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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="">1.8.2.9050</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9051</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">
@ -168,7 +168,7 @@
<h4 data-toc-skip class="author">Dr. Matthijs
Berends</h4>
<h4 data-toc-skip class="date">13 November 2022</h4>
<h4 data-toc-skip class="date">14 November 2022</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/AMR.Rmd" class="external-link"><code>vignettes/AMR.Rmd</code></a></small>
<div class="d-none name"><code>AMR.Rmd</code></div>
@ -180,7 +180,7 @@ Berends</h4>
website update since they are based on randomly created values and the
page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
Markdown</a>. However, the methodology remains unchanged. This page was
generated on 13 November 2022.</p>
generated on 14 November 2022.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@ -236,21 +236,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2022-11-13</td>
<td align="center">2022-11-14</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="center">2022-11-13</td>
<td align="center">2022-11-14</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<tr class="odd">
<td align="center">2022-11-13</td>
<td align="center">2022-11-14</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -380,12 +380,12 @@ data set:</p>
<col width="13%">
<col width="13%">
<col width="13%">
<col width="28%">
<col width="26%">
<col width="5%">
<col width="5%">
<col width="5%">
<col width="5%">
<col width="8%">
<col width="9%">
</colgroup>
<thead><tr class="header">
<th align="center">date</th>
@ -400,53 +400,31 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2013-01-01</td>
<td align="center">Z8</td>
<td align="center">Hospital B</td>
<td align="center">2011-09-28</td>
<td align="center">W5</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2010-04-10</td>
<td align="center">I9</td>
<td align="center">Hospital B</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2017-06-19</td>
<td align="center">I1</td>
<td align="center">2013-01-09</td>
<td align="center">A10</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2014-01-26</td>
<td align="center">L2</td>
<td align="center">Hospital C</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">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2011-03-14</td>
<td align="center">T1</td>
<td align="center">Hospital B</td>
<td align="center">2010-03-15</td>
<td align="center">W2</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
@ -455,13 +433,35 @@ data set:</p>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2010-11-28</td>
<td align="center">E3</td>
<td align="center">Hospital B</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">2010-01-24</td>
<td align="center">W4</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2012-08-18</td>
<td align="center">P7</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2010-11-08</td>
<td align="center">J2</td>
<td align="center">Hospital B</td>
<td align="center">Klebsiella pneumoniae</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>
@ -499,18 +499,18 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,557</td>
<td align="right">52.79%</td>
<td align="right">10,557</td>
<td align="right">52.79%</td>
<td align="right">10,420</td>
<td align="right">52.1%</td>
<td align="right">10,420</td>
<td align="right">52.1%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,443</td>
<td align="right">47.22%</td>
<td align="right">9,580</td>
<td align="right">47.9%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
<td align="right">100.0%</td>
</tr>
</tbody>
</table>
@ -621,9 +621,9 @@ takes into account the antimicrobial susceptibility test results using
<span><span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span></span>
<span><span class="co"># 2</span></span>
<span><span class="co"># Including isolates from ICU.</span></span>
<span><span class="co"># =&gt; Found 10,739 'phenotype-based' first isolates (53.7% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,650 'phenotype-based' first isolates (53.3% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 53.7% is suitable for resistance analysis! We can now filter
<p>So only 53.3% is suitable for resistance analysis! We can now filter
on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the
<code>dplyr</code> package:</p>
<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
@ -634,7 +634,7 @@ on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html"
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="co"># Including isolates from ICU.</span></span></code></pre></div>
