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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="">1.8.2.9042</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</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">
@ -395,65 +395,65 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2017-05-11</td>
<td align="center">P2</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">2013-01-16</td>
<td align="center">B4</td>
<td align="center">Hospital A</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">R</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">2014-09-24</td>
<td align="center">W9</td>
<td align="center">Hospital B</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2015-03-26</td>
<td align="center">P5</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">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2010-10-29</td>
<td align="center">B9</td>
<td align="center">Hospital D</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">R</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2016-04-21</td>
<td align="center">S8</td>
<td align="center">Hospital C</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">F</td>
</tr>
<tr class="odd">
<td align="center">2013-04-29</td>
<td align="center">U9</td>
<td align="center">2013-01-04</td>
<td align="center">E1</td>
<td align="center">Hospital A</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="even">
<td align="center">2011-07-13</td>
<td align="center">Y4</td>
<td align="center">Hospital C</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2010-07-12</td>
<td align="center">U6</td>
<tr class="odd">
<td align="center">2013-12-18</td>
<td align="center">A10</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">M</td>
</tr>
<tr class="even">
<td align="center">2013-01-16</td>
<td align="center">N7</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>
@ -494,16 +494,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,235</td>
<td align="right">51.18%</td>
<td align="right">10,235</td>
<td align="right">51.18%</td>
<td align="right">10,495</td>
<td align="right">52.48%</td>
<td align="right">10,495</td>
<td align="right">52.48%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,765</td>
<td align="right">48.83%</td>
<td align="right">9,505</td>
<td align="right">47.53%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -616,10 +616,10 @@ 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 10,603 'phenotype-based' first isolates (53.0% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,707 '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 53% 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
<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">
<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>
@ -629,7 +629,7 @@ it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" cl
<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 10,603 isolates for analysis. Now our data looks
<p>So we end up with 10,707 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>
@ -668,63 +668,31 @@ like:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2017-05-11</td>
<td align="center">P2</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">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="even">
<td align="left">2</td>
<td align="center">2014-09-24</td>
<td align="center">W9</td>
<td align="center">Hospital B</td>
<td align="left">3</td>
<td align="center">2013-01-04</td>
<td align="center">E1</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">F</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="center">2015-03-26</td>
<td align="center">P5</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="even">
<td align="left">5</td>
<td align="center">2013-04-29</td>
<td align="center">U9</td>
<td align="center">Hospital A</td>
<td align="left">4</td>
<td align="center">2011-07-13</td>
<td align="center">Y4</td>
<td align="center">Hospital C</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
@ -733,9 +701,9 @@ like:</p>
</tr>
<tr class="odd">
<td align="left">6</td>
<td align="center">2010-07-12</td>
<td align="center">U6</td>
<td align="center">Hospital B</td>
<td align="center">2013-01-16</td>
<td align="center">N7</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -748,19 +716,51 @@ like:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">10</td>
<td align="center">2015-03-25</td>
<td align="center">B1</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="left">7</td>
<td align="center">2013-07-13</td>
<td align="center">X9</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">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">9</td>
<td align="center">2014-01-13</td>
<td align="center">L1</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">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">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">2017-10-15</td>
<td align="center">F1</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">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
</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: 10,603<br>
Available: 10,603 (100%, NA: 0 = 0%)<br>
Length: 10,707<br>
Available: 10,707 (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">4,603</td>
<td align="right">43.41%</td>
<td align="right">4,603</td>
<td align="right">43.41%</td>
<td align="right">4,763</td>
