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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="">1.8.2.9122</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9123</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">
@ -411,70 +411,70 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2017-03-28</td>
<td align="center">X1</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia coli</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">2010-03-06</td>
<td align="center">O2</td>
<td align="center">Hospital B</td>
<td align="center">2013-09-28</td>
<td align="center">G4</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</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="odd">
<td align="center">2013-12-31</td>
<td align="center">W3</td>
<td align="center">Hospital C</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">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2017-04-25</td>
<td align="center">C6</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">S</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2014-08-23</td>
<td align="center">P4</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">I</td>
<td align="center">I</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2014-12-18</td>
<td align="center">D2</td>
<td align="center">2016-01-14</td>
<td align="center">C3</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2013-02-05</td>
<td align="center">L7</td>
<td align="center">Hospital A</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">2012-06-19</td>
<td align="center">V6</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2017-11-27</td>
<td align="center">N6</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2010-02-05</td>
<td align="center">U8</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">M</td>
<td align="center">F</td>
</tr>
</tbody>
</table>
@ -510,16 +510,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,453</td>
<td align="right">52.27%</td>
<td align="right">10,453</td>
<td align="right">52.27%</td>
<td align="right">10,387</td>
<td align="right">51.94%</td>
<td align="right">10,387</td>
<td align="right">51.94%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,547</td>
<td align="right">47.74%</td>
<td align="right">9,613</td>
<td align="right">48.07%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -632,9 +632,9 @@ 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 12,321 'phenotype-based' first isolates (61.6% of total where a</span></span>
<span><span class="co"># =&gt; Found 12,362 'phenotype-based' first isolates (61.8% of total where a</span></span>
<span><span class="co"># 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 61.8% 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">
@ -644,29 +644,27 @@ 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 12 321 isolates for analysis. Now our data looks
<p>So we end up with 12 362 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%">
<col width="9%">
<col width="9%">
<col width="10%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="6%">
<col width="11%">
<col width="4%">
<col width="4%">
<col width="4%">
<col width="4%">
<col width="6%">
<col width="12%">
<col width="9%">
<col width="12%">
<col width="7%">
<col width="5%">
</colgroup>
<thead><tr class="header">
<th align="left"></th>
<th align="center">date</th>
<th align="center">patient_id</th>
<th align="center">hospital</th>
@ -683,47 +681,74 @@ like:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2017-03-28</td>
<td align="center">X1</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">2013-09-28</td>
<td align="center">G4</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">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="even">
<td align="center">2014-08-23</td>
<td align="center">P4</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</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="even">
<td align="left">2</td>
<td align="center">2010-03-06</td>
<td align="center">O2</td>
<tr class="odd">
<td align="center">2016-01-14</td>
<td align="center">C3</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</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="center">2012-06-19</td>
<td align="center">V6</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">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">Staphylococcus</td>
<td align="center">aureus</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">2013-12-31</td>
<td align="center">W3</td>
<td align="center">Hospital C</td>
<td align="center">2017-11-27</td>
<td align="center">N6</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">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">Escherichia</td>
@ -731,51 +756,18 @@ like:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">6</td>
<td align="center">2013-02-05</td>
<td align="center">L7</td>
<td align="center">Hospital A</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">7</td>
<td align="center">2010-09-28</td>