<p>So we end up with 10,739 isolates for analysis. Now our data looks
<p>So we end up with 10,650 isolates for analysis. Now our data looks
like:</p>
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">data_1st</span><span class="op">)</span></span></code></pre></div>
@ -673,30 +673,14 @@ like:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2013-01-01</td>
<td align="center">Z8</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">3</td>
<td align="center">2017-06-19</td>
<td align="center">I1</td>
<td align="left">2</td>
<td align="center">2013-01-09</td>
<td align="center">A10</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
@ -704,11 +688,11 @@ like:</p>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="center">2011-03-14</td>
<td align="center">T1</td>
<td align="center">Hospital B</td>
<tr class="even">
<td align="left">3</td>
<td align="center">2010-03-15</td>
<td align="center">W2</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -720,15 +704,47 @@ like:</p>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">4</td>
<td align="center">2010-01-24</td>
<td align="center">W4</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">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="left">6</td>
<td align="center">2010-11-28</td>
<td align="center">E3</td>
<td align="left">5</td>
<td align="center">2012-08-18</td>
<td align="center">P7</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">8</td>
<td align="center">2012-07-26</td>
<td align="center">J5</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
@ -736,36 +752,20 @@ like:</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">7</td>
<td align="center">2015-07-19</td>
<td align="center">Y3</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">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">2014-02-08</td>
<td align="center">U4</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">2015-03-14</td>
<td align="center">I4</td>
<td align="center">Hospital C</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">S</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">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
</tbody>
@ -801,8 +801,8 @@ readable:</p>
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://msberends.github.io/cleaner/reference/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></span></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 10,739<br>
Available: 10,739 (100%, NA: 0 = 0%)<br>
Length: 10,650<br>
Available: 10,650 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -827,33 +827,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">4,749</td>
<td align="right">44.22%</td>
<td align="right">4,749</td>
<td align="right">44.22%</td>
<td align="right">4,668</td>
<td align="right">43.83%</td>
<td align="right">4,668</td>
<td align="right">43.83%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,673</td>
<td align="right">24.89%</td>
<td align="right">7,422</td>
<td align="right">69.11%</td>
<td align="right">2,688</td>
<td align="right">25.24%</td>
<td align="right">7,356</td>
<td align="right">69.07%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,118</td>
<td align="right">19.72%</td>
<td align="right">9,540</td>
<td align="right">88.84%</td>
<td align="right">2,093</td>
<td align="right">19.65%</td>
<td align="right">9,449</td>
<td align="right">88.72%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,199</td>
<td align="right">11.16%</td>
<td align="right">10,739</td>
<td align="right">1,201</td>
<td align="right">11.28%</td>
<td align="right">10,650</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -874,14 +874,14 @@ antibiotic class they are in:</p>
<col width="9%">
<col width="9%">
<col width="9%">
<col width="11%">
<col width="10%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="6%">
<col width="11%">
<col width="11%">
<col width="12%">
<col width="9%">
<col width="5%">
</colgroup>
@ -902,87 +902,57 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2011-03-14</td>
<td align="center">T1</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">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">2010-11-28</td>
<td align="center">E3</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2014-02-08</td>
<td align="center">U4</td>
<td align="center">2010-03-15</td>
<td align="center">W2</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">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">2017-10-23</td>
<td align="center">Q3</td>
<td align="center">Hospital C</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2017-05-27</td>
<td align="center">W10</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<tr class="even">
