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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="">1.8.2.9079</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9080</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">
@ -400,20 +400,42 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2010-10-28</td>
<td align="center">M5</td>
<td align="center">2017-01-07</td>
<td align="center">A3</td>
<td align="center">Hospital A</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">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2016-07-14</td>
<td align="center">O7</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">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2012-11-17</td>
<td align="center">Y4</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2010-12-17</td>
<td align="center">U4</td>
<td align="center">Hospital B</td>
<td align="center">2012-05-10</td>
<td align="center">V8</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td>
@ -422,49 +444,27 @@ data set:</p>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2015-04-24</td>
<td align="center">W10</td>
<td align="center">2012-08-22</td>
<td align="center">R2</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2016-01-14</td>
<td align="center">M10</td>
<td align="center">Hospital B</td>
<td align="center">2017-10-16</td>
<td align="center">P2</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">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2011-08-05</td>
<td align="center">O2</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2011-11-02</td>
<td align="center">N3</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
</tbody>
</table>
<p>Now, let’s start the cleaning and the analysis!</p>
@ -621,9 +621,9 @@ takes into account the antimicrobial susceptibility test results using
<span><span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span></span>
<span><span class="co"># 2</span></span>
<span><span class="co"># Including isolates from ICU.</span></span>
<span><span class="co"># =&gt; Found 10,536 'phenotype-based' first isolates (52.7% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,690 'phenotype-based' first isolates (53.5% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 52.7% is suitable for resistance analysis! We can now filter
<p>So only 53.5% 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">
@ -634,11 +634,11 @@ on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html"
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="co"># Including isolates from ICU.</span></span></code></pre></div>
<p>So we end up with 10,536 isolates for analysis. Now our data looks
<p>So we end up with 10,690 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%">
@ -652,7 +652,7 @@ like:</p>
<col width="6%">
<col width="11%">
<col width="12%">
<col width="9%">
<col width="7%">
<col width="5%">
</colgroup>
<thead><tr class="header">
@ -673,25 +673,9 @@ like:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">5</td>
<td align="center">2011-08-05</td>
<td align="center">O2</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">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">2017-05-04</td>
<td align="center">T10</td>
<td align="left">2</td>
<td align="center">2016-07-14</td>
<td align="center">O7</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
@ -704,47 +688,63 @@ like:</p>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">9</td>
<td align="center">2013-05-12</td>
<td align="center">L8</td>
<td align="center">Hospital A</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">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">10</td>
<td align="center">2016-03-11</td>
<td align="center">Q7</td>
<td align="left">4</td>
<td align="center">2012-05-10</td>
<td align="center">V8</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">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">12</td>
<td align="center">2016-04-09</td>
<td align="center">E4</td>
<td align="center">Hospital A</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">S</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="center">2012-08-22</td>
<td align="center">R2</td>
<td align="center">Hospital A</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">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">8</td>
<td align="center">2010-08-18</td>
<td align="center">N8</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">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">11</td>
<td align="center">2012-09-30</td>
<td align="center">M3</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
@ -753,19 +753,19 @@ like:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">13</td>
<td align="center">2010-02-22</td>
<td align="center">K4</td>
<td align="left">14</td>
<td align="center">2015-11-13</td>
<td align="center">D3</td>
<td align="center">Hospital A</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</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">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
</tbody>
@ -801,8 +801,8 @@ readable:</p>
