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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="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</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="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</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">
@ -163,7 +163,7 @@
<h4 data-toc-skip class="author">Dr. Matthijs
Berends</h4>
<h4 data-toc-skip class="date">29 October 2022</h4>
<h4 data-toc-skip class="date">30 October 2022</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/AMR.Rmd" class="external-link"><code>vignettes/AMR.Rmd</code></a></small>
<div class="d-none name"><code>AMR.Rmd</code></div>
@ -175,7 +175,7 @@ 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 29 October 2022.</p>
generated on 30 October 2022.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@ -231,21 +231,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2022-10-29</td>
<td align="center">2022-10-30</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="center">2022-10-29</td>
<td align="center">2022-10-30</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<tr class="odd">
<td align="center">2022-10-29</td>
<td align="center">2022-10-30</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -395,69 +395,69 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2012-02-21</td>
<td align="center">S5</td>
<td align="center">Hospital D</td>
<td align="center">2017-02-09</td>
<td align="center">A8</td>
<td align="center">Hospital A</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2012-01-01</td>
<td align="center">S5</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">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2014-08-14</td>
<td align="center">B9</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2013-06-17</td>
<td align="center">J1</td>
<td align="center">Hospital C</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2017-06-22</td>
<td align="center">V10</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2011-05-13</td>
<td align="center">C3</td>
<td align="center">2010-10-01</td>
<td align="center">X8</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2012-04-05</td>
<td align="center">I6</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2013-02-02</td>
<td align="center">J7</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2017-04-23</td>
<td align="center">H1</td>
<td align="center">Hospital A</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">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2013-08-13</td>
<td align="center">N9</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
</tbody>
@ -494,16 +494,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,313</td>
<td align="right">51.57%</td>
<td align="right">10,313</td>
<td align="right">51.57%</td>
<td align="right">10,425</td>
<td align="right">52.13%</td>
<td align="right">10,425</td>
<td align="right">52.13%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,687</td>
<td align="right">48.44%</td>
<td align="right">9,575</td>
<td align="right">47.88%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -616,9 +616,9 @@ takes into account the antimicrobial susceptibility test results using
<span><span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span></span>
<span><span class="co"># 2</span></span>
<span><span class="co"># Including isolates from ICU.</span></span>
<span><span class="co"># =&gt; Found 10,638 'phenotype-based' first isolates (53.2% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,672 'phenotype-based' first isolates (53.4% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 53.2% is suitable for resistance analysis! We can now filter
<p>So only 53.4% 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">
@ -629,7 +629,7 @@ on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html"
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="co"># Including isolates from ICU.</span></span></code></pre></div>
<p>So we end up with 10,638 isolates for analysis. Now our data looks
<p>So we end up with 10,672 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>
@ -668,13 +668,29 @@ like:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2012-02-21</td>
<td align="center">S5</td>
<td align="center">Hospital D</td>
<td align="left">7</td>
<td align="center">2010-08-01</td>
<td align="center">X2</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">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">9</td>
<td align="center">2012-09-22</td>
<td align="center">U1</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">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
@ -683,15 +699,31 @@ like:</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="center">2011-05-13</td>
<td align="center">C3</td>
<tr class="odd">
<td align="left">10</td>
<td align="center">2015-07-29</td>
<td align="center">Y1</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">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">11</td>
<td align="center">2012-05-29</td>
<td align="center">C5</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
@ -700,64 +732,32 @@ like:</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">6</td>
<td align="center">2013-08-13</td>
<td align="center">N9</td>
<td align="left">12</td>
<td align="center">2011-02-06</td>
<td align="center">S1</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">7</td>
<td align="center">2017-03-07</td>
<td align="center">G5</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">10</td>
<td align="center">2011-06-18</td>
<td align="center">C3</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">11</td>
<td align="center">2011-09-13</td>
<td align="center">U2</td>
<td align="center">Hospital D</td>
<td align="left">14</td>
<td align="center">2012-10-27</td>
<td align="center">E2</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
@ -796,8 +796,8 @@ readable:</p>
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://msberends.github.io/cleaner/reference/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></span></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 10,638<br>
Available: 10,638 (100%, NA: 0 = 0%)<br>
Length: 10,672<br>
Available: 10,672 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -822,33 +822,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">4,698</td>
<td align="right">44.16%</td>
<td align="right">4,698</td>
<td align="right">44.16%</td>
<td align="right">4,695</td>
<td align="right">43.99%</td>
<td align="right">4,695</td>
<td align="right">43.99%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,683</td>
<td align="right">25.22%</td>
<td align="right">7,381</td>
<td align="right">69.38%</td>
<td align="right">2,749</td>
<td align="right">25.76%</td>
<td align="right">7,444</td>
<td align="right">69.75%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,070</td>
<td align="right">19.46%</td>
<td align="right">9,451</td>
<td align="right">88.84%</td>
<td align="right">2,073</td>
<td align="right">19.42%</td>
<td align="right">9,517</td>
<td align="right">89.18%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,187</td>
<td align="right">11.16%</td>
<td align="right">10,638</td>
<td align="right">1,155</td>
<td align="right">10.82%</td>
<td align="right">10,672</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -897,12 +897,12 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2012-02-21</td>
<td align="center">S5</td>
<td align="center">Hospital D</td>
<td align="center">2012-09-22</td>
<td align="center">U1</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">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
@ -912,12 +912,27 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2017-03-07</td>
<td align="center">G5</td>
<td align="center">Hospital D</td>
<td align="center">2015-07-29</td>
<td align="center">Y1</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">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2012-07-31</td>
<td align="center">J9</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
@ -926,9 +941,9 @@ antibiotic class they are in:</p>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2011-03-18</td>
<td align="center">F8</td>
<tr class="even">
<td align="center">2013-04-30</td>
<td align="center">F4</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
@ -941,30 +956,15 @@ antibiotic class they are in:</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2017-06-06</td>
<td align="center">M4</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">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">2012-12-07</td>
<td align="center">C6</td>
<td align="center">Hospital B</td>
<td align="center">2010-10-16</td>
<td align="center">A3</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
@ -972,18 +972,18 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2012-02-15</td>
<td align="center">M4</td>
<td align="center">2010-06-06</td>
<td align="center">D9</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">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-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
</tbody>
@ -1009,50 +1009,50 @@ different bug/drug combinations, you can use the
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">2229</td>
<td align="center">110</td>
<td align="center">2359</td>
<td align="center">4698</td>
<td align="center">2219</td>
<td align="center">120</td>
<td align="center">2356</td>
<td align="center">4695</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3438</td>
<td align="center">153</td>
<td align="center">1107</td>
<td align="center">4698</td>
<td align="center">3496</td>
<td align="center">146</td>
<td align="center">1053</td>
<td align="center">4695</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3430</td>
<td align="center">3403</td>
<td align="center">0</td>
<td align="center">1268</td>
<td align="center">4698</td>
<td align="center">1292</td>
<td align="center">4695</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4120</td>
<td align="center">4103</td>
<td align="center">0</td>
<td align="center">578</td>
<td align="center">4698</td>
<td align="center">592</td>
<td align="center">4695</td>
</tr>
<tr class="odd">
<td align="center">K. pneumoniae</td>
<td align="center">AMX</td>
<td align="center">0</td>
<td align="center">0</td>
<td align="center">1187</td>
<td align="center">1187</td>
<td align="center">1155</td>
<td align="center">1155</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">939</td>
<td align="center">48</td>
<td align="center">200</td>
<td align="center">1187</td>
<td align="center">913</td>
<td align="center">41</td>
<td align="center">201</td>
<td align="center">1155</td>
</tr>
</tbody>
</table>
@ -1075,34 +1075,34 @@ 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">4120</td>
<td align="center">4103</td>
<td align="center">0</td>
<td align="center">578</td>
<td align="center">4698</td>
<td align="center">592</td>
<td align="center">4695</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1081</td>
<td align="center">1056</td>
<td align="center">0</td>
<td align="center">106</td>
<td align="center">1187</td>
<td align="center">99</td>
<td align="center">1155</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2424</td>
<td align="center">2425</td>
<td align="center">0</td>
<td align="center">259</td>
<td align="center">2683</td>
<td align="center">324</td>
<td align="center">2749</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">2070</td>
<td align="center">2070</td>
<td align="center">2073</td>
<td align="center">2073</td>
</tr>
</tbody>
</table>
@ -1134,7 +1134,7 @@ I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equa
own:</p>
<div class="sourceCode" id="cb26"><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] 0.5418312</span></span></code></pre></div>
<span><span class="co"># [1] 0.5438531</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="cb27"><pre class="downlit sourceCode r">
@ -1149,19 +1149,19 @@ own:</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5577628</td>
<td align="center">0.5467467</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5364725</td>
<td align="center">0.5433633</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5250313</td>
<td align="center">0.5498433</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5391595</td>
<td align="center">0.5359324</td>
</tr>
</tbody>
</table>
@ -1186,23 +1186,23 @@ 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">0.5577628</td>
<td align="center">3272</td>
<td align="center">0.5467467</td>
<td align="center">3166</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5364725</td>
<td align="center">3674</td>
<td align="center">0.5433633</td>
<td align="center">3782</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5250313</td>
<td align="center">1598</td>
<td align="center">0.5498433</td>
<td align="center">1595</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5391595</td>
<td align="center">2094</td>
<td align="center">0.5359324</td>
<td align="center">2129</td>
</tr>
</tbody>
</table>
@ -1227,27 +1227,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7643678</td>
<td align="center">0.8769689</td>
<td align="center">0.9753086</td>
<td align="center">0.7757188</td>
<td align="center">0.8739084</td>
<td align="center">0.9782748</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8315080</td>
<td align="center">0.9106992</td>
<td align="center">0.9831508</td>
<td align="center">0.8259740</td>
<td align="center">0.9142857</td>
<td align="center">0.9844156</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7935147</td>
<td align="center">0.9034663</td>
<td align="center">0.9836004</td>
<td align="center">0.7937432</td>
<td align="center">0.8821390</td>
<td align="center">0.9792652</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5526570</td>
<td align="center">0.5344911</td>
<td align="center">0.0000000</td>
<td align="center">0.5526570</td>
<td align="center">0.5344911</td>
</tr>
</tbody>
</table>
@ -1275,23 +1275,23 @@ classes, use a antibiotic class selector such as
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">55.8%</td>
<td align="right">26.8%</td>
<td align="right">54.7%</td>
<td align="right">26.2%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">53.6%</td>
<td align="right">26.5%</td>
<td align="right">54.3%</td>
<td align="right">25.5%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">52.5%</td>
<td align="right">25.1%</td>
<td align="right">55.0%</td>
<td align="right">27.5%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">53.9%</td>
<td align="right">25.5%</td>
<td align="right">53.6%</td>
<td align="right">26.0%</td>
</tr>
</tbody>
</table>
@ -1407,18 +1407,16 @@ 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] 8 &lt;=0.001 64 128 8 0.01 16 0.0625 0.5 </span></span>
<span><span class="co"># [10] 0.01 128 8 0.125 1 0.25 8 0.01 32 </span></span>
<span><span class="co"># [19] 4 0.5 1 0.002 0.25 1 4 0.025 0.005 </span></span>
<span><span class="co"># [28] 0.01 128 0.005 0.125 0.125 2 32 16 16 </span></span>
<span><span class="co"># [37] &lt;=0.001 0.01 0.125 0.5 &lt;=0.001 4 0.25 8 8 </span></span>
<span><span class="co"># [46] 0.025 4 1 128 0.0625 0.025 1 0.125 1 </span></span>
<span><span class="co"># [55] 0.025 &lt;=0.001 8 0.002 0.25 2 &gt;=256 32 0.005 </span></span>
<span><span class="co"># [64] 2 0.0625 4 0.5 128 0.002 0.01 1 0.005 </span></span>
<span><span class="co"># [73] 0.125 0.125 0.25 &lt;=0.001 8 128 0.125 128 4 </span></span>
<span><span class="co"># [82] &gt;=256 16 8 16 64 8 &lt;=0.001 4 0.002 </span></span>
<span><span class="co"># [91] 64 0.005 128 1 0.5 32 1 0.0625 0.01 </span></span>
<span><span class="co"># [100] 0.0625</span></span></code></pre></div>
<span><span class="co"># [1] 0.125 1 0.125 0.001 32 0.001 4 &gt;=256 0.0625 0.002 </span></span>
<span><span class="co"># [11] 0.001 0.5 0.025 0.01 16 2 64 8 2 0.5 </span></span>
<span><span class="co"># [21] 0.125 32 0.5 0.5 0.005 4 &gt;=256 16 2 0.005 </span></span>
<span><span class="co"># [31] 0.01 0.005 0.5 0.002 4 1 64 2 16 0.0625</span></span>
<span><span class="co"># [41] 0.025 0.025 0.01 &gt;=256 0.005 64 8 0.01 0.001 128 </span></span>
<span><span class="co"># [51] 0.001 64 4 64 &gt;=256 1 0.5 32 0.125 0.002 </span></span>
<span><span class="co"># [61] 8 16 128 2 &gt;=256 0.01 1 16 128 0.002 </span></span>
<span><span class="co"># [71] 128 16 0.01 1 2 0.25 0.01 0.25 1 0.005 </span></span>
<span><span class="co"># [81] 8 0.025 &gt;=256 0.002 0.002 0.0625 0.125 0.005 &gt;=256 0.5 </span></span>
<span><span class="co"># [91] &gt;=256 128 2 128 0.25 1 0.005 0.125 0.0625 0.25</span></span></code></pre></div>
<div class="sourceCode" id="cb37"><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>
@ -1452,10 +1450,10 @@ 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] 22 30 22 24 23 21 30 20 25 25 31 26 21 31 20 24 18 31 28 28 27 28 20 18 29</span></span>
<span><span class="co"># [26] 27 31 26 19 28 28 17 29 30 23 22 31 24 31 17 18 24 26 21 26 17 21 26 19 27</span></span>
<span><span class="co"># [51] 22 19 19 21 23 24 27 20 31 18 23 22 30 24 31 26 25 22 22 24 23 30 19 28 18</span></span>
<span><span class="co"># [76] 28 29 25 22 25 23 27 20 23 20 19 23 18 22 28 21 23 26 17 17 18 27 26 28 30</span></span></code></pre></div>
<span><span class="co"># [1] 17 24 27 27 17 30 28 20 18 30 23 23 18 30 24 31 22 26 24 18 31 25 17 18 23</span></span>
<span><span class="co"># [26] 26 25 19 22 21 22 29 19 21 28 22 24 26 20 23 19 23 18 25 28 21 29 23 20 24</span></span>
<span><span class="co"># [51] 29 24 17 17 30 29 18 21 30 29 29 22 27 22 17 17 28 21 27 20 24 26 31 20 17</span></span>
<span><span class="co"># [76] 19 31 17 22 21 19 22 25 19 29 30 25 22 17 31 24 24 25 28 22 26 27 27 21 27</span></span></code></pre></div>
<div class="sourceCode" id="cb43"><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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articles/EUCAST.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="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</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">

