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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="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</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 18 February 2023.</p>
generated on 22 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">2023-02-18</td>
<td align="center">2023-02-22</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">2023-02-18</td>
<td align="center">2023-02-22</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">2023-02-18</td>
<td align="center">2023-02-22</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -408,69 +408,69 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2015-08-25</td>
<td align="center">Z2</td>
<td align="center">Hospital B</td>
<td align="center">2014-12-01</td>
<td align="center">V4</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2010-08-12</td>
<td align="center">I7</td>
<td align="center">Hospital C</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2012-07-28</td>
<td align="center">V1</td>
<td align="center">Hospital B</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2011-07-03</td>
<td align="center">F3</td>
<td align="center">2012-09-30</td>
<td align="center">D9</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2015-06-20</td>
<td align="center">R4</td>
<td align="center">Hospital B</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">2011-08-02</td>
<td align="center">M4</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2012-08-20</td>
<td align="center">U4</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2014-04-29</td>
<td align="center">J7</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2015-10-22</td>
<td align="center">H6</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">2015-05-14</td>
<td align="center">N5</td>
<td align="center">Hospital C</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
</tbody>
@ -507,16 +507,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,346</td>
<td align="right">51.73%</td>
<td align="right">10,346</td>
<td align="right">51.73%</td>
<td align="right">10,361</td>
<td align="right">51.81%</td>
<td align="right">10,361</td>
<td align="right">51.81%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,654</td>
<td align="right">48.27%</td>
<td align="right">9,639</td>
<td align="right">48.20%</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 12,322 'phenotype-based' first isolates (61.6% of total where a</span></span>
<span><span class="co">#&gt; =&gt; Found 12,431 'phenotype-based' first isolates (62.2% of total where a</span></span>
<span><span class="co">#&gt; microbial ID was available)</span></span></code></pre></div>
<p>So only 61.6% is suitable for resistance analysis! We can now filter
<p>So only 62.2% 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">
@ -641,7 +641,7 @@ on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html"
<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<p>So we end up with 12 322 isolates for analysis. Now our data looks
<p>So we end up with 12 431 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>
@ -680,78 +680,30 @@ like:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2014-12-01</td>
<td align="center">V4</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">I</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="left">2</td>
<td align="center">2011-07-03</td>
<td align="center">F3</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">I</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">3</td>
<td align="center">2015-06-20</td>
<td align="center">R4</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">4</td>
<td align="center">2012-08-20</td>
<td align="center">U4</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">7</td>
<td align="center">2017-10-28</td>
<td align="center">J6</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">8</td>
<td align="center">2017-08-19</td>
<td align="center">I1</td>
<td align="center">Hospital D</td>
<td align="center">2010-08-12</td>
<td align="center">I7</td>
<td align="center">Hospital C</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">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
@ -759,22 +711,70 @@ like:</p>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">9</td>
<td align="center">2017-07-16</td>
<td align="center">S8</td>
<tr class="odd">
<td align="left">3</td>
<td align="center">2012-07-28</td>
<td align="center">V1</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">6</td>
<td align="center">2015-05-14</td>
<td align="center">N5</td>
<td align="center">Hospital C</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">7</td>
<td align="center">2011-03-07</td>
<td align="center">X4</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</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">8</td>
<td align="center">2016-11-12</td>
<td align="center">T7</td>
<td align="center">Hospital A</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
<p>Time for the analysis!</p>
@ -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: 12,322<br>
Available: 12,322 (100%, NA: 0 = 0%)<br>
Length: 12,431<br>
Available: 12,431 (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">5,843</td>
<td align="right">47.42%</td>
<td align="right">5,843</td>
<td align="right">47.42%</td>
<td align="right">5,970</td>
