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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="">1.8.2.9038</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9039</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">
@ -375,12 +375,12 @@ data set:</p>
<col width="13%">
<col width="13%">
<col width="13%">
<col width="28%">
<col width="26%">
<col width="5%">
<col width="5%">
<col width="5%">
<col width="5%">
<col width="8%">
<col width="9%">
</colgroup>
<thead><tr class="header">
<th align="center">date</th>
@ -395,68 +395,68 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2017-02-09</td>
<td align="center">A8</td>
<td align="center">Hospital A</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">2016-08-09</td>
<td align="center">B3</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</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">2012-01-01</td>
<td align="center">S5</td>
<td align="center">2017-05-13</td>
<td align="center">F3</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</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>
<tr class="odd">
<td align="center">2014-03-18</td>
<td align="center">N4</td>
<td align="center">Hospital B</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">2011-05-13</td>
<td align="center">X4</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">I</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">2014-08-14</td>
<td align="center">B9</td>
<td align="center">2016-07-24</td>
<td align="center">R2</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2010-11-05</td>
<td align="center">Q1</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">M</td>
</tr>
<tr class="even">
<td align="center">2013-06-17</td>
<td align="center">J1</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">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2017-06-22</td>
<td align="center">V10</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2010-10-01</td>
<td align="center">X8</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
@ -494,16 +494,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,425</td>
<td align="right">52.13%</td>
<td align="right">10,425</td>
<td align="right">52.13%</td>
<td align="right">10,433</td>
<td align="right">52.17%</td>
<td align="right">10,433</td>
<td align="right">52.17%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,575</td>
<td align="right">47.88%</td>
<td align="right">9,567</td>
<td align="right">47.84%</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 10,672 'phenotype-based' first isolates (53.4% of total where a</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"># microbial ID was available)</span></span></code></pre></div>
<p>So only 53.4% 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">
@ -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 10,672 isolates for analysis. Now our data looks
<p>So we end up with 10,691 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>
@ -668,58 +668,10 @@ like:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">7</td>
<td align="center">2010-08-01</td>
<td align="center">X2</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">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">9</td>
<td align="center">2012-09-22</td>
<td align="center">U1</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="odd">
<td align="left">10</td>
<td align="center">2015-07-29</td>
<td align="center">Y1</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">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="left">11</td>
<td align="center">2012-05-29</td>
<td align="center">C5</td>
<td align="center">Hospital B</td>
<td align="left">1</td>
<td align="center">2016-08-09</td>
<td align="center">B3</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
@ -731,16 +683,64 @@ like:</p>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">12</td>
<td align="center">2011-02-06</td>
<td align="center">S1</td>
<tr class="even">
<td align="left">2</td>
<td align="center">2017-05-13</td>
<td align="center">F3</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</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-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">2014-03-18</td>
<td align="center">N4</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</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">4</td>
<td align="center">2011-05-13</td>
<td align="center">X4</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">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">2016-07-24</td>
<td align="center">R2</td>
<td align="center">Hospital D</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">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
@ -748,19 +748,19 @@ like:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">14</td>
<td align="center">2012-10-27</td>
<td align="center">E2</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</td>
<td align="left">8</td>
<td align="center">2011-10-07</td>
<td align="center">R2</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">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
</tbody>
@ -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: 10,672<br>
Available: 10,672 (100%, NA: 0 = 0%)<br>
Length: 10,691<br>
Available: 10,691 (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">4,695</td>
<td align="right">43.99%</td>
<td align="right">4,695</td>
<td align="right">43.99%</td>
<td align="right">4,653</td>
<td align="right">43.52%</td>
