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@ -36,7 +36,7 @@
<a class="navbar-brand me-2" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9082</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9083</small>
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9082</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9083</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="">1.8.2.9082</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9083</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">
@ -400,71 +400,71 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2013-11-17</td>
<td align="center">D4</td>
<td align="center">2017-09-27</td>
<td align="center">K9</td>
<td align="center">Hospital A</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">Escherichia coli</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2014-12-24</td>
<td align="center">S2</td>
<td align="center">Hospital B</td>
<td align="center">2012-09-19</td>
<td align="center">M7</td>
<td align="center">Hospital A</td>
<td align="center">Streptococcus pneumoniae</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="odd">
<td align="center">2010-01-21</td>
<td align="center">Q3</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2016-11-24</td>
<td align="center">N1</td>
<td align="center">Hospital D</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">2014-08-31</td>
<td align="center">Q4</td>
<td align="center">2016-07-29</td>
<td align="center">J7</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2012-08-04</td>
<td align="center">N10</td>
<td align="center">Hospital B</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2016-03-16</td>
<td align="center">D5</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">2016-06-19</td>
<td align="center">E7</td>
<td align="center">Hospital C</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">2016-10-07</td>
<td align="center">O7</td>
<td align="center">Hospital D</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
</tbody>
</table>
<p>Now, let’s start the cleaning and the analysis!</p>
@ -499,16 +499,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,466</td>
<td align="right">52.33%</td>
<td align="right">10,466</td>
<td align="right">52.33%</td>
<td align="right">10,357</td>
<td align="right">51.79%</td>
<td align="right">10,357</td>
<td align="right">51.79%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,534</td>
<td align="right">47.67%</td>
<td align="right">9,643</td>
<td align="right">48.22%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -621,9 +621,9 @@ takes into account the antimicrobial susceptibility test results using
<span><span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span></span>
<span><span class="co"># 2</span></span>
<span><span class="co"># Including isolates from ICU.</span></span>
<span><span class="co"># =&gt; Found 10,633 'phenotype-based' first isolates (53.2% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,726 'phenotype-based' first isolates (53.6% 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 53.6% 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">
@ -634,7 +634,7 @@ 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 10,633 isolates for analysis. Now our data looks
<p>So we end up with 10,726 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>
@ -673,14 +673,14 @@ like:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2013-11-17</td>
<td align="center">D4</td>
<td align="left">2</td>
<td align="center">2012-09-19</td>
<td align="center">M7</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
@ -689,29 +689,13 @@ like:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="center">2014-12-24</td>
<td align="center">S2</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="center">2016-03-16</td>
<td align="center">D5</td>
<td align="left">4</td>
<td align="center">2016-11-24</td>
<td align="center">N1</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
@ -720,42 +704,10 @@ like:</p>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">7</td>
<td align="center">2011-09-05</td>
<td align="center">Z1</td>
<td align="center">Hospital C</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">8</td>
<td align="center">2015-09-14</td>
<td align="center">B4</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="even">
<td align="left">9</td>
<td align="center">2013-09-14</td>
<td align="center">G4</td>
<td align="left">10</td>
<td align="center">2013-06-30</td>
<td align="center">M8</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
@ -768,6 +720,54 @@ like:</p>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">11</td>
<td align="center">2017-03-10</td>
<td align="center">N8</td>
<td align="center">Hospital A</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="odd">
<td align="left">12</td>
<td align="center">2016-12-09</td>
<td align="center">T3</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">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">14</td>
<td align="center">2014-04-02</td>
<td align="center">I2</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">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
<p>Time for the analysis!</p>
@ -801,8 +801,8 @@ readable:</p>
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://msberends.github.io/cleaner/reference/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></span></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 10,633<br>
Available: 10,633 (100%, NA: 0 = 0%)<br>
Length: 10,726<br>
Available: 10,726 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -827,33 +827,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">4,608</td>
<td align="right">43.34%</td>
<td align="right">4,608</td>
<td align="right">43.34%</td>
<td align="right">4,697</td>
<td align="right">43.79%</td>
<td align="right">4,697</td>
<td align="right">43.79%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,724</td>
<td align="right">25.62%</td>
<td align="right">7,332</td>
<td align="right">68.96%</td>
<td align="right">2,746</td>
<td align="right">25.60%</td>
<td align="right">7,443</td>
<td align="right">69.39%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,080</td>
<td align="right">19.56%</td>
<td align="right">9,412</td>
<td align="right">88.52%</td>
<td align="right">2,106</td>
<td align="right">19.63%</td>
<td align="right">9,549</td>
<td align="right">89.03%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,221</td>
<td align="right">11.48%</td>
<td align="right">10,633</td>
<td align="right">1,177</td>
<td align="right">10.97%</td>
<td align="right">10,726</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -874,14 +874,14 @@ antibiotic class they are in:</p>
<col width="9%">
<col width="9%">
<col width="9%">
<col width="11%">
<col width="10%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="6%">
<col width="11%">
<col width="11%">
<col width="12%">
<col width="9%">
<col width="5%">
</colgroup>
@ -902,13 +902,13 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2013-11-17</td>
<td align="center">D4</td>
<td align="center">2012-09-19</td>
<td align="center">M7</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
@ -917,39 +917,69 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2014-12-24</td>
<td align="center">S2</td>
<td align="center">Hospital B</td>
<td align="center">2010-02-14</td>
<td align="center">B5</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">F</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2015-09-14</td>
<td align="center">B4</td>
<td align="center">2016-09-23</td>
<td align="center">O10</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2015-05-01</td>
<td align="center">W1</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2017-08-13</td>
<td align="center">I9</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2011-02-25</td>
<td align="center">P4</td>
<td align="center">Hospital C</td>
<td align="center">2014-05-21</td>
<td align="center">O10</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
@ -961,36 +991,6 @@ antibiotic class they are in:</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2015-04-27</td>
<td align="center">C10</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">R</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2011-03-11</td>
<td align="center">J4</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
<p>If you want to get a quick glance of the number of isolates in
@ -1013,50 +1013,50 @@ 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">2140</td>
<td align="center">128</td>
<td align="center">2340</td>
<td align="center">4608</td>
<td align="center">2194</td>
<td align="center">130</td>
<td align="center">2373</td>
<td align="center">4697</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3336</td>
<td align="center">178</td>
<td align="center">1094</td>
