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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="">1.8.2.9138</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9139</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">
@ -408,67 +408,67 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2014-12-01</td>
<td align="center">V4</td>
<td align="center">2011-02-12</td>
<td align="center">O4</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">I</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2012-09-30</td>
<td align="center">D9</td>
<td align="center">Hospital D</td>
<td align="center">2011-03-08</td>
<td align="center">W5</td>
<td align="center">Hospital C</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">I</td>
<td align="center">I</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2015-09-22</td>
<td align="center">R6</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2013-03-03</td>
<td align="center">E2</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">I</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">M</td>
</tr>
<tr class="odd">
<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">2014-09-08</td>
<td align="center">I5</td>
<td align="center">Hospital B</td>
<td align="center">Klebsiella pneumoniae</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">I</td>
<td align="center">M</td>
</tr>
<tr class="even">
<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">2017-10-13</td>
<td align="center">F8</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">M</td>
@ -507,16 +507,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,361</td>
<td align="right">51.81%</td>
<td align="right">10,361</td>
<td align="right">51.81%</td>
<td align="right">10,425</td>
<td align="right">52.13%</td>
<td align="right">10,425</td>
<td align="right">52.13%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,639</td>
<td align="right">48.20%</td>
<td align="right">9,575</td>
<td align="right">47.88%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -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 12,431 'phenotype-based' first isolates (62.2% of total where a</span></span>
<span><span class="co">#&gt; =&gt; Found 12,293 'phenotype-based' first isolates (61.5% of total where a</span></span>
<span><span class="co">#&gt; microbial ID was available)</span></span></code></pre></div>
<p>So only 62.2% is suitable for resistance analysis! We can now filter
<p>So only 61.5% 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 12 431 isolates for analysis. Now our data looks
<p>So we end up with 12 293 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 style="width:100%;" class="table">
<table 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="12%">
<col width="11%">
<col width="9%">
<col width="5%">
</colgroup>
@ -681,45 +681,13 @@ like:</p>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2014-12-01</td>
<td align="center">V4</td>
<td align="center">2011-02-12</td>
<td align="center">O4</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">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">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="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_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">I</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-positive</td>
@ -728,30 +696,30 @@ like:</p>
<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="left">2</td>
<td align="center">2011-03-08</td>
<td align="center">W5</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">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="odd">
<td align="left">3</td>
<td align="center">2015-09-22</td>
<td align="center">R6</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">R</td>
<td align="center">I</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
@ -760,19 +728,51 @@ like:</p>
<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="left">6</td>
<td align="center">2017-10-13</td>
<td align="center">F8</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</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="odd">
<td align="left">7</td>
<td align="center">2013-03-22</td>
<td align="center">H3</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">I</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">8</td>
<td align="center">2014-11-05</td>
<td align="center">Y10</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">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>
</tbody>
@ -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: 12,431<br>
Available: 12,431 (100%, NA: 0 = 0%)<br>
Length: 12,293<br>
Available: 12,293 (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">5,970</td>
<td align="right">48.03%</td>
<td align="right">5,970</td>
<td align="right">48.03%</td>
<td align="right">5,873</td>
<td align="right">47.78%</td>
<td align="right">5,873</td>
<td align="right">47.78%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</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>
<td align="right">3,225</td>
<td align="right">26.23%</td>
<td align="right">9,098</td>
<td align="right">74.01%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</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>
<td align="right">1,844</td>
<td align="right">15.00%</td>
<td align="right">10,942</td>
<td align="right">89.01%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,309</td>
<td align="right">10.53%</td>
<td align="right">12,431</td>
<td align="right">1,351</td>
<td align="right">10.99%</td>
<td align="right">12,293</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -909,13 +909,43 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2014-12-01</td>
<td align="center">V4</td>
<td align="center">2011-02-12</td>
