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<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="">1.8.2.9142</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9143</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="">1.8.2.9142</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9143</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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@ -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="">1.8.2.9142</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9143</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">
@ -187,7 +187,7 @@
website update since they are based on randomly created values and the
page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
Markdown</a>. However, the methodology remains unchanged. This page was
generated on 23 February 2023.</p>
generated on 24 February 2023.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@ -243,21 +243,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2023-02-23</td>
<td align="center">2023-02-24</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="center">2023-02-23</td>
<td align="center">2023-02-24</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<tr class="odd">
<td align="center">2023-02-23</td>
<td align="center">2023-02-24</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -388,12 +388,12 @@ data set:</p>
<col width="13%">
<col width="13%">
<col width="13%">
<col width="26%">
<col width="28%">
<col width="5%">
<col width="5%">
<col width="5%">
<col width="5%">
<col width="9%">
<col width="8%">
</colgroup>
<thead><tr class="header">
<th align="center">date</th>
@ -408,65 +408,65 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2014-03-08</td>
<td align="center">B5</td>
<td align="center">Hospital C</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">S</td>
<td align="center">2010-07-25</td>
<td align="center">E7</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2017-02-25</td>
<td align="center">S6</td>
<td align="center">2011-10-24</td>
<td align="center">Y9</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2014-12-01</td>
<td align="center">P7</td>
<td align="center">2016-05-31</td>
<td align="center">N6</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2014-04-25</td>
<td align="center">M9</td>
<td align="center">2012-12-23</td>
<td align="center">N3</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2010-05-05</td>
<td align="center">T6</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia coli</td>
<td align="center">2012-09-03</td>
<td align="center">J8</td>
<td align="center">Hospital D</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">F</td>
<td align="center">I</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2011-10-26</td>
<td align="center">B6</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">2012-06-18</td>
<td align="center">L8</td>
<td align="center">Hospital C</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
@ -507,16 +507,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,313</td>
<td align="right">51.57%</td>
<td align="right">10,313</td>
<td align="right">51.57%</td>
<td align="right">10,443</td>
<td align="right">52.22%</td>
<td align="right">10,443</td>
<td align="right">52.22%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,687</td>
<td align="right">48.44%</td>
<td align="right">9,557</td>
<td align="right">47.79%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -629,9 +629,9 @@ takes into account the antimicrobial susceptibility test results using
<span><span class="co">#&gt; Basing inclusion on all antimicrobial results, using a points threshold of</span></span>
<span><span class="co">#&gt; 2</span></span>
<span><span class="co">#&gt; Including isolates from ICU.</span></span>
<span><span class="co">#&gt; =&gt; Found 12,263 'phenotype-based' first isolates (61.3% of total where a</span></span>
<span><span class="co">#&gt; =&gt; Found 12,276 'phenotype-based' first isolates (61.4% of total where a</span></span>
<span><span class="co">#&gt; microbial ID was available)</span></span></code></pre></div>
<p>So only 61.3% is suitable for resistance analysis! We can now filter
<p>So only 61.4% is suitable for resistance analysis! We can now filter
on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the
<code>dplyr</code> package:</p>
<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
@ -641,11 +641,11 @@ on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html"
<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<p>So we end up with 12 263 isolates for analysis. Now our data looks
<p>So we end up with 12 276 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>
<table class="table">
<table style="width:100%;" class="table">
<colgroup>
<col width="2%">
<col width="9%">
@ -658,7 +658,7 @@ like:</p>
<col width="3%">
<col width="6%">
<col width="11%">
<col width="10%">
<col width="12%">
<col width="9%">
<col width="5%">
</colgroup>
@ -680,32 +680,32 @@ like:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2014-03-08</td>
<td align="center">B5</td>
<td align="center">Hospital C</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="left">2</td>
<td align="center">2011-10-24</td>
<td align="center">Y9</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">3</td>
<td align="center">2014-12-01</td>
<td align="center">P7</td>
<td align="left">4</td>
<td align="center">2012-12-23</td>
<td align="center">N3</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">F</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>
@ -713,60 +713,60 @@ like:</p>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="center">2010-05-05</td>
<td align="center">T6</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">I</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">6</td>
<td align="center">2011-10-26</td>
<td align="center">B6</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">7</td>
<td align="center">2014-09-23</td>
<td align="center">Q2</td>
<td align="center">2012-09-03</td>
<td align="center">J8</td>
<td align="center">Hospital D</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">10</td>
<td align="center">2011-08-26</td>
<td align="center">P9</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</td>
<td align="left">6</td>
<td align="center">2012-06-18</td>
<td align="center">L8</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>
<tr class="odd">
<td align="left">7</td>
<td align="center">2017-07-20</td>
<td align="center">K10</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">9</td>
<td align="center">2015-09-17</td>
<td align="center">Z10</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">F</td>
@ -808,8 +808,8 @@ readable:</p>
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://msberends.github.io/cleaner/reference/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></span></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 12,263<br>
Available: 12,263 (100%, NA: 0 = 0%)<br>
Length: 12,276<br>
Available: 12,276 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -834,33 +834,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">5,863</td>
<td align="right">47.81%</td>
<td align="right">5,863</td>
<td align="right">47.81%</td>
<td align="right">5,930</td>
<td align="right">48.31%</td>
<td align="right">5,930</td>
<td align="right">48.31%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,213</td>
<td align="right">26.20%</td>
<td align="right">9,076</td>
<td align="right">74.01%</td>
<td align="right">3,288</td>
<td align="right">26.78%</td>
<td align="right">9,218</td>
<td align="right">75.09%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">1,879</td>
<td align="right">15.32%</td>
<td align="right">10,955</td>
<td align="right">89.33%</td>
<td align="right">1,744</td>
<td align="right">14.21%</td>
<td align="right">10,962</td>
<td align="right">89.30%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,308</td>
<td align="right">10.67%</td>
<td align="right">12,263</td>
<td align="right">1,314</td>
<td align="right">10.70%</td>
<td align="right">12,276</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -909,69 +909,69 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2011-10-26</td>
<td align="center">B6</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">2012-06-18</td>
<td align="center">L8</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>
<tr class="even">
<td align="center">2017-10-16</td>
<td align="center">H9</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</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">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2016-02-22</td>
<td align="center">O1</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">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">2015-10-31</td>
<td align="center">X3</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2014-09-23</td>
<td align="center">Q2</td>
<td align="center">Hospital D</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2014-06-16</td>
<td align="center">S3</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2013-07-11</td>
<td align="center">L9</td>
<td align="center">2017-12-30</td>
<td align="center">G1</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2011-11-10</td>
<td align="center">N1</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">I</td>
<td align="center">I</td>