<td align="right">44.48%</td>
<td align="right">4,763</td>
<td align="right">44.48%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,709</td>
<td align="right">25.55%</td>
<td align="right">7,312</td>
<td align="right">68.96%</td>
<td align="right">2,688</td>
<td align="right">25.11%</td>
<td align="right">7,451</td>
<td align="right">69.59%</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">19.86%</td>
<td align="right">9,418</td>
<td align="right">88.82%</td>
<td align="right">2,091</td>
<td align="right">19.53%</td>
<td align="right">9,542</td>
<td align="right">89.12%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,185</td>
<td align="right">11.18%</td>
<td align="right">10,603</td>
<td align="right">1,165</td>
<td align="right">10.88%</td>
<td align="right">10,707</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -897,42 +897,12 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2014-09-24</td>
<td align="center">W9</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">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">2014-11-16</td>
<td align="center">M1</td>
<td align="center">2013-01-04</td>
<td align="center">E1</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">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2016-07-19</td>
<td align="center">G10</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">M</td>
@ -942,28 +912,13 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2015-01-12</td>
<td align="center">W8</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>
<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">2014-10-02</td>
<td align="center">X5</td>
<td align="center">Hospital D</td>
<td align="center">2011-07-13</td>
<td align="center">Y4</td>
<td align="center">Hospital C</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
@ -971,13 +926,13 @@ antibiotic class they are in:</p>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2010-11-15</td>
<td align="center">M5</td>
<td align="center">Hospital C</td>
<tr class="odd">
<td align="center">2010-11-23</td>
<td align="center">B2</td>
<td align="center">Hospital B</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">M</td>
@ -986,6 +941,51 @@ antibiotic class they are in:</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2016-09-07</td>
<td align="center">I6</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">R</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2010-04-16</td>
<td align="center">T8</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">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2013-04-19</td>
<td align="center">G5</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>
</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">2197</td>
<td align="center">137</td>
<td align="center">2269</td>
<td align="center">4603</td>
<td align="center">2209</td>
<td align="center">126</td>
<td align="center">2428</td>
<td align="center">4763</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3391</td>
<td align="center">167</td>
<td align="center">1045</td>
<td align="center">4603</td>
<td align="center">3491</td>
<td align="center">158</td>
<td align="center">1114</td>
<td align="center">4763</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3413</td>
<td align="center">3463</td>
<td align="center">0</td>
<td align="center">1190</td>
<td align="center">4603</td>
<td align="center">1300</td>
<td align="center">4763</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">3980</td>
<td align="center">4154</td>
<td align="center">0</td>
<td align="center">623</td>
<td align="center">4603</td>
<td align="center">609</td>
<td align="center">4763</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">1185</td>
<td align="center">1185</td>
<td align="center">1165</td>
<td align="center">1165</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">942</td>
<td align="center">43</td>
<td align="center">200</td>
<td align="center">1185</td>
<td align="center">905</td>
<td align="center">49</td>
<td align="center">211</td>
<td align="center">1165</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">3980</td>
<td align="center">4154</td>
<td align="center">0</td>
<td align="center">623</td>
<td align="center">4603</td>
<td align="center">609</td>
<td align="center">4763</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1060</td>
<td align="center">1057</td>
<td align="center">0</td>
<td align="center">125</td>
<td align="center">1185</td>
<td align="center">108</td>
<td align="center">1165</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2422</td>
<td align="center">2378</td>
<td align="center">0</td>
<td align="center">287</td>
<td align="center">2709</td>
<td align="center">310</td>
<td align="center">2688</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">2091</td>
<td align="center">2091</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] 0.5352259</span></span></code></pre></div>
<span><span class="co"># [1] 0.5443168</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">0.5432099</td>
<td align="center">0.5446860</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5246981</td>
<td align="center">0.5468415</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5336856</td>
<td align="center">0.5404884</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5419501</td>