<td align="center">2010-01-24</td>
<td align="center">W4</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">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">2012-07-26</td>
<td align="center">J5</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">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2016-10-31</td>
<td align="center">L4</td>
<td align="center">Hospital B</td>
<td align="center">2010-02-12</td>
<td align="center">E10</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">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
@ -991,6 +961,36 @@ antibiotic class they are in:</p>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2011-12-23</td>
<td align="center">R5</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2017-05-04</td>
<td align="center">X9</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
<p>If you want to get a quick glance of the number of isolates in
@ -1014,50 +1014,50 @@ different bug/drug combinations, you can use the
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">2232</td>
<td align="center">132</td>
<td align="center">2385</td>
<td align="center">4749</td>
<td align="center">2216</td>
<td align="center">123</td>
<td align="center">2329</td>
<td align="center">4668</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3526</td>
<td align="center">160</td>
<td align="center">1063</td>
<td align="center">4749</td>
<td align="center">3459</td>
<td align="center">138</td>
<td align="center">1071</td>
<td align="center">4668</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3417</td>
<td align="center">3368</td>
<td align="center">0</td>
<td align="center">1332</td>
<td align="center">4749</td>
<td align="center">1300</td>
<td align="center">4668</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4139</td>
<td align="center">4117</td>
<td align="center">0</td>
<td align="center">610</td>
<td align="center">4749</td>
<td align="center">551</td>
<td align="center">4668</td>
</tr>
<tr class="odd">
<td align="center">K. pneumoniae</td>
<td align="center">AMX</td>
<td align="center">0</td>
<td align="center">0</td>
<td align="center">1199</td>
<td align="center">1199</td>
<td align="center">1201</td>
<td align="center">1201</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">933</td>
<td align="center">44</td>
<td align="center">222</td>
<td align="center">1199</td>
<td align="center">952</td>
<td align="center">36</td>
<td align="center">213</td>
<td align="center">1201</td>
</tr>
</tbody>
</table>
@ -1080,34 +1080,34 @@ 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">4139</td>
<td align="center">4117</td>
<td align="center">0</td>
<td align="center">610</td>
<td align="center">4749</td>
<td align="center">551</td>
<td align="center">4668</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1089</td>
<td align="center">1100</td>
<td align="center">0</td>
<td align="center">110</td>
<td align="center">1199</td>
<td align="center">101</td>
<td align="center">1201</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2352</td>
<td align="center">2397</td>
<td align="center">0</td>
<td align="center">321</td>
<td align="center">2673</td>
<td align="center">291</td>
<td align="center">2688</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">2118</td>
<td align="center">2118</td>
<td align="center">2093</td>
<td align="center">2093</td>
</tr>
</tbody>
</table>
@ -1139,7 +1139,7 @@ I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equa
own:</p>
<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span></span>
<span><span class="co"># [1] 0.5423224</span></span></code></pre></div>
<span><span class="co"># [1] 0.5415962</span></span></code></pre></div>
<p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and
<code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r">
@ -1154,19 +1154,19 @@ own:</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5322120</td>
<td align="center">0.5346793</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5366357</td>
<td align="center">0.5482421</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5579757</td>
<td align="center">0.5480192</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5560205</td>
<td align="center">0.5347418</td>
</tr>
</tbody>
</table>
@ -1191,23 +1191,23 @@ 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">0.5322120</td>
<td align="center">3151</td>
<td align="center">0.5346793</td>
<td align="center">3071</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5366357</td>
<td align="center">3876</td>
<td align="center">0.5482421</td>
<td align="center">3783</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5579757</td>