@ -984,18 +984,18 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2016-02-01</td>
<td align="center">H9</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">2015-11-07</td>
<td align="center">D3</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
</tbody>
@ -1020,50 +1020,50 @@ different bug/drug combinations, you can use the
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">2727</td>
<td align="center">1251</td>
<td align="center">1885</td>
<td align="center">5863</td>
<td align="center">2798</td>
<td align="center">1114</td>
<td align="center">2018</td>
<td align="center">5930</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">1482</td>
<td align="center">1242</td>
<td align="center">3139</td>
<td align="center">5863</td>
<td align="center">1504</td>
<td align="center">1245</td>
<td align="center">3181</td>
<td align="center">5930</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">2084</td>
<td align="center">1802</td>
<td align="center">1977</td>
<td align="center">5863</td>
<td align="center">2027</td>
<td align="center">1808</td>
<td align="center">2095</td>
<td align="center">5930</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">1999</td>
<td align="center">1799</td>
<td align="center">2065</td>
<td align="center">5863</td>
<td align="center">2054</td>
<td align="center">1817</td>
<td align="center">2059</td>
<td align="center">5930</td>
</tr>
<tr class="odd">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">546</td>
<td align="center">264</td>
<td align="center">498</td>
<td align="center">1308</td>
<td align="center">582</td>
<td align="center">275</td>
<td align="center">457</td>
<td align="center">1314</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMX</td>
<td align="center">0</td>
<td align="center">0</td>
<td align="center">1308</td>
<td align="center">1308</td>
<td align="center">1314</td>
<td align="center">1314</td>
</tr>
</tbody>
</table>
@ -1085,34 +1085,34 @@ 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">1999</td>
<td align="center">1799</td>
<td align="center">2065</td>
<td align="center">5863</td>
<td align="center">2054</td>
<td align="center">1817</td>
<td align="center">2059</td>
<td align="center">5930</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">475</td>
<td align="center">389</td>
<td align="center">444</td>
<td align="center">1308</td>
<td align="center">464</td>
<td align="center">407</td>
<td align="center">443</td>
<td align="center">1314</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">1105</td>
<td align="center">1034</td>
<td align="center">1074</td>
<td align="center">3213</td>
<td align="center">1122</td>
<td align="center">1047</td>
<td align="center">1119</td>
<td align="center">3288</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">1879</td>
<td align="center">1879</td>
<td align="center">1744</td>
<td align="center">1744</td>
</tr>
</tbody>
</table>
@ -1144,7 +1144,7 @@ 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">#&gt; [1] 0.5849303</span></span></code></pre></div>
<span><span class="co">#&gt; [1] 0.5847181</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">
@ -1159,19 +1159,19 @@ own:</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5897998</td>
<td align="center">0.5877193</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5851407</td>
<td align="center">0.5747854</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5656620</td>
<td align="center">0.5892857</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5919967</td>
<td align="center">0.5948136</td>
</tr>
</tbody>
</table>
@ -1196,23 +1196,23 @@ 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">0.5897998</td>
<td align="center">3647</td>
<td align="center">0.5877193</td>
<td align="center">3534</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5851407</td>
<td align="center">4334</td>
<td align="center">0.5747854</td>
<td align="center">4426</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5656620</td>
<td align="center">1858</td>
<td align="center">0.5892857</td>
<td align="center">1848</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5919967</td>
<td align="center">2424</td>
<td align="center">0.5948136</td>
<td align="center">2468</td>
</tr>
</tbody>
</table>
@ -1237,27 +1237,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.6784922</td>
<td align="center">0.6477912</td>
<td align="center">0.8882824</td>
<td align="center">0.6596965</td>
<td align="center">0.6527825</td>
<td align="center">0.8831366</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.6192661</td>
<td align="center">0.6605505</td>
<td align="center">0.8631498</td>
<td align="center">0.6522070</td>
<td align="center">0.6628615</td>
<td align="center">0.8896499</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.6616869</td>
<td align="center">0.6657330</td>
<td align="center">0.8882664</td>
<td align="center">0.6727494</td>
<td align="center">0.6596715</td>
<td align="center">0.8892944</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.4827036</td>
<td align="center">0.4678899</td>
<td align="center">0.0000000</td>
<td align="center">0.4827036</td>
<td align="center">0.4678899</td>
</tr>
</tbody>
</table>
@ -1285,23 +1285,23 @@ classes, use a antibiotic class selector such as
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">59.0%</td>
<td align="right">36.9%</td>
<td align="right">58.8%</td>
<td align="right">36.5%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">58.5%</td>
<td align="right">35.8%</td>
<td align="right">57.5%</td>
<td align="right">36.2%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">56.6%</td>
<td align="right">34.6%</td>
<td align="right">58.9%</td>
<td align="right">36.7%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">59.2%</td>
<td align="right">37.3%</td>
<td align="right">59.5%</td>
<td align="right">36.8%</td>
</tr>
</tbody>
</table>
@ -1417,18 +1417,18 @@ 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">#&gt; Class 'mic'</span></span>
<span><span class="co">#&gt; [1] 1 &gt;=256 32 128 &gt;=256 0.025 &gt;=256 0.025 2 </span></span>
<span><span class="co">#&gt; [10] 64 8 1 128 0.0625 0.01 1 128 &lt;=0.001</span></span>
<span><span class="co">#&gt; [19] 8 32 32 0.0625 128 8 0.125 128 0.25 </span></span>
<span><span class="co">#&gt; [28] 0.25 &lt;=0.001 4 128 16 32 0.01 4 &lt;=0.001</span></span>
<span><span class="co">#&gt; [37] &lt;=0.001 16 0.01 0.25 8 32 0.25 &gt;=256 0.0625 </span></span>
<span><span class="co">#&gt; [46] 16 0.002 &gt;=256 0.25 0.025 0.0625 4 0.005 4 </span></span>
<span><span class="co">#&gt; [55] 128 0.125 0.0625 32 0.002 4 8 0.002 0.005 </span></span>
<span><span class="co">#&gt; [64] 0.0625 &gt;=256 0.25 0.01 1 0.5 0.01 0.125 16 </span></span>
<span><span class="co">#&gt; [73] 128 16 1 0.25 0.0625 1 &gt;=256 1 8 </span></span>
<span><span class="co">#&gt; [82] 0.5 32 32 &lt;=0.001 64 0.5 0.5 0.5 0.025 </span></span>
<span><span class="co">#&gt; [91] 16 0.5 &lt;=0.001 1 2 64 &gt;=256 1 0.25 </span></span>
<span><span class="co">#&gt; [100] 2</span></span></code></pre></div>
<span><span class="co">#&gt; [1] 0.5 0.0625 8 16 8 64 32 256 32 </span></span>
<span><span class="co">#&gt; [10] 0.025 1 0.002 16 256 0.025 2 0.01 8 </span></span>
<span><span class="co">#&gt; [19] 64 0.25 0.005 &lt;=0.001 &lt;=0.001 2 0.002 0.125 4 </span></span>
<span><span class="co">#&gt; [28] 1 2 256 4 32 0.125 1 2 0.0625 </span></span>
<span><span class="co">#&gt; [37] 0.01 0.0625 0.125 &lt;=0.001 0.01 256 256 128 32 </span></span>
<span><span class="co">#&gt; [46] 8 256 32 8 0.25 1 32 256 128 </span></span>
<span><span class="co">#&gt; [55] &lt;=0.001 16 128 0.25 0.005 0.25 8 16 0.125 </span></span>
<span><span class="co">#&gt; [64] 0.002 4 0.125 256 8 &lt;=0.001 0.005 0.025 64 </span></span>
<span><span class="co">#&gt; [73] 2 256 0.25 16 4 0.125 32 0.5 0.002 </span></span>
<span><span class="co">#&gt; [82] 0.025 256 0.025 1 64 0.5 0.01 0.01 64 </span></span>
<span><span class="co">#&gt; [91] &lt;=0.001 16 256 64 0.25 0.25 64 4 0.025 </span></span>
<span><span class="co">#&gt; [100] 0.005</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>
@ -1462,10 +1462,10 @@ 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">#&gt; Class 'disk'</span></span>
<span><span class="co">#&gt; [1] 28 24 26 18 22 19 28 20 30 27 21 31 21 17 18 30 27 23 20 24 29 29 24 30 26</span></span>
<span><span class="co">#&gt; [26] 21 19 18 25 26 17 17 18 28 26 27 21 21 25 20 18 31 27 21 25 19 22 25 27 20</span></span>
<span><span class="co">#&gt; [51] 31 19 28 28 24 24 31 30 29 30 27 21 22 28 30 22 28 31 31 29 20 31 27 19 28</span></span>
<span><span class="co">#&gt; [76] 25 22 20 28 22 23 26 24 23 27 20 31 19 22 30 27 24 17 27 17 29 23 17 29 26</span></span></code></pre></div>
<span><span class="co">#&gt; [1] 27 25 28 20 31 23 27 18 23 19 25 22 21 20 18 28 27 30 18 29 31 18 21 20 23</span></span>
<span><span class="co">#&gt; [26] 27 27 30 29 27 21 18 28 27 23 31 21 30 17 20 29 20 18 18 21 26 25 26 29 20</span></span>
<span><span class="co">#&gt; [51] 21 26 21 31 19 18 21 26 22 25 22 21 20 20 31 25 24 19 20 30 19 24 28 23 23</span></span>
<span><span class="co">#&gt; [76] 20 29 22 18 26 26 27 31 27 30 29 21 31 20 17 18 19 27 29 20 19 26 17 20 21</span></span></code></pre></div>
<div class="sourceCode" id="cb42"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">disk_values</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></code></pre></div>