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://msberends.github.io/cleaner/reference/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></span></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 10,536<br>
Available: 10,536 (100%, NA: 0 = 0%)<br>
Length: 10,690<br>
Available: 10,690 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -827,33 +827,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">4,550</td>
<td align="right">43.19%</td>
<td align="right">4,550</td>
<td align="right">43.19%</td>
<td align="right">4,641</td>
<td align="right">43.41%</td>
<td align="right">4,641</td>
<td align="right">43.41%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,742</td>
<td align="right">26.03%</td>
<td align="right">7,292</td>
<td align="right">69.21%</td>
<td align="right">2,706</td>
<td align="right">25.31%</td>
<td align="right">7,347</td>
<td align="right">68.73%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,069</td>
<td align="right">19.64%</td>
<td align="right">9,361</td>
<td align="right">88.85%</td>
<td align="right">2,165</td>
<td align="right">20.25%</td>
<td align="right">9,512</td>
<td align="right">88.98%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,175</td>
<td align="right">11.15%</td>
<td align="right">10,536</td>
<td align="right">1,178</td>
<td align="right">11.02%</td>
<td align="right">10,690</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -874,14 +874,14 @@ antibiotic class they are in:</p>
<col width="9%">
<col width="9%">
<col width="9%">
<col width="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>
@ -902,27 +902,57 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2011-08-05</td>
<td align="center">O2</td>
<td align="center">Hospital C</td>
<td align="center">2011-09-20</td>
<td align="center">H7</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2013-05-12</td>
<td align="center">L8</td>
<td align="center">2013-09-09</td>
<td align="center">P2</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2010-07-23</td>
<td align="center">O5</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2015-09-18</td>
<td align="center">H3</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
@ -932,58 +962,28 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2016-05-21</td>
<td align="center">T4</td>
<td align="center">Hospital A</td>
<td align="center">2016-02-29</td>
<td align="center">G4</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">S</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="even">
<td align="center">2013-09-09</td>
<td align="center">Q4</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2011-03-13</td>
<td align="center">U1</td>
<td align="center">2011-04-27</td>
<td align="center">O6</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2014-08-28</td>
<td align="center">N9</td>
<td align="center">Hospital A</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">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
@ -1013,50 +1013,50 @@ different bug/drug combinations, you can use the
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">2128</td>
<td align="center">120</td>
<td align="center">2302</td>
<td align="center">4550</td>
<td align="center">2238</td>
<td align="center">123</td>
<td align="center">2280</td>
<td align="center">4641</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3331</td>
<td align="center">152</td>
<td align="center">1067</td>
<td align="center">4550</td>
<td align="center">3380</td>
<td align="center">192</td>
<td align="center">1069</td>
<td align="center">4641</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3321</td>
<td align="center">3354</td>
<td align="center">0</td>
<td align="center">1229</td>
<td align="center">4550</td>
<td align="center">1287</td>
<td align="center">4641</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4005</td>
<td align="center">4053</td>
<td align="center">0</td>
<td align="center">545</td>
<td align="center">4550</td>
<td align="center">588</td>
<td align="center">4641</td>
</tr>
<tr class="odd">
<td align="center">K. pneumoniae</td>
<td align="center">AMX</td>
<td align="center">0</td>
<td align="center">0</td>
<td align="center">1175</td>
<td align="center">1175</td>
<td align="center">1178</td>
<td align="center">1178</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">923</td>
<td align="center">49</td>
<td align="center">203</td>
<td align="center">1175</td>
<td align="center">950</td>
<td align="center">35</td>
<td align="center">193</td>
<td align="center">1178</td>
</tr>
</tbody>
</table>
@ -1078,34 +1078,34 @@ 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">4005</td>
<td align="center">4053</td>
<td align="center">0</td>
<td align="center">545</td>
<td align="center">4550</td>
<td align="center">588</td>
<td align="center">4641</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1053</td>
<td align="center">1060</td>
<td align="center">0</td>
<td align="center">122</td>
<td align="center">1175</td>
<td align="center">118</td>
<td align="center">1178</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2441</td>
<td align="center">2400</td>
<td align="center">0</td>
<td align="center">301</td>
<td align="center">2742</td>
<td align="center">306</td>
