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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="">1.8.2.9114</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9115</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">
@ -391,12 +391,12 @@ 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>
@ -411,68 +411,68 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2013-06-16</td>
<td align="center">R2</td>
<td align="center">Hospital C</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2014-07-04</td>
<td align="center">Z4</td>
<td align="center">Hospital A</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2017-06-03</td>
<td align="center">F5</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">R</td>
<td align="center">R</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2011-12-22</td>
<td align="center">H10</td>
<td align="center">Hospital A</td>
<td align="center">2010-12-30</td>
<td align="center">O7</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2016-09-08</td>
<td align="center">K1</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">M</td>
</tr>
<tr class="odd">
<td align="center">2017-01-25</td>
<td align="center">Y7</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">2010-07-19</td>
<td align="center">W2</td>
<td align="center">Hospital D</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2014-10-21</td>
<td align="center">Y1</td>
<td align="center">2016-09-29</td>
<td align="center">O10</td>
<td align="center">Hospital B</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">F</td>
</tr>
<tr class="odd">
<td align="center">2015-11-01</td>
<td align="center">M1</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2013-03-20</td>
<td align="center">T1</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
</tr>
@ -510,18 +510,18 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,343</td>
<td align="right">51.72%</td>
<td align="right">10,343</td>
<td align="right">51.72%</td>
<td align="right">10,479</td>
<td align="right">52.40%</td>
<td align="right">10,479</td>
<td align="right">52.4%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,657</td>
<td align="right">48.29%</td>
<td align="right">9,521</td>
<td align="right">47.61%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
<td align="right">100.0%</td>
</tr>
</tbody>
</table>
@ -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 12,360 'phenotype-based' first isolates (61.8% of total where a</span></span>
<span><span class="co"># =&gt; Found 12,291 'phenotype-based' first isolates (61.5% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 61.8% 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">
@ -644,11 +644,11 @@ 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 12 360 isolates for analysis. Now our data looks
<p>So we end up with 12 291 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%">
@ -661,7 +661,7 @@ like:</p>
<col width="3%">
<col width="6%">
<col width="11%">
<col width="12%">
<col width="11%">
<col width="9%">
<col width="5%">
</colgroup>
@ -683,96 +683,96 @@ like:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2013-06-16</td>
<td align="center">R2</td>
<td align="left">4</td>
<td align="center">2016-09-29</td>
<td align="center">O10</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">5</td>
<td align="center">2015-11-01</td>
<td align="center">M1</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">S</td>
<td align="center">I</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">9</td>
<td align="center">2011-03-28</td>
<td align="center">W6</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">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="left">12</td>
<td align="center">2016-01-01</td>
<td align="center">J2</td>
<td align="center">Hospital B</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">I</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="center">2014-07-04</td>
<td align="center">Z4</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">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">6</td>
<td align="center">2014-10-21</td>
<td align="center">Y1</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">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">7</td>
<td align="center">2017-08-18</td>
<td align="center">E9</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">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="left">8</td>
<td align="center">2017-10-08</td>
<td align="center">P4</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">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="left">10</td>
<td align="center">2012-08-30</td>
<td align="center">C4</td>
<td align="left">14</td>
<td align="center">2013-09-11</td>
<td align="center">C2</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_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">16</td>
<td align="center">2017-06-17</td>
<td align="center">W2</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">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>