<td align="center">4608</td>
<td align="center">3459</td>
<td align="center">180</td>
<td align="center">1058</td>
<td align="center">4697</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3373</td>
<td align="center">3421</td>
<td align="center">0</td>
<td align="center">1235</td>
<td align="center">4608</td>
<td align="center">1276</td>
<td align="center">4697</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4042</td>
<td align="center">4111</td>
<td align="center">0</td>
<td align="center">566</td>
<td align="center">4608</td>
<td align="center">586</td>
<td align="center">4697</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">1221</td>
<td align="center">1221</td>
<td align="center">1177</td>
<td align="center">1177</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">951</td>
<td align="center">51</td>
<td align="center">219</td>
<td align="center">1221</td>
<td align="center">938</td>
<td align="center">48</td>
<td align="center">191</td>
<td align="center">1177</td>
</tr>
</tbody>
</table>
@ -1078,34 +1078,34 @@ 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">4042</td>
<td align="center">4111</td>
<td align="center">0</td>
<td align="center">566</td>
<td align="center">4608</td>
<td align="center">586</td>
<td align="center">4697</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1121</td>
<td align="center">1045</td>
<td align="center">0</td>
<td align="center">100</td>
<td align="center">1221</td>
<td align="center">132</td>
<td align="center">1177</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2432</td>
<td align="center">2430</td>
<td align="center">0</td>
<td align="center">292</td>
<td align="center">2724</td>
<td align="center">316</td>
<td align="center">2746</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">2080</td>
<td align="center">2080</td>
<td align="center">2106</td>
<td align="center">2106</td>
</tr>
</tbody>
</table>
@ -1137,7 +1137,7 @@ I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equa
own:</p>
<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span></span>
<span><span class="co"># [1] 0.5483871</span></span></code></pre></div>
<span><span class="co"># [1] 0.5466157</span></span></code></pre></div>
<p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and
<code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
@ -1152,19 +1152,19 @@ own:</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5436433</td>
<td align="center">0.5586592</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5441137</td>
<td align="center">0.5431104</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5588420</td>
<td align="center">0.5266836</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5550395</td>
<td align="center">0.5491618</td>
</tr>
</tbody>
</table>
@ -1189,23 +1189,23 @@ 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">0.5436433</td>
<td align="center">3162</td>
<td align="center">0.5586592</td>
<td align="center">3222</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5441137</td>
<td align="center">3729</td>
<td align="center">0.5431104</td>
<td align="center">3723</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5588420</td>
<td align="center">1589</td>
<td align="center">0.5266836</td>
<td align="center">1574</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5550395</td>
<td align="center">2153</td>
<td align="center">0.5491618</td>
<td align="center">2207</td>
</tr>
</tbody>
</table>
@ -1230,27 +1230,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7625868</td>
<td align="center">0.8771701</td>
<td align="center">0.9743924</td>
<td align="center">0.7747498</td>
<td align="center">0.8752395</td>
<td align="center">0.9774324</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8206388</td>
<td align="center">0.9180999</td>
<td align="center">0.9844390</td>
<td align="center">0.8377230</td>
<td align="center">0.8878505</td>
<td align="center">0.9770603</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7830396</td>
<td align="center">0.8928047</td>
<td align="center">0.9805433</td>
<td align="center">0.7760379</td>
<td align="center">0.8849235</td>
<td align="center">0.9756009</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5447115</td>
<td align="center">0.5394112</td>
<td align="center">0.0000000</td>
<td align="center">0.5447115</td>
<td align="center">0.5394112</td>
</tr>
</tbody>
</table>
@ -1278,23 +1278,23 @@ classes, use a antibiotic class selector such as
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">54.4%</td>
<td align="right">25.9%</td>
<td align="right">55.9%</td>
<td align="right">26.0%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">54.4%</td>
<td align="right">27.1%</td>
<td align="right">54.3%</td>
<td align="right">25.9%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">55.9%</td>
<td align="right">28.1%</td>
<td align="right">52.7%</td>
<td align="right">25.9%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">55.5%</td>
<td align="right">26.6%</td>
<td align="right">54.9%</td>
<td align="right">28.3%</td>
</tr>
</tbody>
</table>
@ -1410,16 +1410,18 @@ classes) <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code>:</p>
<code class="sourceCode R"><span><span class="va">mic_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span></span>
<span><span class="va">mic_values</span></span>
<span><span class="co"># Class 'mic'</span></span>
<span><span class="co"># [1] 0.025 2 128 0.0625 0.005 16 0.125 0.5 0.5 64 </span></span>
<span><span class="co"># [11] 0.002 0.025 16 0.0625 2 2 1 0.01 4 0.002 </span></span>
<span><span class="co"># [21] 128 1 0.025 64 128 16 0.01 0.002 2 0.5 </span></span>
<span><span class="co"># [31] 2 8 0.125 0.125 0.005 0.001 0.01 2 0.0625 4 </span></span>
<span><span class="co"># [41] 0.01 32 0.01 32 32 0.25 1 0.25 64 0.5 </span></span>
<span><span class="co"># [51] 2 128 0.005 1 0.0625 64 0.125 1 0.5 0.5 </span></span>
<span><span class="co"># [61] 0.5 2 0.125 256 128 16 64 0.25 2 0.01 </span></span>
<span><span class="co"># [71] 0.025 0.125 0.005 16 1 8 0.001 0.125 32 256 </span></span>
<span><span class="co"># [81] 0.5 16 0.005 4 1 16 256 8 0.25 0.01 </span></span>
<span><span class="co"># [91] 0.5 16 0.002 32 128 16 1 0.001 16 32</span></span></code></pre></div>
<span><span class="co"># [1] 0.0625 0.005 16 0.005 0.0625 8 1 0.25 0.01 </span></span>
<span><span class="co"># [10] &gt;=256 0.01 0.0625 0.0625 128 0.025 0.01 1 4 </span></span>
<span><span class="co"># [19] 0.01 128 0.125 0.025 16 &lt;=0.001 &lt;=0.001 8 0.125 </span></span>
<span><span class="co"># [28] 0.25 0.25 0.125 0.025 0.01 0.0625 16 0.002 8 </span></span>
<span><span class="co"># [37] 2 128 128 &lt;=0.001 0.0625 0.125 0.002 &lt;=0.001 0.025 </span></span>
<span><span class="co"># [46] 0.5 0.0625 128 0.5 64 0.5 0.005 0.5 16 </span></span>
<span><span class="co"># [55] 0.125 0.002 0.5 2 &gt;=256 &gt;=256 0.125 64 0.005 </span></span>
<span><span class="co"># [64] 64 32 16 4 16 8 8 0.125 0.5 </span></span>
<span><span class="co"># [73] 32 0.025 1 64 1 0.125 0.125 0.025 32 </span></span>
<span><span class="co"># [82] 64 0.01 0.25 2 0.125 0.0625 8 2 0.01 </span></span>
<span><span class="co"># [91] 64 0.005 8 0.25 0.125 8 128 0.5 &lt;=0.001</span></span>
<span><span class="co"># [100] 0.0625</span></span></code></pre></div>
<div class="sourceCode" id="cb36"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">mic_values</span><span class="op">)</span></span></code></pre></div>
@ -1453,10 +1455,10 @@ plotting:</p>
<code class="sourceCode R"><span><span class="va">disk_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_disk</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span>
<span><span class="va">disk_values</span></span>
<span><span class="co"># Class 'disk'</span></span>
<span><span class="co"># [1] 21 18 31 26 31 22 21 22 22 27 21 28 24 29 30 27 31 22 30 31 25 29 30 22 22</span></span>
<span><span class="co"># [26] 20 29 18 31 28 18 19 18 25 30 28 25 20 22 20 17 20 21 24 19 23 25 19 30 30</span></span>
<span><span class="co"># [51] 23 24 23 17 17 17 25 24 26 17 24 19 31 27 24 21 27 21 25 31 22 24 22 19 24</span></span>
<span><span class="co"># [76] 23 24 18 29 24 21 28 19 26 23 24 18 20 31 31 26 19 24 17 18 27 25 26 28 25</span></span></code></pre></div>
<span><span class="co"># [1] 27 19 29 18 21 24 23 21 17 28 17 27 23 22 23 18 30 30 22 24 22 22 20 26 17</span></span>
<span><span class="co"># [26] 17 29 22 23 19 24 28 27 28 17 17 27 28 17 23 28 18 28 23 21 22 22 19 29 27</span></span>
<span><span class="co"># [51] 17 18 22 22 24 19 30 24 31 29 26 17 28 26 27 17 17 27 22 20 28 25 17 20 30</span></span>
<span><span class="co"># [76] 25 31 25 28 27 27 20 31 25 23 24 22 20 18 26 29 18 25 31 20 22 26 29 20 31</span></span></code></pre></div>