<td align="center">G1</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">I</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="even">
<td align="left">9</td>
<td align="center">2012-08-19</td>
<td align="center">X8</td>
<td align="center">2010-02-05</td>
<td align="center">U8</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
</tbody>
@ -811,8 +803,8 @@ 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: 12,321<br>
Available: 12,321 (100%, NA: 0 = 0%)<br>
Length: 12,362<br>
Available: 12,362 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -837,33 +829,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">5,929</td>
<td align="right">48.12%</td>
<td align="right">5,929</td>
<td align="right">48.12%</td>
<td align="right">5,901</td>
<td align="right">47.73%</td>
<td align="right">5,901</td>
<td align="right">47.73%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,237</td>
<td align="right">26.27%</td>
<td align="right">9,166</td>
<td align="right">74.39%</td>
<td align="right">3,281</td>
<td align="right">26.54%</td>
<td align="right">9,182</td>
<td align="right">74.28%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">1,835</td>
<td align="right">14.89%</td>
<td align="right">11,001</td>
<td align="right">89.29%</td>
<td align="right">1,852</td>
<td align="right">14.98%</td>
<td align="right">11,034</td>
<td align="right">89.26%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,320</td>
<td align="right">10.71%</td>
<td align="right">12,321</td>
<td align="right">1,328</td>
<td align="right">10.74%</td>
<td align="right">12,362</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -912,95 +904,95 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2010-03-06</td>
<td align="center">O2</td>
<td align="center">2012-06-19</td>
<td align="center">V6</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</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">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">Staphylococcus</td>
<td align="center">aureus</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">2012-08-19</td>
<td align="center">X8</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2017-02-17</td>
<td align="center">F10</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2011-05-23</td>
<td align="center">R7</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2016-08-09</td>
<td align="center">Y9</td>
<td align="center">Hospital C</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2011-10-07</td>
<td align="center">C4</td>
<td align="center">Hospital A</td>
<td align="center">2017-11-27</td>
<td align="center">N6</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">R</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2010-05-19</td>
<td align="center">L4</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2016-05-08</td>
<td align="center">P1</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">S</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>
<tr class="odd">
<td align="center">2017-02-17</td>
<td align="center">D3</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">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="center">2012-12-04</td>
<td align="center">N7</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-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
@ -1025,46 +1017,46 @@ different bug/drug combinations, you can use the
<td align="left">2</td>
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">2773</td>
<td align="center">1159</td>
<td align="center">1997</td>
<td align="center">5929</td>
<td align="center">2771</td>
<td align="center">1155</td>
<td align="center">1975</td>
<td align="center">5901</td>
</tr>
<tr class="even">
<td align="left">1</td>
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">1452</td>
<td align="center">1281</td>
<td align="center">3196</td>
<td align="center">5929</td>
<td align="center">1531</td>
<td align="center">1205</td>
<td align="center">3165</td>
<td align="center">5901</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">2044</td>
<td align="center">1853</td>
<td align="center">2032</td>
<td align="center">5929</td>
<td align="center">2061</td>
<td align="center">1749</td>
<td align="center">2091</td>
<td align="center">5901</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">2047</td>
<td align="center">1881</td>
<td align="center">2001</td>
<td align="center">5929</td>
<td align="center">2045</td>
<td align="center">1817</td>
<td align="center">2039</td>
<td align="center">5901</td>
</tr>
<tr class="odd">
<td align="left">6</td>
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">589</td>
<td align="center">282</td>
<td align="center">449</td>
<td align="center">1320</td>
<td align="center">583</td>
<td align="center">278</td>
<td align="center">467</td>
<td align="center">1328</td>
</tr>
<tr class="even">
<td align="left">5</td>
@ -1072,8 +1064,8 @@ different bug/drug combinations, you can use the
<td align="center">AMX</td>
<td align="center">0</td>
<td align="center">0</td>
<td align="center">1320</td>
<td align="center">1320</td>
<td align="center">1328</td>