@ -811,8 +811,8 @@ 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: 12,360<br>
Available: 12,360 (100%, NA: 0 = 0%)<br>
Length: 12,291<br>
Available: 12,291 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -837,33 +837,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">5,976</td>
<td align="right">48.35%</td>
<td align="right">5,976</td>
<td align="right">48.35%</td>
<td align="right">5,932</td>
<td align="right">48.26%</td>
<td align="right">5,932</td>
<td align="right">48.26%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,242</td>
<td align="right">26.23%</td>
<td align="right">9,218</td>
<td align="right">74.58%</td>
<td align="right">3,234</td>
<td align="right">26.31%</td>
<td align="right">9,166</td>
<td align="right">74.57%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">1,860</td>
<td align="right">15.05%</td>
<td align="right">11,078</td>
<td align="right">89.63%</td>
<td align="right">1,831</td>
<td align="right">14.90%</td>
<td align="right">10,997</td>
<td align="right">89.47%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,282</td>
<td align="right">10.37%</td>
<td align="right">12,360</td>
<td align="right">1,294</td>
<td align="right">10.53%</td>
<td align="right">12,291</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -884,14 +884,14 @@ antibiotic class they are in:</p>
<col width="9%">
<col width="9%">
<col width="9%">
<col width="10%">
<col width="11%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="6%">
<col width="11%">
<col width="12%">
<col width="11%">
<col width="9%">
<col width="5%">
</colgroup>
@ -912,57 +912,57 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2014-07-04</td>
<td align="center">Z4</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">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2014-10-21</td>
<td align="center">Y1</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">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="odd">
<td align="center">2017-08-18</td>
<td align="center">E9</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">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="even">
<td align="center">2017-10-08</td>
<td align="center">P4</td>
<td align="center">2011-03-28</td>
<td align="center">W6</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">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">2017-06-17</td>
<td align="center">W2</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">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="odd">
<td align="center">2015-08-02</td>
<td align="center">T7</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">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">2012-04-29</td>
<td align="center">Q6</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">R</td>
<td align="center">R</td>
<td align="center">F</td>
@ -972,13 +972,13 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2012-08-30</td>
<td align="center">C4</td>
<td align="center">Hospital D</td>
<td align="center">2014-12-09</td>
<td align="center">E7</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
@ -987,18 +987,18 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2012-12-24</td>
<td align="center">Q5</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">2010-08-29</td>
<td align="center">N8</td>
<td align="center">Hospital B</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">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>
</tbody>
@ -1025,46 +1025,46 @@ 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">2812</td>
<td align="center">1160</td>
<td align="center">2004</td>
<td align="center">5976</td>
<td align="center">2766</td>
<td align="center">1182</td>
<td align="center">1984</td>
<td align="center">5932</td>
</tr>
<tr class="even">
<td align="left">1</td>
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">1563</td>
<td align="center">1221</td>
<td align="center">3192</td>
<td align="center">5976</td>
<td align="center">1503</td>
<td align="center">1271</td>
<td align="center">3158</td>
<td align="center">5932</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">2049</td>
<td align="center">1816</td>
<td align="center">2111</td>
<td align="center">5976</td>
<td align="center">2090</td>
<td align="center">1798</td>
<td align="center">2044</td>
<td align="center">5932</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">1864</td>
<td align="center">2065</td>
<td align="center">5976</td>
<td align="center">2053</td>
<td align="center">1791</td>
<td align="center">2088</td>
<td align="center">5932</td>
</tr>
<tr class="odd">
<td align="left">6</td>
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">555</td>
<td align="center">281</td>
<td align="center">446</td>
<td align="center">1282</td>
<td align="center">590</td>
<td align="center">264</td>
<td align="center">440</td>
<td align="center">1294</td>
</tr>
<tr class="even">
<td align="left">5</td>
@ -1072,8 +1072,8 @@ 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">1282</td>