<td align="right">48.03%</td>
<td align="right">5,970</td>
<td align="right">48.03%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,319</td>
<td align="right">26.94%</td>
<td align="right">9,162</td>
<td align="right">74.35%</td>
<td align="right">3,335</td>
<td align="right">26.83%</td>
<td align="right">9,305</td>
<td align="right">74.85%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">1,857</td>
<td align="right">15.07%</td>
<td align="right">11,019</td>
<td align="right">89.43%</td>
<td align="right">1,817</td>
<td align="right">14.62%</td>
<td align="right">11,122</td>
<td align="right">89.47%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,303</td>
<td align="right">10.57%</td>
<td align="right">12,322</td>
<td align="right">1,309</td>
<td align="right">10.53%</td>
<td align="right">12,431</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -909,41 +909,11 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2015-06-20</td>
<td align="center">R4</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2014-01-08</td>
<td align="center">V3</td>
<td align="center">Hospital C</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="odd">
<td align="center">2013-07-30</td>
<td align="center">Y4</td>
<td align="center">Hospital B</td>
<td align="center">2014-12-01</td>
<td align="center">V4</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">R</td>
@ -954,13 +924,58 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2013-03-23</td>
<td align="center">E6</td>
<td align="center">Hospital A</td>
<td align="center">2012-07-28</td>
<td align="center">V1</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2016-08-30</td>
<td align="center">Q3</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">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2013-03-03</td>
<td align="center">F7</td>
<td align="center">Hospital B</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">2010-10-30</td>
<td align="center">H10</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
@ -968,36 +983,21 @@ antibiotic class they are in:</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2013-12-04</td>
<td align="center">S8</td>
<td align="center">Hospital B</td>
<tr class="even">
<td align="center">2011-04-07</td>
<td align="center">D8</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2013-02-27</td>
<td align="center">Z2</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">I</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>
</tbody>
</table>
<p>If you want to get a quick glance of the number of isolates in
@ -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">2759</td>
<td align="center">1167</td>
<td align="center">1917</td>
<td align="center">5843</td>
<td align="center">2855</td>
<td align="center">1161</td>
<td align="center">1954</td>
<td align="center">5970</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">1459</td>
<td align="center">1245</td>
<td align="center">3139</td>
<td align="center">5843</td>
<td align="center">1518</td>
<td align="center">1282</td>
<td align="center">3170</td>
<td align="center">5970</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">2071</td>
<td align="center">1788</td>
<td align="center">1984</td>
<td align="center">5843</td>
<td align="center">2087</td>
<td align="center">1796</td>
<td align="center">2087</td>
<td align="center">5970</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">2002</td>
<td align="center">1833</td>
<td align="center">2008</td>
<td align="center">5843</td>
<td align="center">2119</td>
<td align="center">1854</td>
<td align="center">1997</td>
<td align="center">5970</td>
</tr>
<tr class="odd">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">583</td>
<td align="center">292</td>
<td align="center">428</td>
<td align="center">1303</td>
<td align="center">615</td>
<td align="center">256</td>
<td align="center">438</td>
<td align="center">1309</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">1303</td>
<td align="center">1303</td>
<td align="center">1309</td>
<td align="center">1309</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">2002</td>
<td align="center">1833</td>
<td align="center">2008</td>
<td align="center">5843</td>
<td align="center">2119</td>
<td align="center">1854</td>
<td align="center">1997</td>
<td align="center">5970</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">456</td>
<td align="center">423</td>
<td align="center">424</td>
<td align="center">1303</td>
<td align="center">409</td>
<td align="center">444</td>
<td align="center">1309</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">1144</td>
<td align="center">1045</td>
<td align="center">1130</td>
<td align="center">3319</td>
<td align="center">1122</td>
<td align="center">1075</td>
<td align="center">1138</td>
<td align="center">3335</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">1857</td>
<td align="center">1857</td>
<td align="center">1817</td>
<td align="center">1817</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] 0.5842396</span></span></code></pre></div>
<span><span class="co">#&gt; [1] 0.5810474</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">0.5827676</td>
<td align="center">0.5871733</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5907183</td>
<td align="center">0.5822430</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5845813</td>