<td align="center">0.5420827</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">0.5432099</td>
<td align="center">3240</td>
<td align="center">0.5446860</td>
<td align="center">3312</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5246981</td>
<td align="center">3644</td>
<td align="center">0.5468415</td>
<td align="center">3736</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5336856</td>
<td align="center">1514</td>
<td align="center">0.5404884</td>
<td align="center">1556</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5419501</td>
<td align="center">2205</td>
<td align="center">0.5420827</td>
<td align="center">2103</td>
</tr>
</tbody>
</table>
@ -1227,27 +1227,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7729741</td>
<td align="center">0.8646535</td>
<td align="center">0.9761025</td>
<td align="center">0.7661138</td>
<td align="center">0.8721394</td>
<td align="center">0.9777451</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8312236</td>
<td align="center">0.8945148</td>
<td align="center">0.9746835</td>
<td align="center">0.8188841</td>
<td align="center">0.9072961</td>
<td align="center">0.9785408</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7958656</td>
<td align="center">0.8940568</td>
<td align="center">0.9778516</td>
<td align="center">0.7898065</td>
<td align="center">0.8846726</td>
<td align="center">0.9825149</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5413105</td>
<td align="center">0.5538020</td>
<td align="center">0.0000000</td>
<td align="center">0.5413105</td>
<td align="center">0.5538020</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">26.5%</td>
<td align="right">54.5%</td>
<td align="right">27.2%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">52.5%</td>
<td align="right">25.0%</td>
<td align="right">54.7%</td>
<td align="right">26.8%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">53.4%</td>
<td align="right">26.4%</td>
<td align="right">54.0%</td>
<td align="right">25.1%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">54.2%</td>
<td align="right">27.0%</td>
<td align="right">25.3%</td>
</tr>
</tbody>
</table>
@ -1407,16 +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] 0.125 64 32 0.01 0.25 0.01 1 0.005 4 8 </span></span>
<span><span class="co"># [11] 64 0.001 8 0.005 4 0.5 0.005 16 0.001 128 </span></span>
<span><span class="co"># [21] 64 16 64 8 2 2 0.25 128 0.001 &gt;=256 </span></span>
<span><span class="co"># [31] 4 4 8 2 4 16 0.5 2 0.25 0.025 </span></span>
<span><span class="co"># [41] 2 8 8 0.005 128 2 0.01 16 1 1 </span></span>
<span><span class="co"># [51] 0.002 64 16 32 1 0.025 0.0625 16 64 0.001 </span></span>
<span><span class="co"># [61] 0.001 0.002 2 0.002 0.025 0.01 0.025 0.01 16 16 </span></span>
<span><span class="co"># [71] &gt;=256 64 16 0.25 0.01 64 0.25 64 0.001 0.001 </span></span>
<span><span class="co"># [81] 64 16 &gt;=256 4 0.25 0.002 0.5 1 128 0.002 </span></span>
<span><span class="co"># [91] 0.025 0.125 0.025 0.025 0.002 0.25 0.025 64 4 8</span></span></code></pre></div>
<span><span class="co"># [1] 0.125 8 2 8 0.0625 16 8 0.01 0.125 </span></span>
<span><span class="co"># [10] 0.005 8 64 8 0.002 0.25 0.5 8 0.125 </span></span>
<span><span class="co"># [19] 8 &lt;=0.001 0.125 &gt;=256 32 0.025 0.0625 2 4 </span></span>
<span><span class="co"># [28] 2 0.125 0.002 16 0.125 4 &lt;=0.001 1 0.125 </span></span>
<span><span class="co"># [37] 1 128 16 4 1 16 4 32 &lt;=0.001</span></span>
<span><span class="co"># [46] 2 0.005 0.025 0.005 8 0.25 64 64 8 </span></span>
<span><span class="co"># [55] 8 2 2 0.005 4 4 0.5 4 0.01 </span></span>
<span><span class="co"># [64] 0.25 0.01 0.0625 128 0.01 0.01 1 4 8 </span></span>
<span><span class="co"># [73] &gt;=256 0.002 0.5 0.5 128 0.005 16 4 0.125 </span></span>
<span><span class="co"># [82] 8 0.005 0.005 128 0.125 1 0.25 &gt;=256 &gt;=256 </span></span>
<span><span class="co"># [91] 0.125 0.25 0.5 0.125 4 32 0.125 0.025 8 </span></span>
<span><span class="co"># [100] 0.005</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>
@ -1450,10 +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] 21 22 20 24 22 19 26 17 18 29 25 23 23 30 27 29 23 27 17 26 28 17 23 22 24</span></span>
<span><span class="co"># [26] 19 17 18 21 18 19 26 23 28 20 26 29 20 29 21 30 23 31 22 31 22 27 20 25 22</span></span>
<span><span class="co"># [51] 19 24 26 29 21 21 23 22 24 31 24 20 17 18 20 21 29 20 18 23 18 17 30 21 18</span></span>
<span><span class="co"># [76] 18 17 23 21 26 29 25 26 30 30 29 29 18 18 23 26 19 29 28 24 28 24 23 17 20</span></span></code></pre></div>
<span><span class="co"># [1] 31 20 26 28 17 30 25 27 30 18 29 25 25 29 18 27 30 19 21 22 26 23 23 21 20</span></span>
<span><span class="co"># [26] 27 20 17 17 30 26 21 17 30 29 19 25 24 23 17 18 18 18 29 26 30 29 20 19 30</span></span>
<span><span class="co"># [51] 30 27 18 18 23 23 25 23 31 19 30 23 27 21 24 19 26 27 21 29 17 25 29 29 26</span></span>
<span><span class="co"># [76] 22 28 19 28 26 23 22 29 28 18 29 17 19 29 29 17 27 20 23 21 24 27 25 20 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="">1.8.2.9042</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</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
View File

@ -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="">1.8.2.9042</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</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">