<td align="center">1328</td>
</tr>
</tbody>
</table>
@ -1095,34 +1087,34 @@ 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">2047</td>
<td align="center">1881</td>
<td align="center">2001</td>
<td align="center">5929</td>
<td align="center">2045</td>
<td align="center">1817</td>
<td align="center">2039</td>
<td align="center">5901</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">460</td>
<td align="center">405</td>
<td align="center">455</td>
<td align="center">1320</td>
<td align="center">458</td>
<td align="center">417</td>
<td align="center">453</td>
<td align="center">1328</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">1151</td>
<td align="center">1041</td>
<td align="center">1045</td>
<td align="center">3237</td>
<td align="center">1126</td>
<td align="center">1065</td>
<td align="center">1090</td>
<td align="center">3281</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">1835</td>
<td align="center">1835</td>
<td align="center">1852</td>
<td align="center">1852</td>
</tr>
</tbody>
</table>
@ -1154,7 +1146,7 @@ I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equa
own:</p>
<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span></span>
<span><span class="co"># [1] 0.5912669</span></span></code></pre></div>
<span><span class="co"># [1] 0.5856657</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">
@ -1169,19 +1161,19 @@ own:</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5871212</td>
<td align="center">0.5945799</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5979070</td>
<td align="center">0.5890156</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5780315</td>
<td align="center">0.5738308</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5957361</td>
<td align="center">0.5756472</td>
</tr>
</tbody>
</table>
@ -1206,23 +1198,23 @@ 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">0.5871212</td>
<td align="center">3696</td>
<td align="center">0.5945799</td>
<td align="center">3690</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5979070</td>
<td align="center">4300</td>
<td align="center">0.5890156</td>
<td align="center">4297</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5780315</td>
<td align="center">1839</td>
<td align="center">0.5738308</td>
<td align="center">1903</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5957361</td>
<td align="center">2486</td>
<td align="center">0.5756472</td>
<td align="center">2472</td>
</tr>
</tbody>
</table>
@ -1247,27 +1239,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.6631810</td>
<td align="center">0.6625063</td>
<td align="center">0.8891887</td>
<td align="center">0.6653110</td>
<td align="center">0.6544653</td>
<td align="center">0.8818844</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.6598485</td>
<td align="center">0.6553030</td>
<td align="center">0.8818182</td>
<td align="center">0.6483434</td>
<td align="center">0.6588855</td>
<td align="center">0.8734940</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.6663577</td>
<td align="center">0.6771702</td>
<td align="center">0.8884770</td>
<td align="center">0.6638220</td>
<td align="center">0.6677842</td>
<td align="center">0.8857056</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.4621253</td>
<td align="center">0.4649028</td>
<td align="center">0.0000000</td>
<td align="center">0.4621253</td>
<td align="center">0.4649028</td>
</tr>
</tbody>
</table>
@ -1295,23 +1287,23 @@ 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">36.6%</td>
<td align="right">59.5%</td>
<td align="right">36.3%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">59.8%</td>
<td align="right">36.8%</td>
<td align="right">58.9%</td>
<td align="right">36.9%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">57.8%</td>
<td align="right">36.5%</td>
<td align="right">57.4%</td>
<td align="right">36.6%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">59.6%</td>
<td align="right">36.4%</td>
<td align="right">57.6%</td>
<td align="right">37.0%</td>
</tr>
</tbody>
</table>
@ -1427,18 +1419,18 @@ 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] 64 0.01 2 0.01 0.0625 32 &lt;=0.001 0.01 8 </span></span>
<span><span class="co"># [10] 0.005 64 64 8 128 0.002 32 16 32 </span></span>
<span><span class="co"># [19] 2 2 0.25 64 64 32 64 128 128 </span></span>
<span><span class="co"># [28] 2 0.0625 0.25 0.5 4 0.025 0.25 0.125 8 </span></span>
<span><span class="co"># [37] &lt;=0.001 0.5 0.01 0.0625 8 32 0.0625 0.5 64 </span></span>
<span><span class="co"># [46] 0.025 0.5 0.005 1 2 4 0.005 0.5 64 </span></span>
<span><span class="co"># [55] 0.0625 256 0.025 0.125 0.125 0.125 0.25 4 0.5 </span></span>
<span><span class="co"># [64] 128 4 0.002 0.5 1 0.005 2 8 0.005 </span></span>
<span><span class="co"># [73] 0.002 1 256 256 0.025 32 0.01 0.25 0.005 </span></span>
<span><span class="co"># [82] 2 0.025 1 128 64 1 32 16 64 </span></span>
<span><span class="co"># [91] 0.0625 0.025 0.5 256 &lt;=0.001 16 &lt;=0.001 32 128 </span></span>
<span><span class="co"># [100] 8</span></span></code></pre></div>