<td align="center">0.5788635</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5747605</td>
<td align="center">0.5717638</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">0.5827676</td>
<td align="center">3830</td>
<td align="center">0.5871733</td>
<td align="center">3711</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5907183</td>
<td align="center">4288</td>
<td align="center">0.5822430</td>
<td align="center">4280</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5845813</td>
<td align="center">1803</td>
<td align="center">0.5788635</td>
<td align="center">1883</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5747605</td>
<td align="center">2401</td>
<td align="center">0.5717638</td>
<td align="center">2557</td>
</tr>
</tbody>
</table>
@ -1237,27 +1237,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.6719151</td>
<td align="center">0.6563409</td>
<td align="center">0.8921787</td>
<td align="center">0.6726968</td>
<td align="center">0.6654941</td>
<td align="center">0.8934673</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.6715272</td>
<td align="center">0.6745971</td>
<td align="center">0.8879509</td>
<td align="center">0.6653934</td>
<td align="center">0.6608098</td>
<td align="center">0.8800611</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.6776137</td>
<td align="center">0.6595360</td>
<td align="center">0.8945466</td>
<td align="center">0.6773613</td>
<td align="center">0.6587706</td>
<td align="center">0.8917541</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.4717286</td>
<td align="center">0.4777105</td>
<td align="center">0.0000000</td>
<td align="center">0.4717286</td>
<td align="center">0.4777105</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">58.3%</td>
<td align="right">35.1%</td>
<td align="right">58.7%</td>
<td align="right">36.2%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">59.1%</td>
<td align="right">35.8%</td>
<td align="right">58.2%</td>
<td align="right">35.9%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">58.5%</td>
<td align="right">37.4%</td>
<td align="right">57.9%</td>
<td align="right">34.9%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">57.5%</td>
<td align="right">34.9%</td>
<td align="right">57.2%</td>
<td align="right">34.5%</td>
</tr>
</tbody>
</table>
@ -1417,16 +1417,16 @@ classes) <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code>:</p>
<code class="sourceCode R"><span><span class="va">mic_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span></span>
<span><span class="va">mic_values</span></span>
<span><span class="co">#&gt; Class 'mic'</span></span>
<span><span class="co">#&gt; [1] 0.25 0.5 0.125 0.125 16 32 0.002 &gt;=256 0.025 1 </span></span>
<span><span class="co">#&gt; [11] 64 128 32 0.25 0.5 0.0625 128 &gt;=256 8 0.002 </span></span>
<span><span class="co">#&gt; [21] 0.005 0.002 4 0.125 0.005 0.125 0.01 4 64 0.005 </span></span>
<span><span class="co">#&gt; [31] 32 0.002 0.25 0.002 0.0625 32 16 128 0.001 128 </span></span>
<span><span class="co">#&gt; [41] 0.001 0.5 0.025 0.5 128 4 0.005 0.25 0.125 0.002 </span></span>
<span><span class="co">#&gt; [51] 16 0.025 0.005 0.0625 4 32 0.005 4 0.025 0.001 </span></span>
<span><span class="co">#&gt; [61] 128 0.125 0.025 2 4 0.0625 0.001 8 0.25 0.025 </span></span>
<span><span class="co">#&gt; [71] 1 32 &gt;=256 1 16 8 0.0625 0.01 2 0.005 </span></span>
<span><span class="co">#&gt; [81] 16 0.025 1 0.002 128 0.002 0.5 8 8 64 </span></span>
<span><span class="co">#&gt; [91] 128 0.01 0.005 16 0.002 0.005 &gt;=256 8 0.002 0.25</span></span></code></pre></div>
<span><span class="co">#&gt; [1] 0.0625 0.125 16 0.025 0.005 128 8 4 0.002 32 </span></span>
<span><span class="co">#&gt; [11] 64 0.5 0.025 0.01 8 0.002 0.5 1 0.125 0.001 </span></span>
<span><span class="co">#&gt; [21] 0.005 0.025 0.005 0.125 0.001 128 0.01 2 64 128 </span></span>
<span><span class="co">#&gt; [31] 8 1 1 128 8 4 16 0.5 0.25 0.25 </span></span>
<span><span class="co">#&gt; [41] 16 256 0.002 8 0.025 0.5 128 8 256 64 </span></span>
<span><span class="co">#&gt; [51] 0.025 128 0.025 0.001 1 0.002 0.125 0.001 256 0.01 </span></span>
<span><span class="co">#&gt; [61] 64 0.0625 0.025 16 0.5 0.125 256 1 1 128 </span></span>
<span><span class="co">#&gt; [71] 32 0.01 0.01 0.0625 128 4 16 0.005 256 8 </span></span>
<span><span class="co">#&gt; [81] 8 0.005 0.01 0.025 32 64 1 0.005 128 0.25 </span></span>
<span><span class="co">#&gt; [91] 16 0.001 0.5 0.001 0.25 0.0625 2 2 0.001 0.125</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>
@ -1438,7 +1438,8 @@ classes) <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code>:</p>
<p>But we could also be more specific, by generating MICs that are
likely to be found in <em>E. coli</em> for ciprofloxacin:</p>
<div class="sourceCode" id="cb38"><pre class="downlit sourceCode r">
<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>, 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>
<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>, 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="co">#&gt; [1] "here"</span></span></code></pre></div>
<p>For the <code><a href="../reference/plot.html">plot()</a></code> and <code><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot()</a></code> function, we
can define the microorganism and an antimicrobial agent the same way.
