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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="">1.8.2.9034</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9035</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">
@ -395,31 +395,64 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2017-07-03</td>
<td align="center">M8</td>
<td align="center">2016-06-08</td>
<td align="center">H2</td>
<td align="center">Hospital B</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">R</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2015-10-26</td>
<td align="center">B10</td>
<td align="center">2017-12-08</td>
<td align="center">T3</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2013-11-26</td>
<td align="center">C9</td>
<td align="center">Hospital B</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="even">
<td align="center">2011-09-18</td>
<td align="center">Y5</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">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2014-08-30</td>
<td align="center">I4</td>
<td align="center">Hospital A</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2011-11-13</td>
<td align="center">N6</td>
<td align="center">Hospital A</td>
<tr class="even">
<td align="center">2012-11-04</td>
<td align="center">T9</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
@ -427,39 +460,6 @@ data set:</p>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2010-08-24</td>
<td align="center">J7</td>
<td align="center">Hospital C</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2012-03-12</td>
<td align="center">H2</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">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2017-06-02</td>
<td align="center">J9</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia 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">M</td>
</tr>
</tbody>
</table>
<p>Now, let’s start the cleaning and the analysis!</p>
@ -494,16 +494,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,313</td>
<td align="right">51.57%</td>
<td align="right">10,313</td>
<td align="right">51.57%</td>
<td align="right">10,377</td>
<td align="right">51.89%</td>
<td align="right">10,377</td>
<td align="right">51.89%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,687</td>
<td align="right">48.44%</td>
<td align="right">9,623</td>
<td align="right">48.12%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -616,9 +616,9 @@ 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 10,691 'phenotype-based' first isolates (53.5% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,687 'phenotype-based' first isolates (53.4% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 53.5% is suitable for resistance analysis! We can now filter
<p>So only 53.4% 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">
@ -629,7 +629,7 @@ on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html"
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="co"># Including isolates from ICU.</span></span></code></pre></div>
<p>So we end up with 10,691 isolates for analysis. Now our data looks
<p>So we end up with 10,687 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>
@ -646,8 +646,8 @@ like:</p>
<col width="3%">
<col width="6%">
<col width="11%">
<col width="10%">
<col width="9%">
<col width="12%">
<col width="7%">
<col width="5%">
</colgroup>
<thead><tr class="header">
@ -669,41 +669,57 @@ like:</p>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2017-07-03</td>
<td align="center">M8</td>
<td align="center">2016-06-08</td>
<td align="center">H2</td>
<td align="center">Hospital B</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</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-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</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">2</td>
<td align="center">2015-10-26</td>
<td align="center">B10</td>
<td align="center">2017-12-08</td>
<td align="center">T3</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</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">S</td>
<td align="center">S</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">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">3</td>
<td align="center">2011-11-13</td>
<td align="center">N6</td>
<td align="center">Hospital A</td>
<td align="center">2013-11-26</td>
<td align="center">C9</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">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="left">6</td>
<td align="center">2012-11-04</td>
<td align="center">T9</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -715,52 +731,36 @@ like:</p>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">7</td>
<td align="center">2014-07-24</td>
<td align="center">M2</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">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="odd">
<td align="left">11</td>
<td align="center">2015-01-28</td>
<td align="center">D3</td>
<td align="center">Hospital B</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="left">8</td>
<td align="center">2011-09-02</td>
<td align="center">U9</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">S</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">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">18</td>