<td align="right">4,653</td>
<td align="right">43.52%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,749</td>
<td align="right">25.76%</td>
<td align="right">7,444</td>
<td align="right">69.75%</td>
<td align="right">2,711</td>
<td align="right">25.36%</td>
<td align="right">7,364</td>
<td align="right">68.88%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,073</td>
<td align="right">19.42%</td>
<td align="right">9,517</td>
<td align="right">89.18%</td>
<td align="right">2,142</td>
<td align="right">20.04%</td>
<td align="right">9,506</td>
<td align="right">88.92%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,155</td>
<td align="right">10.82%</td>
<td align="right">10,672</td>
<td align="right">1,185</td>
<td align="right">11.08%</td>
<td align="right">10,691</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -897,58 +897,58 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2012-09-22</td>
<td align="center">U1</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">2015-07-29</td>
<td align="center">Y1</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">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">2012-07-31</td>
<td align="center">J9</td>
<td align="center">Hospital A</td>
<td align="center">2016-07-24</td>
<td align="center">R2</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2013-04-30</td>
<td align="center">F4</td>
<td align="center">2011-10-07</td>
<td align="center">R2</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">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">2016-06-18</td>
<td align="center">R8</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">2015-09-18</td>
<td align="center">D3</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">I</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
@ -957,33 +957,33 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2010-10-16</td>
<td align="center">A3</td>
<td align="center">Hospital A</td>
<td align="center">2017-02-04</td>
<td align="center">Y10</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">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">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">2010-06-06</td>
<td align="center">D9</td>
<td align="center">2013-11-13</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">B_ESCHR_COLI</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">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>
</tbody>
@ -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">2219</td>
<td align="center">120</td>
<td align="center">2356</td>
<td align="center">4695</td>
<td align="center">2175</td>
<td align="center">152</td>
<td align="center">2326</td>
<td align="center">4653</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3496</td>
<td align="center">146</td>
<td align="center">1053</td>
<td align="center">4695</td>
<td align="center">3423</td>
<td align="center">161</td>
<td align="center">1069</td>
<td align="center">4653</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3403</td>
<td align="center">3409</td>
<td align="center">0</td>
<td align="center">1292</td>
<td align="center">4695</td>
<td align="center">1244</td>
<td align="center">4653</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4103</td>
<td align="center">4080</td>
<td align="center">0</td>
<td align="center">592</td>
<td align="center">4695</td>
<td align="center">573</td>
<td align="center">4653</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">1155</td>
<td align="center">1155</td>
<td align="center">1185</td>
<td align="center">1185</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">913</td>
<td align="center">41</td>
<td align="center">201</td>
<td align="center">1155</td>
<td align="center">939</td>
<td align="center">39</td>
<td align="center">207</td>
<td align="center">1185</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">4080</td>
<td align="center">0</td>
<td align="center">592</td>
<td align="center">4695</td>
<td align="center">573</td>
<td align="center">4653</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1056</td>
<td align="center">1060</td>
<td align="center">0</td>
<td align="center">99</td>
<td align="center">1155</td>
<td align="center">125</td>
<td align="center">1185</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2425</td>
<td align="center">2400</td>
<td align="center">0</td>
<td align="center">324</td>
<td align="center">2749</td>
<td align="center">311</td>
<td align="center">2711</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">2073</td>
<td align="center">2073</td>
<td align="center">2142</td>
<td align="center">2142</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] 0.5438531</span></span></code></pre></div>
<span><span class="co"># [1] 0.5446637</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">0.5467467</td>
<td align="center">0.5453964</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5433633</td>
<td align="center">0.5342941</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5498433</td>
<td align="center">0.5604129</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5359324</td>
<td align="center">0.5495620</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">0.5467467</td>
<td align="center">3166</td>
<td align="center">0.5453964</td>
<td align="center">3128</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5433633</td>
<td align="center">3782</td>
<td align="center">0.5342941</td>
<td align="center">3747</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5498433</td>
