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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="">1.8.2.9125</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9126</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">
@ -411,70 +411,70 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2010-01-28</td>
<td align="center">Q1</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">2010-12-31</td>
<td align="center">U7</td>
<td align="center">Hospital C</td>
<td align="center">Streptococcus pneumoniae</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>
</tr>
<tr class="even">
<td align="center">2011-02-02</td>
<td align="center">C8</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</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>
</tr>
<tr class="odd">
<td align="center">2014-01-19</td>
<td align="center">G10</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">R</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2012-08-24</td>
<td align="center">J7</td>
<td align="center">Hospital B</td>
<td align="center">2012-10-26</td>
<td align="center">C3</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2015-08-11</td>
<td align="center">M1</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2016-03-05</td>
<td align="center">Z6</td>
<td align="center">Hospital D</td>
<td align="center">2015-12-06</td>
<td align="center">A7</td>
<td align="center">Hospital C</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2016-07-03</td>
<td align="center">J4</td>
<td align="center">Hospital A</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2016-04-02</td>
<td align="center">A4</td>
<td align="center">Hospital A</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2016-06-10</td>
<td align="center">F6</td>
<td align="center">Hospital B</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">M</td>
</tr>
</tbody>
</table>
@ -510,16 +510,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,478</td>
<td align="right">52.39%</td>
<td align="right">10,478</td>
<td align="right">52.39%</td>
<td align="right">10,376</td>
<td align="right">51.88%</td>
<td align="right">10,376</td>
<td align="right">51.88%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,522</td>
<td align="right">47.61%</td>
<td align="right">9,624</td>
<td align="right">48.12%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -632,9 +632,9 @@ takes into account the antimicrobial susceptibility test results using
<span><span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span></span>
<span><span class="co"># 2</span></span>
<span><span class="co"># Including isolates from ICU.</span></span>
<span><span class="co"># =&gt; Found 12,223 'phenotype-based' first isolates (61.1% of total where a</span></span>
<span><span class="co"># =&gt; Found 12,299 'phenotype-based' first isolates (61.5% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 61.1% is suitable for resistance analysis! We can now filter
<p>So only 61.5% is suitable for resistance analysis! We can now filter
on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the
<code>dplyr</code> package:</p>
<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
@ -644,7 +644,7 @@ on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html"
<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<p>So we end up with 12 223 isolates for analysis. Now our data looks
<p>So we end up with 12 299 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>
@ -683,99 +683,99 @@ like:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2010-01-28</td>
<td align="center">Q1</td>
<td align="center">Hospital B</td>
<td align="left">2</td>
<td align="center">2012-10-26</td>
<td align="center">C3</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">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="center">2011-02-02</td>
<td align="center">C8</td>
<td align="left">7</td>
<td align="center">2013-06-13</td>
<td align="center">Q4</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</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">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">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">3</td>
<td align="center">2014-01-19</td>
<td align="center">G10</td>
<td align="left">11</td>
<td align="center">2014-08-27</td>
<td align="center">K9</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</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">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">5</td>
<td align="center">2015-08-11</td>
<td align="center">M1</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="left">14</td>
<td align="center">2016-03-09</td>
<td align="center">F2</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-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">6</td>
<td align="center">2016-03-05</td>
<td align="center">Z6</td>
<td align="center">Hospital D</td>
<td align="left">15</td>
<td align="center">2011-09-20</td>
<td align="center">C6</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="left">7</td>
<td align="center">2015-03-06</td>
<td align="center">Y8</td>
<td align="left">16</td>
<td align="center">2017-02-27</td>
<td align="center">Y6</td>
<td align="center">Hospital B</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">I</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">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>
</tbody>
@ -811,8 +811,8 @@ readable:</p>
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://msberends.github.io/cleaner/reference/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></span></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 12,223<br>