This will add the interpretation of those values according to a chosen
@ -1460,10 +1461,10 @@ 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 18 29 27 31 26 27 30 31 18 30 25 17 20 20 31 22 22 30 26 24 26 23 28 28</span></span>
<span><span class="co">#&gt; [26] 24 27 29 20 30 25 25 25 22 23 27 27 23 29 27 23 20 19 23 23 18 29 21 31 29</span></span>
<span><span class="co">#&gt; [51] 19 31 27 27 31 20 22 28 31 19 21 30 28 21 24 21 20 20 19 27 26 30 19 24 29</span></span>
<span><span class="co">#&gt; [76] 17 26 18 27 23 19 29 24 27 27 20 25 28 17 21 29 29 17 22 20 26 24 23 17 25</span></span></code></pre></div>
<span><span class="co">#&gt; [1] 27 29 20 31 27 23 30 27 19 24 31 20 19 28 23 25 17 22 20 24 24 28 17 29 26</span></span>
<span><span class="co">#&gt; [26] 29 31 23 23 30 18 29 30 23 21 19 25 24 22 18 28 25 24 18 25 25 27 24 24 27</span></span>
<span><span class="co">#&gt; [51] 27 18 18 25 22 27 30 24 31 26 19 30 21 22 23 19 23 23 22 26 22 29 29 29 29</span></span>
<span><span class="co">#&gt; [76] 26 26 24 30 17 30 17 25 27 17 27 20 23 17 21 17 27 18 23 30 19 22 20 30 17</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="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</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">

56
articles/MDR.html
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -385,18 +385,18 @@ names or codes, this would have worked exactly the same way:</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span>
<span><span class="co">#&gt; rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
<span><span class="co">#&gt; 1 S R R R S S</span></span>
<span><span class="co">#&gt; 2 I I S I R R</span></span>
<span><span class="co">#&gt; 3 S S S I R I</span></span>
<span><span class="co">#&gt; 4 I I R R R S</span></span>
<span><span class="co">#&gt; 5 I I S I R S</span></span>
<span><span class="co">#&gt; 6 S R I I R S</span></span>
<span><span class="co">#&gt; 1 S I I I R R</span></span>
<span><span class="co">#&gt; 2 I S I R I S</span></span>
<span><span class="co">#&gt; 3 I S I R R I</span></span>
<span><span class="co">#&gt; 4 I I R R S I</span></span>
<span><span class="co">#&gt; 5 S S R S R R</span></span>
<span><span class="co">#&gt; 6 R I I S S I</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 R</span></span>
<span><span class="co">#&gt; 3 S</span></span>
<span><span class="co">#&gt; 2 S</span></span>
<span><span class="co">#&gt; 3 I</span></span>
<span><span class="co">#&gt; 4 R</span></span>
<span><span class="co">#&gt; 5 I</span></span>
<span><span class="co">#&gt; 5 S</span></span>
<span><span class="co">#&gt; 6 I</span></span></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can
use:</p>
@ -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">3165</td>
<td align="right">63.30%</td>
<td align="right">3165</td>
<td align="right">63.30%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">966</td>
<td align="right">19.32%</td>
<td align="right">4187</td>
<td align="right">83.74%</td>
<td align="right">1009</td>
<td align="right">20.18%</td>
<td align="right">4174</td>
<td align="right">83.48%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">448</td>
<td align="right">8.96%</td>
<td align="right">4635</td>
<td align="right">92.70%</td>
<td align="right">455</td>
<td align="right">9.10%</td>
<td align="right">4629</td>
<td align="right">92.58%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">256</td>
<td align="right">5.12%</td>
<td align="right">4891</td>
<td align="right">97.82%</td>
<td align="right">270</td>
<td align="right">5.40%</td>
<td align="right">4899</td>
<td align="right">97.98%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">109</td>
<td align="right">2.18%</td>
<td align="right">101</td>
<td align="right">2.02%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

6
articles/PCA.html
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</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">
@ -280,8 +280,8 @@ that contain numeric values in all selected variables, so we now only
need to do:</p>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">pca_result</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/pca.html">pca</a></span><span class="op">(</span><span class="va">resistance_data</span><span class="op">)</span></span>