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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9142</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9143</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
View File

@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9142</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9143</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">
@ -386,18 +386,18 @@ names or codes, this would have worked exactly the same way:</p>
<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">#&gt; rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
<span><span class="co">#&gt; 1 R I S R S R</span></span>
<span><span class="co">#&gt; 2 R R R S R S</span></span>
<span><span class="co">#&gt; 3 I R I R S I</span></span>
<span><span class="co">#&gt; 4 S R I I R R</span></span>
<span><span class="co">#&gt; 5 I R I I R S</span></span>
<span><span class="co">#&gt; 6 R I S I I R</span></span>
<span><span class="co">#&gt; 2 R R I I R I</span></span>
<span><span class="co">#&gt; 3 I R S S I R</span></span>
<span><span class="co">#&gt; 4 R S I S R S</span></span>
<span><span class="co">#&gt; 5 S R S S S S</span></span>
<span><span class="co">#&gt; 6 S R S I S R</span></span>
<span><span class="co">#&gt; kanamycin</span></span>
<span><span class="co">#&gt; 1 R</span></span>
<span><span class="co">#&gt; 2 I</span></span>
<span><span class="co">#&gt; 3 R</span></span>
<span><span class="co">#&gt; 1 I</span></span>
<span><span class="co">#&gt; 2 R</span></span>
<span><span class="co">#&gt; 3 S</span></span>
<span><span class="co">#&gt; 4 R</span></span>
<span><span class="co">#&gt; 5 R</span></span>
<span><span class="co">#&gt; 6 R</span></span></code></pre></div>
<span><span class="co">#&gt; 5 S</span></span>
<span><span class="co">#&gt; 6 S</span></span></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can
use:</p>
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
@ -438,40 +438,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3221</td>
<td align="right">64.42%</td>
<td align="right">3221</td>
<td align="right">64.42%</td>
<td align="right">3217</td>
<td align="right">64.34%</td>
<td align="right">3217</td>
<td align="right">64.34%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">969</td>
<td align="right">19.38%</td>
<td align="right">4190</td>
<td align="right">83.80%</td>
<td align="right">960</td>
<td align="right">19.20%</td>
<td align="right">4177</td>
<td align="right">83.54%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">466</td>
<td align="right">9.32%</td>
<td align="right">4656</td>
<td align="right">93.12%</td>
<td align="right">461</td>
<td align="right">9.22%</td>
<td align="right">4638</td>
<td align="right">92.76%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">261</td>
<td align="right">5.22%</td>
<td align="right">4917</td>
<td align="right">98.34%</td>
<td align="right">257</td>
<td align="right">5.14%</td>
<td align="right">4895</td>
<td align="right">97.90%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">83</td>
<td align="right">1.66%</td>
<td align="right">105</td>
<td align="right">2.10%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

2
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -38,7 +38,7 @@
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@ -178,7 +178,7 @@
<h4 data-toc-skip class="author">Dr. Matthijs
Berends</h4>
<h4 data-toc-skip class="date">23 February 2023</h4>
<h4 data-toc-skip class="date">24 February 2023</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/SPSS.Rmd" class="external-link"><code>vignettes/SPSS.Rmd</code></a></small>
<div class="d-none name"><code>SPSS.Rmd</code></div>

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@ -38,7 +38,7 @@
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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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@ -176,7 +176,7 @@
<main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
<h4 data-toc-skip class="date">23 February 2023</h4>
<h4 data-toc-skip class="date">24 February 2023</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<div class="d-none name"><code>datasets.Rmd</code></div>