<td align="center">2016-05-13</td>
<td align="center">L1</td>
<td align="center">Hospital B</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="left">10</td>
<td align="center">2015-12-26</td>
<td align="center">Q6</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">I</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">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
</tbody>
@ -796,8 +796,8 @@ 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: 10,691<br>
Available: 10,691 (100%, NA: 0 = 0%)<br>
Length: 10,687<br>
Available: 10,687 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -822,33 +822,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">4,678</td>
<td align="right">43.76%</td>
<td align="right">4,678</td>
<td align="right">43.76%</td>
<td align="right">4,686</td>
<td align="right">43.85%</td>
<td align="right">4,686</td>
<td align="right">43.85%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,713</td>
<td align="right">25.38%</td>
<td align="right">7,391</td>
<td align="right">69.13%</td>
<td align="right">2,764</td>
<td align="right">25.86%</td>
<td align="right">7,450</td>
<td align="right">69.71%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,106</td>
<td align="right">19.70%</td>
<td align="right">9,497</td>
<td align="right">88.83%</td>
<td align="right">2,087</td>
<td align="right">19.53%</td>
<td align="right">9,537</td>
<td align="right">89.24%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,194</td>
<td align="right">11.17%</td>
<td align="right">10,691</td>
<td align="right">1,150</td>
<td align="right">10.76%</td>
<td align="right">10,687</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -869,14 +869,14 @@ antibiotic class they are in:</p>
<col width="9%">
<col width="9%">
<col width="9%">
<col width="11%">
<col width="10%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="6%">
<col width="11%">
<col width="11%">
<col width="12%">
<col width="9%">
<col width="5%">
</colgroup>
@ -897,26 +897,56 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2017-07-03</td>
<td align="center">M8</td>
<td align="center">Hospital B</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">2017-01-02</td>
<td align="center">H1</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">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</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">2014-07-24</td>
<td align="center">M2</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">2014-06-28</td>
<td align="center">F2</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2013-11-15</td>
<td align="center">R3</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="even">
<td align="center">2016-09-25</td>
<td align="center">A7</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">S</td>
<td align="center">R</td>
@ -927,65 +957,35 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2015-10-21</td>
<td align="center">E5</td>
<td align="center">Hospital C</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">2017-07-08</td>
<td align="center">T1</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">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">2016-07-03</td>
<td align="center">I7</td>
<td align="center">Hospital C</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">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">2012-11-08</td>
<td align="center">P10</td>
<td align="center">2017-08-10</td>
<td align="center">D9</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">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2010-12-30</td>
<td align="center">J6</td>
<td align="center">Hospital C</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</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>
</tbody>
</table>
<p>If you want to get a quick glance of the number of isolates in
@ -1009,50 +1009,50 @@ 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">2228</td>
<td align="center">114</td>
<td align="center">2336</td>
<td align="center">4678</td>
<td align="center">2208</td>
<td align="center">140</td>
<td align="center">2338</td>
<td align="center">4686</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3442</td>
<td align="center">167</td>
<td align="center">1069</td>
<td align="center">4678</td>
<td align="center">3438</td>
<td align="center">171</td>
<td align="center">1077</td>
<td align="center">4686</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3424</td>
<td align="center">3403</td>
<td align="center">0</td>
<td align="center">1254</td>
<td align="center">4678</td>
<td align="center">1283</td>
<td align="center">4686</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4103</td>
<td align="center">4139</td>
<td align="center">0</td>
<td align="center">575</td>
<td align="center">4678</td>
<td align="center">547</td>
<td align="center">4686</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">1194</td>
<td align="center">1194</td>
<td align="center">1150</td>
<td align="center">1150</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">964</td>
<td align="center">40</td>
<td align="center">190</td>
<td align="center">1194</td>
<td align="center">902</td>
<td align="center">50</td>
<td align="center">198</td>
<td align="center">1150</td>
</tr>
</tbody>