Available: 12,223 (100%, NA: 0 = 0%)<br>
Length: 12,299<br>
Available: 12,299 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -837,33 +837,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">5,786</td>
<td align="right">47.34%</td>
<td align="right">5,786</td>
<td align="right">47.34%</td>
<td align="right">5,867</td>
<td align="right">47.70%</td>
<td align="right">5,867</td>
<td align="right">47.70%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,288</td>
<td align="right">26.90%</td>
<td align="right">9,074</td>
<td align="right">74.24%</td>
<td align="right">3,232</td>
<td align="right">26.28%</td>
<td align="right">9,099</td>
<td align="right">73.98%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">1,803</td>
<td align="right">14.75%</td>
<td align="right">10,877</td>
<td align="right">88.99%</td>
<td align="right">1,853</td>
<td align="right">15.07%</td>
<td align="right">10,952</td>
<td align="right">89.05%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,346</td>
<td align="right">11.01%</td>
<td align="right">12,223</td>
<td align="right">1,347</td>
<td align="right">10.95%</td>
<td align="right">12,299</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -912,12 +912,42 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2010-01-28</td>
<td align="center">Q1</td>
<td align="center">Hospital B</td>
<td align="center">2016-03-09</td>
<td align="center">F2</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-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2011-09-20</td>
<td align="center">C6</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">2015-05-24</td>
<td align="center">Q4</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
@ -927,73 +957,28 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2011-02-02</td>
<td align="center">C8</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">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2014-01-19</td>
<td align="center">G10</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">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2015-08-11</td>
<td align="center">M1</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">2014-10-15</td>
<td align="center">N1</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">I</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">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">2016-03-05</td>
<td align="center">Z6</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">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2011-04-18</td>
<td align="center">W9</td>
<td align="center">2012-01-21</td>
<td align="center">U5</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
@ -1001,6 +986,21 @@ antibiotic class they are in:</p>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2016-08-02</td>
<td align="center">F4</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">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>
</table>
<p>If you want to get a quick glance of the number of isolates in
@ -1025,46 +1025,46 @@ different bug/drug combinations, you can use the
<td align="left">2</td>
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">2751</td>
<td align="center">1090</td>
<td align="center">1945</td>
<td align="center">5786</td>
<td align="center">2757</td>
<td align="center">1154</td>
<td align="center">1956</td>
<td align="center">5867</td>
</tr>
<tr class="even">
<td align="left">1</td>
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">1493</td>
<td align="center">1209</td>
<td align="center">3084</td>
<td align="center">5786</td>
<td align="center">1536</td>
<td align="center">1221</td>
<td align="center">3110</td>
<td align="center">5867</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">2007</td>
<td align="center">2046</td>
<td align="center">1793</td>
<td align="center">1986</td>
<td align="center">5786</td>
<td align="center">2028</td>
<td align="center">5867</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">1994</td>
<td align="center">1783</td>
<td align="center">2009</td>
<td align="center">5786</td>
<td align="center">2007</td>
<td align="center">1817</td>
<td align="center">2043</td>
<td align="center">5867</td>
</tr>
<tr class="odd">
<td align="left">6</td>
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">595</td>
<td align="center">309</td>
<td align="center">442</td>
<td align="center">1346</td>
<td align="center">600</td>
<td align="center">285</td>
<td align="center">462</td>
<td align="center">1347</td>
</tr>
<tr class="even">
<td align="left">5</td>
@ -1072,8 +1072,8 @@ different bug/drug combinations, you can use the
<td align="center">AMX</td>
<td align="center">0</td>
<td align="center">0</td>
<td align="center">1346</td>
<td align="center">1346</td>
<td align="center">1347</td>
<td align="center">1347</td>
</tr>
</tbody>
</table>
@ -1095,34 +1095,34 @@ different bug/drug combinations, you can use the
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">1994</td>
<td align="center">1783</td>
<td align="center">2009</td>
<td align="center">5786</td>
<td align="center">2007</td>
<td align="center">1817</td>
<td align="center">2043</td>
<td align="center">5867</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">461</td>
<td align="center">430</td>
<td align="center">455</td>
<td align="center">1346</td>
<td align="center">462</td>
<td align="center">409</td>
<td align="center">476</td>
<td align="center">1347</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">1095</td>