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authors.html
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@ -10,7 +10,7 @@
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@ -42,7 +42,7 @@
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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="">1.8.2.9142</small>
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@ -142,7 +142,7 @@
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="1.8.2.9142" id="amr-1829142">AMR 1.8.2.9142<a class="anchor" aria-label="anchor" href="#amr-1829142"></a></h2>
<h2 class="pkg-version" data-toc-text="1.8.2.9143" id="amr-1829143">AMR 1.8.2.9143<a class="anchor" aria-label="anchor" href="#amr-1829143"></a></h2>
<p><em>(this beta version will eventually become v2.0! We’re happy to reach a new major milestone soon!)</em></p>
<p>This is a new major release of the AMR package, with great new additions but also some breaking changes for current users. These are all listed below.</p>
<p><strong><a href="https://en.wikipedia.org/wiki/TL;DR" class="external-link">TL;DR</a></strong></p>
@ -156,32 +156,32 @@
<li>Now available in 20 languages</li>
<li>Many small bug fixes</li>
</ul><div class="section level3">
<h3 id="new-1-8-2-9142">New<a class="anchor" aria-label="anchor" href="#new-1-8-2-9142"></a></h3>
<h3 id="new-1-8-2-9143">New<a class="anchor" aria-label="anchor" href="#new-1-8-2-9143"></a></h3>
<div class="section level4">
<h4 id="sir-vs-rsi-1-8-2-9142">SIR vs. RSI<a class="anchor" aria-label="anchor" href="#sir-vs-rsi-1-8-2-9142"></a></h4>
<h4 id="sir-vs-rsi-1-8-2-9143">SIR vs. RSI<a class="anchor" aria-label="anchor" href="#sir-vs-rsi-1-8-2-9143"></a></h4>
<p>For this milestone version, we replaced all mentions of RSI with SIR, to comply with what is actually being commonly used in the field of clinical microbiology when it comes to this tri-form regarding AMR.</p>
<p>While existing functions such as <code><a href="../reference/AMR-deprecated.html">as.rsi()</a></code>, <code><a href="../reference/AMR-deprecated.html">rsi_df()</a></code> and <code><a href="../reference/AMR-deprecated.html">ggplot_rsi()</a></code> still work, their replacements <code><a href="../reference/as.sir.html">as.sir()</a></code>, <code><a href="../reference/proportion.html">sir_df()</a></code>, <code><a href="../reference/ggplot_sir.html">ggplot_sir()</a></code> are now the current functions for AMR data analysis. A warning will be thrown once a session to remind users about this. The data set <code>rsi_translation</code> is now called <code>clinical_breakpoints</code> to better reflect its content.</p>
<p>The ‘RSI functions’ will be removed in a future version, but not before late 2023 / early 2024.</p>
</div>
<div class="section level4">
<h4 id="new-antibiogram-function-1-8-2-9142">New antibiogram function<a class="anchor" aria-label="anchor" href="#new-antibiogram-function-1-8-2-9142"></a></h4>
<h4 id="new-antibiogram-function-1-8-2-9143">New antibiogram function<a class="anchor" aria-label="anchor" href="#new-antibiogram-function-1-8-2-9143"></a></h4>
<p>With the new <code><a href="../reference/antibiogram.html">antibiogram()</a></code> function, users can now generate traditional, combined, syndromic, and even weighted-incidence syndromic combination antibiograms (WISCA). With this, we follow the logic in the previously described work of Klinker <em>et al.</em> (2021, DOI <a href="https://doi.org/10.1177/20499361211011373" class="external-link">10.1177/20499361211011373</a>) and Barbieri <em>et al.</em> (2021, DOI <a href="https://doi.org/10.1186/s13756-021-00939-2" class="external-link">10.1186/s13756-021-00939-2</a>).</p>
<p>The help page for <code><a href="../reference/antibiogram.html">antibiogram()</a></code> extensively elaborates on use cases, and <code><a href="../reference/antibiogram.html">antibiogram()</a></code> also supports printing in R Markdown and Quarto, with support for 20 languages.</p>
<p>Furthermore, different plotting methods were implemented to allow for graphical visualisations as well.</p>
</div>
<div class="section level4">
<h4 id="interpretation-of-mic-and-disk-diffusion-values-1-8-2-9142">Interpretation of MIC and disk diffusion values<a class="anchor" aria-label="anchor" href="#interpretation-of-mic-and-disk-diffusion-values-1-8-2-9142"></a></h4>
<h4 id="interpretation-of-mic-and-disk-diffusion-values-1-8-2-9143">Interpretation of MIC and disk diffusion values<a class="anchor" aria-label="anchor" href="#interpretation-of-mic-and-disk-diffusion-values-1-8-2-9143"></a></h4>
<p>The clinical breakpoints and intrinsic resistance of EUCAST 2022 and CLSI 2022 have been added for <code><a href="../reference/as.sir.html">as.sir()</a></code>. EUCAST 2022 (v12.0) is now the new default guideline for all MIC and disks diffusion interpretations, and for <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> to apply EUCAST Expert Rules. The default guideline (EUCAST) can now be changed with the new <code>AMR_guideline</code> option, such as: <code>options(AMR_guideline = "CLSI 2020")</code>.</p>
<p>With the new arguments <code>include_PKPD</code> (default: <code>TRUE</code>) and <code>include_screening</code> (default: <code>FALSE</code>), users can now specify whether breakpoints for screening and from the PK/PD table should be included when interpreting MICs and disks diffusion values. These options can be set globally, which can be read in <a href="https://msberends.github.io/AMR/reference/AMR-options.html">our new manual</a>.</p>
<p>Interpretation guidelines older than 10 years were removed, the oldest now included guidelines of EUCAST and CLSI are from 2013.</p>
</div>
<div class="section level4">
<h4 id="supported-languages-1-8-2-9142">Supported languages<a class="anchor" aria-label="anchor" href="#supported-languages-1-8-2-9142"></a></h4>
<h4 id="supported-languages-1-8-2-9143">Supported languages<a class="anchor" aria-label="anchor" href="#supported-languages-1-8-2-9143"></a></h4>
<p>We added support for the following ten languages: Chinese (simplified), Czech, Finnish, Greek, Japanese, Norwegian (bokmål), Polish, Romanian, Turkish and Ukrainian. All antibiotic names are now available in these languages, and the AMR package will automatically determine a supported language based on the user’s system language.</p>
<p>We are very grateful for the valuable input by our colleagues from other countries. The <code>AMR</code> package is now available in 20 languages in total, and according to download stats used in almost all countries in the world!</p>
</div>
<div class="section level4">
<h4 id="microbiological-taxonomy-1-8-2-9142">Microbiological taxonomy<a class="anchor" aria-label="anchor" href="#microbiological-taxonomy-1-8-2-9142"></a></h4>
<h4 id="microbiological-taxonomy-1-8-2-9143">Microbiological taxonomy<a class="anchor" aria-label="anchor" href="#microbiological-taxonomy-1-8-2-9143"></a></h4>
<p>The <code>microorganisms</code> data set no longer relies on the Catalogue of Life, but on the List of Prokaryotic names with Standing in Nomenclature (LPSN) and is supplemented with the ‘backbone taxonomy’ from the Global Biodiversity Information Facility (GBIF). The structure of this data set has changed to include separate LPSN and GBIF identifiers. Almost all previous MO codes were retained. It contains over 1,400 taxonomic names from 2022.</p>