60
articles/MDR.html
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</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">
@ -370,19 +370,19 @@ 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 S R S R R I</span></span>
<span><span class="co"># 2 R S I I S I</span></span>
<span><span class="co"># 3 I S I I S I</span></span>
<span><span class="co"># 4 I I S R S R</span></span>
<span><span class="co"># 5 S I S S R I</span></span>
<span><span class="co"># 6 R S I R S R</span></span>
<span><span class="co"># 1 S I R S S R</span></span>
<span><span class="co"># 2 I I I I S I</span></span>
<span><span class="co"># 3 I I R I I S</span></span>
<span><span class="co"># 4 I S I R I R</span></span>
<span><span class="co"># 5 I R I R R I</span></span>
<span><span class="co"># 6 I R I R S S</span></span>
<span><span class="co"># kanamycin</span></span>
<span><span class="co"># 1 I</span></span>
<span><span class="co"># 2 I</span></span>
<span><span class="co"># 1 S</span></span>
<span><span class="co"># 2 S</span></span>
<span><span class="co"># 3 R</span></span>
<span><span class="co"># 4 I</span></span>
<span><span class="co"># 5 I</span></span>
<span><span class="co"># 6 S</span></span></code></pre></div>
<span><span class="co"># 4 S</span></span>
<span><span class="co"># 5 R</span></span>
<span><span class="co"># 6 I</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">
@ -423,40 +423,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3190</td>
<td align="right">63.80%</td>
<td align="right">3190</td>
<td align="right">63.80%</td>
<td align="right">3192</td>
<td align="right">63.84%</td>
<td align="right">3192</td>
<td align="right">63.84%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">978</td>
<td align="right">19.56%</td>
<td align="right">4168</td>
<td align="right">83.36%</td>
<td align="right">989</td>
<td align="right">19.78%</td>
<td align="right">4181</td>
<td align="right">83.62%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">498</td>
<td align="right">9.96%</td>
<td align="right">4666</td>
<td align="right">93.32%</td>
<td align="right">453</td>
<td align="right">9.06%</td>
<td align="right">4634</td>
<td align="right">92.68%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">242</td>
<td align="right">4.84%</td>
<td align="right">4908</td>
<td align="right">98.16%</td>
<td align="right">268</td>
<td align="right">5.36%</td>
<td align="right">4902</td>
<td align="right">98.04%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">92</td>
<td align="right">1.84%</td>
<td align="right">98</td>
<td align="right">1.96%</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="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</small>
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13
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="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</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">
@ -163,7 +163,7 @@
<h4 data-toc-skip class="author">Dr. Matthijs
Berends</h4>
<h4 data-toc-skip class="date">29 October 2022</h4>
<h4 data-toc-skip class="date">30 October 2022</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/SPSS.Rmd" class="external-link"><code>vignettes/SPSS.Rmd</code></a></small>
<div class="d-none name"><code>SPSS.Rmd</code></div>
@ -242,7 +242,7 @@ data using a custom made website. The webdesign knowledge needed
<li>
<p><strong>R has a huge community.</strong></p>
<p>Many R users just ask questions on websites like <a href="https://stackoverflow.com" class="external-link">StackOverflow.com</a>, the largest
online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">467,961
online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">468,730
R-related questions</a> have already been asked on this platform (that
covers questions and answers for any programming language). In my own
experience, most questions are answered within a couple of
@ -336,9 +336,10 @@ would be of any better use than R.</p>
<span><span class="fu"><a href="../reference/ab_property.html">ab_name</a></span><span class="op">(</span><span class="st">"floxapen"</span><span class="op">)</span></span>
<span><span class="co"># [1] "Flucloxacillin"</span></span>
<span><span class="fu"><a href="../reference/ab_property.html">ab_tradenames</a></span><span class="op">(</span><span class="st">"floxapen"</span><span class="op">)</span></span>
<span><span class="co"># [1] "floxacillin" "floxapen" "floxapen sodium salt"</span></span>
<span><span class="co"># [4] "fluclox" "flucloxacilina" "flucloxacillin" </span></span>
<span><span class="co"># [7] "flucloxacilline" "flucloxacillinum" "fluorochloroxacillin"</span></span>
<span><span class="co"># [1] "culpen" "floxacillin" "floxacillin sodium" </span></span>
<span><span class="co"># [4] "floxapen" "floxapen sodium salt" "fluclox" </span></span>
<span><span class="co"># [7] "flucloxacilina" "flucloxacillin" "flucloxacilline" </span></span>
<span><span class="co"># [10] "flucloxacillinum" "fluorochloroxacillin" "staphylex"</span></span>
<span><span class="fu"><a href="../reference/ab_property.html">ab_atc</a></span><span class="op">(</span><span class="st">"floxapen"</span><span class="op">)</span></span>
<span><span class="co"># [1] "J01CF05"</span></span></code></pre></div>
</div>

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="">1.8.2.9037</small>
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56
articles/datasets.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="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</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">
@ -161,7 +161,7 @@
<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">29 October 2022</h4>
<h4 data-toc-skip class="date">30 October 2022</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<div class="d-none name"><code>datasets.Rmd</code></div>
@ -191,7 +191,7 @@ column names:<br><em>mo</em>, <em>fullname</em>, <em>status</em>, <em>kingdom</e
<em>gbif_renamed_to</em>, <em>prevalence</em> and <em>snomed</em>.</p>
<p>This data set is in R available as <code>microorganisms</code>, after
you load the <code>AMR</code> package.</p>
<p>It was last updated on 29 October 2022 17:02:33 UTC. Find more info
<p>It was last updated on 30 October 2022 13:33:29 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
@ -483,40 +483,40 @@ Set Name ‘Microoganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href
<h2 id="antibiotics-antibiotic-agents">
<code>antibiotics</code>: Antibiotic Agents<a class="anchor" aria-label="anchor" href="#antibiotics-antibiotic-agents"></a>
</h2>
<p>A data set with 464 rows and 14 columns, containing the following
<p>A data set with 484 rows and 14 columns, containing the following
column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>atc</em>,
<em>atc_group1</em>, <em>atc_group2</em>, <em>abbreviations</em>,
<em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>,
<em>iv_ddd</em>, <em>iv_units</em> and <em>loinc</em>.</p>
<p>This data set is in R available as <code>antibiotics</code>, after
you load the <code>AMR</code> package.</p>
<p>It was last updated on 29 October 2022 17:02:33 UTC. Find more info
<p>It was last updated on 30 October 2022 13:33:29 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.rds" class="external-link">original
R Data Structure (RDS) file</a> (36 kB)<br>
R Data Structure (RDS) file</a> (39 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.txt" class="external-link">tab-separated
text file</a> (0.1 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.xlsx" class="external-link">Microsoft
Excel workbook</a> (63 kB)<br>
Excel workbook</a> (66 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.feather" class="external-link">Apache
Feather file</a> (97 kB)<br>
Feather file</a> (0.1 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.parquet" class="external-link">Apache
Parquet file</a> (74 kB)<br>
Parquet file</a> (97 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.sas" class="external-link">SAS
data file</a> (1.8 MB)<br>
data file</a> (1.9 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.sav" class="external-link">IBM
SPSS Statistics data file</a> (0.3 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.dta" class="external-link">Stata
DTA file</a> (0.3 MB)</li>
DTA file</a> (0.4 MB)</li>
</ul>
<p>The tab-separated text file and Microsoft Excel workbook, and SAS,
SPSS and Stata files all contain the ATC codes, common abbreviations,
@ -650,7 +650,7 @@ inhibitors</td>
<td align="center">Macrolides, lincosamides and streptogramins</td>
<td align="center">Macrolides</td>
<td align="center">az, azi, azit, …</td>
<td align="center">aritromicina, azasite, azenil, …</td>
<td align="center">aritromicina, aruzilina, azasite, …</td>
<td align="center">0.3</td>
<td align="center">g</td>
<td align="center">0.5</td>
@ -671,7 +671,7 @@ inhibitors</td>
<td align="center"></td>
<td align="center">3.6</td>
<td align="center">g</td>
<td align="center">3913-1</td>
<td align="center"></td>
</tr>
</tbody>
</table>
@ -687,7 +687,7 @@ column names:<br><em>atc</em>, <em>cid</em>, <em>name</em>, <em>atc_group</em>,
<em>iv_ddd</em> and <em>iv_units</em>.</p>
<p>This data set is in R available as <code>antivirals</code>, after you
load the <code>AMR</code> package.</p>
<p>It was last updated on 29 October 2022 17:02:33 UTC. Find more info
<p>It was last updated on 30 October 2022 13:33:29 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
@ -847,7 +847,7 @@ column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>
<em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
<p>This data set is in R available as <code>rsi_translation</code>,
after you load the <code>AMR</code> package.</p>
<p>It was last updated on 29 October 2022 17:02:33 UTC. Find more info
<p>It was last updated on 30 October 2022 13:33:29 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
@ -1020,7 +1020,7 @@ Resistance<a class="anchor" aria-label="anchor" href="#intrinsic_resistant-intri
column names:<br><em>mo</em> and <em>ab</em>.</p>
<p>This data set is in R available as <code>intrinsic_resistant</code>,
after you load the <code>AMR</code> package.</p>
<p>It was last updated on 29 October 2022 17:02:33 UTC. Find more info
<p>It was last updated on 30 October 2022 13:33:29 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
@ -1046,7 +1046,7 @@ data file</a> (9.8 MB)<br>
SPSS Statistics data file</a> (7.4 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.dta" class="external-link">Stata
DTA file</a> (9.6 MB)</li>
DTA file</a> (9.5 MB)</li>
</ul>
<div class="section level3">
<h3 id="source-4">Source<a class="anchor" aria-label="anchor" href="#source-4"></a>
@ -1112,6 +1112,14 @@ v3.3</a> (2021).</p>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Cefalexin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Cefalotin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Cefazolin</td>
</tr>
<tr class="odd">
@ -1120,14 +1128,6 @@ v3.3</a> (2021).</p>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Cephalexin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Cephalothin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Clarithromycin</td>
</tr>
<tr class="odd">
@ -1308,7 +1308,7 @@ column names:<br><em>ab</em>, <em>name</em>, <em>type</em>, <em>dose</em>,
<em>original_txt</em> and <em>eucast_version</em>.</p>
<p>This data set is in R available as <code>dosage</code>, after you
load the <code>AMR</code> package.</p>
<p>It was last updated on 29 October 2022 17:02:33 UTC. Find more info
<p>It was last updated on 30 October 2022 13:33:29 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
@ -1458,7 +1458,7 @@ column names:<br><em>date</em>, <em>patient</em>, <em>age</em>, <em>gender</em>,
<em>MUP</em> and <em>RIF</em>.</p>
<p>This data set is in R available as <code>example_isolates</code>,
after you load the <code>AMR</code> package.</p>
<p>It was last updated on 29 October 2022 17:02:33 UTC. Find more info
<p>It was last updated on 30 October 2022 13:33:29 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates.html">here</a>.</p>
<div class="section level3">
<h3 id="source-6">Source<a class="anchor" aria-label="anchor" href="#source-6"></a>
@ -1871,7 +1871,7 @@ column names:<br><em>patient_id</em>, <em>hospital</em>, <em>date</em>,
<p>This data set is in R available as
<code>example_isolates_unclean</code>, after you load the
<code>AMR</code> package.</p>
<p>It was last updated on 29 October 2022 17:02:33 UTC. Find more info
<p>It was last updated on 30 October 2022 13:33:29 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates_unclean.html">here</a>.</p>
<div class="section level3">
<h3 id="source-7">Source<a class="anchor" aria-label="anchor" href="#source-7"></a>