<td align="center">1595</td>
<td align="center">0.5604129</td>
<td align="center">1647</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5359324</td>
<td align="center">2129</td>
<td align="center">0.5495620</td>
<td align="center">2169</td>
</tr>
</tbody>
</table>
@ -1227,27 +1227,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7757188</td>
<td align="center">0.8739084</td>
<td align="center">0.9782748</td>
<td align="center">0.7702557</td>
<td align="center">0.8768536</td>
<td align="center">0.9735654</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8259740</td>
<td align="center">0.9142857</td>
<td align="center">0.9844156</td>
<td align="center">0.8253165</td>
<td align="center">0.8945148</td>
<td align="center">0.9839662</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7937432</td>
<td align="center">0.8821390</td>
<td align="center">0.9792652</td>
<td align="center">0.7941719</td>
<td align="center">0.8852822</td>
<td align="center">0.9793434</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5344911</td>
<td align="center">0.5359477</td>
<td align="center">0.0000000</td>
<td align="center">0.5344911</td>
<td align="center">0.5359477</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">54.7%</td>
<td align="right">26.2%</td>
<td align="right">54.5%</td>
<td align="right">26.7%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">54.3%</td>
<td align="right">25.5%</td>
<td align="right">53.4%</td>
<td align="right">26.2%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">55.0%</td>
<td align="right">27.5%</td>
<td align="right">56.0%</td>
<td align="right">27.6%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">53.6%</td>
<td align="right">26.0%</td>
<td align="right">55.0%</td>
<td align="right">25.7%</td>
</tr>
</tbody>
</table>
@ -1407,16 +1407,16 @@ 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] 0.125 1 0.125 0.001 32 0.001 4 &gt;=256 0.0625 0.002 </span></span>
<span><span class="co"># [11] 0.001 0.5 0.025 0.01 16 2 64 8 2 0.5 </span></span>
<span><span class="co"># [21] 0.125 32 0.5 0.5 0.005 4 &gt;=256 16 2 0.005 </span></span>
<span><span class="co"># [31] 0.01 0.005 0.5 0.002 4 1 64 2 16 0.0625</span></span>
<span><span class="co"># [41] 0.025 0.025 0.01 &gt;=256 0.005 64 8 0.01 0.001 128 </span></span>
<span><span class="co"># [51] 0.001 64 4 64 &gt;=256 1 0.5 32 0.125 0.002 </span></span>
<span><span class="co"># [61] 8 16 128 2 &gt;=256 0.01 1 16 128 0.002 </span></span>
<span><span class="co"># [71] 128 16 0.01 1 2 0.25 0.01 0.25 1 0.005 </span></span>
<span><span class="co"># [81] 8 0.025 &gt;=256 0.002 0.002 0.0625 0.125 0.005 &gt;=256 0.5 </span></span>
<span><span class="co"># [91] &gt;=256 128 2 128 0.25 1 0.005 0.125 0.0625 0.25</span></span></code></pre></div>
<span><span class="co"># [1] 0.005 0.5 16 0.25 0.0625 128 0.025 0.01 0.005 0.125 </span></span>
<span><span class="co"># [11] 2 8 0.01 8 128 2 0.025 0.25 128 0.002 </span></span>
<span><span class="co"># [21] 0.001 0.25 0.025 0.001 1 32 0.25 &gt;=256 0.025 0.002 </span></span>
<span><span class="co"># [31] 32 0.025 2 4 0.125 128 8 0.25 2 4 </span></span>
<span><span class="co"># [41] 32 0.0625 8 4 0.125 8 0.125 0.025 16 0.01 </span></span>
<span><span class="co"># [51] 32 0.125 1 64 64 0.01 128 0.5 0.001 0.125 </span></span>
<span><span class="co"># [61] 32 4 0.005 0.001 0.005 0.002 0.5 0.01 0.25 2 </span></span>
<span><span class="co"># [71] &gt;=256 4 128 1 1 0.125 16 0.005 0.001 32 </span></span>
<span><span class="co"># [81] 128 0.5 0.0625 0.0625 32 0.002 4 0.025 0.0625 128 </span></span>
<span><span class="co"># [91] 4 2 2 &gt;=256 16 0.0625 &gt;=256 0.125 0.5 1</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 +1450,10 @@ 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] 17 24 27 27 17 30 28 20 18 30 23 23 18 30 24 31 22 26 24 18 31 25 17 18 23</span></span>
<span><span class="co"># [26] 26 25 19 22 21 22 29 19 21 28 22 24 26 20 23 19 23 18 25 28 21 29 23 20 24</span></span>
<span><span class="co"># [51] 29 24 17 17 30 29 18 21 30 29 29 22 27 22 17 17 28 21 27 20 24 26 31 20 17</span></span>
<span><span class="co"># [76] 19 31 17 22 21 19 22 25 19 29 30 25 22 17 31 24 24 25 28 22 26 27 27 21 27</span></span></code></pre></div>
<span><span class="co"># [1] 18 26 18 24 26 31 22 22 22 26 27 26 30 20 23 30 30 25 25 17 18 27 25 25 28</span></span>
<span><span class="co"># [26] 31 17 23 27 20 29 22 19 31 27 30 21 22 30 24 17 21 28 31 31 17 20 20 28 29</span></span>
<span><span class="co"># [51] 29 19 24 18 28 23 27 17 26 17 28 17 18 30 27 25 26 27 25 31 17 17 17 23 28</span></span>
<span><span class="co"># [76] 29 23 25 25 24 21 24 18 20 17 24 25 30 27 19 23 25 20 18 28 23 24 23 18 20</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="">1.8.2.9038</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9039</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">

54
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="">1.8.2.9038</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9039</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 R S S R</span></span>
<span><span class="co"># 2 I I I I S I</span></span>
<span><span class="co"># 3 I I R I I S</span></span>
<span><span class="co"># 4 I S I R I R</span></span>
<span><span class="co"># 5 I R I R R I</span></span>
<span><span class="co"># 6 I R I R S S</span></span>
<span><span class="co"># 1 S S R R R R</span></span>
<span><span class="co"># 2 R I S R S S</span></span>