<td align="center">2706</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">2069</td>
<td align="center">2069</td>
<td align="center">2165</td>
<td align="center">2165</td>
</tr>
</tbody>
</table>
@ -1137,7 +1137,7 @@ 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] 0.542426</span></span></code></pre></div>
<span><span class="co"># [1] 0.5403181</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">
@ -1152,19 +1152,19 @@ own:</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5308011</td>
<td align="center">0.5356587</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5414217</td>
<td align="center">0.5376112</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5430925</td>
<td align="center">0.5159194</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5612098</td>
<td align="center">0.5683550</td>
</tr>
</tbody>
</table>
@ -1189,23 +1189,23 @@ 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">0.5308011</td>
<td align="center">3133</td>
<td align="center">0.5356587</td>
<td align="center">3211</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5414217</td>
<td align="center">3742</td>
<td align="center">0.5376112</td>
<td align="center">3709</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5430925</td>
<td align="center">1578</td>
<td align="center">0.5159194</td>
<td align="center">1539</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5612098</td>
<td align="center">2083</td>
<td align="center">0.5683550</td>
<td align="center">2231</td>
</tr>
</tbody>
</table>
@ -1230,27 +1230,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7654945</td>
<td align="center">0.8802198</td>
<td align="center">0.9753846</td>
<td align="center">0.7696617</td>
<td align="center">0.8733032</td>
<td align="center">0.9790993</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8272340</td>
<td align="center">0.8961702</td>
<td align="center">0.9889362</td>
<td align="center">0.8361630</td>
<td align="center">0.8998302</td>
<td align="center">0.9830221</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7943107</td>
<td align="center">0.8902261</td>
<td align="center">0.9788476</td>
<td align="center">0.7949002</td>
<td align="center">0.8869180</td>
<td align="center">0.9837398</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5427743</td>
<td align="center">0.5376443</td>
<td align="center">0.0000000</td>
<td align="center">0.5427743</td>
<td align="center">0.5376443</td>
</tr>
</tbody>
</table>
@ -1278,23 +1278,23 @@ classes, use a antibiotic class selector such as
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">53.1%</td>
<td align="right">26.0%</td>
<td align="right">53.6%</td>
<td align="right">26.2%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">54.1%</td>
<td align="right">26.4%</td>
<td align="right">53.8%</td>
<td align="right">25.6%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">54.3%</td>
<td align="right">26.3%</td>
<td align="right">51.6%</td>
<td align="right">26.0%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">56.1%</td>
<td align="right">27.0%</td>
<td align="right">56.8%</td>
<td align="right">28.1%</td>
</tr>
</tbody>
</table>
@ -1410,16 +1410,16 @@ classes) <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code>:</p>
<code class="sourceCode R"><span><span class="va">mic_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span></span>
<span><span class="va">mic_values</span></span>
<span><span class="co"># Class 'mic'</span></span>
<span><span class="co"># [1] 0.005 256 0.0625 0.005 32 0.001 2 16 256 128 </span></span>
<span><span class="co"># [11] 0.25 4 256 0.125 0.001 0.125 256 4 8 0.002 </span></span>
<span><span class="co"># [21] 32 0.0625 256 0.002 0.002 256 64 8 0.002 0.5 </span></span>
<span><span class="co"># [31] 128 1 1 4 0.001 0.25 0.005 0.01 16 0.001 </span></span>
<span><span class="co"># [41] 0.125 16 0.25 256 1 256 0.001 64 0.01 256 </span></span>
<span><span class="co"># [51] 0.0625 0.001 4 16 0.5 0.025 0.5 0.01 2 0.001 </span></span>
<span><span class="co"># [61] 0.001 0.025 16 0.001 1 0.005 32 256 0.002 8 </span></span>
<span><span class="co"># [71] 8 256 256 0.0625 256 2 0.001 1 0.025 0.005 </span></span>
<span><span class="co"># [81] 0.025 0.5 0.01 0.01 0.001 0.005 4 32 16 256 </span></span>
<span><span class="co"># [91] 32 2 256 128 0.5 0.025 0.001 32 8 128</span></span></code></pre></div>
<span><span class="co"># [1] 0.01 0.5 &gt;=256 64 128 0.01 16 0.0625 8 &gt;=256 </span></span>
<span><span class="co"># [11] 64 0.01 128 0.125 4 0.025 0.025 0.01 0.125 2 </span></span>
<span><span class="co"># [21] 32 128 &gt;=256 0.125 &gt;=256 64 0.01 0.25 0.5 4 </span></span>
<span><span class="co"># [31] 2 0.025 0.025 1 0.0625 0.001 8 &gt;=256 8 0.5 </span></span>
<span><span class="co"># [41] 4 32 1 0.125 4 0.0625 0.001 8 0.001 0.001 </span></span>
<span><span class="co"># [51] 2 0.01 1 64 0.002 8 1 64 0.005 128 </span></span>
<span><span class="co"># [61] 0.002 1 0.025 0.25 0.001 1 0.125 0.001 1 0.025 </span></span>
<span><span class="co"># [71] 0.001 0.25 16 128 2 16 4 0.5 &gt;=256 0.125 </span></span>
<span><span class="co"># [81] 0.125 2 0.001 0.25 0.01 4 128 &gt;=256 0.001 4 </span></span>