<p>We previously relied on our own experience to categorise species into pathogenic groups, but we were very happy to encounter the very recent work of Bartlett <em>et al.</em> (2022, DOI <a href="https://doi.org/10.1099/mic.0.001269" class="external-link">10.1099/mic.0.001269</a>) who extensively studied medical-scientific literature to categorise all bacterial species into groups. See <code><a href="../reference/mo_matching_score.html">mo_matching_score()</a></code> on how their work was incorporated into the <code>prevalence</code> column of the <code>microorganisms</code> data set. Using their results, the <code><a href="../reference/as.mo.html">as.mo()</a></code> and all <code>mo_*()</code> functions are now much better capable of converting user input to valid taxonomic records.</p>
<p>The new function <code><a href="../reference/add_custom_microorganisms.html">add_custom_microorganisms()</a></code> allows users to add custom microorganisms to the <code>AMR</code> package.</p>
@ -205,7 +205,7 @@
<li>The <code>microorganisms.old</code> data set was removed, and all previously accepted names are now included in the <code>microorganisms</code> data set. A new column <code>status</code> contains <code>"accepted"</code> for currently accepted names and <code>"synonym"</code> for taxonomic synonyms; currently invalid names. All previously accepted names now have a microorganisms ID and - if available - an LPSN, GBIF and SNOMED CT identifier.</li>
</ul></div>
<div class="section level4">
<h4 id="antibiotic-agents-and-selectors-1-8-2-9142">Antibiotic agents and selectors<a class="anchor" aria-label="anchor" href="#antibiotic-agents-and-selectors-1-8-2-9142"></a></h4>
<h4 id="antibiotic-agents-and-selectors-1-8-2-9143">Antibiotic agents and selectors<a class="anchor" aria-label="anchor" href="#antibiotic-agents-and-selectors-1-8-2-9143"></a></h4>
<p>The new function <code><a href="../reference/add_custom_antimicrobials.html">add_custom_antimicrobials()</a></code> allows users to add custom antimicrobial codes and names to the <code>AMR</code> package.</p>
<p>The <code>antibiotics</code> data set was greatly updated:</p>
<ul><li>The following 20 antibiotics have been added (also includes the <a href="https://www.whocc.no/atc_ddd_index/?code=J01RA&amp;showdescription=no" class="external-link">new J01RA ATC group</a>): azithromycin/fluconazole/secnidazole (AFC), cefepime/amikacin (CFA), cefixime/ornidazole (CEO), ceftriaxone/beta-lactamase inhibitor (CEB), ciprofloxacin/metronidazole (CIM), ciprofloxacin/ornidazole (CIO), ciprofloxacin/tinidazole (CIT), furazidin (FUR), isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST), lascufloxacin (LSC), levofloxacin/ornidazole (LEO), nemonoxacin (NEM), norfloxacin/metronidazole (NME), norfloxacin/tinidazole (NTI), ofloxacin/ornidazole (OOR), oteseconazole (OTE), rifampicin/ethambutol/isoniazid (REI), sarecycline (SRC), tetracycline/oleandomycin (TOL), and thioacetazone (TAT)</li>
@ -217,14 +217,14 @@
</ul><p>Also, we added support for using antibiotic selectors in scoped <code>dplyr</code> verbs (with or without using <code><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars()</a></code>), such as in: <code>... %&gt;% summarise_at(aminoglycosides(), resistance)</code>, please see <code><a href="../reference/proportion.html">resistance()</a></code> for examples.</p>
</div>
<div class="section level4">
<h4 id="antiviral-agents-1-8-2-9142">Antiviral agents<a class="anchor" aria-label="anchor" href="#antiviral-agents-1-8-2-9142"></a></h4>
<h4 id="antiviral-agents-1-8-2-9143">Antiviral agents<a class="anchor" aria-label="anchor" href="#antiviral-agents-1-8-2-9143"></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-1-8-2-9142">Other new functions<a class="anchor" aria-label="anchor" href="#other-new-functions-1-8-2-9142"></a></h4>
<h4 id="other-new-functions-1-8-2-9143">Other new functions<a class="anchor" aria-label="anchor" href="#other-new-functions-1-8-2-9143"></a></h4>
<ul><li>Function <code><a href="../reference/proportion.html">sir_confidence_interval()</a></code> to add confidence intervals in AMR calculation. This is now also included in <code><a href="../reference/proportion.html">sir_df()</a></code> and <code><a href="../reference/proportion.html">proportion_df()</a></code>.</li>
<li>Function <code><a href="../reference/mean_amr_distance.html">mean_amr_distance()</a></code> to calculate the mean AMR distance. The mean AMR distance is a normalised numeric value to compare AMR test results and can help to identify similar isolates, without comparing antibiograms by hand.</li>
<li>Function <code><a href="../reference/as.sir.html">sir_interpretation_history()</a></code> to view the history of previous runs of <code><a href="../reference/as.sir.html">as.sir()</a></code> (previously <code><a href="../reference/AMR-deprecated.html">as.rsi()</a></code>). This returns a ‘logbook’ with the selected guideline, reference table and specific interpretation of each row in a data set on which <code><a href="../reference/as.sir.html">as.sir()</a></code> was run.</li>
@ -233,7 +233,7 @@
</ul></div>
</div>
<div class="section level3">
<h3 id="changes-1-8-2-9142">Changes<a class="anchor" aria-label="anchor" href="#changes-1-8-2-9142"></a></h3>
<h3 id="changes-1-8-2-9143">Changes<a class="anchor" aria-label="anchor" href="#changes-1-8-2-9143"></a></h3>
<ul><li>Argument <code>combine_IR</code> has been removed from this package (affecting functions <code><a href="../reference/count.html">count_df()</a></code>, <code><a href="../reference/proportion.html">proportion_df()</a></code>, and <code><a href="../reference/proportion.html">sir_df()</a></code> and some plotting functions), since it was replaced with <code>combine_SI</code> three years ago</li>
<li>Using <code>units</code> in <code>ab_ddd(..., units = "...")</code> had been deprecated for some time and is now not supported anymore. Use <code><a href="../reference/ab_property.html">ab_ddd_units()</a></code> instead.</li>
<li>Support for <code>data.frame</code>-enhancing R packages, more specifically: <code><a href="https://Rdatatable.gitlab.io/data.table/reference/data.table.html" class="external-link">data.table::data.table</a></code>, <code><a href="https://sfirke.github.io/janitor/reference/tabyl.html" class="external-link">janitor::tabyl</a></code>, <code><a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble::tibble</a></code>, and <code><a href="https://tsibble.tidyverts.org/reference/tsibble.html" class="external-link">tsibble::tsibble</a></code>. AMR package functions that have a data set as output (such as <code><a href="../reference/proportion.html">sir_df()</a></code> and <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code>), will now return the same data type as the input.</li>
@ -277,7 +277,7 @@
<code>mo_synonyns()</code> now contains the scientific reference as names</li>
</ul></div>
<div class="section level3">
<h3 id="other-1-8-2-9142">Other<a class="anchor" aria-label="anchor" href="#other-1-8-2-9142"></a></h3>
<h3 id="other-1-8-2-9143">Other<a class="anchor" aria-label="anchor" href="#other-1-8-2-9143"></a></h3>
<ul><li>Added Peter Dutey-Magni, Dmytro Mykhailenko, Anton Mymrikov, Andrew Norgan, Jonas Salm, and Anita Williams as contributors, to thank them for their valuable input</li>
<li>New website to make use of the new Bootstrap 5 and pkgdown 2.0. The website now contains results for all examples and will be automatically regenerated with every change to our repository, using GitHub Actions</li>
<li>All R and Rmd files in this project are now styled using the <code>styler</code> package</li>