<td align="center">1045</td>
<td align="center">1148</td>
<td align="center">3288</td>
<td align="center">1091</td>
<td align="center">1034</td>
<td align="center">1107</td>
<td align="center">3232</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">1803</td>
<td align="center">1803</td>
<td align="center">1853</td>
<td align="center">1853</td>
</tr>
</tbody>
</table>
@ -1154,7 +1154,7 @@ I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equa
own:</p>
<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span></span>
<span><span class="co"># [1] 0.5847173</span></span></code></pre></div>
<span><span class="co"># [1] 0.5841125</span></span></code></pre></div>
<p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and
<code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
@ -1169,19 +1169,19 @@ own:</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5854654</td>
<td align="center">0.5842217</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5881089</td>
<td align="center">0.5908142</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5802920</td>
<td align="center">0.5761879</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5812526</td>
<td align="center">0.5779626</td>
</tr>
</tbody>
</table>
@ -1206,23 +1206,23 @@ all isolates available for every group (i.e. values S, I or R):</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5854654</td>
<td align="center">3674</td>
<td align="center">0.5842217</td>
<td align="center">3752</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5881089</td>
<td align="center">4188</td>
<td align="center">0.5908142</td>
<td align="center">4311</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5802920</td>
<td align="center">1918</td>
<td align="center">0.5761879</td>
<td align="center">1831</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5812526</td>
<td align="center">2443</td>
<td align="center">0.5779626</td>
<td align="center">2405</td>
</tr>
</tbody>
</table>
@ -1247,27 +1247,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.6638438</td>
<td align="center">0.6527826</td>
<td align="center">0.8840304</td>
<td align="center">0.6666099</td>
<td align="center">0.6517811</td>
<td align="center">0.8825635</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.6716196</td>
<td align="center">0.6619614</td>
<td align="center">0.8893016</td>
<td align="center">0.6570156</td>
<td align="center">0.6466221</td>
<td align="center">0.8619154</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.6843066</td>
<td align="center">0.6508516</td>
<td align="center">0.8886861</td>
<td align="center">0.6667698</td>
<td align="center">0.6574876</td>
<td align="center">0.8932550</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.4608985</td>
<td align="center">0.4700486</td>
<td align="center">0.0000000</td>
<td align="center">0.4608985</td>
<td align="center">0.4700486</td>
</tr>
</tbody>
</table>
@ -1295,23 +1295,23 @@ classes, use a antibiotic class selector such as
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">58.5%</td>
<td align="right">35.8%</td>
<td align="right">58.4%</td>
<td align="right">37.3%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">58.8%</td>
<td align="right">35.8%</td>
<td align="right">59.1%</td>
<td align="right">37.2%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">58.0%</td>
<td align="right">36.7%</td>
<td align="right">57.6%</td>
<td align="right">35.2%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">58.1%</td>
<td align="right">36.0%</td>
<td align="right">57.8%</td>
<td align="right">34.3%</td>
</tr>
</tbody>
</table>
@ -1427,16 +1427,18 @@ classes) <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code>:</p>
<code class="sourceCode R"><span><span class="va">mic_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span></span>
<span><span class="va">mic_values</span></span>
<span><span class="co"># Class 'mic'</span></span>
<span><span class="co"># [1] &gt;=256 0.0625 0.0625 0.01 0.25 0.002 8 0.25 128 1 </span></span>
<span><span class="co"># [11] 4 1 0.01 2 0.002 8 1 0.001 128 0.002 </span></span>
<span><span class="co"># [21] 8 0.002 0.005 0.001 128 0.01 16 8 0.125 1 </span></span>
<span><span class="co"># [31] 0.25 16 0.002 0.025 128 0.0625 64 0.5 &gt;=256 2 </span></span>
<span><span class="co"># [41] 4 8 0.25 64 0.25 128 0.005 4 0.005 2 </span></span>
<span><span class="co"># [51] &gt;=256 &gt;=256 &gt;=256 32 0.25 0.0625 64 32 &gt;=256 4 </span></span>
<span><span class="co"># [61] 128 0.025 8 0.5 16 128 128 0.125 0.005 1 </span></span>
<span><span class="co"># [71] &gt;=256 64 0.025 0.001 128 0.005 8 64 0.002 8 </span></span>
<span><span class="co"># [81] 0.005 32 1 0.005 64 16 32 0.5 0.01 0.002 </span></span>
<span><span class="co"># [91] 0.25 2 0.5 32 4 0.005 0.0625 8 0.002 0.005</span></span></code></pre></div>
<span><span class="co"># [1] 0.5 0.25 4 0.002 &lt;=0.001 0.005 0.25 0.005 32 </span></span>
<span><span class="co"># [10] 0.025 64 0.025 0.5 0.125 16 0.25 0.01 32 </span></span>
<span><span class="co"># [19] &lt;=0.001 0.125 0.125 64 2 0.125 16 128 0.002 </span></span>
<span><span class="co"># [28] 0.002 1 0.0625 0.125 8 64 128 0.0625 64 </span></span>
<span><span class="co"># [37] 128 0.005 0.125 0.005 32 64 64 32 256 </span></span>
<span><span class="co"># [46] 128 0.0625 &lt;=0.001 &lt;=0.001 256 8 4 2 1 </span></span>
<span><span class="co"># [55] 16 0.002 1 1 &lt;=0.001 1 8 0.5 2 </span></span>
<span><span class="co"># [64] 2 2 1 &lt;=0.001 2 32 16 0.01 0.002 </span></span>