<td align="center">1561</td>
<td align="center">0.5480192</td>
<td align="center">1666</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5560205</td>
<td align="center">2151</td>
<td align="center">0.5347418</td>
<td align="center">2130</td>
</tr>
</tbody>
</table>
@ -1232,27 +1232,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7761634</td>
<td align="center">0.8715519</td>
<td align="center">0.9816804</td>
<td align="center">0.7705656</td>
<td align="center">0.8819623</td>
<td align="center">0.9777207</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8148457</td>
<td align="center">0.9082569</td>
<td align="center">0.9824854</td>
<td align="center">0.8226478</td>
<td align="center">0.9159034</td>
<td align="center">0.9866778</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.8017209</td>
<td align="center">0.8799102</td>
<td align="center">0.9816685</td>
<td align="center">0.7979911</td>
<td align="center">0.8917411</td>
<td align="center">0.9769345</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5325779</td>
<td align="center">0.5470616</td>
<td align="center">0.0000000</td>
<td align="center">0.5325779</td>
<td align="center">0.5470616</td>
</tr>
</tbody>
</table>
@ -1280,23 +1280,23 @@ classes, use a antibiotic class selector such as
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">53.2%</td>
<td align="right">26.1%</td>
<td align="right">53.5%</td>
<td align="right">25.9%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">53.7%</td>
<td align="right">25.5%</td>
<td align="right">54.8%</td>
<td align="right">26.6%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">55.8%</td>
<td align="right">27.9%</td>
<td align="right">54.8%</td>
<td align="right">26.8%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">55.6%</td>
<td align="right">26.0%</td>
<td align="right">53.5%</td>
<td align="right">24.8%</td>
</tr>
</tbody>
</table>
@ -1412,16 +1412,18 @@ classes) <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code>:</p>
<code class="sourceCode R"><span><span class="va">mic_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span></span>
<span><span class="va">mic_values</span></span>
<span><span class="co"># Class 'mic'</span></span>
<span><span class="co"># [1] 0.0625 0.005 0.005 0.001 256 128 0.125 0.5 0.125 0.025 </span></span>
<span><span class="co"># [11] 8 64 0.0625 0.5 0.001 4 0.01 8 0.0625 4 </span></span>
<span><span class="co"># [21] 16 8 0.5 0.0625 0.01 0.001 0.01 8 8 0.01 </span></span>
<span><span class="co"># [31] 0.5 1 32 8 4 0.5 0.25 32 0.005 8 </span></span>
<span><span class="co"># [41] 128 32 0.001 128 8 0.025 64 8 16 0.0625</span></span>
<span><span class="co"># [51] 0.01 0.5 0.025 16 32 256 0.001 16 8 0.01 </span></span>
<span><span class="co"># [61] 0.5 8 8 0.0625 0.01 0.125 128 16 0.002 128 </span></span>
<span><span class="co"># [71] 64 128 64 32 32 16 64 0.01 64 2 </span></span>
<span><span class="co"># [81] 0.25 0.002 0.025 128 0.002 64 0.001 2 32 16 </span></span>
<span><span class="co"># [91] 0.005 8 0.25 0.002 16 32 1 0.25 16 0.005</span></span></code></pre></div>
<span><span class="co"># [1] 0.125 2 0.01 &lt;=0.002 &gt;=256 16 16 1 0.01 </span></span>
<span><span class="co"># [10] 0.25 0.01 64 &lt;=0.002 16 128 0.125 0.125 0.0625 </span></span>
<span><span class="co"># [19] 0.005 1 0.125 &gt;=256 16 0.01 0.125 2 0.25 </span></span>
<span><span class="co"># [28] 0.025 &gt;=256 0.01 0.0625 0.125 0.025 64 0.125 4 </span></span>
<span><span class="co"># [37] 32 64 &gt;=256 32 128 32 64 32 0.01 </span></span>
<span><span class="co"># [46] 0.005 0.0625 16 32 4 4 0.0625 0.01 2 </span></span>
<span><span class="co"># [55] 8 64 4 &gt;=256 4 &gt;=256 1 0.005 &lt;=0.002</span></span>
<span><span class="co"># [64] 0.25 4 0.125 1 128 0.125 128 0.25 1 </span></span>
<span><span class="co"># [73] &gt;=256 8 0.025 64 4 2 16 16 32 </span></span>
<span><span class="co"># [82] 0.25 8 4 16 0.005 64 0.0625 0.25 0.125 </span></span>
<span><span class="co"># [91] 0.25 0.0625 0.01 0.125 0.125 0.01 64 0.125 0.005 </span></span>
<span><span class="co"># [100] 32</span></span></code></pre></div>
<div class="sourceCode" id="cb37"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">mic_values</span><span class="op">)</span></span></code></pre></div>
@ -1455,10 +1457,10 @@ plotting:</p>
<code class="sourceCode R"><span><span class="va">disk_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_disk</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span>
<span><span class="va">disk_values</span></span>
<span><span class="co"># Class 'disk'</span></span>
<span><span class="co"># [1] 25 31 26 31 24 31 27 17 28 25 21 28 20 20 17 17 26 20 20 29 26 31 30 20 25</span></span>