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@ -11,7 +11,7 @@ articles:
datasets: datasets.html
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
last_built: 2023-02-23T15:32Z
last_built: 2023-02-24T08:47Z
urls:
reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles

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<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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@ -205,16 +205,16 @@
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">df</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> birth_date age age_exact age_at_y2k</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1966-05-28 56 56.74247 33</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1968-06-27 54 54.66027 31</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1969-08-07 53 53.54795 30</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1979-02-13 44 44.02740 20</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1987-09-25 35 35.41370 12</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1949-02-07 74 74.04384 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1950-11-07 72 72.29589 49</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1983-09-03 39 39.47397 16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1941-03-04 81 81.97534 58</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1968-03-30 54 54.90411 31</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1970-09-03 52 52.47671 29</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1961-08-15 61 61.52877 38</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1975-10-03 47 47.39452 24</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1963-12-22 59 59.17534 36</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1957-11-01 65 65.31507 42</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1964-09-04 58 58.47397 35</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1973-11-09 49 49.29315 26</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1945-07-01 77 77.65205 54</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1993-11-25 29 29.24932 6</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1965-10-15 57 57.36164 34</span>
</code></pre></div>
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@ -171,7 +171,8 @@
<span><span class="co"># S3 method for antibiogram</span></span>
<span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">knit_print.antibiogram</span><span class="op">(</span></span>
<span><span class="co"># S3 method for antibiogram</span></span>
<span><span class="fu">knit_print</span><span class="op">(</span></span>
<span> <span class="va">x</span>,</span>
<span> italicise <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> na <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"knitr.kable.NA"</span>, default <span class="op">=</span> <span class="st">""</span><span class="op">)</span>,</span>
@ -253,7 +254,7 @@
<dt>italicise</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether the microorganism names in the <a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">knitr</a> table should be made italic, using <code><a href="italicise_taxonomy.html">italicise_taxonomy()</a></code>. This only works when the output format is markdown, such as in HTML output.</p></dd>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether the microorganism names in the <a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">knitr</a> table should be made italic, using <code><a href="italicise_taxonomy.html">italicise_taxonomy()</a></code>.</p></dd>
<dt>na</dt>
@ -264,6 +265,10 @@
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p>This function returns a table with values between 0 and 100 for <em>susceptibility</em>, not resistance.</p>
<p><strong>Remember that you should filter your data to let it contain only first isolates!</strong> This is needed to exclude duplicates and to reduce selection bias. Use <code><a href="first_isolate.html">first_isolate()</a></code> to determine them in your data set with one of the four available algorithms.</p>
<p>All types of antibiograms as listed below can be plotted (using <code><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">ggplot2::autoplot()</a></code> or base <span style="R">R</span> <code><a href="plot.html">plot()</a></code>/<code><a href="https://rdrr.io/r/graphics/barplot.html" class="external-link">barplot()</a></code>). The <code>antibiogram</code> object can also be used directly in R Markdown / Quarto (i.e., <code>knitr</code>) for reports. In this case, <code><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">knitr::kable()</a></code> will be applied automatically and microorganism names will even be printed in italics at default (see argument <code>italicise</code>). You can also use functions from specific 'table reporting' packages to transform the output of <code>antibiogram()</code> to your needs, e.g. with <code>as_flextable()</code> or <code>gt()</code>.</p><div class="section">
<h3 id="antibiogram-types">Antibiogram Types<a class="anchor" aria-label="anchor" href="#antibiogram-types"></a></h3>
<p>There are four antibiogram types, as proposed by Klinker <em>et al.</em> (2021, <a href="https://doi.org/10.1177/20499361211011373" class="external-link">doi:10.1177/20499361211011373</a>
), and they are all supported by <code>antibiogram()</code>:</p><ol><li><p><strong>Traditional Antibiogram</strong></p>
<p>Case example: Susceptibility of <em>Pseudomonas aeruginosa</em> to piperacillin/tazobactam (TZP)</p>
@ -292,8 +297,7 @@
<span> <span class="va">.</span><span class="op">$</span><span class="va">gender</span> <span class="op">==</span> <span class="st">"Male"</span> <span class="op">&amp;</span></span>
<span> <span class="va">.</span><span class="op">$</span><span class="va">condition</span> <span class="op">==</span> <span class="st">"Heart Disease"</span>,</span>
<span> <span class="st">"Study Group"</span>, <span class="st">"Control Group"</span><span class="op">)</span><span class="op">)</span></span></code></pre><p></p></div></li>
</ol><p>All types of antibiograms can be generated with the functions as described on this page, and can be plotted (using <code><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">ggplot2::autoplot()</a></code> or base <span style="R">R</span> <code><a href="plot.html">plot()</a></code>/<code><a href="https://rdrr.io/r/graphics/barplot.html" class="external-link">barplot()</a></code>) or directly used into R Markdown / Quarto formats for reports (in the last case, <code><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">knitr::kable()</a></code> will be applied automatically). Use functions from specific 'table reporting' packages to transform the output of <code>antibiogram()</code> to your needs, e.g. <code>flextable::as_flextable()</code> or <code>gt::gt()</code>.</p>
<p>Note that for combination antibiograms, it is important to realise that susceptibility can be calculated in two ways, which can be set with the <code>only_all_tested</code> argument (default is <code>FALSE</code>). See this example for two antibiotics, Drug A and Drug B, about how <code>antibiogram()</code> works to calculate the %SI:</p>
</ol><p>Note that for combination antibiograms, it is important to realise that susceptibility can be calculated in two ways, which can be set with the <code>only_all_tested</code> argument (default is <code>FALSE</code>). See this example for two antibiotics, Drug A and Drug B, about how <code>antibiogram()</code> works to calculate the %SI:</p>
<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="sc">--------------------------------------------------------------------</span></span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a> only_all_tested <span class="ot">=</span> <span class="cn">FALSE</span> only_all_tested <span class="ot">=</span> <span class="cn">TRUE</span></span>
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a> <span class="sc">-----------------------</span> <span class="sc">-----------------------</span></span>
@ -310,6 +314,8 @@
<span id="cb1-14"><a href="#cb1-14" aria-hidden="true" tabindex="-1"></a> R <span class="sc">&lt;</span><span class="cn">NA</span><span class="sc">&gt;</span> <span class="sc">-</span> <span class="sc">-</span> <span class="sc">-</span> <span class="sc">-</span></span>
<span id="cb1-15"><a href="#cb1-15" aria-hidden="true" tabindex="-1"></a> <span class="er">&lt;</span><span class="cn">NA</span><span class="sc">&gt;</span> <span class="er">&lt;</span><span class="cn">NA</span><span class="sc">&gt;</span> <span class="sc">-</span> <span class="sc">-</span> <span class="sc">-</span> <span class="sc">-</span></span>
<span id="cb1-16"><a href="#cb1-16" aria-hidden="true" tabindex="-1"></a><span class="sc">--------------------------------------------------------------------</span></span></code></pre><p></p></div>
</div>
</div>
<div class="section level2">
@ -487,6 +493,7 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> WISCA Group 1 Gram-positive (123-406) 76 89 81 95</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> WISCA Group 2 Gram-positive (222-732) 76 89 88 95</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Print the output for R Markdown / Quarto -----------------------------</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">ureido</span> <span class="op">&lt;-</span> <span class="fu">antibiogram</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
@ -499,7 +506,7 @@
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/ns-load.html" class="external-link">requireNamespace</a></span><span class="op">(</span><span class="st">"knitr"</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="fu">knitr</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/knitr/man/knit_print.html" class="external-link">knit_print</a></span><span class="op">(</span><span class="va">ureido</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "\n\n| Pathogen (N) | Piperacillin/tazobactam|\n|:----------------------|-----------------------:|\n| CoNS (33) | 30|\n| *E. coli* (416) | 94|\n| *K. pneumoniae* (53) | 89|\n| *S. pneumoniae* (112) | 100|"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "\n\n|Pathogen (N) | Piperacillin/tazobactam|\n|:---------------------|-----------------------:|\n|CoNS (33) | 30|\n|*E. coli* (416) | 94|\n|*K. pneumoniae* (53) | 89|\n|*S. pneumoniae* (112) | 100|"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> attr(,"class")</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "knit_asis"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> attr(,"knit_cacheable")</span>

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2
reference/as.mo.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="">1.8.2.9142</small>
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22
reference/as.sir.html
View File

@ -12,7 +12,7 @@ All breakpoints used for interpretation are publicly available in the clinical_b
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9142</small>
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@ -534,16 +534,16 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 50 × 17</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index ab_input ab_guid…¹ mo_in…² mo_guideline guide…³</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2023-02-23 <span style="color: #949494;">15:33:48</span> 1 TOB TOB Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2023-02-23 <span style="color: #949494;">15:33:47</span> 1 GEN GEN Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2023-02-23 <span style="color: #949494;">15:33:47</span> 1 CIP CIP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2023-02-23 <span style="color: #949494;">15:33:47</span> 1 AMP AMP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2023-02-23 <span style="color: #949494;">15:33:41</span> 1 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2023-02-23 <span style="color: #949494;">15:33:41</span> 2 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2023-02-23 <span style="color: #949494;">15:33:41</span> 3 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2023-02-23 <span style="color: #949494;">15:33:41</span> 4 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2023-02-23 <span style="color: #949494;">15:33:41</span> 5 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2023-02-23 <span style="color: #949494;">15:33:41</span> 6 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2023-02-24 <span style="color: #949494;">08:48:44</span> 1 TOB TOB Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2023-02-24 <span style="color: #949494;">08:48:43</span> 1 GEN GEN Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2023-02-24 <span style="color: #949494;">08:48:43</span> 1 CIP CIP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2023-02-24 <span style="color: #949494;">08:48:43</span> 1 AMP AMP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2023-02-24 <span style="color: #949494;">08:48:37</span> 1 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2023-02-24 <span style="color: #949494;">08:48:37</span> 2 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2023-02-24 <span style="color: #949494;">08:48:37</span> 3 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2023-02-24 <span style="color: #949494;">08:48:37</span> 4 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2023-02-24 <span style="color: #949494;">08:48:37</span> 5 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2023-02-24 <span style="color: #949494;">08:48:37</span> 6 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 40 more rows, 10 more variables: ref_table &lt;chr&gt;, method &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># input &lt;dbl&gt;, outcome &lt;sir&gt;, breakpoint_S_R &lt;chr&gt;, ab_considered &lt;lgl&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># mo_considered &lt;lgl&gt;, breakpoint_S &lt;lgl&gt;, breakpoint_R &lt;lgl&gt;,</span></span>

2
reference/atc_online.html
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="">1.8.2.9142</small>
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reference/av_from_text.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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reference/av_property.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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2
reference/availability.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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4
reference/bug_drug_combinations.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="">1.8.2.9142</small>
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@ -226,7 +226,7 @@
</div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p>The function <code><a href="https://rdrr.io/r/base/format.html" class="external-link">format()</a></code> calculates the resistance per bug-drug combination. Use <code>combine_SI = TRUE</code> (default) to test R vs. S+I and <code>combine_SI = FALSE</code> to test R+I vs. S.</p>
<p>The function <code><a href="https://rdrr.io/r/base/format.html" class="external-link">format()</a></code> calculates the resistance per bug-drug combination and returns a table ready for reporting/publishing. Use <code>combine_SI = TRUE</code> (default) to test R vs. S+I and <code>combine_SI = FALSE</code> to test R+I vs. S. This table can also directly be used in R Markdown / Quarto without the need for e.g. <code><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">knitr::kable()</a></code>.</p>
</div>
<div class="section level2">