2
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</small>
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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="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</small>
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4
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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="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</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">
@ -188,7 +188,7 @@ treatment evaluation in any setting.</p>
10.33612/diss.177417131</a> and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">DOI
10.33612/diss.192486375</a>).</p>
<p>After installing this package, R knows ~49,000 distinct microbial
species and all ~570 antibiotic, antimycotic and antiviral drugs by name
species and all ~590 antibiotic, antimycotic and antiviral drugs by name
and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED
CT), and knows all about valid R/SI and MIC values. The integral
breakpoint guidelines from CLSI and EUCAST are included from the last 10

2
authors.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="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</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
index.html
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@ -42,7 +42,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</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">

19
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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="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</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">
@ -127,10 +127,10 @@
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="1.8.2.9037" id="amr-1829037">AMR 1.8.2.9037<a class="anchor" aria-label="anchor" href="#amr-1829037"></a></h2>
<h2 class="pkg-version" data-toc-text="1.8.2.9038" id="amr-1829038">AMR 1.8.2.9038<a class="anchor" aria-label="anchor" href="#amr-1829038"></a></h2>
<p>This version will eventually become v2.0! We’re happy to reach a new major milestone soon!</p>
<div class="section level4">
<h4 id="breaking-1-8-2-9037">Breaking<a class="anchor" aria-label="anchor" href="#breaking-1-8-2-9037"></a></h4>
<h4 id="breaking-1-8-2-9038">Breaking<a class="anchor" aria-label="anchor" href="#breaking-1-8-2-9038"></a></h4>
<ul><li>Removed all species of the taxonomic kingdom Chromista from the package. This was done for multiple reasons:
<ul><li>CRAN allows packages to be around 5 MB maximum, some packages are exempted but this package is not one of them</li>
<li>Chromista are not relevant when it comes to antimicrobial resistance, thus lacking the primary scope of this package</li>
@ -143,7 +143,7 @@
<li>Removal of interpretation guidelines older than 10 years, the oldest now included guidelines of EUCAST and CLSI are from 2013</li>
</ul></div>
<div class="section level4">
<h4 id="new-1-8-2-9037">New<a class="anchor" aria-label="anchor" href="#new-1-8-2-9037"></a></h4>
<h4 id="new-1-8-2-9038">New<a class="anchor" aria-label="anchor" href="#new-1-8-2-9038"></a></h4>
<ul><li>EUCAST 2022 and CLSI 2022 guidelines have been added for <code><a href="../reference/as.rsi.html">as.rsi()</a></code>. EUCAST 2022 is now the new default guideline for all MIC and disks diffusion interpretations.</li>
<li>All new algorithm for <code><a href="../reference/as.mo.html">as.mo()</a></code> (and thus all <code>mo_*()</code> functions) while still following our original set-up as described in our paper (DOI 10.18637/jss.v104.i03).
<ul><li>A new argument <code>keep_synonyms</code> allows to <em>not</em> correct for updated taxonomy, in favour of the now deleted argument <code>allow_uncertain</code>
@ -165,9 +165,15 @@
<li>Support for using antibiotic selectors in scoped <code>dplyr</code> verbs (with or without <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>, see <code><a href="../reference/proportion.html">resistance()</a></code>
</li>
<li>Support for antimicrobial interpretation of anaerobic bacteria, by adding a ‘placeholder’ code <code>B_ANAER</code> to the <code>microorganisms</code> data set and add the breakpoints of anaerobics to the <code>rsi_interpretation</code> data set, which is used by <code><a href="../reference/as.rsi.html">as.rsi()</a></code> when interpreting MIC and disk diffusion values</li>
<li>New and updated entries for the <code>antibiotics</code> data set
<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>
<li>Added some missing ATC codes</li>
<li>Updated DDDs and PubChem Compound IDs</li>
<li>Updated some antibiotic name spelling, now used by WHOCC (such as cephalexin -&gt; cefalexin, and phenethicillin -&gt; pheneticillin)</li>
</ul></li>
</ul></div>
<div class="section level4">
<h4 id="changed-1-8-2-9037">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-2-9037"></a></h4>
<h4 id="changed-1-8-2-9038">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-2-9038"></a></h4>
<ul><li>Fix for using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on certain EUCAST breakpoints for MIC values</li>
<li>Fix for using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on <code>NA</code> values (e.g. <code>as.rsi(as.disk(NA), ...)</code>)</li>
<li>Fix for using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on drug-drug combinations with multiple breakpoints for different body sites</li>
@ -195,10 +201,9 @@
<li>Antimicrobial interpretation ‘SDD’ (susceptible dose-dependent, coined by CLSI) will be interpreted as ‘I’ to comply with EUCAST’s ‘I’ in <code><a href="../reference/as.rsi.html">as.rsi()</a></code>
</li>
<li>Fix for <code><a href="../reference/mo_property.html">mo_shortname()</a></code> in case of higher taxonomic ranks (order, class, phylum)</li>
<li>Updated DDDs and ATCs for the <code>antibiotics</code> data set - ATC codes J04AB06 (enviomycin) and D06AX14 (ozenoxacin) were added</li>
</ul></div>
<div class="section level4">
<h4 id="other-1-8-2-9037">Other<a class="anchor" aria-label="anchor" href="#other-1-8-2-9037"></a></h4>
<h4 id="other-1-8-2-9038">Other<a class="anchor" aria-label="anchor" href="#other-1-8-2-9038"></a></h4>
<ul><li>New website to make use of the new Bootstrap 5 and pkgdown 2.0. The website now contains results for all examples and will be automatically regenerated with every change to our repository, using GitHub Actions</li>
<li>Added Peter Dutey-Magni, Dmytro Mykhailenko, Anton Mymrikov, and Jonas Salm as contributors, to thank them for their valuable input</li>
<li>All R and Rmd files in this project are now styled using the <code>styler</code> package</li>

2
pkgdown.yml
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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: 2022-10-29T17:04Z
last_built: 2022-10-30T13:36Z
urls:
reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles

2
reference/AMR-deprecated.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</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">

8
reference/AMR.html
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@ -5,7 +5,7 @@ This work was published in the Journal of Statistical Software (Volume 104(3); d
) and formed the basis of two PhD theses (doi:10.33612/diss.177417131
and doi:10.33612/diss.192486375
).
After installing this package, R knows ~49,000 distinct microbial species and all ~570 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.
After installing this package, R knows ~49,000 distinct microbial species and all ~590 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.
This package is fully independent of any other R package and works on Windows, macOS and Linux with all versions of R since R-3.0.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice and University Medical Center Groningen. This R package is actively maintained and free software; you can freely use and distribute it for both personal and commercial (but not patent) purposes under the terms of the GNU General Public License version 2.0 (GPL-2), as published by the Free Software Foundation.
This package can be used for:
Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the List of Prokaryotic names with Standing in Nomenclature (LPSN) and the Global Biodiversity Information Facility (GBIF)
@ -31,7 +31,7 @@ This work was published in the Journal of Statistical Software (Volume 104(3); d
) and formed the basis of two PhD theses (doi:10.33612/diss.177417131
and doi:10.33612/diss.192486375
).
After installing this package, R knows ~49,000 distinct microbial species and all ~570 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.
After installing this package, R knows ~49,000 distinct microbial species and all ~590 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.
This package is fully independent of any other R package and works on Windows, macOS and Linux with all versions of R since R-3.0.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice and University Medical Center Groningen. This R package is actively maintained and free software; you can freely use and distribute it for both personal and commercial (but not patent) purposes under the terms of the GNU General Public License version 2.0 (GPL-2), as published by the Free Software Foundation.
This package can be used for:
Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the List of Prokaryotic names with Standing in Nomenclature (LPSN) and the Global Biodiversity Information Facility (GBIF)
@ -62,7 +62,7 @@ Principal component analysis for AMR
<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="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</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">
@ -186,7 +186,7 @@ Principal component analysis for AMR
) and formed the basis of two PhD theses (<a href="https://doi.org/10.33612/diss.177417131" class="external-link">doi:10.33612/diss.177417131</a>
and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">doi:10.33612/diss.192486375</a>
).</p>
<p>After installing this package, <span style="R">R</span> knows ~49,000 distinct microbial species and all ~570 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.</p>
<p>After installing this package, <span style="R">R</span> knows ~49,000 distinct microbial species and all ~590 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.</p>
<p>This package is fully independent of any other <span style="R">R</span> package and works on Windows, macOS and Linux with all versions of <span style="R">R</span> since R-3.0.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice and University Medical Center Groningen. This <span style="R">R</span> package is actively maintained and free software; you can freely use and distribute it for both personal and commercial (but not patent) purposes under the terms of the GNU General Public License version 2.0 (GPL-2), as published by the Free Software Foundation.</p>
<p>This package can be used for:</p><ul><li><p>Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the List of Prokaryotic names with Standing in Nomenclature (LPSN) and the Global Biodiversity Information Facility (GBIF)</p></li>
<li><p>Interpreting raw MIC and disk diffusion values, based on any CLSI or EUCAST guideline from the last 10 years</p></li>

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9
reference/WHOCC.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="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</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">
@ -152,9 +152,10 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Meropenem"</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_tradenames</a></span><span class="op">(</span><span class="st">"flucloxacillin"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "floxacillin" "floxapen" "floxapen sodium salt"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [4] "fluclox" "flucloxacilina" "flucloxacillin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] "flucloxacilline" "flucloxacillinum" "fluorochloroxacillin"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "culpen" "floxacillin" "floxacillin sodium" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [4] "floxapen" "floxapen sodium salt" "fluclox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] "flucloxacilina" "flucloxacillin" "flucloxacilline" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] "flucloxacillinum" "fluorochloroxacillin" "staphylex" </span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>

2
reference/WHONET.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/ab_from_text.html
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="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</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">