<div class="sourceCode" id="cb42"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">disk_values</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></code></pre></div>

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2
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="">1.8.2.9082</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9083</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

58
articles/MDR.html
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9082</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9083</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">
@ -375,18 +375,18 @@ names or codes, this would have worked exactly the same way:</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span>
<span><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
<span><span class="co"># 1 I S I S R S</span></span>
<span><span class="co"># 2 S S R S R S</span></span>
<span><span class="co"># 3 I R S I R I</span></span>
<span><span class="co"># 4 R R S S R S</span></span>
<span><span class="co"># 5 S R R S I R</span></span>
<span><span class="co"># 6 I I I S I I</span></span>
<span><span class="co"># 1 R S R S I S</span></span>
<span><span class="co"># 2 R S S S I R</span></span>
<span><span class="co"># 3 R R R S I S</span></span>
<span><span class="co"># 4 S S I S I R</span></span>
<span><span class="co"># 5 R S I I R R</span></span>
<span><span class="co"># 6 R R S I S S</span></span>
<span><span class="co"># kanamycin</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 R</span></span>
<span><span class="co"># 5 R</span></span>
<span><span class="co"># 2 R</span></span>
<span><span class="co"># 3 S</span></span>
<span><span class="co"># 4 S</span></span>
<span><span class="co"># 5 S</span></span>
<span><span class="co"># 6 R</span></span></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can
use:</p>
@ -428,40 +428,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3194</td>
<td align="right">63.88%</td>
<td align="right">3194</td>
<td align="right">63.88%</td>
<td align="right">3249</td>
<td align="right">64.98%</td>
<td align="right">3249</td>
<td align="right">64.98%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">983</td>
<td align="right">19.66%</td>
<td align="right">4177</td>
<td align="right">83.54%</td>
<td align="right">936</td>
<td align="right">18.72%</td>
<td align="right">4185</td>
<td align="right">83.70%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">492</td>
<td align="right">9.84%</td>
<td align="right">4669</td>
<td align="right">93.38%</td>
<td align="right">465</td>
<td align="right">9.30%</td>
<td align="right">4650</td>
<td align="right">93.00%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">235</td>
<td align="right">4.70%</td>
<td align="right">4904</td>
<td align="right">98.08%</td>
<td align="right">249</td>
<td align="right">4.98%</td>
<td align="right">4899</td>
<td align="right">97.98%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">96</td>
<td align="right">1.92%</td>
<td align="right">101</td>
<td align="right">2.02%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

2
articles/PCA.html
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9082</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9083</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
articles/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="">1.8.2.9082</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9083</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
articles/WHONET.html
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9082</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9083</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
articles/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="">1.8.2.9082</small>
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9082</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="">1.8.2.9082</small>
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9082</small>
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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="">1.8.2.9082</small>
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9082</small>
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@ -132,7 +132,7 @@
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="1.8.2.9082" id="amr-1829082">AMR 1.8.2.9082<a class="anchor" aria-label="anchor" href="#amr-1829082"></a></h2>
<h2 class="pkg-version" data-toc-text="1.8.2.9083" id="amr-1829083">AMR 1.8.2.9083<a class="anchor" aria-label="anchor" href="#amr-1829083"></a></h2>
<p><em>(this beta version will eventually become v2.0! We’re happy to reach a new major milestone soon!)</em></p>
<p>This is a new major release of the AMR package, with great new additions but also some breaking changes for current users. These are all listed below.</p>
<p><strong><a href="https://en.wikipedia.org/wiki/TL;DR" class="external-link">TL;DR</a></strong></p>
@ -145,19 +145,19 @@
<li>Many new interesting functions, such as <code><a href="../reference/proportion.html">rsi_confidence_interval()</a></code> and <code><a href="../reference/mean_amr_distance.html">mean_amr_distance()</a></code>, and <code><a href="../reference/add_custom_microorganisms.html">add_custom_microorganisms()</a></code> to add custom microorganisms to this package</li>
<li>Many small bug fixes</li>
</ul><div class="section level3">
<h3 id="new-1-8-2-9082">New<a class="anchor" aria-label="anchor" href="#new-1-8-2-9082"></a></h3>
<h3 id="new-1-8-2-9083">New<a class="anchor" aria-label="anchor" href="#new-1-8-2-9083"></a></h3>
<div class="section level4">
<h4 id="interpretation-of-mic-and-disk-diffusion-values-1-8-2-9082">Interpretation of MIC and disk diffusion values<a class="anchor" aria-label="anchor" href="#interpretation-of-mic-and-disk-diffusion-values-1-8-2-9082"></a></h4>
<h4 id="interpretation-of-mic-and-disk-diffusion-values-1-8-2-9083">Interpretation of MIC and disk diffusion values<a class="anchor" aria-label="anchor" href="#interpretation-of-mic-and-disk-diffusion-values-1-8-2-9083"></a></h4>
<p>The clinical breakpoints and intrinsic resistance of EUCAST 2022 and CLSI 2022 have been added for <code><a href="../reference/as.rsi.html">as.rsi()</a></code>. EUCAST 2022 (v12.0) is now the new default guideline for all MIC and disks diffusion interpretations, and for <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> to apply EUCAST Expert Rules. The default guideline (EUCAST) can now be changed with the new <code>AMR_guideline</code> option, such as: <code>options(AMR_guideline = "CLSI 2020")</code>.</p>
<p>Interpretation guidelines older than 10 years were removed, the oldest now included guidelines of EUCAST and CLSI are from 2013.</p>
</div>
<div class="section level4">
<h4 id="supported-languages-1-8-2-9082">Supported languages<a class="anchor" aria-label="anchor" href="#supported-languages-1-8-2-9082"></a></h4>
<h4 id="supported-languages-1-8-2-9083">Supported languages<a class="anchor" aria-label="anchor" href="#supported-languages-1-8-2-9083"></a></h4>
<p>We added support for the following languages: Chinese, Greek, Japanese, Polish, Turkish and Ukrainian. All antibiotic names are now available in these languages, and the AMR package will automatically determine a supported language based on the user system language.</p>
<p>We are very grateful for the valuable input by our colleagues from other countries. The <code>AMR</code> package is now available in 16 languages and according to download stats used in almost all countries in the world!</p>
</div>
<div class="section level4">
<h4 id="microbiological-taxonomy-1-8-2-9082">Microbiological taxonomy<a class="anchor" aria-label="anchor" href="#microbiological-taxonomy-1-8-2-9082"></a></h4>
<h4 id="microbiological-taxonomy-1-8-2-9083">Microbiological taxonomy<a class="anchor" aria-label="anchor" href="#microbiological-taxonomy-1-8-2-9083"></a></h4>
<p>The <code>microorganisms</code> data set no longer relies on the Catalogue of Life, but on the List of Prokaryotic names with Standing in Nomenclature (LPSN) and is supplemented with the ‘backbone taxonomy’ from the Global Biodiversity Information Facility (GBIF). The structure of this data set has changed to include separate LPSN and GBIF identifiers. Almost all previous MO codes were retained. It contains over 1,400 taxonomic names from 2022.</p>
<p>We previously relied on our own experience to categorise species into pathogenic groups, but we were very happy to encounter the very recent work of Bartlett <em>et al.</em> (2022, DOI <a href="https://doi.org/10.1099/mic.0.001269" class="external-link">10.1099/mic.0.001269</a>) who extensively studied medical-scientific literature to categorise all bacterial species into groups. See <code><a href="../reference/mo_matching_score.html">mo_matching_score()</a></code> on how their work was incorporated into the <code>prevalence</code> column of the <code>microorganisms</code> data set. Using their results, the <code><a href="../reference/as.mo.html">as.mo()</a></code> and all <code>mo_*()</code> functions are now much better capable of converting user input to valid taxonomic records.</p>