<span><span class="co">#&gt; ℹ Columns selected for PCA: "AMC", "CAZ", "CTX", "CXM", "GEN", "SXT", "TMP"</span></span>
<span><span class="co">#&gt; and "TOB". Total observations available: 7.</span></span></code></pre></div>
<span><span class="co">#&gt; ℹ Columns selected for PCA: "AMC", "CAZ", "CTX", "CXM", "GEN", "SXT",</span></span>
<span><span class="co">#&gt; "TMP", and "TOB". Total observations available: 7.</span></span></code></pre></div>
<p>The result can be reviewed with the good old <code><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary()</a></code>
function:</p>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">

6
articles/SPSS.html
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -178,7 +178,7 @@
<h4 data-toc-skip class="author">Dr. Matthijs
Berends</h4>
<h4 data-toc-skip class="date">18 February 2023</h4>
<h4 data-toc-skip class="date">22 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>
@ -257,7 +257,7 @@ data using a custom made website. The webdesign knowledge needed
<li>
<p><strong>R has a huge community.</strong></p>
<p>Many R users just ask questions on websites like <a href="https://stackoverflow.com" class="external-link">StackOverflow.com</a>, the largest
online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">480 788
online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">481 631
R-related questions</a> have already been asked on this platform (that
covers questions and answers for any programming language). In my own
experience, most questions are answered within a couple of

15
articles/WHONET.html
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</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">
@ -230,7 +230,13 @@ In other words, they should only contain values <code>"S"</code>,
<span> <span class="co"># get microbial ID based on given organism</span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>mo <span class="op">=</span> <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="va">Organism</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="co"># transform everything from "AMP_ND10" to "CIP_EE" to the new `sir` class</span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">AMP_ND10</span><span class="op">:</span><span class="va">CIP_EE</span><span class="op">)</span>, <span class="va">as.sir</span><span class="op">)</span></span></code></pre></div>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">AMP_ND10</span><span class="op">:</span><span class="va">CIP_EE</span><span class="op">)</span>, <span class="va">as.sir</span><span class="op">)</span></span>
<span><span class="co">#&gt; Warning: There was 1 warning in `mutate()`.</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> In argument: `AMP_ND10 = (function (x, ...) ...`.</span></span>
<span><span class="co">#&gt; Caused by warning:</span></span>
<span><span class="co">#&gt; <span style="color: #BBBB00;">!</span> The 'rsi' class has been replaced with 'sir'. Transform your 'rsi' columns</span></span>
<span><span class="co">#&gt; to 'sir' with as.sir(), e.g.:</span></span>
<span><span class="co">#&gt; your_data %&gt;% mutate_if(is.rsi, as.sir)</span></span></code></pre></div>
<p>No errors or warnings, so all values are transformed succesfully.</p>
<p>We also created a package dedicated to data cleaning and checking,
called the <code>cleaner</code> package. Its <code><a href="https://msberends.github.io/cleaner/reference/freq.html" class="external-link">freq()</a></code>
@ -352,14 +358,11 @@ Longest: 40</p>
<span><span class="co"># amoxicillin/clavulanic acid (J01CR02) as an example</span></span>
<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 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">AMC_ND2</span><span class="op">)</span></span></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: factor &gt; ordered &gt; sir (numeric)<br>
<p>Class: factor &gt; ordered &gt; rsi (numeric)<br>
Length: 500<br>
Levels: 3: S &lt; I &lt; R<br>
Available: 481 (96.2%, NA: 19 = 3.8%)<br>
Unique: 3</p>
<p>Drug: Amoxicillin/clavulanic acid (AMC, J01CR02)<br>
Drug group: Beta-lactams/penicillins<br>
%SI: 78.59%</p>
<table class="table">
<thead><tr class="header">
<th align="left"></th>

20
articles/datasets.html
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -176,7 +176,7 @@
<main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
<h4 data-toc-skip class="date">18 February 2023</h4>