2
reference/clinical_breakpoints.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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reference/count.html
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@ -12,7 +12,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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reference/custom_eucast_rules.html
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@ -10,7 +10,7 @@
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reference/dosage.html
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@ -10,7 +10,7 @@
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reference/eucast_rules.html
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@ -12,7 +12,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
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reference/example_isolates.html
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@ -10,7 +10,7 @@
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reference/example_isolates_unclean.html
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@ -10,7 +10,7 @@
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reference/first_isolate.html
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@ -12,7 +12,7 @@
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reference/g.test.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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106
reference/get_episode.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -192,27 +192,27 @@
<span class="r-in"><span><span class="va">df</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq_len</a></span><span class="op">(</span><span class="fl">2000</span><span class="op">)</span>, size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># indices</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 8 35 40 37 41 12 38 37 11 46 3 25 20 29 7 46 15 30 29 16 26 44 22 20 14</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 25 45 2 38 18 44 39 4 28 9 20 6 27 31 34 22 18 11 45 4 17 24 32 48 5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 34 36 12 47 37 29 2 39 11 29 27 45 35 27 45 23 22 25 7 37 17 40 46 9 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 12 42 21 10 15 14 25 44 25 8 12 26 33 43 45 41 19 33 4 32 6 13 1 18 9</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 14 42 21 14 39 21 36 28 23 18 43 10 36 41 37 1 39 7 13 36 7 40 29 42 25</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 10 30 18 38 35 10 19 6 16 8 28 13 10 11 45 40 32 5 5 31 9 24 22 26 41</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 20 39 17 43 11 11 27 8 12 28 20 1 43 8 33 44 22 17 27 15 16 35 18 42 22</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 34 13 35 11 31 2 17 4 29 43 10 20 22 21 3 34 26 8 44 13 12 6 27 44 7</span>
<span class="r-in"><span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># TRUE/FALSE</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE TRUE TRUE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] TRUE TRUE TRUE FALSE TRUE TRUE FALSE TRUE TRUE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] TRUE FALSE TRUE TRUE FALSE TRUE FALSE TRUE TRUE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] TRUE TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE TRUE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] TRUE TRUE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] FALSE FALSE TRUE FALSE TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] FALSE FALSE FALSE TRUE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE TRUE TRUE FALSE TRUE FALSE TRUE TRUE TRUE TRUE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] FALSE TRUE TRUE TRUE FALSE TRUE TRUE FALSE FALSE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] TRUE FALSE TRUE FALSE TRUE TRUE FALSE TRUE TRUE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] FALSE FALSE TRUE TRUE FALSE TRUE TRUE FALSE TRUE TRUE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] TRUE FALSE TRUE FALSE TRUE FALSE FALSE FALSE TRUE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] FALSE FALSE FALSE FALSE</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: 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;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2003-01-25 088256 73 F ICU B_STPHY_HMNS R NA R R </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-07-21 955940 82 F Clinical B_PSDMN_AERG R NA NA R </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># FEP &lt;sir&gt;, CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># GEN &lt;sir&gt;, TOB &lt;sir&gt;, AMK &lt;sir&gt;, KAN &lt;sir&gt;, TMP &lt;sir&gt;, SXT &lt;sir&gt;,</span></span>
@ -247,19 +247,19 @@
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">patient</span>, <span class="va">condition</span>, <span class="va">date</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 100 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, condition [98]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, condition [91]</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> 004531 2013-12-02 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 023456 2012-11-24 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 005088 2007-08-22 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 021648 2004-08-21 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 067927 2002-02-14 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 088256 2003-01-25 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 092034 2006-06-12 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 0F9638 2014-09-22 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 114570 2003-04-22 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 119392 2010-11-01 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 151041 2006-02-09 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 1710B8 2008-01-22 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 077922 2009-08-24 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 078381 2014-06-28 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 078381 2014-08-17 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 083080 2010-02-25 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 092034 2016-08-07 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 0E2483 2007-05-29 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 0F9638 2014-09-22 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 90 more rows</span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
@ -273,19 +273,19 @@
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">patient</span>, <span class="va">ward</span>, <span class="va">date</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 100 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: ward, patient [95]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: ward, patient [90]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward date patient new_index new_logical</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical 2013-12-02 004531 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical 2012-11-24 023456 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical 2007-08-22 005088 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical 2004-08-21 021648 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> ICU 2002-02-14 067927 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> ICU 2003-01-25 088256 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> ICU 2006-06-12 092034 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Clinical 2014-09-22 0F9638 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> ICU 2003-04-22 114570 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical 2010-11-01 119392 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Clinical 2006-02-09 151041 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical 2008-01-22 1710B8 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical 2009-08-24 077922 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> ICU 2014-06-28 078381 1 FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> ICU 2014-08-17 078381 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Clinical 2010-02-25 083080 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical 2016-08-07 092034 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Clinical 2007-05-29 0E2483 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical 2014-09-22 0F9638 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 90 more rows</span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
@ -301,9 +301,9 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 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 55 12 36 42</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 30 11 21 24</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 10 7 10 10</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 58 12 36 45</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 28 10 23 28</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 4 3 4 4</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># grouping on patients and microorganisms leads to the same</span></span></span>
<span class="r-in"><span><span class="co"># results as first_isolate() when using 'episode-based':</span></span></span>
@ -332,19 +332,19 @@
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_data.html" class="external-link">group_vars</a></span><span class="op">(</span><span class="va">.</span><span class="op">)</span>, <span class="va">flag_episode</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 100 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, mo, ward [95]</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> 4F6B71 B_STRPT_GRPB Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 516F62 B_GRNLC_ADCN ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> A76045 B_STPHY_EPDR ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 414858 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 329C35 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> D27987 B_ENTRBC_CLOC ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 590035 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 960698 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 151041 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 987C84 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, mo, ward [97]</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> 895298 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> D08278 B_ESCHR_COLI Outpatient TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 445249 B_STPHY_CONS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 968584 B_PSDMN_AERG Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 976813 B_STPHY_AURS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> AB0003 B_STRPT Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 715822 B_STPHY_EPDR Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 387C40 B_KLBSL_PNMN Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> B13757 B_STPHY_EPDR Outpatient TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 005088 B_SLMNL_ENTR Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 90 more rows</span></span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>

2
reference/ggplot_pca.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9142</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9143</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_sir.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="">1.8.2.9142</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9143</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="">1.8.2.9142</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9143</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

4
reference/index.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9142</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9143</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -256,7 +256,7 @@
<dl><dt>
<code><a href="antibiogram.html">antibiogram()</a></code> <code><a href="antibiogram.html">plot(<i>&lt;antibiogram&gt;</i>)</a></code> <code><a href="antibiogram.html">autoplot(<i>&lt;antibiogram&gt;</i>)</a></code> <code><a href="antibiogram.html">knit_print.antibiogram()</a></code>
<code><a href="antibiogram.html">antibiogram()</a></code> <code><a href="antibiogram.html">plot(<i>&lt;antibiogram&gt;</i>)</a></code> <code><a href="antibiogram.html">autoplot(<i>&lt;antibiogram&gt;</i>)</a></code> <code><a href="antibiogram.html">knit_print(<i>&lt;antibiogram&gt;</i>)</a></code>
</dt>
<dd>Generate Antibiogram: Traditional, Combined, Syndromic, or Weighted-Incidence Syndromic Combination (WISCA)</dd>
</dl><dl><dt>

2
reference/intrinsic_resistant.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9142</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9143</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="">1.8.2.9142</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9143</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="">1.8.2.9142</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9143</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="">1.8.2.9142</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9143</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="">1.8.2.9142</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9143</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -182,9 +182,9 @@
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 3.027456</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2.990683</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] -0.06012916</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.00935699</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="">1.8.2.9142</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9143</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="">1.8.2.9142</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9143</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">