<td align="center">1282</td>
<td align="center">1294</td>
<td align="center">1294</td>
</tr>
</tbody>
</table>
@ -1095,34 +1095,34 @@ 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">1864</td>
<td align="center">2065</td>
<td align="center">5976</td>
<td align="center">2053</td>
<td align="center">1791</td>
<td align="center">2088</td>
<td align="center">5932</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">461</td>
<td align="center">406</td>
<td align="center">415</td>
<td align="center">1282</td>
<td align="center">443</td>
<td align="center">418</td>
<td align="center">433</td>
<td align="center">1294</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">1122</td>
<td align="center">989</td>
<td align="center">1131</td>
<td align="center">3242</td>
<td align="center">1084</td>
<td align="center">1013</td>
<td align="center">1137</td>
<td align="center">3234</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">1860</td>
<td align="center">1860</td>
<td align="center">1831</td>
<td align="center">1831</td>
</tr>
</tbody>
</table>
@ -1154,7 +1154,7 @@ 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] 0.5843042</span></span></code></pre></div>
<span><span class="co"># [1] 0.5826214</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 +1169,19 @@ own:</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5790487</td>
<td align="center">0.5758659</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5752233</td>
<td align="center">0.5828610</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5984384</td>
<td align="center">0.5882029</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5973469</td>
<td align="center">0.5881384</td>
</tr>
</tbody>
</table>
@ -1206,23 +1206,23 @@ 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">0.5790487</td>
<td align="center">3637</td>
<td align="center">0.5758659</td>
<td align="center">3638</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5752233</td>
<td align="center">4367</td>
<td align="center">0.5828610</td>
<td align="center">4411</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5984384</td>
<td align="center">1793</td>
<td align="center">0.5882029</td>
<td align="center">1814</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5973469</td>
<td align="center">2563</td>
<td align="center">0.5881384</td>
<td align="center">2428</td>
</tr>
</tbody>
</table>
@ -1247,27 +1247,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.6646586</td>
<td align="center">0.6544511</td>
<td align="center">0.8840361</td>
<td align="center">0.6655428</td>
<td align="center">0.6480108</td>
<td align="center">0.8833446</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.6521061</td>
<td align="center">0.6762871</td>
<td align="center">0.8892356</td>
<td align="center">0.6599691</td>
<td align="center">0.6653787</td>
<td align="center">0.8802164</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.6748920</td>
<td align="center">0.6511413</td>
<td align="center">0.8834053</td>
<td align="center">0.6719233</td>
<td align="center">0.6484230</td>
<td align="center">0.8862090</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.4698925</td>
<td align="center">0.4729656</td>
<td align="center">0.0000000</td>
<td align="center">0.4698925</td>
<td align="center">0.4729656</td>
</tr>
</tbody>
</table>
@ -1295,23 +1295,23 @@ classes, use a antibiotic class selector such as
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">57.9%</td>
<td align="right">36.8%</td>
<td align="right">57.6%</td>
<td align="right">36.5%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">57.5%</td>
<td align="right">35.8%</td>
<td align="right">58.3%</td>
<td align="right">36.2%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">59.8%</td>
<td align="right">37.4%</td>
<td align="right">58.8%</td>
<td align="right">36.3%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">59.7%</td>
<td align="right">35.8%</td>
<td align="right">58.8%</td>
<td align="right">35.7%</td>
</tr>
</tbody>
</table>
@ -1427,18 +1427,18 @@ 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] 0.25 32 0.0625 1 0.125 16 0.0625 16 0.025 </span></span>
<span><span class="co"># [10] 0.25 &gt;=256 0.5 1 0.01 &gt;=256 2 0.5 8 </span></span>
<span><span class="co"># [19] 64 &gt;=256 1 2 0.005 0.002 0.5 0.01 0.0625 </span></span>
<span><span class="co"># [28] 0.125 0.002 0.002 &gt;=256 &gt;=256 0.025 4 1 2 </span></span>
<span><span class="co"># [37] 0.01 1 32 128 &gt;=256 &lt;=0.001 0.01 2 0.002 </span></span>
<span><span class="co"># [46] 2 4 0.002 0.25 &gt;=256 0.125 0.125 0.25 16 </span></span>
<span><span class="co"># [55] 128 0.25 0.0625 8 16 0.002 64 64 &gt;=256 </span></span>
<span><span class="co"># [64] 0.5 8 0.5 16 0.002 0.25 &lt;=0.001 &gt;=256 0.002 </span></span>
<span><span class="co"># [73] 4 0.005 128 2 8 32 1 1 2 </span></span>
<span><span class="co"># [82] 0.025 &lt;=0.001 &gt;=256 0.025 0.5 16 4 2 128 </span></span>
<span><span class="co"># [91] 64 0.002 0.002 1 &gt;=256 0.125 0.01 0.01 0.0625 </span></span>