<span><span class="co"># [73] 16 0.025 0.002 0.01 1 0.25 0.25 64 1 </span></span>
<span><span class="co"># [82] 0.125 &lt;=0.001 16 0.25 8 4 0.25 0.002 0.0625 </span></span>
<span><span class="co"># [91] 128 0.005 128 256 64 2 256 0.025 0.25 </span></span>
<span><span class="co"># [100] 4</span></span></code></pre></div>
<div class="sourceCode" id="cb36"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">mic_values</span><span class="op">)</span></span></code></pre></div>
@ -1470,10 +1472,10 @@ plotting:</p>
<code class="sourceCode R"><span><span class="va">disk_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_disk</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span>
<span><span class="va">disk_values</span></span>
<span><span class="co"># Class 'disk'</span></span>
<span><span class="co"># [1] 28 20 23 25 19 22 25 19 24 22 23 24 27 30 18 31 19 28 28 26 21 20 21 30 30</span></span>
<span><span class="co"># [26] 27 30 22 27 30 23 27 27 27 30 18 28 21 20 26 21 19 24 21 19 28 19 18 29 27</span></span>
<span><span class="co"># [51] 18 26 18 28 17 21 30 21 21 20 21 22 30 27 28 31 24 29 27 18 27 25 30 27 25</span></span>
<span><span class="co"># [76] 24 28 24 29 27 17 30 25 24 21 17 26 22 23 24 26 18 26 20 23 24 28 17 25 22</span></span></code></pre></div>
<span><span class="co"># [1] 18 29 29 26 17 27 24 26 25 24 23 20 19 25 22 24 20 19 24 17 23 21 19 21 20</span></span>
<span><span class="co"># [26] 26 18 17 26 22 25 19 25 26 17 26 19 29 20 27 19 22 31 25 19 28 25 17 29 31</span></span>
<span><span class="co"># [51] 26 31 29 21 19 28 30 30 31 28 30 22 22 22 17 31 22 19 21 17 28 29 17 28 26</span></span>
<span><span class="co"># [76] 20 20 20 19 25 17 28 28 31 24 28 21 28 20 25 21 28 27 23 27 22 31 27 27 18</span></span></code></pre></div>
<div class="sourceCode" id="cb42"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">disk_values</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></code></pre></div>

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2
articles/EUCAST.html
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9125</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9126</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">

56
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="">1.8.2.9125</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9126</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -385,17 +385,17 @@ 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 I I S I S I</span></span>
<span><span class="co"># 2 I I R R R I</span></span>
<span><span class="co"># 3 R R S S I R</span></span>
<span><span class="co"># 4 S S I R S S</span></span>
<span><span class="co"># 5 R R R S R I</span></span>
<span><span class="co"># 6 I S S I I R</span></span>
<span><span class="co"># 1 R S S R I S</span></span>
<span><span class="co"># 2 S I I S I I</span></span>
<span><span class="co"># 3 R I S R R R</span></span>
<span><span class="co"># 4 S R S I S R</span></span>
<span><span class="co"># 5 R S R S S R</span></span>
<span><span class="co"># 6 I I S S S I</span></span>
<span><span class="co"># kanamycin</span></span>
<span><span class="co"># 1 R</span></span>
<span><span class="co"># 1 I</span></span>
<span><span class="co"># 2 R</span></span>
<span><span class="co"># 3 I</span></span>
<span><span class="co"># 4 S</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 R</span></span></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can
@ -438,40 +438,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3187</td>
<td align="right">63.74%</td>
<td align="right">3187</td>
<td align="right">63.74%</td>
<td align="right">3263</td>
<td align="right">65.26%</td>
<td align="right">3263</td>
<td align="right">65.26%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">996</td>
<td align="right">19.92%</td>
<td align="right">4183</td>
<td align="right">83.66%</td>
<td align="right">970</td>
<td align="right">19.40%</td>
<td align="right">4233</td>
<td align="right">84.66%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">449</td>
<td align="right">8.98%</td>
<td align="right">4632</td>
<td align="right">92.64%</td>
<td align="right">433</td>
<td align="right">8.66%</td>
<td align="right">4666</td>
<td align="right">93.32%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">271</td>
<td align="right">5.42%</td>
<td align="right">4903</td>
<td align="right">98.06%</td>
<td align="right">229</td>
<td align="right">4.58%</td>
<td align="right">4895</td>
<td align="right">97.90%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">97</td>
<td align="right">1.94%</td>
<td align="right">105</td>
<td align="right">2.10%</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="">1.8.2.9125</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9126</small>
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2
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9125</small>
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@ -38,7 +38,7 @@
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9125</small>
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@ -38,7 +38,7 @@
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9125</small>
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2
articles/index.html
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@ -10,7 +10,7 @@
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articles/resistance_predict.html
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9125</small>
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