104
reference/ab_property.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</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">
@ -256,37 +256,45 @@
<span class="r-in"><span><span class="fu">ab_cid</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span> <span class="co"># 33613 (Compound ID from PubChem)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 33613</span>
<span class="r-in"><span><span class="fu">ab_synonyms</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span> <span class="co"># a list with brand names of amoxicillin</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "actimoxi" "amoclen" "amolin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [4] "amopen" "amopenixin" "amoxibiotic" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] "amoxicaps" "amoxicilina" "amoxicillin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] "amoxicilline" "amoxicillinum" "amoxiden" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] "amoxil" "amoxivet" "amoxy" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [16] "amoxycillin" "anemolin" "aspenil" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] "biomox" "bristamox" "cemoxin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [22] "clamoxyl" "delacillin" "dispermox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] "efpenix" "flemoxin" "hiconcil" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [28] "histocillin" "hydroxyampicillin" "ibiamox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [31] "imacillin" "lamoxy" "metafarma capsules"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [34] "metifarma capsules" "moxacin" "moxatag" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] "ospamox" "pamoxicillin" "piramox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [40] "robamox" "sawamox pm" "tolodina" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [43] "unicillin" "utimox" "vetramox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "actimoxi" "amoclen" "amolin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [4] "amopen" "amopenixin" "amoxibiotic" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] "amoxicaps" "amoxicilina" "amoxicillin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] "amoxicillin hydrate" "amoxicilline" "amoxicillinum" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] "amoxiden" "amoxil" "amoxivet" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [16] "amoxy" "amoxycillin" "amoxyke" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] "anemolin" "aspenil" "atoksilin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [22] "biomox" "bristamox" "cemoxin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] "clamoxyl" "damoxy" "delacillin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [28] "demoksil" "dispermox" "efpenix" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [31] "flemoxin" "hiconcil" "histocillin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [34] "hydroxyampicillin" "ibiamox" "imacillin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] "lamoxy" "largopen" "metafarma capsules" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [40] "metifarma capsules" "moksilin" "moxacin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [43] "moxatag" "ospamox" "pamoxicillin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [46] "piramox" "promoxil" "remoxil" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] "robamox" "sawamox pm" "tolodina" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [52] "topramoxin" "unicillin" "utimox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [55] "vetramox" </span>
<span class="r-in"><span><span class="fu">ab_tradenames</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span> <span class="co"># same</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "actimoxi" "amoclen" "amolin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [4] "amopen" "amopenixin" "amoxibiotic" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] "amoxicaps" "amoxicilina" "amoxicillin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] "amoxicilline" "amoxicillinum" "amoxiden" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] "amoxil" "amoxivet" "amoxy" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [16] "amoxycillin" "anemolin" "aspenil" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] "biomox" "bristamox" "cemoxin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [22] "clamoxyl" "delacillin" "dispermox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] "efpenix" "flemoxin" "hiconcil" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [28] "histocillin" "hydroxyampicillin" "ibiamox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [31] "imacillin" "lamoxy" "metafarma capsules"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [34] "metifarma capsules" "moxacin" "moxatag" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] "ospamox" "pamoxicillin" "piramox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [40] "robamox" "sawamox pm" "tolodina" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [43] "unicillin" "utimox" "vetramox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "actimoxi" "amoclen" "amolin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [4] "amopen" "amopenixin" "amoxibiotic" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] "amoxicaps" "amoxicilina" "amoxicillin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] "amoxicillin hydrate" "amoxicilline" "amoxicillinum" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] "amoxiden" "amoxil" "amoxivet" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [16] "amoxy" "amoxycillin" "amoxyke" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] "anemolin" "aspenil" "atoksilin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [22] "biomox" "bristamox" "cemoxin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] "clamoxyl" "damoxy" "delacillin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [28] "demoksil" "dispermox" "efpenix" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [31] "flemoxin" "hiconcil" "histocillin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [34] "hydroxyampicillin" "ibiamox" "imacillin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] "lamoxy" "largopen" "metafarma capsules" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [40] "metifarma capsules" "moksilin" "moxacin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [43] "moxatag" "ospamox" "pamoxicillin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [46] "piramox" "promoxil" "remoxil" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] "robamox" "sawamox pm" "tolodina" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [52] "topramoxin" "unicillin" "utimox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [55] "vetramox" </span>
<span class="r-in"><span><span class="fu">ab_group</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span> <span class="co"># "Beta-lactams/penicillins"</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Beta-lactams/penicillins"</span>
<span class="r-in"><span><span class="fu">ab_atc_group1</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span> <span class="co"># "Beta-lactam antibacterials, penicillins"</span></span></span>
@ -339,21 +347,25 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Penicillins with extended spectrum"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $tradenames</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "actimoxi" "amoclen" "amolin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [4] "amopen" "amopenixin" "amoxibiotic" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] "amoxicaps" "amoxicilina" "amoxicillin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] "amoxicilline" "amoxicillinum" "amoxiden" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] "amoxil" "amoxivet" "amoxy" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [16] "amoxycillin" "anemolin" "aspenil" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] "biomox" "bristamox" "cemoxin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [22] "clamoxyl" "delacillin" "dispermox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] "efpenix" "flemoxin" "hiconcil" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [28] "histocillin" "hydroxyampicillin" "ibiamox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [31] "imacillin" "lamoxy" "metafarma capsules"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [34] "metifarma capsules" "moxacin" "moxatag" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] "ospamox" "pamoxicillin" "piramox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [40] "robamox" "sawamox pm" "tolodina" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [43] "unicillin" "utimox" "vetramox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "actimoxi" "amoclen" "amolin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [4] "amopen" "amopenixin" "amoxibiotic" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] "amoxicaps" "amoxicilina" "amoxicillin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] "amoxicillin hydrate" "amoxicilline" "amoxicillinum" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] "amoxiden" "amoxil" "amoxivet" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [16] "amoxy" "amoxycillin" "amoxyke" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] "anemolin" "aspenil" "atoksilin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [22] "biomox" "bristamox" "cemoxin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] "clamoxyl" "damoxy" "delacillin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [28] "demoksil" "dispermox" "efpenix" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [31] "flemoxin" "hiconcil" "histocillin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [34] "hydroxyampicillin" "ibiamox" "imacillin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] "lamoxy" "largopen" "metafarma capsules" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [40] "metifarma capsules" "moksilin" "moxacin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [43] "moxatag" "ospamox" "pamoxicillin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [46] "piramox" "promoxil" "remoxil" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] "robamox" "sawamox pm" "tolodina" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [52] "topramoxin" "unicillin" "utimox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [55] "vetramox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $loinc</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "16365-9" "25274-2" "3344-9" "80133-2"</span>

34
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="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</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">
@ -169,16 +169,18 @@
<span class="r-in"><span> <span class="fu"><a href="as.ab.html">as.ab</a></span><span class="op">(</span><span class="st">"test"</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> Class 'ab'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] &lt;NA&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] FUS</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># now add a custom entry - it will be considered by as.ab() and</span></span></span>
<span class="r-in"><span><span class="co"># all ab_*() functions</span></span></span>
<span class="r-in"><span><span class="fu">add_custom_antimicrobials</span><span class="op">(</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>ab <span class="op">=</span> <span class="st">"TEST"</span>,</span></span>
<span class="r-in"><span> name <span class="op">=</span> <span class="st">"Test Antibiotic"</span>,</span></span>
<span class="r-in"><span> <span class="co"># you can add any property present in the</span></span></span>
<span class="r-in"><span> <span class="co"># 'antibiotics' data set, such as 'group':</span></span></span>
<span class="r-in"><span> group <span class="op">=</span> <span class="st">"Test Group"</span><span class="op">)</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
<span class="r-in"><span> ab <span class="op">=</span> <span class="st">"TEST"</span>,</span></span>
<span class="r-in"><span> name <span class="op">=</span> <span class="st">"Test Antibiotic"</span>,</span></span>
<span class="r-in"><span> <span class="co"># you can add any property present in the</span></span></span>
<span class="r-in"><span> <span class="co"># 'antibiotics' data set, such as 'group':</span></span></span>
<span class="r-in"><span> group <span class="op">=</span> <span class="st">"Test Group"</span></span></span>
<span class="r-in"><span> <span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Added one record to the internal `antibiotics` data set.</span>
<span class="r-in"><span></span></span>
@ -242,10 +244,12 @@
<span class="r-in"><span><span class="co"># Add Co-fluampicil, which is one of the many J01CR50 codes, see</span></span></span>
<span class="r-in"><span><span class="co"># https://www.whocc.no/ddd/list_of_ddds_combined_products/</span></span></span>
<span class="r-in"><span><span class="fu">add_custom_antimicrobials</span><span class="op">(</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>ab <span class="op">=</span> <span class="st">"COFLU"</span>,</span></span>
<span class="r-in"><span> name <span class="op">=</span> <span class="st">"Co-fluampicil"</span>,</span></span>
<span class="r-in"><span> atc <span class="op">=</span> <span class="st">"J01CR50"</span>,</span></span>
<span class="r-in"><span> group <span class="op">=</span> <span class="st">"Beta-lactams/penicillines"</span><span class="op">)</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
<span class="r-in"><span> ab <span class="op">=</span> <span class="st">"COFLU"</span>,</span></span>
<span class="r-in"><span> name <span class="op">=</span> <span class="st">"Co-fluampicil"</span>,</span></span>
<span class="r-in"><span> atc <span class="op">=</span> <span class="st">"J01CR50"</span>,</span></span>
<span class="r-in"><span> group <span class="op">=</span> <span class="st">"Beta-lactams/penicillines"</span></span></span>
<span class="r-in"><span> <span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Added one record to the internal `antibiotics` data set.</span>
<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_atc</a></span><span class="op">(</span><span class="st">"Co-fluampicil"</span><span class="op">)</span></span></span>
@ -254,9 +258,11 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Co-fluampicil"</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># even antibiotic selectors work</span></span></span>
<span class="r-in"><span><span class="va">x</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>random_column <span class="op">=</span> <span class="st">"test"</span>,</span></span>
<span class="r-in"><span> coflu <span class="op">=</span> <span class="fu"><a href="as.rsi.html">as.rsi</a></span><span class="op">(</span><span class="st">"S"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> ampicillin <span class="op">=</span> <span class="fu"><a href="as.rsi.html">as.rsi</a></span><span class="op">(</span><span class="st">"R"</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">x</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> random_column <span class="op">=</span> <span class="st">"test"</span>,</span></span>
<span class="r-in"><span> coflu <span class="op">=</span> <span class="fu"><a href="as.rsi.html">as.rsi</a></span><span class="op">(</span><span class="st">"S"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> ampicillin <span class="op">=</span> <span class="fu"><a href="as.rsi.html">as.rsi</a></span><span class="op">(</span><span class="st">"R"</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">x</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> random_column coflu ampicillin</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 test S R</span>

22
reference/age.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</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">
@ -190,16 +190,16 @@
<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 1933-11-08 88 88.97260 66</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1932-04-27 90 90.50685 67</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1969-07-28 53 53.25479 30</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1977-03-14 45 45.62740 22</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1998-05-31 24 24.41370 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1990-01-02 32 32.82192 9</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1999-06-09 23 23.38904 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1939-10-15 83 83.03836 60</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1995-01-21 27 27.76986 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1936-03-11 86 86.63562 63</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1979-10-11 43 43.05205 20</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1941-08-25 81 81.18082 58</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1936-03-04 86 86.65753 63</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1986-08-24 36 36.18356 13</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1998-01-06 24 24.81370 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1972-12-06 49 49.89863 27</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1954-01-12 68 68.79726 45</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1987-04-28 35 35.50685 12</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1941-09-12 81 81.13151 58</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1937-11-01 84 84.99452 62</span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>

2
reference/age_groups.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="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</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">