<span><span class="co"># [100] 0.0625</span></span></code></pre></div>
<span><span class="co"># [1] 0.005 2 2 128 8 0.01 0.005 0.25 2 </span></span>
<span><span class="co"># [10] 8 256 0.125 256 0.002 0.0625 0.025 8 16 </span></span>
<span><span class="co"># [19] 0.002 0.5 0.25 256 16 2 0.002 0.01 0.01 </span></span>
<span><span class="co"># [28] 1 256 2 64 0.002 128 8 2 128 </span></span>
<span><span class="co"># [37] 0.002 4 0.025 32 8 0.125 32 0.5 8 </span></span>
<span><span class="co"># [46] 0.125 0.5 128 0.005 0.005 0.5 2 &lt;=0.001 0.025 </span></span>
<span><span class="co"># [55] 0.002 0.0625 1 32 0.125 64 0.002 0.025 0.01 </span></span>
<span><span class="co"># [64] 32 8 0.01 4 0.125 0.125 64 0.5 0.0625 </span></span>
<span><span class="co"># [73] 1 256 1 32 16 0.0625 1 16 64 </span></span>
<span><span class="co"># [82] 0.125 0.002 16 0.0625 128 32 64 0.0625 64 </span></span>
<span><span class="co"># [91] 2 2 0.005 256 0.25 0.0625 0.01 4 &lt;=0.001</span></span>
<span><span class="co"># [100] 1</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 +1472,10 @@ 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] 31 22 24 20 23 20 22 27 19 20 20 23 28 30 23 21 17 17 25 19 21 31 18 31 19</span></span>
<span><span class="co"># [26] 26 28 31 17 21 31 20 30 26 22 24 30 18 31 25 17 29 29 18 26 27 24 21 22 18</span></span>
<span><span class="co"># [51] 17 19 22 27 19 23 24 20 30 30 19 17 31 31 17 25 24 31 22 22 19 27 17 19 19</span></span>
<span><span class="co"># [76] 31 22 22 23 26 29 20 17 29 31 27 30 18 17 31 26 17 27 22 20 19 23 24 28 20</span></span></code></pre></div>
<span><span class="co"># [1] 17 30 22 31 20 25 23 17 24 17 30 26 21 20 28 19 28 29 24 17 29 30 31 27 25</span></span>
<span><span class="co"># [26] 29 21 21 18 25 19 25 22 26 28 18 25 19 24 30 23 22 24 22 22 22 18 24 19 19</span></span>
<span><span class="co"># [51] 17 17 28 29 28 24 20 23 25 29 31 21 31 18 18 18 28 22 18 25 29 24 27 29 23</span></span>
<span><span class="co"># [76] 21 31 17 29 30 24 29 21 29 24 17 28 18 19 31 27 25 26 18 27 27 29 28 25 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="">1.8.2.9114</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9115</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

58
articles/MDR.html
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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="">1.8.2.9114</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9115</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -385,18 +385,18 @@ names or codes, this would have worked exactly the same way:</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span>
<span><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
<span><span class="co"># 1 R I S R R I</span></span>
<span><span class="co"># 2 I R S I R R</span></span>
<span><span class="co"># 3 I I R S I R</span></span>
<span><span class="co"># 4 R I R I R I</span></span>
<span><span class="co"># 5 R S I R R S</span></span>
<span><span class="co"># 6 S R R R R R</span></span>
<span><span class="co"># 1 S R R S R R</span></span>
<span><span class="co"># 2 R R I R S R</span></span>
<span><span class="co"># 3 S S R S S S</span></span>
<span><span class="co"># 4 R S S I S S</span></span>
<span><span class="co"># 5 I S S R S R</span></span>
<span><span class="co"># 6 I I S R R R</span></span>
<span><span class="co"># kanamycin</span></span>
<span><span class="co"># 1 R</span></span>
<span><span class="co"># 2 R</span></span>
<span><span class="co"># 3 I</span></span>
<span><span class="co"># 4 S</span></span>
<span><span class="co"># 5 S</span></span>
<span><span class="co"># 2 S</span></span>
<span><span class="co"># 3 S</span></span>
<span><span class="co"># 4 R</span></span>
<span><span class="co"># 5 I</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>
@ -438,40 +438,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3194</td>
<td align="right">63.88%</td>
<td align="right">3194</td>
<td align="right">63.88%</td>
<td align="right">3202</td>
<td align="right">64.04%</td>
<td align="right">3202</td>
<td align="right">64.04%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">998</td>
<td align="right">19.96%</td>
<td align="right">4192</td>
<td align="right">83.84%</td>
<td align="right">1007</td>
<td align="right">20.14%</td>
<td align="right">4209</td>
<td align="right">84.18%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">468</td>
<td align="right">9.36%</td>
<td align="right">4660</td>
<td align="right">93.20%</td>
<td align="right">453</td>
<td align="right">9.06%</td>
<td align="right">4662</td>
<td align="right">93.24%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">232</td>
<td align="right">4.64%</td>
<td align="right">4892</td>
<td align="right">97.84%</td>
<td align="right">227</td>
<td align="right">4.54%</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">108</td>
<td align="right">2.16%</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>
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