</table>
@ -1075,34 +1075,34 @@ 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">4103</td>
<td align="center">4139</td>
<td align="center">0</td>
<td align="center">575</td>
<td align="center">4678</td>
<td align="center">547</td>
<td align="center">4686</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1069</td>
<td align="center">1039</td>
<td align="center">0</td>
<td align="center">125</td>
<td align="center">1194</td>
<td align="center">111</td>
<td align="center">1150</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2406</td>
<td align="center">2463</td>
<td align="center">0</td>
<td align="center">307</td>
<td align="center">2713</td>
<td align="center">301</td>
<td align="center">2764</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">2106</td>
<td align="center">2106</td>
<td align="center">2087</td>
<td align="center">2087</td>
</tr>
</tbody>
</table>
@ -1134,7 +1134,7 @@ I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equa
own:</p>
<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span></span>
<span><span class="co"># [1] 0.5445702</span></span></code></pre></div>
<span><span class="co"># [1] 0.5448676</span></span></code></pre></div>
<p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and
<code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r">
@ -1149,19 +1149,19 @@ own:</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5426092</td>
<td align="center">0.5442717</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5458619</td>
<td align="center">0.5377861</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5291508</td>
<td align="center">0.5453991</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5568834</td>
<td align="center">0.5577913</td>
</tr>
</tbody>
</table>
@ -1186,23 +1186,23 @@ 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">0.5426092</td>
<td align="center">3227</td>
<td align="center">0.5442717</td>
<td align="center">3151</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5458619</td>
<td align="center">3794</td>
<td align="center">0.5377861</td>
<td align="center">3758</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5291508</td>
<td align="center">1578</td>
<td align="center">0.5453991</td>
<td align="center">1641</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5568834</td>
<td align="center">2092</td>
<td align="center">0.5577913</td>
<td align="center">2137</td>
</tr>
</tbody>
</table>
@ -1227,27 +1227,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7714835</td>
<td align="center">0.8770842</td>
<td align="center">0.9803335</td>
<td align="center">0.7701665</td>
<td align="center">0.8832693</td>
<td align="center">0.9812207</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8408710</td>
<td align="center">0.8953099</td>
<td align="center">0.9824121</td>
<td align="center">0.8278261</td>
<td align="center">0.9034783</td>
<td align="center">0.9860870</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7906377</td>
<td align="center">0.8868411</td>
<td align="center">0.9808330</td>
<td align="center">0.7948625</td>
<td align="center">0.8910999</td>
<td align="center">0.9851664</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5365622</td>
<td align="center">0.5304264</td>
<td align="center">0.0000000</td>
<td align="center">0.5365622</td>
<td align="center">0.5304264</td>
</tr>
</tbody>
</table>
@ -1275,23 +1275,23 @@ classes, use a antibiotic class selector such as
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">54.3%</td>
<td align="right">27.6%</td>
<td align="right">54.4%</td>
<td align="right">25.9%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">54.6%</td>
<td align="right">25.6%</td>
<td align="right">53.8%</td>
<td align="right">26.2%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">52.9%</td>
<td align="right">25.8%</td>
<td align="right">54.5%</td>
<td align="right">27.5%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">55.7%</td>
<td align="right">25.6%</td>
<td align="right">55.8%</td>
<td align="right">26.6%</td>
</tr>
</tbody>
</table>
@ -1407,18 +1407,18 @@ 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] 1 0.0625 0.25 8 32 0.5 128 0.0625 0.025 </span></span>
<span><span class="co"># [10] 1 4 0.125 0.025 0.125 0.125 4 32 4 </span></span>
<span><span class="co"># [19] &lt;=0.001 256 0.0625 0.125 0.01 4 64 0.0625 128 </span></span>
<span><span class="co"># [28] 4 &lt;=0.001 0.002 &lt;=0.001 64 &lt;=0.001 0.25 0.5 32 </span></span>
<span><span class="co"># [37] 0.125 32 &lt;=0.001 16 0.002 0.01 1 2 0.0625 </span></span>
<span><span class="co"># [46] 8 0.125 0.002 128 256 0.0625 32 2 32 </span></span>
<span><span class="co"># [55] 0.25 0.01 0.002 32 4 1 0.01 64 0.125 </span></span>
<span><span class="co"># [64] 0.5 0.005 0.125 0.005 0.0625 0.002 8 2 0.005 </span></span>
<span><span class="co"># [73] 64 0.5 0.125 0.0625 0.0625 128 0.002 0.125 2 </span></span>
<span><span class="co"># [82] 64 0.0625 0.01 4 &lt;=0.001 0.25 &lt;=0.001 8 4 </span></span>
<span><span class="co"># [91] 4 0.005 0.01 4 0.005 2 4 0.025 0.005 </span></span>
<span><span class="co"># [100] 0.5</span></span></code></pre></div>
<span><span class="co"># [1] 128 8 0.5 0.01 4 0.025 0.002 256 &lt;=0.001</span></span>
<span><span class="co"># [10] 0.002 2 4 0.5 32 0.025 0.002 0.5 16 </span></span>