<p>The new function <code><a href="../reference/add_custom_microorganisms.html">add_custom_microorganisms()</a></code> allows users to add custom microorganisms to the <code>AMR</code> package.</p>
@ -181,7 +181,7 @@
<li>The <code>microorganisms.old</code> data set was removed, and all previously accepted names are now included in the <code>microorganisms</code> data set. A new column <code>status</code> contains <code>"accepted"</code> for currently accepted names and <code>"synonym"</code> for taxonomic synonyms; currently invalid names. All previously accepted names now have a microorganisms ID and - if available - an LPSN, GBIF and SNOMED CT identifier.</li>
</ul></div>
<div class="section level4">
<h4 id="antibiotic-agents-and-selectors-1-8-2-9082">Antibiotic agents and selectors<a class="anchor" aria-label="anchor" href="#antibiotic-agents-and-selectors-1-8-2-9082"></a></h4>
<h4 id="antibiotic-agents-and-selectors-1-8-2-9083">Antibiotic agents and selectors<a class="anchor" aria-label="anchor" href="#antibiotic-agents-and-selectors-1-8-2-9083"></a></h4>
<p>The new function <code><a href="../reference/add_custom_antimicrobials.html">add_custom_antimicrobials()</a></code> allows users to add custom antimicrobial codes and names to the <code>AMR</code> package.</p>
<p>The <code>antibiotics</code> data set was greatly updated:</p>
<ul><li>The following 20 antibiotics have been added (also includes the <a href="https://www.whocc.no/atc_ddd_index/?code=J01RA&amp;showdescription=no" class="external-link">new J01RA ATC group</a>): azithromycin/fluconazole/secnidazole (AFC), cefepime/amikacin (CFA), cefixime/ornidazole (CEO), ceftriaxone/beta-lactamase inhibitor (CEB), ciprofloxacin/metronidazole (CIM), ciprofloxacin/ornidazole (CIO), ciprofloxacin/tinidazole (CIT), furazidin (FUR), isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST), lascufloxacin (LSC), levofloxacin/ornidazole (LEO), nemonoxacin (NEM), norfloxacin/metronidazole (NME), norfloxacin/tinidazole (NTI), ofloxacin/ornidazole (OOR), oteseconazole (OTE), rifampicin/ethambutol/isoniazid (REI), sarecycline (SRC), tetracycline/oleandomycin (TOL), and thioacetazone (TAT)</li>
@ -193,14 +193,14 @@
</ul><p>Also, we added support for using antibiotic selectors in scoped <code>dplyr</code> verbs (with or without using <code><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars()</a></code>), such as in: <code>... %&gt;% summarise_at(aminoglycosides(), resistance)</code>, please see <code><a href="../reference/proportion.html">resistance()</a></code> for examples.</p>
</div>
<div class="section level4">
<h4 id="antiviral-agents-1-8-2-9082">Antiviral agents<a class="anchor" aria-label="anchor" href="#antiviral-agents-1-8-2-9082"></a></h4>
<h4 id="antiviral-agents-1-8-2-9083">Antiviral agents<a class="anchor" aria-label="anchor" href="#antiviral-agents-1-8-2-9083"></a></h4>
<p>We now added extensive support for antiviral agents! For the first time, the <code>AMR</code> package has extensive support for antiviral drugs and to work with their names, codes and other data in any way.</p>
<ul><li>The <code>antivirals</code> data set has been extended with 18 new drugs (also from the <a href="https://www.whocc.no/atc_ddd_index/?code=J05AJ&amp;showdescription=no" class="external-link">new J05AJ ATC group</a>) and now also contains antiviral identifiers and LOINC codes</li>
<li>A new data type <code>av</code> (<em>antivirals</em>) has been added, which is functionally similar to <code>ab</code> for antibiotics</li>
<li>Functions <code><a href="../reference/as.av.html">as.av()</a></code>, <code><a href="../reference/av_property.html">av_name()</a></code>, <code><a href="../reference/av_property.html">av_atc()</a></code>, <code><a href="../reference/av_property.html">av_synonyms()</a></code>, <code><a href="../reference/av_from_text.html">av_from_text()</a></code> have all been added as siblings to their <code>ab_*()</code> equivalents</li>
</ul></div>
<div class="section level4">
<h4 id="other-new-functions-1-8-2-9082">Other new functions<a class="anchor" aria-label="anchor" href="#other-new-functions-1-8-2-9082"></a></h4>
<h4 id="other-new-functions-1-8-2-9083">Other new functions<a class="anchor" aria-label="anchor" href="#other-new-functions-1-8-2-9083"></a></h4>
<ul><li>Function <code><a href="../reference/proportion.html">rsi_confidence_interval()</a></code> to add confidence intervals in AMR calculation. This is now also included in <code><a href="../reference/proportion.html">rsi_df()</a></code> and <code><a href="../reference/proportion.html">proportion_df()</a></code>.</li>
<li>Function <code><a href="../reference/mean_amr_distance.html">mean_amr_distance()</a></code> to calculate the mean AMR distance. The mean AMR distance is a normalised numeric value to compare AMR test results and can help to identify similar isolates, without comparing antibiograms by hand.</li>
<li>Function <code><a href="../reference/as.rsi.html">rsi_interpretation_history()</a></code> to view the history of previous runs of <code><a href="../reference/as.rsi.html">as.rsi()</a></code>. This returns a ‘logbook’ with the selected guideline, reference table and specific interpretation of each row in a data set on which <code><a href="../reference/as.rsi.html">as.rsi()</a></code> was run.</li>
@ -209,7 +209,7 @@
</ul></div>
</div>
<div class="section level3">
<h3 id="changes-1-8-2-9082">Changes<a class="anchor" aria-label="anchor" href="#changes-1-8-2-9082"></a></h3>
<h3 id="changes-1-8-2-9083">Changes<a class="anchor" aria-label="anchor" href="#changes-1-8-2-9083"></a></h3>
<ul><li>Argument <code>combine_IR</code> has been removed from this package (affecting functions <code><a href="../reference/count.html">count_df()</a></code>, <code><a href="../reference/proportion.html">proportion_df()</a></code>, and <code><a href="../reference/proportion.html">rsi_df()</a></code> and some plotting functions), since it was replaced with <code>combine_SI</code> three years ago</li>
<li>Using <code>units</code> in <code>ab_ddd(..., units = "...")</code> had been deprecated for some time and is now not supported anymore. Use <code><a href="../reference/ab_property.html">ab_ddd_units()</a></code> instead.</li>
<li>Support for <code>data.frame</code>-enhancing R packages, more specifically: <code><a href="https://Rdatatable.gitlab.io/data.table/reference/data.table.html" class="external-link">data.table::data.table</a></code>, <code><a href="https://rdrr.io/pkg/janitor/man/tabyl.html" class="external-link">janitor::tabyl</a></code>, <code><a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble::tibble</a></code>, and <code><a href="https://tsibble.tidyverts.org/reference/tsibble.html" class="external-link">tsibble::tsibble</a></code>. AMR package functions that have a data set as output (such as <code><a href="../reference/proportion.html">rsi_df()</a></code> and <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code>), will now return the same data type as the input.</li>
@ -248,7 +248,7 @@
<li>Cleaning columns with <code><a href="../reference/as.rsi.html">as.rsi()</a></code>, <code><a href="../reference/as.mic.html">as.mic()</a></code>, or <code><a href="../reference/as.disk.html">as.disk()</a></code> will now show the column name in the warning for invalid results</li>
</ul></div>
<div class="section level3">
<h3 id="other-1-8-2-9082">Other<a class="anchor" aria-label="anchor" href="#other-1-8-2-9082"></a></h3>
<h3 id="other-1-8-2-9083">Other<a class="anchor" aria-label="anchor" href="#other-1-8-2-9083"></a></h3>
<ul><li>New website to make use of the new Bootstrap 5 and pkgdown 2.0. The website now contains results for all examples and will be automatically regenerated with every change to our repository, using GitHub Actions</li>
<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
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@ -11,7 +11,7 @@ articles:
datasets: datasets.html
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
last_built: 2023-01-06T09:12Z
last_built: 2023-01-06T10:25Z
urls:
reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles

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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9082</small>
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@ -62,7 +62,7 @@ Principal component analysis for AMR
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -10,7 +10,7 @@
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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reference/add_custom_antimicrobials.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9082</small>