24
reference/antibiotic_class_selectors.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</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">
@ -252,27 +252,27 @@
<ul><li><p><code>aminoglycosides()</code> can select: <br> amikacin (AMK), amikacin/fosfomycin (AKF), amphotericin B-high (AMH), apramycin (APR), arbekacin (ARB), astromicin (AST), bekanamycin (BEK), dibekacin (DKB), framycetin (FRM), gentamicin (GEN), gentamicin-high (GEH), habekacin (HAB), hygromycin (HYG), isepamicin (ISE), kanamycin (KAN), kanamycin-high (KAH), kanamycin/cephalexin (KAC), micronomicin (MCR), neomycin (NEO), netilmicin (NET), pentisomicin (PIM), plazomicin (PLZ), propikacin (PKA), ribostamycin (RST), sisomicin (SIS), streptoduocin (STR), streptomycin (STR1), streptomycin-high (STH), tobramycin (TOB) and tobramycin-high (TOH)</p></li>
<li><p><code>aminopenicillins()</code> can select: <br> amoxicillin (AMX) and ampicillin (AMP)</p></li>
<li><p><code>antifungals()</code> can select: <br> 5-fluorocytosine (FCT), amphotericin B (AMB), anidulafungin (ANI), butoconazole (BUT), caspofungin (CAS), ciclopirox (CIX), clotrimazole (CTR), econazole (ECO), fluconazole (FLU), fosfluconazole (FFL), griseofulvin (GRI), hachimycin (HCH), ibrexafungerp (IBX), isavuconazole (ISV), isoconazole (ISO), itraconazole (ITR), ketoconazole (KET), manogepix (MGX), micafungin (MIF), miconazole (MCZ), nystatin (NYS), pimaricin (PMR), posaconazole (POS), rezafungin (RZF), ribociclib (RBC), sulconazole (SUC), terbinafine (TRB), terconazole (TRC) and voriconazole (VOR)</p></li>
<li><p><code>antimycobacterials()</code> can select: <br> 4-aminosalicylic acid (AMA), calcium aminosalicylate (CLA), capreomycin (CAP), clofazimine (CLF), delamanid (DLM), enviomycin (ENV), ethambutol (ETH), ethambutol/isoniazid (ETI), ethionamide (ETI1), isoniazid (INH), morinamide (MRN), p-aminosalicylic acid (PAS), pretomanid (PMD), prothionamide (PTH), pyrazinamide (PZA), rifabutin (RIB), rifampicin (RIF), rifampicin/isoniazid (RFI), rifampicin/pyrazinamide/ethambutol/isoniazid (RPEI), rifampicin/pyrazinamide/isoniazid (RPI), rifamycin (RFM), rifapentine (RFP), simvastatin/fenofibrate (SMF), sodium aminosalicylate (SDA), streptomycin/isoniazid (STI), terizidone (TRZ), thioacetazone/isoniazid (THI1), tiocarlide (TCR) and viomycin (VIO)</p></li>
<li><p><code>betalactams()</code> can select: <br> amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), avibactam (AVB), azidocillin (AZD), azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), biapenem (BIA), carbenicillin (CRB), carindacillin (CRN), cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefaloridine (RID), cefamandole (MAN), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/nacubactam (FNC), cefepime/tazobactam (FPT), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (CCL), cefetrizole (CZL), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening (FOX1), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/enzyme inhibitor (CEI), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), cefuroxime (CXM), cefuroxime axetil (CXA), cephalexin (LEX), cephalothin (CEP), cephapirin (HAP), cephradine (CED), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), doripenem (DOR), epicillin (EPC), ertapenem (ETP), flucloxacillin (FLC), hetacillin (HET), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), latamoxef (LTM), lenampicillin (LEN), loracarbef (LOR), mecillinam (MEC), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), metampicillin (MTM), methicillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nacubactam (NAC), nafcillin (NAF), oxacillin (OXA), panipenem (PAN), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), phenethicillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), sarmoxicillin (SRX), sulbactam (SUL), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), tazobactam (TAZ), tebipenem (TBP), temocillin (TEM), ticarcillin (TIC) and ticarcillin/clavulanic acid (TCC)</p></li>
<li><p><code>antifungals()</code> can select: <br> amphotericin B (AMB), anidulafungin (ANI), butoconazole (BUT), caspofungin (CAS), ciclopirox (CIX), clotrimazole (CTR), econazole (ECO), fluconazole (FLU), flucytosine (FCT), fosfluconazole (FFL), griseofulvin (GRI), hachimycin (HCH), ibrexafungerp (IBX), isavuconazole (ISV), isoconazole (ISO), itraconazole (ITR), ketoconazole (KET), manogepix (MGX), micafungin (MIF), miconazole (MCZ), nystatin (NYS), oteseconazole (OTE), pimaricin (PMR), posaconazole (POS), rezafungin (RZF), ribociclib (RBC), sulconazole (SUC), terbinafine (TRB), terconazole (TRC) and voriconazole (VOR)</p></li>
<li><p><code>antimycobacterials()</code> can select: <br> 4-aminosalicylic acid (AMA), calcium aminosalicylate (CLA), capreomycin (CAP), clofazimine (CLF), delamanid (DLM), enviomycin (ENV), ethambutol (ETH), ethambutol/isoniazid (ETI), ethionamide (ETI1), isoniazid (INH), isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST), morinamide (MRN), p-aminosalicylic acid (PAS), pretomanid (PMD), protionamide (PTH), pyrazinamide (PZA), rifabutin (RIB), rifampicin (RIF), rifampicin/ethambutol/isoniazid (REI), rifampicin/isoniazid (RFI), rifampicin/pyrazinamide/ethambutol/isoniazid (RPEI), rifampicin/pyrazinamide/isoniazid (RPI), rifamycin (RFM), rifapentine (RFP), simvastatin/fenofibrate (SMF), sodium aminosalicylate (SDA), streptomycin/isoniazid (STI), terizidone (TRZ), thioacetazone (TAT), thioacetazone/isoniazid (THI1), tiocarlide (TCR) and viomycin (VIO)</p></li>
<li><p><code>betalactams()</code> can select: <br> amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), avibactam (AVB), azidocillin (AZD), azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), biapenem (BIA), carbenicillin (CRB), carindacillin (CRN), cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefamandole (MAN), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/nacubactam (FNC), cefepime/tazobactam (FPT), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (CCL), cefetrizole (CZL), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening (FOX1), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/tazobactam (CEI), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), cefuroxime (CXM), cefuroxime axetil (CXA), cephradine (CED), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), doripenem (DOR), epicillin (EPC), ertapenem (ETP), flucloxacillin (FLC), hetacillin (HET), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), latamoxef (LTM), lenampicillin (LEN), loracarbef (LOR), mecillinam (MEC), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), metampicillin (MTM), meticillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nacubactam (NAC), nafcillin (NAF), oxacillin (OXA), panipenem (PAN), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), pheneticillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), sarmoxicillin (SRX), sulbactam (SUL), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), tazobactam (TAZ), tebipenem (TBP), temocillin (TEM), ticarcillin (TIC) and ticarcillin/clavulanic acid (TCC)</p></li>
<li><p><code>carbapenems()</code> can select: <br> biapenem (BIA), doripenem (DOR), ertapenem (ETP), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), panipenem (PAN), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA) and tebipenem (TBP)</p></li>
<li><p><code>cephalosporins()</code> can select: <br> cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefaloridine (RID), cefamandole (MAN), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/tazobactam (FPT), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (CCL), cefetrizole (CZL), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening (FOX1), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/enzyme inhibitor (CEI), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), cefuroxime (CXM), cefuroxime axetil (CXA), cephalexin (LEX), cephalothin (CEP), cephapirin (HAP), cephradine (CED), latamoxef (LTM) and loracarbef (LOR)</p></li>
<li><p><code>cephalosporins_1st()</code> can select: <br> cefacetrile (CAC), cefadroxil (CFR), cefaloridine (RID), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefroxadine (CRD), ceftezole (CTL), cephalexin (LEX), cephalothin (CEP), cephapirin (HAP) and cephradine (CED)</p></li>
<li><p><code>cephalosporins()</code> can select: <br> cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefamandole (MAN), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/tazobactam (FPT), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (CCL), cefetrizole (CZL), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening (FOX1), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/tazobactam (CEI), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), cefuroxime (CXM), cefuroxime axetil (CXA), cephradine (CED), latamoxef (LTM) and loracarbef (LOR)</p></li>
<li><p><code>cephalosporins_1st()</code> can select: <br> cefacetrile (CAC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefroxadine (CRD), ceftezole (CTL) and cephradine (CED)</p></li>
<li><p><code>cephalosporins_2nd()</code> can select: <br> cefaclor (CEC), cefamandole (MAN), cefmetazole (CMZ), cefonicid (CID), ceforanide (CND), cefotetan (CTT), cefotiam (CTF), cefoxitin (FOX), cefoxitin screening (FOX1), cefprozil (CPR), cefuroxime (CXM), cefuroxime axetil (CXA) and loracarbef (LOR)</p></li>
<li><p><code>cephalosporins_3rd()</code> can select: <br> cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefetamet (CAT), cefetamet pivoxil (CPI), cefixime (CFM), cefmenoxime (CMX), cefodizime (DIZ), cefoperazone (CFP), cefoperazone/sulbactam (CSL), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotiam hexetil (CHE), cefovecin (FOV), cefpimizole (CFZ), cefpiramide (CPM), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefsulodin (CFS), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftriaxone (CRO) and latamoxef (LTM)</p></li>
<li><p><code>cephalosporins_3rd()</code> can select: <br> cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefetamet (CAT), cefetamet pivoxil (CPI), cefixime (CFM), cefmenoxime (CMX), cefodizime (DIZ), cefoperazone (CFP), cefoperazone/sulbactam (CSL), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotiam hexetil (CHE), cefovecin (FOV), cefpimizole (CFZ), cefpiramide (CPM), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefsulodin (CFS), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB) and latamoxef (LTM)</p></li>
<li><p><code>cephalosporins_4th()</code> can select: <br> cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/tazobactam (FPT), cefetecol (CCL), cefoselis (CSE), cefozopran (ZOP), cefpirome (CPO) and cefquinome (CEQ)</p></li>
<li><p><code>cephalosporins_5th()</code> can select: <br> ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/enzyme inhibitor (CEI) and ceftolozane/tazobactam (CZT)</p></li>
<li><p><code>fluoroquinolones()</code> can select: <br> besifloxacin (BES), ciprofloxacin (CIP), clinafloxacin (CLX), danofloxacin (DAN), delafloxacin (DFX), difloxacin (DIF), enoxacin (ENX), enrofloxacin (ENR), finafloxacin (FIN), fleroxacin (FLE), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), levofloxacin (LVX), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nifuroquine (NIF), norfloxacin (NOR), ofloxacin (OFX), orbifloxacin (ORB), pazufloxacin (PAZ), pefloxacin (PEF), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX) and trovafloxacin (TVA)</p></li>
<li><p><code>cephalosporins_5th()</code> can select: <br> ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/tazobactam (CEI) and ceftolozane/tazobactam (CZT)</p></li>
<li><p><code>fluoroquinolones()</code> can select: <br> besifloxacin (BES), ciprofloxacin (CIP), clinafloxacin (CLX), danofloxacin (DAN), delafloxacin (DFX), difloxacin (DIF), enoxacin (ENX), enrofloxacin (ENR), finafloxacin (FIN), fleroxacin (FLE), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), lascufloxacin (LSC), levofloxacin (LVX), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nifuroquine (NIF), norfloxacin (NOR), ofloxacin (OFX), orbifloxacin (ORB), pazufloxacin (PAZ), pefloxacin (PEF), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX) and trovafloxacin (TVA)</p></li>
<li><p><code>glycopeptides()</code> can select: <br> avoparcin (AVO), dalbavancin (DAL), norvancomycin (NVA), oritavancin (ORI), ramoplanin (RAM), teicoplanin (TEC), teicoplanin-macromethod (TCM), telavancin (TLV), vancomycin (VAN) and vancomycin-macromethod (VAM)</p></li>
<li><p><code>lincosamides()</code> can select: <br> acetylmidecamycin (ACM), acetylspiramycin (ASP), clindamycin (CLI), gamithromycin (GAM), kitasamycin (KIT), lincomycin (LIN), meleumycin (MEL), nafithromycin (ZWK), pirlimycin (PRL), primycin (PRM), solithromycin (SOL), tildipirosin (TIP), tilmicosin (TIL), tulathromycin (TUL), tylosin (TYL) and tylvalosin (TYL1)</p></li>
<li><p><code>lipoglycopeptides()</code> can select: <br> dalbavancin (DAL), oritavancin (ORI) and telavancin (TLV)</p></li>
<li><p><code>macrolides()</code> can select: <br> acetylmidecamycin (ACM), acetylspiramycin (ASP), azithromycin (AZM), clarithromycin (CLR), dirithromycin (DIR), erythromycin (ERY), flurithromycin (FLR1), gamithromycin (GAM), josamycin (JOS), kitasamycin (KIT), meleumycin (MEL), midecamycin (MID), miocamycin (MCM), nafithromycin (ZWK), oleandomycin (OLE), pirlimycin (PRL), primycin (PRM), rokitamycin (ROK), roxithromycin (RXT), solithromycin (SOL), spiramycin (SPI), telithromycin (TLT), tildipirosin (TIP), tilmicosin (TIL), troleandomycin (TRL), tulathromycin (TUL), tylosin (TYL) and tylvalosin (TYL1)</p></li>
<li><p><code>oxazolidinones()</code> can select: <br> cadazolid (CDZ), cycloserine (CYC), linezolid (LNZ), tedizolid (TZD) and thiacetazone (THA)</p></li>
<li><p><code>penicillins()</code> can select: <br> amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), avibactam (AVB), azidocillin (AZD), azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), carbenicillin (CRB), carindacillin (CRN), cefepime/nacubactam (FNC), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), epicillin (EPC), flucloxacillin (FLC), hetacillin (HET), lenampicillin (LEN), mecillinam (MEC), metampicillin (MTM), methicillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nacubactam (NAC), nafcillin (NAF), oxacillin (OXA), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), phenethicillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), sarmoxicillin (SRX), sulbactam (SUL), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), tazobactam (TAZ), temocillin (TEM), ticarcillin (TIC) and ticarcillin/clavulanic acid (TCC)</p></li>
<li><p><code>penicillins()</code> can select: <br> amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), avibactam (AVB), azidocillin (AZD), azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), carbenicillin (CRB), carindacillin (CRN), cefepime/nacubactam (FNC), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), epicillin (EPC), flucloxacillin (FLC), hetacillin (HET), lenampicillin (LEN), mecillinam (MEC), metampicillin (MTM), meticillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nacubactam (NAC), nafcillin (NAF), oxacillin (OXA), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), pheneticillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), sarmoxicillin (SRX), sulbactam (SUL), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), tazobactam (TAZ), temocillin (TEM), ticarcillin (TIC) and ticarcillin/clavulanic acid (TCC)</p></li>
<li><p><code>polymyxins()</code> can select: <br> colistin (COL), polymyxin B (PLB) and polymyxin B/polysorbate 80 (POP)</p></li>
<li><p><code>quinolones()</code> can select: <br> besifloxacin (BES), cinoxacin (CIN), ciprofloxacin (CIP), clinafloxacin (CLX), danofloxacin (DAN), delafloxacin (DFX), difloxacin (DIF), enoxacin (ENX), enrofloxacin (ENR), finafloxacin (FIN), fleroxacin (FLE), flumequine (FLM), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), levofloxacin (LVX), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nalidixic acid (NAL), nifuroquine (NIF), nitroxoline (NTR), norfloxacin (NOR), ofloxacin (OFX), orbifloxacin (ORB), oxolinic acid (OXO), pazufloxacin (PAZ), pefloxacin (PEF), pipemidic acid (PPA), piromidic acid (PIR), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rosoxacin (ROS), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX) and trovafloxacin (TVA)</p></li>
<li><p><code>quinolones()</code> can select: <br> besifloxacin (BES), cinoxacin (CIN), ciprofloxacin (CIP), clinafloxacin (CLX), danofloxacin (DAN), delafloxacin (DFX), difloxacin (DIF), enoxacin (ENX), enrofloxacin (ENR), finafloxacin (FIN), fleroxacin (FLE), flumequine (FLM), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), lascufloxacin (LSC), levofloxacin (LVX), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nalidixic acid (NAL), nemonoxacin (NEM), nifuroquine (NIF), nitroxoline (NTR), norfloxacin (NOR), ofloxacin (OFX), orbifloxacin (ORB), oxolinic acid (OXO), pazufloxacin (PAZ), pefloxacin (PEF), pipemidic acid (PPA), piromidic acid (PIR), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rosoxacin (ROS), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX) and trovafloxacin (TVA)</p></li>
<li><p><code>streptogramins()</code> can select: <br> pristinamycin (PRI) and quinupristin/dalfopristin (QDA)</p></li>
<li><p><code>tetracyclines()</code> can select: <br> cetocycline (CTO), chlortetracycline (CTE), clomocycline (CLM1), demeclocycline (DEM), doxycycline (DOX), eravacycline (ERV), lymecycline (LYM), metacycline (MTC), minocycline (MNO), omadacycline (OMC), oxytetracycline (OXY), penimepicycline (PNM1), rolitetracycline (RLT), tetracycline (TCY) and tigecycline (TGC)</p></li>
<li><p><code>tetracyclines()</code> can select: <br> cetocycline (CTO), chlortetracycline (CTE), clomocycline (CLM1), demeclocycline (DEM), doxycycline (DOX), eravacycline (ERV), lymecycline (LYM), metacycline (MTC), minocycline (MNO), omadacycline (OMC), oxytetracycline (OXY), penimepicycline (PNM1), rolitetracycline (RLT), sarecycline (SRC), tetracycline (TCY) and tigecycline (TGC)</p></li>
<li><p><code>trimethoprims()</code> can select: <br> brodimoprim (BDP), sulfadiazine (SDI), sulfadiazine/tetroxoprim (SLT), sulfadiazine/trimethoprim (SLT1), sulfadimethoxine (SUD), sulfadimidine (SDM), sulfadimidine/trimethoprim (SLT2), sulfafurazole (SLF), sulfaisodimidine (SLF1), sulfalene (SLF2), sulfamazone (SZO), sulfamerazine (SLF3), sulfamerazine/trimethoprim (SLT3), sulfamethizole (SLF4), sulfamethoxazole (SMX), sulfamethoxypyridazine (SLF5), sulfametomidine (SLF6), sulfametoxydiazine (SLF7), sulfametrole/trimethoprim (SLT4), sulfamoxole (SLF8), sulfamoxole/trimethoprim (SLT5), sulfanilamide (SLF9), sulfaperin (SLF10), sulfaphenazole (SLF11), sulfapyridine (SLF12), sulfathiazole (SUT), sulfathiourea (SLF13), trimethoprim (TMP) and trimethoprim/sulfamethoxazole (SXT)</p></li>
<li><p><code>ureidopenicillins()</code> can select: <br> azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP) and piperacillin/tazobactam (TZP)</p></li>
</ul></div>