71
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="">1.8.2.9142</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9143</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -201,30 +201,29 @@
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">sir</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_sir</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">sir</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] I R I R S R R I S S</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] I I S I S I I I I S</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">sir</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.7745967 1.1618950 -0.7745967 1.1618950 -0.7745967 1.1618950</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 1.1618950 -0.7745967 -0.7745967 -0.7745967</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN</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] 128 0.125 0.025 1 1 8 0.125 &lt;=0.01 1 0.0625</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 256 16 0.025 8 0.001 128 0.001 0.005 0.025 0.025</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] 2.0067688 -0.4415318 -1.0100096 0.2929584 0.2929584 1.0274486</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.4415318 -1.3336573 0.2929584 -0.6863619</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1.4628662 0.8866012 -0.4563741 0.7425349 -1.1253971 1.3187999</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -1.1253971 -0.7908856 -0.4563741 -0.4563741</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] 2.0067688 -0.4415318 -1.0100096 0.2929584 0.2929584 1.0274486</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.4415318 -1.3336573 0.2929584 -0.6863619</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1.4628662 0.8866012 -0.4563741 0.7425349 -1.1253971 1.3187999</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -1.1253971 -0.7908856 -0.4563741 -0.4563741</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] 19 33 9 33 40 43 40 7 39 44</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 50 32 24 26 49 40 9 34 41 14</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] -0.8390265 0.1649368 -1.5561432 0.1649368 0.6669185 0.8820535</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.6669185 -1.6995665 0.5952068 0.9537652</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1.311234687 0.007244391 -0.572306852 -0.427419042 1.238790782</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [6] 0.586795633 -1.658965433 0.152132201 0.659239539 -1.296745906</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>
@ -234,22 +233,22 @@
<span class="r-in"><span> tobr <span class="op">=</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span>, ab <span class="op">=</span> <span class="st">"tobr"</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">y</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A R 20 1 &gt;=16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B R 17 &gt;=16 &lt;=0.25</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C I 22 2 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D R 18 &gt;=16 0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E S 25 8 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F I 18 1 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G I 28 4 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H R 19 &gt;=16 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I R 21 1 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J I 18 8 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A I 21 2 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B S 24 0.5 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C R 29 0.5 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D I 29 &gt;=4 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E I 31 2 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F R 24 0.5 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G I 20 1 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H S 23 0.5 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I I 19 1 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J S 21 2 16</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> and "tobr"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.210274980 -0.189659861 -0.361042252 0.008770745 0.395772293</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [6] -0.660927881 0.080327628 0.590266790 0.025640147 -0.099422589</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.3578553 -0.2633009 0.2567155 0.7156924 0.4223198 0.1444269</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.6445214 -0.1375992 -0.5188196 0.3829419</span>
<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op">&lt;-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in .subset(x, j):</span> invalid subscript type 'list'</span>
<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
@ -265,17 +264,17 @@
<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",</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> and "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 I 22 2 2 -0.361042252 0.0000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B R 17 &gt;=16 &lt;=0.25 -0.189659861 0.1713824</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 J I 18 8 8 -0.099422589 0.2616197</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 F I 18 1 4 -0.660927881 0.2998856</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 D R 18 &gt;=16 0.5 0.008770745 0.3698130</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 I R 21 1 4 0.025640147 0.3866824</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G I 28 4 1 0.080327628 0.4413699</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 A R 20 1 &gt;=16 0.210274980 0.5713172</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 E S 25 8 8 0.395772293 0.7568145</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 H R 19 &gt;=16 8 0.590266790 0.9513090</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 0.5 1 0.2567155 0.0000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 F R 24 0.5 2 0.1444269 0.1122886</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 J S 21 2 16 0.3829419 0.1262264</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 E I 31 2 2 0.4223198 0.1656043</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 H S 23 0.5 8 -0.1375992 0.3943147</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 D I 29 &gt;=4 4 0.7156924 0.4589769</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 B S 24 0.5 4 -0.2633009 0.5200164</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 A I 21 2 1 -0.3578553 0.6145708</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I I 19 1 2 -0.5188196 0.7755351</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 G I 20 1 1 -0.6445214 0.9012368</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="">1.8.2.9142</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9143</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/microorganisms.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9142</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9143</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 @@
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@ -12,7 +12,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
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@ -10,7 +10,7 @@
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@ -193,42 +193,44 @@
<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] 0.025 16 2 64 0.5 0.01 8 2 16 0.025 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 0.125 0.002 0.001 16 0.0625 1 0.001 0.001 0.0625 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 0.025 0.001 64 32 64 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 8 0.002 0.005 0.125 &gt;=256 16 32 &gt;=256 0.025 0.125 &gt;=256 0.005</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] &gt;=256 &gt;=256 &gt;=256 0.025 16 1 0.125 128 8 0.001 128 0.005</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 64 </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] 26 50 43 50 14 13 12 7 15 49 10 6 48 40 38 45 43 50 36 45 36 29 27 37 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 49 42 10 37 12 22 29 28 11 50 44 39 14 41 6 16 47 46 43 38 24 15 42 45 38</span>
<span class="r-in"><span><span class="fu">random_sir</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] R I S I R R R S I S S R R I S I R S I R I I R R I</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] I R I S I I R I R R I R I I I S I I R I I S R 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] &lt;=0.001 &gt;=64 4 0.01 4 16 0.0625 &lt;=0.001 &gt;=64 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] &lt;=0.001 0.005 0.002 0.01 &lt;=0.001 0.0625 2 0.0625 &lt;=0.001</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 2 1 0.025 8 0.0625 &gt;=64 0.005 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1 1 64 8 0.025 0.001 0.001 2 0.5 16 0.005 32 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] 0.125 1 32 0.25 0.125 0.002 2 0.5 4 0.125 0.01 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 0.001</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] 1 0.5 0.5 4 &gt;=32 4 1 2 4 4 2 0.5 1 2 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [16] 1 &gt;=32 &gt;=32 0.5 8 0.5 2 0.5 4 &gt;=32</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 4 1 &gt;=16 4 &gt;=16 1 &lt;=0.5 2 &gt;=16 &lt;=0.5 &lt;=0.5 &gt;=16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] 8 4 8 &gt;=16 2 &lt;=0.5 &lt;=0.5 1 &gt;=16 2 1 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 1 </span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-4</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1 0.0625 0.0625 0.125 0.25 2 0.0625 0.0625 0.125 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 0.0625 0.125 0.125 4 0.0625 4 0.125 0.25 0.5 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 0.0625 0.0625 0.5 0.125 0.5 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1 8 0.5 0.25 4 &gt;=16 8 0.25 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [9] &lt;=0.0625 0.125 1 8 &gt;=16 &gt;=16 &gt;=16 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [17] 4 0.5 &lt;=0.0625 0.5 2 2 0.125 0.5 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 8 </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] 40 12 48 48 41 39 44 22 46 45 19 9 37 49 50 18 9 42 14 16 50 39 14 45 44</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 30 23 42 49 27 45 39 9 28 12 43 30 29 49 45 25 13 46 41 47 10 26 37 14 27</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 13 17 14 17 12 11 11 14 17 15 15 14 15 13 13 15 11 11 17 12 12 14 13 14</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 11 14 16 14 14 14 17 13 15 17 13 13 15 11 13 14 13 14 12 13 11 12 15 14 15</span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 12-27</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 25 23 24 18 15 27 25 17 24 18 17 15 16 21 27 16 24 20 17 23 25 22 19 23 24</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 22 20 21 17 20 27 17 24 17 25 27 18 27 25 16 21 25 20 19 27 15 17 20 24 20</span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
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reference/resistance_predict.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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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>
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@ -181,7 +181,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">skewness</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Uniform.html" class="external-link">runif</a></span><span class="op">(</span><span class="fl">1000</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.01690184</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.003828091</span>
</code></pre></div>
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