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9082</small>
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9082</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9083</small>
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@ -195,16 +195,16 @@
<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 1938-11-04 84 84.17260 61</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1943-11-30 79 79.10137 56</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1974-01-26 48 48.94521 25</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1979-09-12 43 43.31781 20</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1974-05-22 48 48.62740 25</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1946-11-24 76 76.11781 53</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1983-12-25 39 39.03288 16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1952-07-07 70 70.50137 47</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1972-03-28 50 50.77808 27</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1995-07-31 27 27.43562 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1998-12-26 24 24.03014 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1963-01-07 59 59.99726 36</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1946-08-28 76 76.35890 53</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1940-02-07 82 82.91233 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1983-07-22 39 39.46027 16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1938-09-09 84 84.32603 61</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1982-06-27 40 40.52877 17</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1981-11-26 41 41.11233 18</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1976-03-08 46 46.83288 23</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1994-03-10 28 28.82740 5</span>
</code></pre></div>
</div>
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -10,7 +10,7 @@
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@ -506,16 +506,16 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 50 × 12</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index ab_input ab_gu…¹ mo_in…² mo_guideline guide…³</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2023-01-06 <span style="color: #949494;">09:13:06</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> 2023-01-06 <span style="color: #949494;">09:13:07</span> 1 AMP AMP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2023-01-06 <span style="color: #949494;">09:13:07</span> 1 CIP CIP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2023-01-06 <span style="color: #949494;">09:13:07</span> 1 GEN GEN Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2023-01-06 <span style="color: #949494;">09:13:08</span> 1 TOB TOB Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2023-01-06 <span style="color: #949494;">09:13:09</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> 2023-01-06 <span style="color: #949494;">09:13:09</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> 2023-01-06 <span style="color: #949494;">09:13:09</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> 2023-01-06 <span style="color: #949494;">09:13:09</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> 2023-01-06 <span style="color: #949494;">09:13:09</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> 2023-01-06 <span style="color: #949494;">10:26:04</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> 2023-01-06 <span style="color: #949494;">10:26:04</span> 1 AMP AMP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2023-01-06 <span style="color: #949494;">10:26:05</span> 1 CIP CIP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2023-01-06 <span style="color: #949494;">10:26:05</span> 1 GEN GEN Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2023-01-06 <span style="color: #949494;">10:26:06</span> 1 TOB TOB Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2023-01-06 <span style="color: #949494;">10:26:07</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> 2023-01-06 <span style="color: #949494;">10:26:07</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> 2023-01-06 <span style="color: #949494;">10:26:07</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> 2023-01-06 <span style="color: #949494;">10:26:07</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> 2023-01-06 <span style="color: #949494;">10:26:07</span> 4 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 40 more rows, 5 more variables: ref_table &lt;chr&gt;, method &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># input &lt;dbl&gt;, outcome &lt;rsi&gt;, breakpoint_S_R &lt;chr&gt;, and abbreviated variable</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># names ¹​ab_guideline, ²​mo_input, ³​guideline</span></span>

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>
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@ -10,7 +10,7 @@
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@ -10,7 +10,7 @@
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@ -12,7 +12,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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@ -10,7 +10,7 @@
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@ -10,7 +10,7 @@
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@ -12,7 +12,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
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@ -10,7 +10,7 @@
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@ -10,7 +10,7 @@
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@ -12,7 +12,7 @@
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2
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@ -10,7 +10,7 @@
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135
reference/get_episode.html
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@ -10,7 +10,7 @@
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@ -182,44 +182,39 @@
<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] 38 61 52 31 46 25 45 60 7 31 63 47 7 10 31 45 9 33 6 14 36 25 14 59 36</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 51 63 8 27 7 47 58 47 22 43 24 12 33 13 38 19 44 34 22 16 63 62 60 23 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 56 59 52 7 6 57 26 15 18 58 33 19 52 28 9 43 48 60 55 43 40 57 54 49 51</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 5 16 27 46 4 44 52 18 44 9 43 25 18 8 9 48 40 26 48 17 27 59 9 13 36</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [101] 63 24 45 55 1 15 2 56 34 54 32 5 14 2 23 37 60 2 22 53 3 32 50 63 42</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [126] 58 35 10 26 10 17 13 3 59 3 41 48 30 50 1 6 10 37 50 40 2 39 47 5 51</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [151] 9 60 8 40 3 62 21 2 7 3 30 4 30 26 14 41 48 13 29 22 31 5 11 38 56</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [176] 56 58 11 56 39 9 40 60 32 39 52 37 4 1 59 20 18 2 24 61 21 28 3 54 62</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 60 32 64 53 16 36 44 56 18 28 21 26 16 25 28 61 21 23 43 13 34 13 43 44 47</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 55 65 65 19 65 7 41 20 49 53 19 44 57 33 51 6 33 22 32 36 46 62 55 38 56</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 59 7 25 63 36 29 10 13 31 27 28 54 11 25 31 17 59 48 23 30 54 36 27 63 24</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 9 25 11 17 50 41 49 56 27 21 12 48 37 48 5 15 18 20 22 11 41 12 43 43 13</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [101] 49 39 55 20 10 64 43 50 14 43 47 60 40 26 32 3 41 26 59 35 44 61 24 18 42</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [126] 36 41 41 54 1 1 53 8 29 45 2 59 60 48 53 35 30 41 63 58 46 18 53 61 9</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [151] 30 10 14 4 7 62 62 39 30 27 54 29 24 60 40 41 63 6 42 21 25 23 19 15 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [176] 8 54 36 11 43 10 33 56 30 2 45 23 1 57 64 65 22 31 35 10 25 15 2 34 53</span>