@ -370,19 +370,19 @@ 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 I S S I R</span></span>
<span><span class="co"># 2 I R I S R R</span></span>
<span><span class="co"># 3 S I I S R R</span></span>
<span><span class="co"># 4 R I S S I I</span></span>
<span><span class="co"># 5 I I R I I I</span></span>
<span><span class="co"># 6 I I S I S I</span></span>
<span><span class="co"># 1 R R S I R S</span></span>
<span><span class="co"># 2 R I S S R S</span></span>
<span><span class="co"># 3 R I S S S S</span></span>
<span><span class="co"># 4 S I S I I I</span></span>
<span><span class="co"># 5 S I S S R S</span></span>
<span><span class="co"># 6 S S S I S S</span></span>
<span><span class="co"># kanamycin</span></span>
<span><span class="co"># 1 S</span></span>
<span><span class="co"># 2 S</span></span>
<span><span class="co"># 3 S</span></span>
<span><span class="co"># 4 R</span></span>
<span><span class="co"># 2 R</span></span>
<span><span class="co"># 3 R</span></span>
<span><span class="co"># 4 I</span></span>
<span><span class="co"># 5 I</span></span>
<span><span class="co"># 6 S</span></span></code></pre></div>
<span><span class="co"># 6 I</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">
@ -423,40 +423,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3206</td>
<td align="right">64.12%</td>
<td align="right">3206</td>
<td align="right">64.12%</td>
<td align="right">3210</td>
<td align="right">64.20%</td>
<td align="right">3210</td>
<td align="right">64.20%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">983</td>
<td align="right">19.66%</td>
<td align="right">4189</td>
<td align="right">83.78%</td>
<td align="right">1040</td>
<td align="right">20.80%</td>
<td align="right">4250</td>
<td align="right">85.00%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">464</td>
<td align="right">9.28%</td>
<td align="right">4653</td>
<td align="right">93.06%</td>
<td align="right">427</td>
<td align="right">8.54%</td>
<td align="right">4677</td>
<td align="right">93.54%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">236</td>
<td align="right">4.72%</td>
<td align="right">4889</td>
<td align="right">97.78%</td>
<td align="right">235</td>
<td align="right">4.70%</td>
<td align="right">4912</td>
<td align="right">98.24%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">111</td>
<td align="right">2.22%</td>
<td align="right">88</td>
<td align="right">1.76%</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="">1.8.2.9042</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</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="">1.8.2.9042</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</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="">1.8.2.9042</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</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">

18
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="">1.8.2.9042</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9043</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">
@ -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 5 November 2022 07:20:03 UTC. Find more info
<p>It was last updated on 5 November 2022 08:32:50 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>
@ -490,7 +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 5 November 2022 07:20:03 UTC. Find more info
<p>It was last updated on 5 November 2022 08:32:50 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>
@ -687,7 +687,7 @@ 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 5 November 2022 07:20:03 UTC. Find more info
<p>It was last updated on 5 November 2022 08:32:50 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>
@ -847,7 +847,7 @@ 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 5 November 2022 07:20:03 UTC. Find more info
<p>It was last updated on 5 November 2022 08:32:50 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>
@ -1020,7 +1020,7 @@ 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 5 November 2022 07:20:03 UTC. Find more info
<p>It was last updated on 5 November 2022 08:32:50 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>
@ -1308,7 +1308,7 @@ 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 5 November 2022 07:20:03 UTC. Find more info
<p>It was last updated on 5 November 2022 08:32:50 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>
@ -1458,7 +1458,7 @@ 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 5 November 2022 07:20:03 UTC. Find more info
<p>It was last updated on 5 November 2022 08:32:50 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>
@ -1871,7 +1871,7 @@ 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 5 November 2022 07:20:03 UTC. Find more info
<p>It was last updated on 5 November 2022 08:32:50 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
articles/index.html
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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="">1.8.2.9042</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="">1.8.2.9042</small>
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articles/welcome_to_AMR.html
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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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