46
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reference/as.ab.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</small>
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2
reference/as.disk.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</small>
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2
reference/as.mic.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</small>
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2
reference/as.mo.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</small>
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22
reference/as.rsi.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</small>
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@ -496,16 +496,16 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 50 × 13</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index ab_input ab_consid…¹ mo_in…² mo_conside…³ guide…⁴</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2022-10-29 <span style="color: #949494;">17:04:55</span> 1 ampicillin AMP Strep … B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2022-10-29 <span style="color: #949494;">17:04:55</span> 1 AMP AMP Escher… B_ESCHR_COLI EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2022-10-29 <span style="color: #949494;">17:04:55</span> 1 CIP CIP Escher… B_ESCHR_COLI EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2022-10-29 <span style="color: #949494;">17:04:56</span> 1 GEN GEN Escher… B_ESCHR_COLI EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2022-10-29 <span style="color: #949494;">17:04:56</span> 1 TOB TOB Escher… B_ESCHR_COLI EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2022-10-29 <span style="color: #949494;">17:04:56</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2022-10-29 <span style="color: #949494;">17:04:57</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2022-10-29 <span style="color: #949494;">17:04:57</span> 2 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2022-10-29 <span style="color: #949494;">17:04:57</span> 3 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2022-10-29 <span style="color: #949494;">17:04:57</span> 4 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2022-10-30 <span style="color: #949494;">13:36:47</span> 1 ampicillin AMP Strep … B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2022-10-30 <span style="color: #949494;">13:36:47</span> 1 AMP AMP Escher… B_ESCHR_COLI EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2022-10-30 <span style="color: #949494;">13:36:48</span> 1 CIP CIP Escher… B_ESCHR_COLI EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2022-10-30 <span style="color: #949494;">13:36:48</span> 1 GEN GEN Escher… B_ESCHR_COLI EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2022-10-30 <span style="color: #949494;">13:36:48</span> 1 TOB TOB Escher… B_ESCHR_COLI EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2022-10-30 <span style="color: #949494;">13:36:49</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2022-10-30 <span style="color: #949494;">13:36:49</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2022-10-30 <span style="color: #949494;">13:36:49</span> 2 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2022-10-30 <span style="color: #949494;">13:36:50</span> 3 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2022-10-30 <span style="color: #949494;">13:36:50</span> 4 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 40 more rows, 6 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;"># breakpoint_S &lt;dbl&gt;, breakpoint_R &lt;dbl&gt;, input &lt;dbl&gt;, interpretation &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># and abbreviated variable names ¹​ab_considered, ²​mo_input, ³​mo_considered,</span></span>

2
reference/atc_online.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
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2
reference/availability.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="">1.8.2.9037</small>
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2
reference/bug_drug_combinations.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="">1.8.2.9037</small>
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2
reference/count.html
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@ -12,7 +12,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
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28
reference/custom_eucast_rules.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="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</small>
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@ -208,30 +208,30 @@
<p>It is possible to define antibiotic groups instead of single antibiotics for the rule consequence, the part <em>after</em> the tilde. In above examples, the antibiotic group <code>aminopenicillins</code> is used to include ampicillin and amoxicillin. The following groups are allowed (case-insensitive). Within parentheses are the agents that will be matched when running the rule.</p><ul><li><p>"aminoglycosides"<br>(amikacin, amikacin/fosfomycin, amphotericin B-high, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin and tobramycin-high)</p></li>
<li><p>"aminopenicillins"<br>(amoxicillin and ampicillin)</p></li>
<li><p>"antifungals"<br>(5-fluorocytosine, amphotericin B, anidulafungin, butoconazole, caspofungin, ciclopirox, clotrimazole, econazole, fluconazole, fosfluconazole, griseofulvin, hachimycin, ibrexafungerp, isavuconazole, isoconazole, itraconazole, ketoconazole, manogepix, micafungin, miconazole, nystatin, pimaricin, posaconazole, rezafungin, ribociclib, sulconazole, terbinafine, terconazole and voriconazole)</p></li>
<li><p>"antimycobacterials"<br>(4-aminosalicylic acid, calcium aminosalicylate, capreomycin, clofazimine, delamanid, enviomycin, ethambutol, ethambutol/isoniazid, ethionamide, isoniazid, morinamide, p-aminosalicylic acid, pretomanid, prothionamide, pyrazinamide, rifabutin, rifampicin, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, rifapentine, simvastatin/fenofibrate, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone/isoniazid, tiocarlide and viomycin)</p></li>
<li><p>"betalactams"<br>(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, avibactam, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, biapenem, carbenicillin, carindacillin, cefacetrile, cefaclor, cefadroxil, cefaloridine, cefamandole, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/nacubactam, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/enzyme inhibitor, ceftolozane/tazobactam, ceftriaxone, cefuroxime, cefuroxime axetil, cephalexin, cephalothin, cephapirin, cephradine, ciclacillin, clometocillin, cloxacillin, dicloxacillin, doripenem, epicillin, ertapenem, flucloxacillin, hetacillin, imipenem, imipenem/EDTA, imipenem/relebactam, latamoxef, lenampicillin, loracarbef, mecillinam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, metampicillin, methicillin, mezlocillin, mezlocillin/sulbactam, nacubactam, nafcillin, oxacillin, panipenem, penamecillin, penicillin/novobiocin, penicillin/sulbactam, phenethicillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, razupenem, ritipenem, ritipenem acoxil, sarmoxicillin, sulbactam, sulbenicillin, sultamicillin, talampicillin, tazobactam, tebipenem, temocillin, ticarcillin and ticarcillin/clavulanic acid)</p></li>
<li><p>"antifungals"<br>(amphotericin B, anidulafungin, butoconazole, caspofungin, ciclopirox, clotrimazole, econazole, fluconazole, flucytosine, fosfluconazole, griseofulvin, hachimycin, ibrexafungerp, isavuconazole, isoconazole, itraconazole, ketoconazole, manogepix, micafungin, miconazole, nystatin, oteseconazole, pimaricin, posaconazole, rezafungin, ribociclib, sulconazole, terbinafine, terconazole and voriconazole)</p></li>
<li><p>"antimycobacterials"<br>(4-aminosalicylic acid, calcium aminosalicylate, capreomycin, clofazimine, delamanid, enviomycin, ethambutol, ethambutol/isoniazid, ethionamide, isoniazid, isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, morinamide, p-aminosalicylic acid, pretomanid, protionamide, pyrazinamide, rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, rifapentine, simvastatin/fenofibrate, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone, thioacetazone/isoniazid, tiocarlide and viomycin)</p></li>
<li><p>"betalactams"<br>(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, avibactam, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, biapenem, carbenicillin, carindacillin, cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/nacubactam, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, ciclacillin, clometocillin, cloxacillin, dicloxacillin, doripenem, epicillin, ertapenem, flucloxacillin, hetacillin, imipenem, imipenem/EDTA, imipenem/relebactam, latamoxef, lenampicillin, loracarbef, mecillinam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, metampicillin, meticillin, mezlocillin, mezlocillin/sulbactam, nacubactam, nafcillin, oxacillin, panipenem, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, razupenem, ritipenem, ritipenem acoxil, sarmoxicillin, sulbactam, sulbenicillin, sultamicillin, talampicillin, tazobactam, tebipenem, temocillin, ticarcillin and ticarcillin/clavulanic acid)</p></li>
<li><p>"carbapenems"<br>(biapenem, doripenem, ertapenem, imipenem, imipenem/EDTA, imipenem/relebactam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, panipenem, razupenem, ritipenem, ritipenem acoxil and tebipenem)</p></li>
<li><p>"cephalosporins"<br>(cefacetrile, cefaclor, cefadroxil, cefaloridine, cefamandole, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/enzyme inhibitor, ceftolozane/tazobactam, ceftriaxone, cefuroxime, cefuroxime axetil, cephalexin, cephalothin, cephapirin, cephradine, latamoxef and loracarbef)</p></li>
<li><p>"cephalosporins_1st"<br>(cefacetrile, cefadroxil, cefaloridine, cefatrizine, cefazedone, cefazolin, cefroxadine, ceftezole, cephalexin, cephalothin, cephapirin and cephradine)</p></li>
<li><p>"cephalosporins"<br>(cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, latamoxef and loracarbef)</p></li>
<li><p>"cephalosporins_1st"<br>(cefacetrile, cefadroxil, cefalexin, cefaloridine, cefalotin, cefapirin, cefatrizine, cefazedone, cefazolin, cefroxadine, ceftezole and cephradine)</p></li>
<li><p>"cephalosporins_2nd"<br>(cefaclor, cefamandole, cefmetazole, cefonicid, ceforanide, cefotetan, cefotiam, cefoxitin, cefoxitin screening, cefprozil, cefuroxime, cefuroxime axetil and loracarbef)</p></li>
<li><p>"cephalosporins_3rd"<br>(cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefetamet, cefetamet pivoxil, cefixime, cefmenoxime, cefodizime, cefoperazone, cefoperazone/sulbactam, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotiam hexetil, cefovecin, cefpimizole, cefpiramide, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefsulodin, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftriaxone and latamoxef)</p></li>
<li><p>"cephalosporins_3rd"<br>(cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefetamet, cefetamet pivoxil, cefixime, cefmenoxime, cefodizime, cefoperazone, cefoperazone/sulbactam, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotiam hexetil, cefovecin, cefpimizole, cefpiramide, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefsulodin, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftriaxone, ceftriaxone/beta-lactamase inhibitor and latamoxef)</p></li>
<li><p>"cephalosporins_4th"<br>(cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetecol, cefoselis, cefozopran, cefpirome and cefquinome)</p></li>
<li><p>"cephalosporins_5th"<br>(ceftaroline, ceftaroline/avibactam, ceftobiprole, ceftobiprole medocaril, ceftolozane/enzyme inhibitor and ceftolozane/tazobactam)</p></li>
<li><p>"cephalosporins_except_caz"<br>(cefacetrile, cefaclor, cefadroxil, cefaloridine, cefamandole, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/enzyme inhibitor, ceftolozane/tazobactam, ceftriaxone, cefuroxime, cefuroxime axetil, cephalexin, cephalothin, cephapirin, cephradine, latamoxef and loracarbef)</p></li>
<li><p>"fluoroquinolones"<br>(besifloxacin, ciprofloxacin, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, levofloxacin, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nifuroquine, norfloxacin, ofloxacin, orbifloxacin, pazufloxacin, pefloxacin, pradofloxacin, premafloxacin, prulifloxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin and trovafloxacin)</p></li>
<li><p>"cephalosporins_5th"<br>(ceftaroline, ceftaroline/avibactam, ceftobiprole, ceftobiprole medocaril and ceftolozane/tazobactam)</p></li>
<li><p>"cephalosporins_except_caz"<br>(cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, latamoxef and loracarbef)</p></li>
<li><p>"fluoroquinolones"<br>(besifloxacin, ciprofloxacin, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nifuroquine, norfloxacin, ofloxacin, orbifloxacin, pazufloxacin, pefloxacin, pradofloxacin, premafloxacin, prulifloxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin and trovafloxacin)</p></li>
<li><p>"glycopeptides"<br>(avoparcin, dalbavancin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, vancomycin and vancomycin-macromethod)</p></li>
<li><p>"glycopeptides_except_lipo"<br>(avoparcin, norvancomycin, ramoplanin, teicoplanin, teicoplanin-macromethod, vancomycin and vancomycin-macromethod)</p></li>
<li><p>"lincosamides"<br>(acetylmidecamycin, acetylspiramycin, clindamycin, gamithromycin, kitasamycin, lincomycin, meleumycin, nafithromycin, pirlimycin, primycin, solithromycin, tildipirosin, tilmicosin, tulathromycin, tylosin and tylvalosin)</p></li>
<li><p>"lipoglycopeptides"<br>(dalbavancin, oritavancin and telavancin)</p></li>
<li><p>"macrolides"<br>(acetylmidecamycin, acetylspiramycin, azithromycin, clarithromycin, dirithromycin, erythromycin, flurithromycin, gamithromycin, josamycin, kitasamycin, meleumycin, midecamycin, miocamycin, nafithromycin, oleandomycin, pirlimycin, primycin, rokitamycin, roxithromycin, solithromycin, spiramycin, telithromycin, tildipirosin, tilmicosin, troleandomycin, tulathromycin, tylosin and tylvalosin)</p></li>
<li><p>"oxazolidinones"<br>(cadazolid, cycloserine, linezolid, tedizolid and thiacetazone)</p></li>
<li><p>"penicillins"<br>(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, avibactam, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, carbenicillin, carindacillin, cefepime/nacubactam, ciclacillin, clometocillin, cloxacillin, dicloxacillin, epicillin, flucloxacillin, hetacillin, lenampicillin, mecillinam, metampicillin, methicillin, mezlocillin, mezlocillin/sulbactam, nacubactam, nafcillin, oxacillin, penamecillin, penicillin/novobiocin, penicillin/sulbactam, phenethicillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, sarmoxicillin, sulbactam, sulbenicillin, sultamicillin, talampicillin, tazobactam, temocillin, ticarcillin and ticarcillin/clavulanic acid)</p></li>
<li><p>"penicillins"<br>(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, avibactam, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, carbenicillin, carindacillin, cefepime/nacubactam, ciclacillin, clometocillin, cloxacillin, dicloxacillin, epicillin, flucloxacillin, hetacillin, lenampicillin, mecillinam, metampicillin, meticillin, mezlocillin, mezlocillin/sulbactam, nacubactam, nafcillin, oxacillin, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, sarmoxicillin, sulbactam, sulbenicillin, sultamicillin, talampicillin, tazobactam, temocillin, ticarcillin and ticarcillin/clavulanic acid)</p></li>
<li><p>"polymyxins"<br>(colistin, polymyxin B and polymyxin B/polysorbate 80)</p></li>
<li><p>"quinolones"<br>(besifloxacin, cinoxacin, ciprofloxacin, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, flumequine, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, levofloxacin, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nalidixic acid, nifuroquine, nitroxoline, norfloxacin, ofloxacin, orbifloxacin, oxolinic acid, pazufloxacin, pefloxacin, pipemidic acid, piromidic acid, pradofloxacin, premafloxacin, prulifloxacin, rosoxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin and trovafloxacin)</p></li>
<li><p>"quinolones"<br>(besifloxacin, cinoxacin, ciprofloxacin, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, flumequine, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nalidixic acid, nemonoxacin, nifuroquine, nitroxoline, norfloxacin, ofloxacin, orbifloxacin, oxolinic acid, pazufloxacin, pefloxacin, pipemidic acid, piromidic acid, pradofloxacin, premafloxacin, prulifloxacin, rosoxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin and trovafloxacin)</p></li>
<li><p>"streptogramins"<br>(pristinamycin and quinupristin/dalfopristin)</p></li>
<li><p>"tetracyclines"<br>(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, tetracycline and tigecycline)</p></li>
<li><p>"tetracyclines_except_tgc"<br>(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline and tetracycline)</p></li>
<li><p>"tetracyclines"<br>(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, tetracycline and tigecycline)</p></li>
<li><p>"tetracyclines_except_tgc"<br>(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline and tetracycline)</p></li>
<li><p>"trimethoprims"<br>(brodimoprim, sulfadiazine, sulfadiazine/tetroxoprim, sulfadiazine/trimethoprim, sulfadimethoxine, sulfadimidine, sulfadimidine/trimethoprim, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamerazine/trimethoprim, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfametrole/trimethoprim, sulfamoxole, sulfamoxole/trimethoprim, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfathiazole, sulfathiourea, trimethoprim and trimethoprim/sulfamethoxazole)</p></li>
<li><p>"ureidopenicillins"<br>(azlocillin, mezlocillin, piperacillin and piperacillin/tazobactam)</p></li>
</ul></div>