<span class="r-in"><span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># TRUE/FALSE</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] FALSE TRUE FALSE TRUE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] TRUE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] FALSE TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] TRUE TRUE TRUE FALSE TRUE FALSE TRUE TRUE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] FALSE FALSE FALSE TRUE TRUE FALSE FALSE TRUE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] TRUE FALSE FALSE TRUE FALSE TRUE FALSE TRUE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [109] TRUE FALSE FALSE FALSE FALSE FALSE TRUE TRUE TRUE TRUE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [121] FALSE TRUE FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [133] FALSE FALSE TRUE TRUE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [145] FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [157] TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [169] TRUE FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [181] TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [193] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] FALSE TRUE FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] TRUE FALSE TRUE TRUE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] TRUE FALSE TRUE FALSE FALSE TRUE FALSE TRUE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] FALSE FALSE TRUE TRUE FALSE TRUE FALSE FALSE TRUE FALSE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] FALSE FALSE FALSE TRUE TRUE TRUE FALSE TRUE TRUE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] TRUE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [109] TRUE FALSE TRUE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [121] FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [133] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [145] TRUE TRUE FALSE TRUE TRUE FALSE FALSE TRUE FALSE TRUE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [157] FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [169] FALSE TRUE FALSE FALSE FALSE TRUE TRUE TRUE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [181] FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE TRUE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [193] FALSE FALSE FALSE TRUE FALSE TRUE TRUE FALSE</span>
<span class="r-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: 6 × 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> 2002-07-28 F54261 69 M Clinical B_STPHY_CONS R NA S NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</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;">3</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;">4</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;">5</span> 2002-07-30 218912 76 F ICU B_ESCHR_COLI R NA NA NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">6</span> 2002-07-15 426426 67 F ICU B_ESCHR_COLI R NA NA NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># 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> 2002-08-14 785317 51 F ICU B_ESCHR_COLI R NA NA NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 36 more variables: AMC &lt;rsi&gt;, AMP &lt;rsi&gt;, TZP &lt;rsi&gt;, CZO &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># 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>
@ -255,16 +250,16 @@
<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> 0D7D34 2011-03-17 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> D80438 2017-07-03 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 590035 2015-02-18 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> A86006 2009-08-09 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2D5F7B 2013-04-08 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 7A1065 2008-02-11 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> E4F322 2012-12-23 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> D39422 2017-05-17 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> C27336 2003-09-22 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 006827 2009-07-24 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 305134 2016-10-28 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 0DBB93 2009-05-08 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> F50400 2017-09-08 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> AC8303 2014-10-20 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 425433 2005-07-11 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> AB0003 2010-04-08 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 452218 2012-05-04 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 904640 2015-11-03 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 968584 2006-01-11 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 773560 2008-05-08 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 190 more rows</span></span>
<span class="r-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>
@ -276,19 +271,19 @@
<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 [188]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: ward, patient [186]</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> ICU 2011-03-17 0D7D34 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical 2017-07-03 D80438 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Clinical 2015-02-18 590035 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical 2009-08-09 A86006 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> ICU 2013-04-08 2D5F7B 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> ICU 2008-02-11 7A1065 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> ICU 2012-12-23 E4F322 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical 2017-05-17 D39422 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> ICU 2003-09-22 C27336 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical 2009-07-24 006827 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> ICU 2016-10-28 305134 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> ICU 2009-05-08 0DBB93 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Clinical 2017-09-08 F50400 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical 2014-10-20 AC8303 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Clinical 2005-07-11 425433 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Clinical 2010-04-08 AB0003 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Clinical 2012-05-04 452218 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical 2015-11-03 904640 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> ICU 2006-01-11 968584 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical 2008-05-08 773560 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>
@ -303,9 +298,9 @@
<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 106 14 49 68</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 69 13 40 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 13 9 13 14</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 110 14 53 71</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 62 12 38 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 14 9 12 13</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>
@ -335,19 +330,19 @@
<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 [193]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, mo, ward [195]</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> 0D7D34 F_CANDD ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> D80438 B_CRYNB_STRT Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 590035 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> A86006 B_STPHY_CONS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2D5F7B B_HMPHL_INFL ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 7A1065 B_ESCHR_COLI ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> E4F322 B_ENTRC ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> D39422 B_KLBSL_PNMN Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> C27336 B_BCTRD_FRGL ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 006827 B_ENTRC_FCLS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 305134 B_PROTS_VLGR ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 0DBB93 B_ESCHR_COLI ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> F50400 B_STPHY_EPDR Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> AC8303 B_STPHY_HMLY Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 425433 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> AB0003 B_STRPT_ANGN Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 452218 B_STPHY_CONS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 904640 B_PROTS_MRBL Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 968584 F_CANDD_ALBC ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 773560 B_STPHY_EPDR Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 190 more rows</span></span>
<span class="r-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="">1.8.2.9082</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9083</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="">1.8.2.9082</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9083</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="">1.8.2.9082</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9083</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/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="">1.8.2.9082</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9083</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/intrinsic_resistant.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9082</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9083</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="">1.8.2.9082</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9083</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="">1.8.2.9082</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9083</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="">1.8.2.9082</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9083</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="">1.8.2.9082</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9083</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">