<span><span class="co"># [26] 25 27 29 29 21 17 27 20 20 17 25 17 20 27 29 19 27 18 28 31 21 23 26 26 27</span></span>
<span><span class="co"># [51] 23 23 21 18 22 23 19 17 22 23 29 28 19 29 20 31 18 25 21 17 18 31 20 21 17</span></span>
<span><span class="co"># [76] 21 28 25 31 24 30 24 17 20 26 31 25 20 30 18 21 29 19 30 20 24 29 23 23 22</span></span></code></pre></div>
<span><span class="co"># [1] 22 22 17 17 30 20 21 18 30 22 28 21 18 25 28 19 30 22 22 19 22 29 27 18 31</span></span>
<span><span class="co"># [26] 17 17 27 26 30 23 21 17 23 31 22 27 31 20 18 20 22 23 17 18 20 24 26 21 29</span></span>
<span><span class="co"># [51] 28 31 21 31 23 24 28 31 28 28 23 27 31 18 31 23 22 21 19 21 21 19 31 27 29</span></span>
<span><span class="co"># [76] 20 22 31 17 24 23 27 21 28 21 28 17 31 23 17 25 25 21 31 23 31 18 23 18 19</span></span></code></pre></div>
<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">disk_values</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></code></pre></div>

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@ -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="">1.8.2.9050</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9051</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">
@ -350,7 +350,7 @@ reading</em>, is basically a form of imputation, and is part of the
<td align="center">-</td>
<td align="center">S</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">S</td>

60
articles/MDR.html
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9050</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9051</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -375,19 +375,19 @@ names or codes, this would have worked exactly the same way:</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span>
<span><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
<span><span class="co"># 1 S S R R S S</span></span>
<span><span class="co"># 2 R R I S I R</span></span>
<span><span class="co"># 3 S I S R I S</span></span>
<span><span class="co"># 4 I S R R I I</span></span>
<span><span class="co"># 5 I I I I I R</span></span>
<span><span class="co"># 6 R S R R R S</span></span>
<span><span class="co"># 1 S S S I R R</span></span>
<span><span class="co"># 2 I S S S R I</span></span>
<span><span class="co"># 3 S R R I I R</span></span>
<span><span class="co"># 4 I I R I I S</span></span>
<span><span class="co"># 5 R I S S R I</span></span>
<span><span class="co"># 6 I S S S R R</span></span>
<span><span class="co"># kanamycin</span></span>
<span><span class="co"># 1 I</span></span>
<span><span class="co"># 2 R</span></span>
<span><span class="co"># 3 I</span></span>
<span><span class="co"># 4 R</span></span>
<span><span class="co"># 1 R</span></span>
<span><span class="co"># 2 I</span></span>
<span><span class="co"># 3 S</span></span>
<span><span class="co"># 4 S</span></span>
<span><span class="co"># 5 S</span></span>
<span><span class="co"># 6 R</span></span></code></pre></div>
<span><span class="co"># 6 I</span></span></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can
use:</p>
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
@ -428,40 +428,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3261</td>
<td align="right">65.22%</td>
<td align="right">3261</td>
<td align="right">65.22%</td>
<td align="right">3195</td>
<td align="right">63.90%</td>
<td align="right">3195</td>
<td align="right">63.90%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">919</td>
<td align="right">18.38%</td>
<td align="right">4180</td>
<td align="right">83.60%</td>
<td align="right">1015</td>
<td align="right">20.30%</td>
<td align="right">4210</td>
<td align="right">84.20%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">488</td>
<td align="right">9.76%</td>
<td align="right">4668</td>
<td align="right">93.36%</td>
<td align="right">437</td>
<td align="right">8.74%</td>
<td align="right">4647</td>
<td align="right">92.94%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">235</td>
<td align="right">4.70%</td>
<td align="right">4903</td>
<td align="right">98.06%</td>
<td align="right">254</td>
<td align="right">5.08%</td>
<td align="right">4901</td>
<td align="right">98.02%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">97</td>
<td align="right">1.94%</td>
<td align="right">99</td>
<td align="right">1.98%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

2
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@ -38,7 +38,7 @@
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@ -168,7 +168,7 @@
<h4 data-toc-skip class="author">Dr. Matthijs
Berends</h4>
<h4 data-toc-skip class="date">13 November 2022</h4>