<span><span class="co"># [19] 0.005 0.025 2 4 4 16 256 4 2 </span></span>
<span><span class="co"># [28] 0.002 2 256 0.025 0.01 0.01 0.01 0.125 &lt;=0.001</span></span>
<span><span class="co"># [37] &lt;=0.001 128 32 0.25 2 0.125 32 32 0.002 </span></span>
<span><span class="co"># [46] 0.002 128 0.002 4 64 0.005 1 8 0.01 </span></span>
<span><span class="co"># [55] &lt;=0.001 0.005 0.005 0.25 0.5 0.0625 0.25 0.0625 0.0625 </span></span>
<span><span class="co"># [64] 0.01 0.002 256 0.5 0.25 0.0625 0.025 0.005 16 </span></span>
<span><span class="co"># [73] 32 0.0625 256 128 128 128 2 256 4 </span></span>
<span><span class="co"># [82] 2 0.005 16 0.005 64 1 0.5 8 0.025 </span></span>
<span><span class="co"># [91] 0.005 0.5 64 0.0625 0.025 0.01 32 128 0.002 </span></span>
<span><span class="co"># [100] 128</span></span></code></pre></div>
<div class="sourceCode" id="cb37"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">mic_values</span><span class="op">)</span></span></code></pre></div>
@ -1452,10 +1452,10 @@ 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] 23 23 17 18 17 19 30 21 31 22 21 28 30 25 17 31 22 26 21 27 23 20 26 26 22</span></span>
<span><span class="co"># [26] 18 28 25 17 22 21 19 27 19 20 25 18 31 22 19 28 23 30 27 24 28 23 23 30 30</span></span>
<span><span class="co"># [51] 23 30 24 23 17 19 18 30 22 24 22 19 19 23 20 19 21 18 26 31 20 20 19 21 24</span></span>
<span><span class="co"># [76] 29 30 18 29 23 22 22 28 23 22 30 18 27 28 26 31 31 22 20 31 28 31 23 31 18</span></span></code></pre></div>
<span><span class="co"># [1] 19 31 30 19 20 26 24 22 22 19 18 20 19 23 20 28 23 28 20 20 21 22 18 17 24</span></span>
<span><span class="co"># [26] 18 22 31 23 22 31 28 29 24 22 26 23 19 18 26 30 23 31 17 27 26 17 17 28 26</span></span>
<span><span class="co"># [51] 17 31 23 30 31 23 17 26 17 23 23 28 23 20 30 17 30 18 23 31 25 31 21 28 19</span></span>
<span><span class="co"># [76] 23 26 29 17 23 29 25 18 25 21 25 22 31 28 24 31 28 19 23 22 17 19 25 23 30</span></span></code></pre></div>
<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">disk_values</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></code></pre></div>

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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="">1.8.2.9034</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9035</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="">1.8.2.9034</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9035</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">
@ -370,18 +370,18 @@ 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 S I R S S</span></span>
<span><span class="co"># 2 R S I I R I</span></span>
<span><span class="co"># 3 R S S R S R</span></span>
<span><span class="co"># 4 R S R S R I</span></span>
<span><span class="co"># 5 R I S R I I</span></span>
<span><span class="co"># 6 S S R S I I</span></span>
<span><span class="co"># 1 I S S R I I</span></span>
<span><span class="co"># 2 S S R R I I</span></span>
<span><span class="co"># 3 I I S I R R</span></span>
<span><span class="co"># 4 S R S S I R</span></span>
<span><span class="co"># 5 R R S R R S</span></span>
<span><span class="co"># 6 R S R I R R</span></span>
<span><span class="co"># kanamycin</span></span>
<span><span class="co"># 1 I</span></span>
<span><span class="co"># 2 I</span></span>
<span><span class="co"># 1 S</span></span>
<span><span class="co"># 2 S</span></span>
<span><span class="co"># 3 I</span></span>
<span><span class="co"># 4 R</span></span>
<span><span class="co"># 5 R</span></span>
<span><span class="co"># 4 S</span></span>
<span><span class="co"># 5 S</span></span>
<span><span class="co"># 6 R</span></span></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can
use:</p>
@ -423,40 +423,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3211</td>
<td align="right">64.22%</td>
<td align="right">3211</td>
<td align="right">64.22%</td>
<td align="right">3255</td>
<td align="right">65.10%</td>
<td align="right">3255</td>
<td align="right">65.10%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">1025</td>
<td align="right">20.50%</td>
<td align="right">4236</td>
<td align="right">84.72%</td>
<td align="right">989</td>
<td align="right">19.78%</td>
<td align="right">4244</td>
<td align="right">84.88%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">425</td>
<td align="right">8.50%</td>
<td align="right">4661</td>
<td align="right">93.22%</td>
<td align="right">427</td>
<td align="right">8.54%</td>
<td align="right">4671</td>
<td align="right">93.42%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">233</td>
<td align="right">4.66%</td>
<td align="right">4894</td>
<td align="right">97.88%</td>
<td align="right">237</td>
<td align="right">4.74%</td>
<td align="right">4908</td>
<td align="right">98.16%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">106</td>
<td align="right">2.12%</td>
<td align="right">92</td>
<td align="right">1.84%</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="">1.8.2.9034</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9035</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