<h4 data-toc-skip class="date">22 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>
@ -203,7 +203,7 @@ column names:<br><em>mo</em>, <em>fullname</em>, <em>status</em>, <em>kingdom</e
<em>genus</em>, <em>species</em>, <em>subspecies</em>, <em>rank</em>,
<em>ref</em>, <em>source</em>, <em>lpsn</em>, <em>lpsn_parent</em>,
<em>lpsn_renamed_to</em>, <em>gbif</em>, <em>gbif_parent</em>,
<em>gbif_renamed_to</em>, <em>prevalence</em> and <em>snomed</em>.</p>
<em>gbif_renamed_to</em>, <em>prevalence</em>, and <em>snomed</em>.</p>
<p>This data set is in R available as <code>microorganisms</code>, after
you load the <code>AMR</code> package.</p>
<p>It was last updated on 6 February 2023 10:57:22 UTC. Find more info
@ -502,10 +502,10 @@ Set Name ‘Microoganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href
column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>atc</em>,
<em>atc_group1</em>, <em>atc_group2</em>, <em>abbreviations</em>,
<em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>,
<em>iv_ddd</em>, <em>iv_units</em> and <em>loinc</em>.</p>
<em>iv_ddd</em>, <em>iv_units</em>, and <em>loinc</em>.</p>
<p>This data set is in R available as <code>antibiotics</code>, after
you load the <code>AMR</code> package.</p>
<p>It was last updated on 30 October 2022 20:05:46 UTC. Find more info
<p>It was last updated on 22 February 2023 13:38:57 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
@ -701,7 +701,7 @@ inhibitors</td>
<p>A data set with 120 rows and 11 columns, containing the following
column names:<br><em>av</em>, <em>name</em>, <em>atc</em>, <em>cid</em>,
<em>atc_group</em>, <em>synonyms</em>, <em>oral_ddd</em>,
<em>oral_units</em>, <em>iv_ddd</em>, <em>iv_units</em> and
<em>oral_units</em>, <em>iv_ddd</em>, <em>iv_units</em>, and
<em>loinc</em>.</p>
<p>This data set is in R available as <code>antivirals</code>, after you
load the <code>AMR</code> package.</p>
@ -880,7 +880,7 @@ inhibitors</td>
<p>A data set with 18 308 rows and 11 columns, containing the following
column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>,
<em>rank_index</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</em>,
<em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
<em>breakpoint_S</em>, <em>breakpoint_R</em>, and <em>uti</em>.</p>
<p>This data set is in R available as <code>clinical_breakpoints</code>,
after you load the <code>AMR</code> package.</p>
<p>It was last updated on 21 January 2023 22:47:20 UTC. Find more info
@ -1341,7 +1341,7 @@ v3.3</a> (2021).</p>
<p>A data set with 336 rows and 9 columns, containing the following
column names:<br><em>ab</em>, <em>name</em>, <em>type</em>, <em>dose</em>,
<em>dose_times</em>, <em>administration</em>, <em>notes</em>,
<em>original_txt</em> and <em>eucast_version</em>.</p>
<em>original_txt</em>, and <em>eucast_version</em>.</p>
<p>This data set is in R available as <code>dosage</code>, after you
load the <code>AMR</code> package.</p>
<p>It was last updated on 14 November 2022 14:20:39 UTC. Find more info
@ -1492,7 +1492,7 @@ column names:<br><em>date</em>, <em>patient</em>, <em>age</em>, <em>gender</em>,
<em>CIP</em>, <em>MFX</em>, <em>VAN</em>, <em>TEC</em>, <em>TCY</em>,
<em>TGC</em>, <em>DOX</em>, <em>ERY</em>, <em>CLI</em>, <em>AZM</em>,
<em>IPM</em>, <em>MEM</em>, <em>MTR</em>, <em>CHL</em>, <em>COL</em>,
<em>MUP</em> and <em>RIF</em>.</p>
<em>MUP</em>, and <em>RIF</em>.</p>
<p>This data set is in R available as <code>example_isolates</code>,
after you load the <code>AMR</code> package.</p>
<p>It was last updated on 21 January 2023 22:47:20 UTC. Find more info
@ -1903,7 +1903,7 @@ Practice<a class="anchor" aria-label="anchor" href="#example_isolates_unclean-ex
</h2>
<p>A data set with 3 000 rows and 8 columns, containing the following
column names:<br><em>patient_id</em>, <em>hospital</em>, <em>date</em>,
<em>bacteria</em>, <em>AMX</em>, <em>AMC</em>, <em>CIP</em> and
<em>bacteria</em>, <em>AMX</em>, <em>AMC</em>, <em>CIP</em>, and
<em>GEN</em>.</p>
<p>This data set is in R available as
<code>example_isolates_unclean</code>, after you load the

2
articles/index.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
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@ -38,7 +38,7 @@
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@ -38,7 +38,7 @@
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