@ -172,9 +172,9 @@
<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] 2.929046</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 3.022562</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] 0.05362037</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.034725</span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>

2
reference/like.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="">1.8.2.9082</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9083</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/mdro.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="">1.8.2.9082</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9083</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">

94
reference/mean_amr_distance.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9082</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9083</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">
@ -191,30 +191,30 @@
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">rsi</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_rsi</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">rsi</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] I I I R R I I S R S</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] S R I R I R I S R I</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">rsi</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.621059 -0.621059 -0.621059 1.449138 1.449138 -0.621059 -0.621059</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [8] -0.621059 1.449138 -0.621059</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.7745967 1.1618950 -0.7745967 1.1618950 -0.7745967 1.1618950</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.7745967 -0.7745967 1.1618950 -0.7745967</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">mic</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">mic</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 64 2 0.25 0.002 0.125 256 8 16 32 0.005</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1 0.025 128 128 0.025 0.125 32 0.01 128 0.0625</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">mic</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.94601143 0.07985353 -0.43984121 -1.64653502 -0.61307279 1.29247458</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.42631669 0.59954827 0.77277985 -1.41753533</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.02978237 -0.95544246 1.18775017 1.18775017 -0.95544246 -0.55158203</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.83988373 -1.18536967 1.18775017 -0.72551525</span>
<span class="r-in"><span><span class="co"># equal to the Z-score of their log2:</span></span></span>
<span class="r-in"><span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span> <span class="op">-</span> <span class="fu"><a href="https://rdrr.io/r/base/mean.html" class="external-link">mean</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="fu"><a href="https://rdrr.io/r/stats/sd.html" class="external-link">sd</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.94601143 0.07985353 -0.43984121 -1.64653502 -0.61307279 1.29247458</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.42631669 0.59954827 0.77277985 -1.41753533</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.02978237 -0.95544246 1.18775017 1.18775017 -0.95544246 -0.55158203</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.83988373 -1.18536967 1.18775017 -0.72551525</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">disk</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_disk</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">disk</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 14 12 9 45 44 22 42 31 47 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 45 44 9 49 49 8 6 35 47 46</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">disk</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -1.08531752 -1.22098221 -1.42447924 1.01748517 0.94965283 -0.54265876</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.81398814 0.06783234 1.15314986 0.27132938</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.60645473 0.55230698 -1.34286403 0.82304570 0.82304570 -1.39701178</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -1.50530726 0.06497729 0.71475021 0.66060247</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>
@ -224,36 +224,36 @@
<span class="r-in"><span> tobr <span class="op">=</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span>, ab <span class="op">=</span> <span class="st">"tobr"</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">y</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A S 27 4 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B I 26 4 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C R 29 16 &lt;=1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D I 31 4 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E I 29 8 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F S 23 8 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G I 25 &lt;=0.5 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H R 23 8 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I S 25 4 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J R 25 1 &lt;=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 I 25 2 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B S 19 2 &gt;=16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C S 27 &gt;=8 &gt;=16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D R 21 2 &gt;=16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E S 26 &gt;=8 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F I 21 2 &gt;=16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G I 27 &lt;=1 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H S 25 &lt;=1 &lt;=1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I I 18 &lt;=1 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J R 27 &gt;=8 8</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "tobr"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.15307753 0.07017847 0.57030268 0.53856269 0.20198126 -0.04314696</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.84354651 0.47440221 -0.34043122 -0.47522509</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.3442580 -0.2743798 0.6961282 0.4613073 0.2926426 -0.1316197</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.4012318 -0.7100447 -0.7115465 1.1230024</span>
<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op">&lt;-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu">where</span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "gent" and "tobr"</span>
<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</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 R 25 1 &lt;=1 -1.43145922</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G I 25 &lt;=0.5 2 -1.13300373</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A S 27 4 2 -0.12677314</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I S 25 4 2 -0.12677314</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C R 29 16 &lt;=1 -0.08981844</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E I 29 8 2 0.20863706</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B I 26 4 4 0.50709255</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D I 31 4 4 0.50709255</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F S 23 8 4 0.84250275</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H R 23 8 4 0.84250275</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> 8 H S 25 &lt;=1 &lt;=1 -1.3827826</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G I 27 &lt;=1 2 -1.0506770</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A I 25 2 2 -0.6512093</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I I 18 &lt;=1 8 -0.3864658</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B S 19 2 &gt;=16 0.3451075</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D R 21 2 &gt;=16 0.3451075</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F I 21 2 &gt;=16 0.3451075</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E S 26 &gt;=8 4 0.4798318</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J R 27 &gt;=8 8 0.8119374</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C S 27 &gt;=8 &gt;=16 1.1440430</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>