articles/SPSS.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="">1.8.2.9034</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9035</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
articles/WHONET.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="">1.8.2.9034</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9035</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">

22
articles/datasets.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="">1.8.2.9034</small>
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@ -191,7 +191,7 @@ column names:<br><em>mo</em>, <em>fullname</em>, <em>status</em>, <em>kingdom</e
<em>gbif_renamed_to</em>, <em>prevalence</em> and <em>snomed</em>.</p>
<p>This data set is in R available as <code>microorganisms</code>, after
you load the <code>AMR</code> package.</p>
<p>It was last updated on 29 October 2022 12:16:58 UTC. Find more info
<p>It was last updated on 29 October 2022 14:10:26 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
@ -199,7 +199,7 @@ about the structure of this data set <a href="https://msberends.github.io/AMR/re
R Data Structure (RDS) file</a> (1.1 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.txt" class="external-link">tab-separated
text file</a> (0.4 kB)<br>
text file</a> (10.6 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.xlsx" class="external-link">Microsoft
Excel workbook</a> (4.8 MB)<br>
@ -223,6 +223,8 @@ DTA file</a> (43.8 MB)</li>
contain only the first 50 SNOMED codes per record, as their file size
would otherwise exceed 100 MB; the file size limit of GitHub.</strong>
Advice? Use R instead.</p>
<p>The tab-separated text file contains all SNOMED codes as comma
separated values.</p>
<div class="section level3">
<h3 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a>
</h3>
@ -488,7 +490,7 @@ column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>a
<em>iv_ddd</em>, <em>iv_units</em> and <em>loinc</em>.</p>
<p>This data set is in R available as <code>antibiotics</code>, after
you load the <code>AMR</code> package.</p>
<p>It was last updated on 29 October 2022 12:16:58 UTC. Find more info
<p>It was last updated on 29 October 2022 14:10:26 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
@ -682,7 +684,7 @@ column names:<br><em>atc</em>, <em>cid</em>, <em>name</em>, <em>atc_group</em>,
<em>iv_ddd</em> and <em>iv_units</em>.</p>
<p>This data set is in R available as <code>antivirals</code>, after you
load the <code>AMR</code> package.</p>
<p>It was last updated on 29 October 2022 12:16:58 UTC. Find more info
<p>It was last updated on 29 October 2022 14:10:26 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
@ -839,7 +841,7 @@ column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>
<em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
<p>This data set is in R available as <code>rsi_translation</code>,
after you load the <code>AMR</code> package.</p>
<p>It was last updated on 29 October 2022 12:16:58 UTC. Find more info
<p>It was last updated on 29 October 2022 14:10:26 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
@ -1012,7 +1014,7 @@ Resistance<a class="anchor" aria-label="anchor" href="#intrinsic_resistant-intri
column names:<br><em>mo</em> and <em>ab</em>.</p>
<p>This data set is in R available as <code>intrinsic_resistant</code>,
after you load the <code>AMR</code> package.</p>
<p>It was last updated on 29 October 2022 12:16:58 UTC. Find more info
<p>It was last updated on 29 October 2022 14:10:26 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
@ -1300,7 +1302,7 @@ column names:<br><em>ab</em>, <em>name</em>, <em>type</em>, <em>dose</em>,
<em>original_txt</em> and <em>eucast_version</em>.</p>
<p>This data set is in R available as <code>dosage</code>, after you
load the <code>AMR</code> package.</p>
<p>It was last updated on 29 October 2022 12:16:58 UTC. Find more info
<p>It was last updated on 29 October 2022 14:10:26 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
@ -1450,7 +1452,7 @@ column names:<br><em>date</em>, <em>patient</em>, <em>age</em>, <em>gender</em>,
<em>MUP</em> and <em>RIF</em>.</p>
<p>This data set is in R available as <code>example_isolates</code>,
after you load the <code>AMR</code> package.</p>
<p>It was last updated on 29 October 2022 12:16:58 UTC. Find more info
<p>It was last updated on 29 October 2022 14:10:26 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates.html">here</a>.</p>
<div class="section level3">
<h3 id="source-6">Source<a class="anchor" aria-label="anchor" href="#source-6"></a>
@ -1863,7 +1865,7 @@ column names:<br><em>patient_id</em>, <em>hospital</em>, <em>date</em>,
<p>This data set is in R available as
<code>example_isolates_unclean</code>, after you load the
<code>AMR</code> package.</p>
<p>It was last updated on 29 October 2022 12:16:58 UTC. Find more info
<p>It was last updated on 29 October 2022 14:10:26 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates_unclean.html">here</a>.</p>
<div class="section level3">
<h3 id="source-7">Source<a class="anchor" aria-label="anchor" href="#source-7"></a>

2
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<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="">1.8.2.9034</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9035</small>
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