<span><span class="co"># 3 R I R S R I</span></span>
<span><span class="co"># 4 I R S I R I</span></span>
<span><span class="co"># 5 S S S R S S</span></span>
<span><span class="co"># 6 S I I R S I</span></span>
<span><span class="co"># kanamycin</span></span>
<span><span class="co"># 1 S</span></span>
<span><span class="co"># 2 S</span></span>
<span><span class="co"># 3 R</span></span>
<span><span class="co"># 4 S</span></span>
<span><span class="co"># 5 R</span></span>
<span><span class="co"># 6 I</span></span></code></pre></div>
<span><span class="co"># 1 R</span></span>
<span><span class="co"># 2 R</span></span>
<span><span class="co"># 3 I</span></span>
<span><span class="co"># 4 I</span></span>
<span><span class="co"># 5 I</span></span>
<span><span class="co"># 6 R</span></span></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can
use:</p>
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
@ -423,32 +423,32 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3192</td>
<td align="right">63.84%</td>
<td align="right">3192</td>
<td align="right">63.84%</td>
<td align="right">3215</td>
<td align="right">64.30%</td>
<td align="right">3215</td>
<td align="right">64.30%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">989</td>
<td align="right">19.78%</td>
<td align="right">4181</td>
<td align="right">83.62%</td>
<td align="right">1001</td>
<td align="right">20.02%</td>
<td align="right">4216</td>
<td align="right">84.32%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">453</td>
<td align="right">9.06%</td>
<td align="right">4634</td>
<td align="right">92.68%</td>
<td align="right">435</td>
<td align="right">8.70%</td>
<td align="right">4651</td>
<td align="right">93.02%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">268</td>
<td align="right">5.36%</td>
<td align="right">251</td>
<td align="right">5.02%</td>
<td align="right">4902</td>
<td align="right">98.04%</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="">1.8.2.9038</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9039</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="">1.8.2.9038</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9039</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="">1.8.2.9038</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9039</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">

20
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="">1.8.2.9038</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9039</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 30 October 2022 13:33:29 UTC. Find more info
<p>It was last updated on 30 October 2022 20:06:52 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>
@ -483,14 +483,14 @@ Set Name ‘Microoganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href
<h2 id="antibiotics-antibiotic-agents">
<code>antibiotics</code>: Antibiotic Agents<a class="anchor" aria-label="anchor" href="#antibiotics-antibiotic-agents"></a>
</h2>
<p>A data set with 484 rows and 14 columns, containing the following
<p>A data set with 483 rows and 14 columns, containing the following
column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>atc</em>,
<em>atc_group1</em>, <em>atc_group2</em>, <em>abbreviations</em>,
<em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>,
<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 30 October 2022 13:33:29 UTC. Find more info
<p>It was last updated on 30 October 2022 20:06:52 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 30 October 2022 13:33:29 UTC. Find more info
<p>It was last updated on 30 October 2022 20:06:52 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 30 October 2022 13:33:29 UTC. Find more info
<p>It was last updated on 30 October 2022 20:06:52 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 30 October 2022 13:33:29 UTC. Find more info
<p>It was last updated on 30 October 2022 20:06:52 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 30 October 2022 13:33:29 UTC. Find more info
<p>It was last updated on 30 October 2022 20:06:52 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 30 October 2022 13:33:29 UTC. Find more info
<p>It was last updated on 30 October 2022 20:06:52 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 30 October 2022 13:33:29 UTC. Find more info
<p>It was last updated on 30 October 2022 20:06:52 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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@ -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="">1.8.2.9038</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9039</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="">1.8.2.9038</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9039</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="">1.8.2.9038</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9039</small>
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@ -188,7 +188,7 @@ treatment evaluation in any setting.</p>
10.33612/diss.177417131</a> and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">DOI
10.33612/diss.192486375</a>).</p>
<p>After installing this package, R knows ~49,000 distinct microbial
species and all ~590 antibiotic, antimycotic and antiviral drugs by name
species and all ~580 antibiotic, antimycotic and antiviral drugs by name
and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED
CT), and knows all about valid R/SI and MIC values. The integral
breakpoint guidelines from CLSI and EUCAST are included from the last 10