<span><span class="co"># [91] 2 64 8 64 0.0625 0.001 0.0625 16 8 8</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>
@ -1453,10 +1453,10 @@ 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] 21 30 25 21 30 30 18 17 24 25 21 23 27 18 31 21 21 21 27 19 29 17 28 23 22</span></span>
<span><span class="co"># [26] 23 26 27 19 29 19 22 23 22 21 24 22 19 27 31 28 29 21 24 31 19 27 17 23 19</span></span>
<span><span class="co"># [51] 25 25 18 20 29 25 26 26 24 26 18 19 19 25 26 24 31 18 17 25 25 26 31 20 31</span></span>
<span><span class="co"># [76] 18 17 28 21 24 31 31 31 28 24 22 17 24 29 19 22 25 20 18 17 25 22 17 22 28</span></span></code></pre></div>
<span><span class="co"># [1] 30 19 17 17 24 26 28 18 19 24 22 26 24 29 24 21 31 27 28 19 29 17 27 30 24</span></span>
<span><span class="co"># [26] 17 19 19 24 24 31 23 30 31 31 19 25 24 20 28 31 30 20 25 19 25 28 25 31 25</span></span>
<span><span class="co"># [51] 17 18 23 23 30 25 24 22 21 24 17 19 28 31 26 23 26 21 21 21 24 20 31 26 28</span></span>
<span><span class="co"># [76] 20 25 25 30 21 29 31 29 22 25 30 18 26 19 17 27 18 20 31 26 28 22 26 22 25</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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2
articles/EUCAST.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="">1.8.2.9079</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9080</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="">1.8.2.9079</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9080</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -375,19 +375,19 @@ names or codes, this would have worked exactly the same way:</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span>
<span><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
<span><span class="co"># 1 S R S R R R</span></span>
<span><span class="co"># 2 R S I S I S</span></span>
<span><span class="co"># 3 R R S S I I</span></span>
<span><span class="co"># 4 I R R S S S</span></span>
<span><span class="co"># 5 S R I I I R</span></span>
<span><span class="co"># 6 R R I S R I</span></span>
<span><span class="co"># 1 I S I I R R</span></span>
<span><span class="co"># 2 I R R I I I</span></span>
<span><span class="co"># 3 R R R I R R</span></span>
<span><span class="co"># 4 R R R I R R</span></span>
<span><span class="co"># 5 S I I I S R</span></span>
<span><span class="co"># 6 I I R I R I</span></span>
<span><span class="co"># kanamycin</span></span>
<span><span class="co"># 1 R</span></span>
<span><span class="co"># 1 I</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 S</span></span>
<span><span class="co"># 6 I</span></span></code></pre></div>
<span><span class="co"># 4 R</span></span>
<span><span class="co"># 5 R</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">
@ -428,40 +428,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3191</td>
<td align="right">63.82%</td>
<td align="right">3191</td>
<td align="right">63.82%</td>
<td align="right">3197</td>
<td align="right">63.94%</td>
<td align="right">3197</td>
<td align="right">63.94%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">1014</td>
<td align="right">20.28%</td>
<td align="right">4205</td>
<td align="right">84.10%</td>
<td align="right">998</td>
<td align="right">19.96%</td>
<td align="right">4195</td>
<td align="right">83.90%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">474</td>
<td align="right">9.48%</td>
<td align="right">4679</td>
<td align="right">93.58%</td>
<td align="right">446</td>
<td align="right">8.92%</td>
<td align="right">4641</td>
<td align="right">92.82%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">225</td>
<td align="right">4.50%</td>
<td align="right">4904</td>
<td align="right">98.08%</td>
<td align="right">241</td>
<td align="right">4.82%</td>
<td align="right">4882</td>
<td align="right">97.64%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">96</td>
<td align="right">1.92%</td>
<td align="right">118</td>
<td align="right">2.36%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

2
articles/PCA.html
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9079</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9080</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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@ -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="">1.8.2.9079</small>
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@ -38,7 +38,7 @@
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9079</small>
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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="">1.8.2.9079</small>
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2
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9079</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9080</small>
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2
articles/resistance_predict.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="">1.8.2.9079</small>
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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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