<td align="center">O4</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">I</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-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2013-03-22</td>
<td align="center">H3</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">I</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">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2014-11-05</td>
<td align="center">Y10</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">F</td>
<td align="center">Gram-negative</td>
@ -924,71 +954,41 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2012-07-28</td>
<td align="center">V1</td>
<td align="center">2013-09-13</td>
<td align="center">A8</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">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">2016-08-30</td>
<td align="center">Q3</td>
<td align="center">2016-08-04</td>
<td align="center">S3</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">B_STPHY_AURS</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-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>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2011-04-07</td>
<td align="center">D8</td>
<td align="center">2013-05-16</td>
<td align="center">K6</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
@ -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">2855</td>
<td align="center">1161</td>
<td align="center">1954</td>
<td align="center">5970</td>
<td align="center">2744</td>
<td align="center">1216</td>
<td align="center">1913</td>
<td align="center">5873</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">1518</td>
<td align="center">1282</td>
<td align="center">3170</td>
<td align="center">5970</td>
<td align="center">1504</td>
<td align="center">1272</td>
<td align="center">3097</td>
<td align="center">5873</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">2087</td>
<td align="center">1796</td>
<td align="center">2087</td>
<td align="center">5970</td>
<td align="center">2018</td>
<td align="center">1818</td>
<td align="center">2037</td>
<td align="center">5873</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">2119</td>
<td align="center">1854</td>
<td align="center">1997</td>
<td align="center">5970</td>
<td align="center">2067</td>
<td align="center">1812</td>
<td align="center">1994</td>
<td align="center">5873</td>
</tr>
<tr class="odd">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">615</td>
<td align="center">256</td>
<td align="center">438</td>
<td align="center">1309</td>
<td align="center">599</td>
<td align="center">275</td>
<td align="center">477</td>
<td align="center">1351</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">1309</td>
<td align="center">1309</td>
<td align="center">1351</td>
<td align="center">1351</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">2119</td>
<td align="center">1854</td>
<td align="center">1997</td>
<td align="center">5970</td>
<td align="center">2067</td>
<td align="center">1812</td>
<td align="center">1994</td>
<td align="center">5873</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">456</td>
<td align="center">409</td>
<td align="center">444</td>
<td align="center">1309</td>
<td align="center">450</td>
<td align="center">437</td>
<td align="center">464</td>
<td align="center">1351</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">1122</td>
<td align="center">1075</td>
<td align="center">1138</td>
<td align="center">3335</td>
<td align="center">1128</td>
<td align="center">980</td>
<td align="center">1117</td>
<td align="center">3225</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">1817</td>
<td align="center">1817</td>
<td align="center">1844</td>
<td align="center">1844</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] 0.5810474</span></span></code></pre></div>
<span><span class="co">#&gt; [1] 0.5805743</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">0.5871733</td>
<td align="center">0.5836502</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5822430</td>
<td align="center">0.5788257</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5788635</td>
<td align="center">0.5675105</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5717638</td>
<td align="center">0.5893679</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">0.5871733</td>
<td align="center">3711</td>
<td align="center">0.5836502</td>
<td align="center">3682</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5822430</td>
<td align="center">4280</td>
<td align="center">0.5788257</td>
<td align="center">4326</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5788635</td>
<td align="center">1883</td>
<td align="center">0.5675105</td>
<td align="center">1896</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5717638</td>
<td align="center">2557</td>
<td align="center">0.5893679</td>
<td align="center">2389</td>
</tr>
</tbody>
</table>
@ -1237,27 +1237,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.6726968</td>
<td align="center">0.6654941</td>
<td align="center">0.8934673</td>
<td align="center">0.6742721</td>
<td align="center">0.6604802</td>
<td align="center">0.8923889</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.6653934</td>
<td align="center">0.6608098</td>
<td align="center">0.8800611</td>
<td align="center">0.6469282</td>
<td align="center">0.6565507</td>
<td align="center">0.8793486</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.6773613</td>
<td align="center">0.6587706</td>
<td align="center">0.8917541</td>
<td align="center">0.6731783</td>
<td align="center">0.6536434</td>
<td align="center">0.8862016</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.4777105</td>
<td align="center">0.4766811</td>
<td align="center">0.0000000</td>
<td align="center">0.4777105</td>
