<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op">&lt;-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in .subset(x, j):</span> invalid subscript type 'list'</span>
<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
@ -266,17 +265,17 @@
<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> "tobr"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance check_id_C</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 C S 28 1 1 -0.12726465 0.00000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 F S 27 1 1 -0.18648338 0.05921873</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 B S 19 1 16 -0.04269298 0.08457167</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 A S 20 &lt;=0.25 16 -0.29224437 0.16497972</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 I I 19 4 8 0.11169208 0.23895672</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 J S 22 2 8 0.13496321 0.26222785</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 E S 29 2 2 0.24072419 0.36798884</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 G I 28 8 1 0.33589052 0.46315517</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 D I 19 &lt;=0.25 2 -0.81461826 0.68735362</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 H R 25 0.5 4 0.64003364 0.76729829</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 R 31 4 1 0.3166812 0.000000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 H R 25 4 2 0.3145374 0.002143877</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 B R 21 &gt;=8 2 0.4406350 0.123953772</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 F R 31 &lt;=2 4 0.6117315 0.295050227</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 J S 20 &gt;=8 2 -0.0868861 0.403567331</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 I R 24 &gt;=8 4 0.9171062 0.600424979</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 A I 29 &lt;=2 2 -0.2859019 0.602583175</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 E I 21 4 1 -0.6894550 1.006136186</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 G S 20 4 1 -0.7426344 1.059315640</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 D S 19 4 1 -0.7958139 1.112495094</span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="co"># support for groups</span></span></span>
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>

2
reference/microorganisms.codes.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9126</small>
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2
reference/microorganisms.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9126</small>
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2
reference/mo_matching_score.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9126</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9131</small>
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2
reference/mo_property.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9126</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9131</small>
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2
reference/mo_source.html
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@ -12,7 +12,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9126</small>
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reference/pca.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9126</small>
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2
reference/plot.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9126</small>
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2
reference/proportion.html
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@ -12,7 +12,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9126</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9131</small>
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35
reference/random.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9126</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9131</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -193,42 +193,43 @@
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 64 0.025 0.01 &lt;=0.001 16 64 0.025 0.125 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.025 16 0.5 &gt;=256 2 64 32 4 0.005 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 0.125 128 0.5 8 0.25 0.002 0.005 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 32 0.01 0.005 0.5 0.025 &gt;=256 0.0625 &gt;=256 &gt;=256 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.25 64 &lt;=0.002 0.025 0.125 128 0.01 0.25 0.25 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 1 128 128 0.005 32 0.0625 2 </span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 20 15 10 41 49 47 42 39 8 46 10 7 17 10 27 22 27 23 11 9 36 14 29 26 16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 19 15 43 41 37 41 46 47 49 9 30 39 8 36 8 19 24 14 25 48 39 7 12 8 49</span>
<span class="r-in"><span><span class="fu">random_sir</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] S I R I S I S R R I I I S I I R S I R R R R S S I</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] I S I R R R R R S R S S I R S S R S I S R S S R S</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
<span class="r-in"><span><span class="co"># make the random generation more realistic by setting a bug and/or drug:</span></span></span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 0.0625-64</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.125 0.005 0.25 0.0625 0.001 0.5 16 0.25 0.0625 0.001 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 0.001 0.001 0.25 2 0.0625 32 4 0.125 0.0625 64 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 32 &gt;=128 0.125 0.0625 64 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.001 8 1 0.01 0.025 8 64 0.5 0.01 0.002 32 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] 128 0.25 4 0.005 0.025 0.125 256 64 128 32 16 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 64 </span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-16</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] &gt;=16 &gt;=16 1 &gt;=16 2 1 1 1 1 2 8 &gt;=16 2 8 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [16] 2 4 8 &gt;=16 8 2 4 8 2 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2 1 0.25 2 32 8 32 16 &gt;=64 0.25 &gt;=64 0.5 2 &gt;=64 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [16] 0.25 8 8 4 &gt;=64 0.25 2 1 16 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-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1 1 0.25 1 2 2 4 0.0625 0.5 0.0625</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 2 0.25 0.25 4 1 0.125 1 0.0625 0.125 0.0625</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 2 0.5 0.0625 0.5 0.5 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 8 1 &lt;=0.0625 0.25 &gt;=16 0.5 1 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [9] 8 0.5 &gt;=16 1 8 0.5 0.25 4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [17] &lt;=0.0625 4 8 8 2 0.5 1 0.5 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 2 </span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 8-50</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 12 17 49 8 49 22 13 47 28 44 43 20 23 45 41 39 50 30 45 48 16 15 40 34 47</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 22 42 48 44 25 31 46 49 21 30 49 22 46 44 21 20 47 33 47 44 45 13 17 24 44</span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 11-17</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 17 17 11 16 12 15 16 16 16 13 12 11 12 16 15 14 16 12 15 13 11 11 17 14 14</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 16 17 17 15 16 11 13 11 11 14 14 14 15 15 13 15 17 12 12 17 15 16 17 14 13</span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 12-27</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 25 17 24 23 17 20 20 19 22 24 25 20 23 21 21 24 18 21 24 17 21 27 21 16 16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 19 24 15 18 17 26 18 19 27 27 19 26 25 25 26 24 27 21 15 15 24 16 18 18 20</span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
</div>

2
reference/resistance_predict.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9126</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9131</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">

4
reference/skewness.html
View File

@ -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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9126</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9131</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">
@ -181,7 +181,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">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] 0.009188111</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.02219704</span>
</code></pre></div>
</div>
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