@ -265,17 +265,17 @@
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "tobr"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance check_id_C</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 C R 29 16 &lt;=1 0.57030268 0.00000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 D I 31 4 4 0.53856269 0.03173999</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 H R 23 8 4 0.47440221 0.09590047</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 E I 29 8 2 0.20198126 0.36832142</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 B I 26 4 4 0.07017847 0.50012421</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F S 23 8 4 -0.04314696 0.61344964</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 A S 27 4 2 -0.15307753 0.72338021</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 I S 25 4 2 -0.34043122 0.91073389</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 J R 25 1 &lt;=1 -0.47522509 1.04552777</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 G I 25 &lt;=0.5 2 -0.84354651 1.41384919</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance check_id_C</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 C S 27 &gt;=8 &gt;=16 0.6961282 0.0000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 D R 21 2 &gt;=16 0.4613073 0.2348209</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 E S 26 &gt;=8 4 0.2926426 0.4034856</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 J R 27 &gt;=8 8 1.1230024 0.4268743</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 F I 21 2 &gt;=16 -0.1316197 0.8277479</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 B S 19 2 &gt;=16 -0.2743798 0.9705080</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 A I 25 2 2 -0.3442580 1.0403862</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 G I 27 &lt;=1 2 -0.4012318 1.0973600</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 H S 25 &lt;=1 &lt;=1 -0.7100447 1.4061728</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 I I 18 &lt;=1 8 -0.7115465 1.4076747</span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="co"># support for groups</span></span></span>
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>

2
reference/microorganisms.codes.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9082</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9083</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
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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="">1.8.2.9082</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9083</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
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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="">1.8.2.9082</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9083</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/mo_property.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9082</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9083</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/mo_source.html
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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="">1.8.2.9082</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9083</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="">1.8.2.9082</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9083</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="">1.8.2.9082</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9083</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/proportion.html
View File

@ -12,7 +12,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9082</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9083</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">

34
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="">1.8.2.9082</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9083</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">
@ -183,42 +183,42 @@
<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] 2 0.002 0.5 0.5 0.125 0.25 32 0.0625 0.002 0.025 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 16 0.125 8 0.002 4 8 0.0625 8 8 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 0.001 0.002 0.01 4 64 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.0625 0.0625 0.0625 1 0.002 16 128 0.5 0.5 64 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 256 4 0.25 0.0625 0.0625 8 0.01 0.25 0.0625 0.005 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 32 0.125 0.25 128 0.5 </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] 24 44 41 19 45 23 10 41 41 41 44 35 33 48 10 19 33 28 22 17 41 32 49 45 10</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 50 28 50 33 47 18 38 25 7 49 43 34 26 27 45 40 42 17 22 42 41 25 31 45 29</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] S I R S S S I I R I S S I I R I R S S R I I R R S</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] S R I R R S S I S I S S S S I I I S S I S R I R I</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
<span class="r-in"><span><span class="co"># make the random generation more realistic by setting a bug and/or drug:</span></span></span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 0.0625-64</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.01 32 8 2 0.005 0.002 0.005 0.025 1 0.5 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 0.125 1 0.01 1 4 0.0625 0.025 0.5 0.125 &gt;=64 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 16 0.5 1 4 0.001 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.025 16 2 16 2 &lt;=0.002 &gt;=64 0.005 4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 8 0.25 0.025 0.0625 &gt;=64 &gt;=64 4 0.0625 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 4 4 32 32 &gt;=64 8 4 </span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-16</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] &lt;=1 &lt;=1 &lt;=1 4 4 16 16 4 &lt;=1 8 4 16 &lt;=1 2 2 16 8 16 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [20] 4 2 4 4 4 4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2 4 1 8 4 2 4 &gt;=16 2 &gt;=16 1 8 2 &gt;=16 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [16] 2 &gt;=16 2 2 8 1 2 1 1 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] 8 &gt;=16 0.125 0.0625 1 0.0625 0.125 2 &gt;=16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 2 &lt;=0.025 1 2 8 1 0.25 0.0625 &gt;=16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 8 1 0.5 &gt;=16 0.125 &gt;=16 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.0625 0.0625 0.25 0.0625 8 2 &lt;=0.025 2 &gt;=16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 2 &lt;=0.025 &gt;=16 1 0.0625 0.125 1 1 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 4 8 0.5 0.5 4 2 0.5 </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] 28 26 38 49 10 27 11 35 47 12 8 45 33 18 8 44 43 21 23 28 48 47 47 24 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 41 24 50 49 30 49 31 45 21 40 45 31 17 31 49 31 12 40 50 19 26 8 41 24 47</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] 13 16 16 15 14 13 12 15 12 16 14 15 17 11 13 13 14 17 13 14 17 12 14 11 17</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 15 16 16 12 12 16 17 11 11 12 14 12 11 12 15 17 16 17 17 12 17 13 17 15 16</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] 17 21 25 24 22 27 15 21 15 26 16 27 26 27 20 17 15 18 17 19 16 20 16 17 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 22 15 20 16 22 26 25 25 19 27 17 22 20 19 19 23 16 16 18 19 19 21 19 15 25</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="">1.8.2.9082</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9083</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
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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="">1.8.2.9082</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9083</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
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@ -12,7 +12,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9082</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9083</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">
@ -171,7 +171,7 @@ 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] -0.08970928</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.02734032</span>
</code></pre></div>
</div>
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reference/translate.html
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9082</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9083</small>
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search.json
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