<td align="center">0.4766811</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">58.7%</td>
<td align="right">36.2%</td>
<td align="right">58.4%</td>
<td align="right">36.1%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">58.2%</td>
<td align="right">35.9%</td>
<td align="right">57.9%</td>
<td align="right">36.2%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">57.9%</td>
<td align="right">34.9%</td>
<td align="right">56.8%</td>
<td align="right">34.6%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">57.2%</td>
<td align="right">34.5%</td>
<td align="right">58.9%</td>
<td align="right">35.8%</td>
</tr>
</tbody>
</table>
@ -1417,16 +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] 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>
<span><span class="co">#&gt; [1] &lt;=0.001 0.5 0.002 0.0625 32 &lt;=0.001 0.125 0.002 0.0625 </span></span>
<span><span class="co">#&gt; [10] 1 0.01 16 0.5 0.25 4 8 2 0.002 </span></span>
<span><span class="co">#&gt; [19] 0.125 8 0.002 1 16 1 2 0.025 &lt;=0.001</span></span>
<span><span class="co">#&gt; [28] 32 16 &lt;=0.001 1 4 0.01 &lt;=0.001 0.002 &gt;=128 </span></span>
<span><span class="co">#&gt; [37] 0.005 2 &lt;=0.001 2 0.002 16 32 4 0.025 </span></span>
<span><span class="co">#&gt; [46] 1 0.01 0.005 0.002 4 2 0.0625 &gt;=128 0.01 </span></span>
<span><span class="co">#&gt; [55] 0.25 32 &gt;=128 0.0625 1 0.5 4 &lt;=0.001 0.005 </span></span>
<span><span class="co">#&gt; [64] 2 16 &lt;=0.001 4 0.25 &gt;=128 64 &lt;=0.001 &gt;=128 </span></span>
<span><span class="co">#&gt; [73] 0.0625 4 0.5 0.025 &gt;=128 &gt;=128 64 32 &gt;=128 </span></span>
<span><span class="co">#&gt; [82] 1 0.0625 0.25 1 0.25 0.0625 8 0.025 2 </span></span>
<span><span class="co">#&gt; [91] 1 0.025 0.002 8 32 2 2 4 16 </span></span>
<span><span class="co">#&gt; [100] 64</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>
@ -1438,8 +1440,7 @@ 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>
<span><span class="co">#&gt; [1] "here"</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></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
@ -1461,10 +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] 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>
<span><span class="co">#&gt; [1] 23 21 21 24 27 18 21 29 31 18 17 26 21 21 27 25 28 31 30 17 29 21 18 30 25</span></span>
<span><span class="co">#&gt; [26] 28 31 17 25 23 22 17 27 24 30 31 24 24 25 27 18 31 20 21 29 30 17 21 20 19</span></span>
<span><span class="co">#&gt; [51] 25 21 17 17 26 25 30 26 19 18 21 28 27 21 30 29 21 17 30 28 26 27 23 31 27</span></span>
<span><span class="co">#&gt; [76] 31 31 26 24 30 31 22 20 17 17 23 31 27 17 28 27 18 27 29 24 24 28 20 19 26</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="">1.8.2.9138</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9139</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="">1.8.2.9138</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9139</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">
@ -385,17 +385,17 @@ 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 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; 1 R S S S I S</span></span>
<span><span class="co">#&gt; 2 I R S R I S</span></span>
<span><span class="co">#&gt; 3 I R R I S R</span></span>
<span><span class="co">#&gt; 4 R R S R S I</span></span>
<span><span class="co">#&gt; 5 S S S S I S</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 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; 1 I</span></span>
<span><span class="co">#&gt; 2 I</span></span>
<span><span class="co">#&gt; 3 S</span></span>
<span><span class="co">#&gt; 4 S</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
@ -438,40 +438,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3165</td>
<td align="right">63.30%</td>
<td align="right">3165</td>
<td align="right">63.30%</td>
<td align="right">3221</td>
<td align="right">64.42%</td>
<td align="right">3221</td>
<td align="right">64.42%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">1009</td>
<td align="right">20.18%</td>
<td align="right">4174</td>
<td align="right">83.48%</td>
<td align="right">985</td>
<td align="right">19.70%</td>
<td align="right">4206</td>
<td align="right">84.12%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">455</td>
<td align="right">9.10%</td>
<td align="right">4629</td>
<td align="right">92.58%</td>
<td align="right">437</td>
<td align="right">8.74%</td>
<td align="right">4643</td>
<td align="right">92.86%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">270</td>
<td align="right">5.40%</td>
<td align="right">4899</td>
<td align="right">97.98%</td>
<td align="right">252</td>
<td align="right">5.04%</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">101</td>
<td align="right">2.02%</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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9139</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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articles/SPSS.html
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@ -38,7 +38,7 @@
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articles/WHONET.html
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@ -38,7 +38,7 @@
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@ -230,13 +230,7 @@ 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>
<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>
<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>
<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>
@ -358,11 +352,14 @@ 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; rsi (numeric)<br>
<p>Class: factor &gt; ordered &gt; sir (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>
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