2
reference/dosage.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="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</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
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2
reference/example_isolates.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="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/example_isolates_unclean.html
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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="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/first_isolate.html
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@ -12,7 +12,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/g.test.html
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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="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</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">

133
reference/get_episode.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="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</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">
@ -177,40 +177,39 @@
<span class="r-in"><span><span class="va">df</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq_len</a></span><span class="op">(</span><span class="fl">2000</span><span class="op">)</span>, size <span class="op">=</span> <span class="fl">200</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span 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] 3 26 59 49 10 61 4 8 14 45 1 4 46 38 48 56 20 27 8 51 63 12 8 37 35</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 26 35 6 8 9 40 40 25 43 34 19 40 1 17 26 10 40 14 33 12 9 55 3 40 29</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 61 29 36 21 53 13 32 6 6 51 49 50 24 17 61 41 48 49 20 41 27 60 23 40 17</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 43 57 36 30 31 9 20 54 39 35 9 8 40 63 6 12 49 32 41 52 6 24 51 30 46</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [101] 58 19 19 21 24 27 26 55 55 23 1 16 32 9 26 43 32 12 57 26 36 56 15 9 30</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [126] 59 34 47 51 4 26 60 55 51 42 48 35 51 8 63 47 63 54 44 41 50 14 9 17 12</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [151] 60 8 62 16 58 29 30 26 22 61 10 7 17 6 38 2 19 9 50 21 23 7 40 5 57</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [176] 26 28 47 15 9 62 61 41 39 11 11 38 53 48 21 8 32 7 55 16 61 44 18 42 5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 56 58 21 46 12 43 36 38 26 65 24 10 57 39 9 61 62 19 16 6 63 35 46 61 27</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 65 54 57 60 5 52 11 35 47 4 53 61 23 63 10 28 15 1 4 18 59 9 41 51 38</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 52 60 10 19 38 2 45 34 41 30 38 27 29 8 8 24 39 2 26 52 34 41 63 16 3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 58 24 17 38 42 30 52 13 18 5 10 63 13 55 48 7 47 40 52 34 38 15 62 28 9</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [101] 16 56 40 6 53 32 5 2 50 23 6 16 1 64 39 27 47 12 19 62 25 52 56 48 28</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [126] 58 21 62 65 44 10 15 10 15 62 55 65 50 28 12 42 61 62 63 6 49 59 33 23 53</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [151] 38 15 20 56 26 46 60 36 40 32 18 29 8 16 37 4 31 15 4 38 62 36 22 43 33</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [176] 40 38 37 64 17 19 9 14 2 22 59 37 11 22 28 53 31 12 56 42 52 7 13 30 22</span>
<span class="r-in"><span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># TRUE/FALSE</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] TRUE TRUE FALSE FALSE TRUE FALSE FALSE TRUE TRUE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] FALSE FALSE FALSE FALSE TRUE TRUE TRUE TRUE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [109] FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [121] FALSE FALSE TRUE FALSE FALSE FALSE TRUE TRUE TRUE TRUE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [133] FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [145] FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [157] FALSE FALSE TRUE TRUE FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [169] TRUE TRUE TRUE TRUE FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [181] TRUE FALSE TRUE TRUE FALSE TRUE TRUE TRUE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [193] FALSE TRUE FALSE FALSE TRUE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE TRUE FALSE TRUE TRUE TRUE TRUE FALSE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] FALSE TRUE FALSE FALSE TRUE FALSE FALSE TRUE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] TRUE TRUE TRUE TRUE FALSE TRUE TRUE FALSE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] TRUE TRUE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] FALSE TRUE TRUE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [109] TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [121] TRUE FALSE FALSE FALSE TRUE FALSE TRUE FALSE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [133] FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [145] FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [157] TRUE FALSE TRUE TRUE FALSE TRUE FALSE FALSE TRUE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [169] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [181] FALSE TRUE TRUE TRUE TRUE TRUE FALSE TRUE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [193] FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># filter on results from the third 60-day episode only, using base R</span></span></span>
<span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, <span class="fl">60</span><span class="op">)</span> <span class="op">==</span> <span class="fl">3</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 1 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-06-23 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> 2002-06-06 24D393 20 F Clinical B_ESCHR_COLI R NA NA NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-12-14 144280 76 F Clinical B_STPHY_AURS R NA S R </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 36 more variables: AMC &lt;rsi&gt;, AMP &lt;rsi&gt;, TZP &lt;rsi&gt;, CZO &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># FEP &lt;rsi&gt;, CXM &lt;rsi&gt;, FOX &lt;rsi&gt;, CTX &lt;rsi&gt;, CAZ &lt;rsi&gt;, CRO &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># GEN &lt;rsi&gt;, TOB &lt;rsi&gt;, AMK &lt;rsi&gt;, KAN &lt;rsi&gt;, TMP &lt;rsi&gt;, SXT &lt;rsi&gt;,</span></span>
@ -246,16 +245,16 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: condition [3]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 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> 798871 2002-06-23 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 800264 2008-04-10 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 620753 2016-10-15 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 997433 2014-01-30 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 05B00F 2004-05-11 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 422833 2017-05-26 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> F35553 2002-09-23 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 739C43 2003-09-26 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 848254 2005-03-29 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 210954 2012-11-01 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 0DBF93 2015-10-12 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> F61180 2016-02-15 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 351193 2007-01-15 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 685398 2013-04-16 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 978187 2004-09-28 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 743093 2012-09-14 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 725779 2010-09-04 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> E16523 2011-06-25 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> F3BD65 2008-01-30 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 3D2C93 2017-12-13 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 190 more rows</span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@ -267,19 +266,19 @@
<span class="r-in"><span> <span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 200 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: ward, patient [172]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: ward, patient [181]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward date patient new_index new_logical</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical 2002-06-23 798871 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Outpatient 2008-04-10 800264 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Clinical 2016-10-15 620753 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical 2014-01-30 997433 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> ICU 2004-05-11 05B00F 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Clinical 2017-05-26 422833 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> ICU 2002-09-23 F35553 2 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical 2003-09-26 739C43 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> ICU 2005-03-29 848254 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical 2012-11-01 210954 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical 2015-10-12 0DBF93 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> ICU 2016-02-15 F61180 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> ICU 2007-01-15 351193 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical 2013-04-16 685398 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> ICU 2004-09-28 978187 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Outpatient 2012-09-14 743093 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Outpatient 2010-09-04 725779 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical 2011-06-25 E16523 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Outpatient 2008-01-30 F3BD65 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> ICU 2017-12-13 3D2C93 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 190 more rows</span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@ -294,9 +293,9 @@
<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 110 15 54 74</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 50 12 36 43</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 12 7 11 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 113 15 51 67</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 53 12 32 38</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 15 8 13 14</span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span> <span class="co"># grouping on patients and microorganisms leads to the same</span></span></span>
@ -315,7 +314,7 @@
<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-msg co"><span class="r-pr">#&gt;</span> Including isolates from ICU.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] FALSE</span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span> <span class="co"># but is_new_episode() has a lot more flexibility than first_isolate(),</span></span></span>
@ -326,19 +325,19 @@
<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: 200 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, mo, ward [182]</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> 798871 B_ENTRC_FCLS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 800264 B_ESCHR_COLI Outpatient TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 620753 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 997433 B_STPHY_HMNS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 05B00F F_CANDD_ALBC ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 422833 B_ENTRC_FCLS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> F35553 B_STPHY_AURS ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 739C43 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 848254 B_STPHY_EPDR ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 210954 B_STPHY_AURS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, mo, ward [190]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> patient mo ward flag_episode</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <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> 0DBF93 B_STPHY_EPDR Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> F61180 B_ESCHR_COLI ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 351193 B_ESCHR_COLI ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 685398 B_STRPT_GRPB Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 978187 B_STRPT_SLVR ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 743093 B_ENTRBC_CLOC Outpatient TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 725779 B_STRPT_PNMN Outpatient TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> E16523 B_STRPT_EQNS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> F3BD65 B_STRPT_ANGN Outpatient TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 3D2C93 B_STPHY_EPDR ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 190 more rows</span></span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>

2
reference/ggplot_pca.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</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/ggplot_rsi.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="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</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/guess_ab_col.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="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</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/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="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</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">
@ -334,7 +334,7 @@
<code><a href="antibiotics.html">antibiotics</a></code> <code><a href="antibiotics.html">antivirals</a></code>
</dt>
<dd>Data Sets with 566 Antimicrobial Drugs</dd>
<dd>Data Sets with 586 Antimicrobial Drugs</dd>
</dl><dl><dt>
<code><a href="intrinsic_resistant.html">intrinsic_resistant</a></code>

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="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</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
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="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</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/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="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</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/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="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</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="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</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">
@ -167,9 +167,9 @@
<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] 2.943874</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 3.044744</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] 0.05253874</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.001382455</span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>