<h4 data-toc-skip class="date">14 November 2022</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/SPSS.Rmd" class="external-link"><code>vignettes/SPSS.Rmd</code></a></small>
<div class="d-none name"><code>SPSS.Rmd</code></div>

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@ -38,7 +38,7 @@
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@ -166,7 +166,7 @@
<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">13 November 2022</h4>
<h4 data-toc-skip class="date">14 November 2022</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<div class="d-none name"><code>datasets.Rmd</code></div>
@ -1328,13 +1328,13 @@ v3.3</a> (2021).</p>
<h2 id="dosage-dosage-guidelines-from-eucast">
<code>dosage</code>: Dosage Guidelines from EUCAST<a class="anchor" aria-label="anchor" href="#dosage-dosage-guidelines-from-eucast"></a>
</h2>
<p>A data set with 169 rows and 9 columns, containing the following
<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>
<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 30 October 2022 20:05:46 UTC. Find more info
<p>It was last updated on 14 November 2022 14:20:39 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
@ -1342,25 +1342,25 @@ about the structure of this data set <a href="https://msberends.github.io/AMR/re
R Data Structure (RDS) file</a> (3 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.txt" class="external-link">tab-separated
text file</a> (15 kB)<br>
text file</a> (29 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.xlsx" class="external-link">Microsoft
Excel workbook</a> (14 kB)<br>
Excel workbook</a> (19 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.feather" class="external-link">Apache
Feather file</a> (11 kB)<br>
Feather file</a> (16 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.parquet" class="external-link">Apache
Parquet file</a> (7 kB)<br>
Parquet file</a> (8 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sas" class="external-link">SAS
data file</a> (52 kB)<br>
data file</a> (92 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sav" class="external-link">IBM
SPSS Statistics data file</a> (23 kB)<br>
SPSS Statistics data file</a> (43 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.dta" class="external-link">Stata
DTA file</a> (44 kB)</li>
DTA file</a> (82 kB)</li>
</ul>
<div class="section level3">
<h3 id="source-5">Source<a class="anchor" aria-label="anchor" href="#source-5"></a>
@ -1368,7 +1368,8 @@ DTA file</a> (44 kB)</li>
<p>EUCAST breakpoints used in this package are based on the dosages in
this data set.</p>
<p>Currently included dosages in the data set are meant for: <a href="https://www.eucast.org/clinical_breakpoints/" class="external-link">‘EUCAST Clinical
Breakpoint Tables’ v11.0</a> (2021).</p>
Breakpoint Tables’ v11.0</a> (2021) and <a href="https://www.eucast.org/clinical_breakpoints/" class="external-link">‘EUCAST Clinical
Breakpoint Tables’ v12.0</a> (2022).</p>
</div>
<div class="section level3">
<h3 id="example-content-5">Example content<a class="anchor" aria-label="anchor" href="#example-content-5"></a>
@ -1406,7 +1407,7 @@ Breakpoint Tables’ v11.0</a> (2021).</p>
<td align="center">iv</td>
<td align="center"></td>
<td align="center">25-30 mg/kg x 1 iv</td>
<td align="center">11</td>
<td align="center">12</td>
</tr>
<tr class="even">
<td align="center">AMX</td>
@ -1417,7 +1418,7 @@ Breakpoint Tables’ v11.0</a> (2021).</p>
<td align="center">iv</td>
<td align="center"></td>
<td align="center">2 g x 6 iv</td>
<td align="center">11</td>
<td align="center">12</td>
</tr>
<tr class="odd">
<td align="center">AMX</td>
@ -1428,7 +1429,7 @@ Breakpoint Tables’ v11.0</a> (2021).</p>
<td align="center">iv</td>
<td align="center"></td>
<td align="center">1 g x 3-4 iv</td>
<td align="center">11</td>
<td align="center">12</td>
</tr>
<tr class="even">
<td align="center">AMX</td>
@ -1439,7 +1440,7 @@ Breakpoint Tables’ v11.0</a> (2021).</p>
<td align="center">oral</td>
<td align="center"></td>
<td align="center">0.75-1 g x 3 oral</td>
<td align="center">11</td>
<td align="center">12</td>
</tr>
<tr class="odd">
<td align="center">AMX</td>
@ -1450,7 +1451,7 @@ Breakpoint Tables’ v11.0</a> (2021).</p>
<td align="center">oral</td>
<td align="center"></td>
<td align="center">0.5 g x 3 oral</td>
<td align="center">11</td>
<td align="center">12</td>
</tr>
<tr class="even">
<td align="center">AMX</td>
@ -1461,7 +1462,7 @@ Breakpoint Tables’ v11.0</a> (2021).</p>
<td align="center">oral</td>
<td align="center"></td>
<td align="center">0.5 g x 3 oral</td>
<td align="center">11</td>
<td align="center">12</td>
</tr>
</tbody>
</table>

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