<span><span class="co"># [1] 1 0.0625 2 8 0.025 64 1 &gt;=256 0.125 </span></span>
<span><span class="co"># [10] 1 1 &lt;=0.001 2 32 0.01 0.005 &gt;=256 0.25 </span></span>
<span><span class="co"># [19] &lt;=0.001 0.25 0.0625 8 16 0.125 128 128 32 </span></span>
<span><span class="co"># [28] 128 2 &lt;=0.001 &lt;=0.001 0.0625 &gt;=256 4 4 1 </span></span>
<span><span class="co"># [37] 8 0.025 &lt;=0.001 64 4 64 32 0.025 &lt;=0.001</span></span>
<span><span class="co"># [46] 128 0.5 16 64 32 64 1 0.002 &gt;=256 </span></span>
<span><span class="co"># [55] 32 4 0.0625 2 &lt;=0.001 0.005 0.125 0.0625 &lt;=0.001</span></span>
<span><span class="co"># [64] &lt;=0.001 0.025 32 4 64 128 0.25 &gt;=256 0.0625 </span></span>
<span><span class="co"># [73] 0.0625 32 8 32 8 &lt;=0.001 0.01 32 8 </span></span>
<span><span class="co"># [82] 64 128 32 8 0.005 0.0625 0.005 4 16 </span></span>
<span><span class="co"># [91] 1 8 &lt;=0.001 2 0.125 0.002 0.025 1 0.002 </span></span>
<span><span class="co"># [100] 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>
@ -1472,10 +1464,10 @@ 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] 24 25 28 31 31 21 29 27 17 27 27 22 27 31 27 24 29 17 30 17 23 20 22 17 24</span></span>
<span><span class="co"># [26] 28 31 28 26 26 22 28 22 26 30 25 21 17 27 25 17 28 25 18 29 21 25 19 30 31</span></span>
<span><span class="co"># [51] 27 18 29 22 20 23 31 19 30 28 21 21 25 28 21 29 25 24 20 17 19 26 26 24 23</span></span>
<span><span class="co"># [76] 17 30 17 17 29 19 18 28 19 25 31 21 29 28 26 28 28 25 22 22 18 21 31 19 29</span></span></code></pre></div>
<span><span class="co"># [1] 20 20 24 24 20 31 20 26 27 29 20 19 17 20 19 23 22 21 20 24 31 21 22 30 18</span></span>
<span><span class="co"># [26] 22 22 22 25 19 24 26 17 26 24 27 31 20 29 19 18 22 19 31 28 26 31 27 25 28</span></span>
<span><span class="co"># [51] 17 18 19 25 27 27 17 17 30 24 26 23 19 26 24 22 27 24 29 24 27 23 27 17 21</span></span>
<span><span class="co"># [76] 21 25 30 25 19 22 25 18 27 31 27 26 28 21 31 19 18 28 18 23 30 28 24 31 27</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="">1.8.2.9122</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9123</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="">1.8.2.9122</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9123</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">
@ -385,19 +385,19 @@ 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 R I S R R S</span></span>
<span><span class="co"># 2 I R I S R S</span></span>
<span><span class="co"># 3 R R I I S I</span></span>
<span><span class="co"># 4 I I R R S I</span></span>
<span><span class="co"># 5 R I I I R I</span></span>
<span><span class="co"># 6 S S I R R S</span></span>
<span><span class="co"># 1 I S R S I S</span></span>
<span><span class="co"># 2 S R R I I S</span></span>
<span><span class="co"># 3 S R I S S R</span></span>
<span><span class="co"># 4 S I I I I I</span></span>
<span><span class="co"># 5 R S R S I R</span></span>
<span><span class="co"># 6 R S I R R I</span></span>
<span><span class="co"># kanamycin</span></span>
<span><span class="co"># 1 S</span></span>
<span><span class="co"># 2 S</span></span>
<span><span class="co"># 3 S</span></span>
<span><span class="co"># 4 I</span></span>
<span><span class="co"># 5 I</span></span>
<span><span class="co"># 6 S</span></span></code></pre></div>
<span><span class="co"># 4 R</span></span>
<span><span class="co"># 5 S</span></span>
<span><span class="co"># 6 R</span></span></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can
use:</p>
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
@ -438,40 +438,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3214</td>
<td align="right">64.28%</td>
<td align="right">3214</td>
<td align="right">64.28%</td>
<td align="right">3246</td>
<td align="right">64.92%</td>
<td align="right">3246</td>
<td align="right">64.92%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">1018</td>
<td align="right">20.36%</td>
<td align="right">4232</td>
<td align="right">84.64%</td>
<td align="right">950</td>
<td align="right">19.00%</td>
<td align="right">4196</td>
<td align="right">83.92%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">439</td>
<td align="right">8.78%</td>
<td align="right">4671</td>
<td align="right">93.42%</td>
<td align="right">462</td>
<td align="right">9.24%</td>
<td align="right">4658</td>
<td align="right">93.16%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">228</td>
<td align="right">4.56%</td>
<td align="right">4899</td>
<td align="right">97.98%</td>
<td align="right">231</td>
<td align="right">4.62%</td>
<td align="right">4889</td>
<td align="right">97.78%</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">111</td>
<td align="right">2.22%</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="">1.8.2.9122</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9123</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
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