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="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</small>
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4
reference/mdro.html
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78
reference/mean_amr_distance.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</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">
@ -195,10 +195,10 @@
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">x</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 4 0.5 2 1 0.125 64 0.5 0.125 128 0.125</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.002 0.005 0.025 0.25 16 0.0625 0.125 0.125 0.5 &gt;=128 </span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.4169169 -0.4169169 0.1389723 -0.1389723 -0.9728062 1.5286955</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.4169169 -0.9728062 1.8066401 -0.9728062</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -1.34831284 -1.07713169 -0.60080993 0.08065244 1.31149613 -0.32962879</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.12448818 -0.12448818 0.28579306 1.92691798</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>
@ -208,38 +208,38 @@
<span class="r-in"><span> tobr <span class="op">=</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span>, ab <span class="op">=</span> <span class="st">"tobr"</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span><span class="op">)</span></span></span>
<span class="r-in"><span><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 &gt;=64 0.125 1 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 1 &gt;=2 1 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 8 0.5 4 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 8 0.125 1 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 4 0.5 0.25 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 4 0.5 1 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G &gt;=64 &gt;=2 4 &gt;=8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H &gt;=64 1 1 &lt;=0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I &gt;=64 0.5 1 &lt;=0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 2 0.5 1 1</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 &lt;=8 1 2 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B &lt;=8 0.125 4 &lt;=2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 16 0.25 &gt;=8 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D &lt;=8 0.25 2 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E &lt;=8 0.125 4 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F &lt;=8 0.5 4 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G &lt;=8 2 1 &lt;=2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 16 2 1 &lt;=2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I &lt;=8 0.25 2 &lt;=2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 16 1 2 4</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "id" and "tobr"</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>NAs introduced by coercion</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.119951582 -0.226246173 0.362260603 -0.443032753 -0.436374819</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [6] 0.004040346 1.429997229 0.047588443 -0.134850653 -0.483430641</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.3264577 -0.5360484 1.0429441 -0.3185842 -0.2191155 0.1089935</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.4068767 0.1106725 -0.6355170 0.5270740</span>
<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op">&lt;-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu">where</span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "tobr"</span>
<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 2 0.5 1 1 -0.483430641</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 8 0.125 1 2 -0.443032753</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 4 0.5 0.25 4 -0.436374819</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 1 &gt;=2 1 1 -0.226246173</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I &gt;=64 0.5 1 &lt;=0.5 -0.134850653</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A &gt;=64 0.125 1 2 -0.119951582</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 4 0.5 1 4 0.004040346</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H &gt;=64 1 1 &lt;=0.5 0.047588443</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 8 0.5 4 2 0.362260603</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G &gt;=64 &gt;=2 4 &gt;=8 1.429997229</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I &lt;=8 0.25 2 &lt;=2 -0.6355170</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B &lt;=8 0.125 4 &lt;=2 -0.5360484</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G &lt;=8 2 1 &lt;=2 -0.4068767</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D &lt;=8 0.25 2 4 -0.3185842</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E &lt;=8 0.125 4 4 -0.2191155</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F &lt;=8 0.5 4 4 0.1089935</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 16 2 1 &lt;=2 0.1106725</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A &lt;=8 1 2 8 0.3264577</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 16 1 2 4 0.5270740</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 16 0.25 &gt;=8 8 1.0429441</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="va">y</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@ -251,17 +251,17 @@
<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 8 0.5 4 2 0.362260603 0.0000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 H &gt;=64 1 1 &lt;=0.5 0.047588443 0.3146722</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 F 4 0.5 1 4 0.004040346 0.3582203</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 A &gt;=64 0.125 1 2 -0.119951582 0.4822122</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 I &gt;=64 0.5 1 &lt;=0.5 -0.134850653 0.4971113</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 B 1 &gt;=2 1 1 -0.226246173 0.5885068</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 E 4 0.5 0.25 4 -0.436374819 0.7986354</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 D 8 0.125 1 2 -0.443032753 0.8052934</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 J 2 0.5 1 1 -0.483430641 0.8456912</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 G &gt;=64 &gt;=2 4 &gt;=8 1.429997229 1.0677366</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance check_id_C</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 C 16 0.25 &gt;=8 8 1.0429441 0.0000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 J 16 1 2 4 0.5270740 0.5158701</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 A &lt;=8 1 2 8 0.3264577 0.7164865</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 H 16 2 1 &lt;=2 0.1106725 0.9322716</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 F &lt;=8 0.5 4 4 0.1089935 0.9339507</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 E &lt;=8 0.125 4 4 -0.2191155 1.2620596</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 D &lt;=8 0.25 2 4 -0.3185842 1.3615283</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 G &lt;=8 2 1 &lt;=2 -0.4068767 1.4498208</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 B &lt;=8 0.125 4 &lt;=2 -0.5360484 1.5789925</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 I &lt;=8 0.25 2 &lt;=2 -0.6355170 1.6784611</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
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="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/microorganisms.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/mo_matching_score.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</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">

8
reference/mo_property.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</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">
@ -575,7 +575,7 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Bacteria"</span>
<span class="r-in"><span><span class="fu">mo_kingdom</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span>, language <span class="op">=</span> <span class="st">"zh"</span><span class="op">)</span> <span class="co"># Chinese, no effect</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Bacteria"</span>
<span class="r-in"><span><span class="fu">mo_type</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span>, language <span class="op">=</span> <span class="st">"zh"</span><span class="op">)</span> <span class="co"># Chinese, translated</span></span></span>
<span class="r-in"><span><span class="fu">mo_type</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span>, language <span class="op">=</span> <span class="st">"zh"</span><span class="op">)</span> <span class="co"># Chinese, translated</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "细菌"</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">mo_fullname</span><span class="op">(</span><span class="st">"S. pyogenes"</span>, Lancefield <span class="op">=</span> <span class="cn">TRUE</span>, language <span class="op">=</span> <span class="st">"de"</span><span class="op">)</span></span></span>
@ -592,7 +592,7 @@
<span class="r-in"><span><span class="co"># gram stains and intrinsic resistance can be used as a filter in dplyr verbs</span></span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu">mo_is_gram_positive</span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span></span>
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu">mo_is_gram_positive</span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="fu"><a href="count.html">count</a></span><span class="op">(</span><span class="fu">mo_genus</span><span class="op">(</span><span class="op">)</span>, sort <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Using column 'mo' as input for `mo_is_gram_positive()`</span>
@ -614,7 +614,7 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">12</span> Paenibacillus 1</span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu">mo_is_intrinsic_resistant</span><span class="op">(</span>ab <span class="op">=</span> <span class="st">"vanco"</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span></span>
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu">mo_is_intrinsic_resistant</span><span class="op">(</span>ab <span class="op">=</span> <span class="st">"vanco"</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="fu"><a href="count.html">count</a></span><span class="op">(</span><span class="fu">mo_genus</span><span class="op">(</span><span class="op">)</span>, sort <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Using column 'mo' as input for `mo_is_intrinsic_resistant()`</span>

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="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/pca.html
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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="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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2
reference/plot.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</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">

14
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="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</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">
@ -303,14 +303,16 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class="r-in"><span><span class="fu">rsi_confidence_interval</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.5688204 0.6218738</span>
<span class="r-in"><span><span class="fu">rsi_confidence_interval</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span>,</span></span>
<span class="r-in"><span> confidence_level <span class="op">=</span> <span class="fl">0.975</span><span class="op">)</span></span></span>
<span class="r-in"><span> confidence_level <span class="op">=</span> <span class="fl">0.975</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] 0.5650148 0.6255670</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># determines %S+I:</span></span></span>
<span class="r-in"><span><span class="fu">susceptibility</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.4044444</span>
<span class="r-in"><span><span class="fu">rsi_confidence_interval</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span>,</span></span>
<span class="r-in"><span> ab_result <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">"S"</span>, <span class="st">"I"</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-in"><span> ab_result <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">"S"</span>, <span class="st">"I"</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] 0.3781262 0.4311796</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># be more specific</span></span></span>
@ -328,14 +330,12 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class="r-in"><span><span class="co"># dplyr -------------------------------------------------------------</span></span></span>
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">ward</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span></span></span>
<span class="r-in"><span> r <span class="op">=</span> <span class="fu">resistance</span><span class="op">(</span><span class="va">CIP</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> n <span class="op">=</span> <span class="fu"><a href="count.html">n_rsi</a></span><span class="op">(</span><span class="va">CIP</span><span class="op">)</span></span></span>
<span class="r-in"><span> <span class="op">)</span> <span class="co"># n_rsi works like n_distinct in dplyr, see ?n_rsi</span></span></span>
<span class="r-in"><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: 3 × 3</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward r n</span>
@ -344,7 +344,6 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 0.190 447</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 0.161 93</span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">ward</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span></span></span>
@ -352,7 +351,6 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class="r-in"><span> ci_min <span class="op">=</span> <span class="fu">rsi_confidence_interval</span><span class="op">(</span><span class="va">CIP</span>, side <span class="op">=</span> <span class="st">"min"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> ci_max <span class="op">=</span> <span class="fu">rsi_confidence_interval</span><span class="op">(</span><span class="va">CIP</span>, side <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> <span class="op">)</span></span></span>
<span class="r-in"><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: 3 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward cipro_R ci_min ci_max</span>
@ -370,7 +368,6 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class="r-in"><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="antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> <span class="va">resistance</span></span></span>
<span class="r-in"><span> <span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (tobramycin), 'AMK' (amikacin) and 'KAN' (kanamycin)</span>
@ -384,7 +381,6 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 0.290 0.400 0.662 1 0.086<span style="text-decoration: underline;">2</span> 0.089<span style="text-decoration: underline;">4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 0.2 0.368 0.605 <span style="color: #BB0000;">NA</span> 0.054<span style="text-decoration: underline;">1</span> 0.054<span style="text-decoration: underline;">1</span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">ward</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span></span></span>

33
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="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</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">
@ -178,41 +178,42 @@
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 128 2 0.001 0.01 0.125 0.25 0.125 4 0.125 64 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] &gt;=256 0.0625 2 32 16 0.01 0.001 64 1 32 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 1 &gt;=256 0.5 64 0.5 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.0625 0.125 0.005 0.01 0.125 1 0.5 0.005 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.002 0.25 &lt;=0.001 8 128 8 1 0.002 0.025 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 0.002 0.0625 &gt;=256 128 16 0.125 4 </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] 18 44 40 45 12 48 17 46 17 35 12 9 26 16 42 15 40 44 25 32 49 42 27 40 15</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 42 13 15 41 49 27 45 44 25 40 42 27 12 47 33 46 43 47 8 29 50 30 46 10 47</span>
<span class="r-in"><span><span class="fu">random_rsi</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'rsi'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] R R I I S I I R S I R S S I S R R I R I I S I S S</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] R I S I S S S R I S R I S R I S S S R I I R I 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] 64 &gt;=256 2 0.01 0.025 0.0625 &lt;=0.001 0.125 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.005 0.01 &lt;=0.001 &lt;=0.001 0.5 &lt;=0.001 8 0.125 &lt;=0.001</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 64 0.005 &lt;=0.001 0.005 &lt;=0.001 0.5 0.125 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 128 &lt;=0.001 128 0.002 32 0.025 0.5 2 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.002 0.25 0.005 16 32 8 0.0625 64 0.5 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 0.002 4 0.125 64 16 0.01 0.002 </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] 2 1 64 8 4 8 8 8 1 64 1 1 8 4 64 2 8 2 2 1 64 1 2 4 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.5 16 2 16 4 16 0.5 2 0.25 2 8 4 2 4 0.5 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [16] 4 0.25 0.25 1 1 1 4 2 16 4 </span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"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 &lt;=0.025 0.125 0.25 0.25 2 0.125 &gt;=8 &lt;=0.025</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.25 &gt;=8 2 &gt;=8 1 2 &gt;=8 4 0.5 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 1 0.25 2 0.0625 &gt;=8 0.25 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] &lt;=0.025 1 0.5 0.5 0.0625 0.0625 &lt;=0.025 1 0.5 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] &lt;=0.025 2 2 0.5 4 &lt;=0.025 1 4 0.25 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 0.25 0.0625 4 0.125 2 0.125 0.0625 </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] 32 45 50 29 50 27 46 34 15 47 9 34 47 22 36 34 23 34 33 13 46 11 32 9 24</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 17 10 48 50 9 49 47 33 25 47 24 45 18 10 46 20 48 10 36 48 38 40 28 17 50</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] 14 16 15 13 12 14 12 14 14 12 16 12 12 15 16 12 12 12 16 17 13 17 11 16 15</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 17 13 12 11 16 15 15 16 17 14 14 15 15 16 17 15 15 14 13 13 16 11 17 15 14</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] 15 19 27 21 22 26 20 24 24 23 22 26 19 18 15 19 22 26 26 26 25 21 20 17 23</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 16 17 20 17 20 16 26 19 20 16 18 22 27 24 16 24 26 26 18 20 18 17 16 15 23</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="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</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/rsi_translation.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="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</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="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</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">
@ -166,7 +166,7 @@ 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] 0.03580118</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.008618361</span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>

2
reference/translate.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="">1.8.2.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</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
search.json
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