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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="">1.8.2.9139</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9140</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">
@ -388,12 +388,12 @@ 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>
@ -408,69 +408,69 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2011-02-12</td>
<td align="center">O4</td>
<td align="center">2014-05-20</td>
<td align="center">U8</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">I</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2011-03-08</td>
<td align="center">W5</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia coli</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2015-09-22</td>
<td align="center">R6</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2013-03-03</td>
<td align="center">E2</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2014-09-08</td>
<td align="center">I5</td>
<td align="center">Hospital B</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">M</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2017-10-13</td>
<td align="center">F8</td>
<td align="center">2017-10-06</td>
<td align="center">A7</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2010-12-13</td>
<td align="center">N3</td>
<td align="center">Hospital C</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">2015-01-26</td>
<td align="center">S8</td>
<td align="center">Hospital B</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">F</td>
</tr>
<tr class="odd">
<td align="center">2010-08-01</td>
<td align="center">V8</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2011-08-06</td>
<td align="center">N5</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">R</td>
<td align="center">M</td>
</tr>
</tbody>
@ -507,16 +507,16 @@ 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">10,292</td>
<td align="right">51.46%</td>
<td align="right">10,292</td>
<td align="right">51.46%</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">9,708</td>
<td align="right">48.54%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -629,7 +629,7 @@ takes into account the antimicrobial susceptibility test results using
<span><span class="co">#&gt; Basing inclusion on all antimicrobial results, using a points threshold of</span></span>
<span><span class="co">#&gt; 2</span></span>
<span><span class="co">#&gt; Including isolates from ICU.</span></span>
<span><span class="co">#&gt; =&gt; Found 12,293 'phenotype-based' first isolates (61.5% of total where a</span></span>
<span><span class="co">#&gt; =&gt; Found 12,307 'phenotype-based' first isolates (61.5% of total where a</span></span>
<span><span class="co">#&gt; microbial ID was available)</span></span></code></pre></div>
<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
@ -641,7 +641,7 @@ 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 12 293 isolates for analysis. Now our data looks
<p>So we end up with 12 307 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>
@ -658,8 +658,8 @@ like:</p>
<col width="3%">
<col width="6%">
<col width="11%">
<col width="11%">
<col width="9%">
<col width="12%">
<col width="7%">
<col width="5%">
</colgroup>
<thead><tr class="header">
@ -681,31 +681,31 @@ like:</p>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2011-02-12</td>
<td align="center">O4</td>
<td align="center">2014-05-20</td>
<td align="center">U8</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">I</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="center">I</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">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="center">2011-03-08</td>
<td align="center">W5</td>
<td align="center">Hospital C</td>
<td align="center">2017-10-06</td>
<td align="center">A7</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">F</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
@ -713,63 +713,63 @@ like:</p>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="center">2015-09-22</td>
<td align="center">R6</td>
<td align="center">Hospital B</td>
<td align="center">2010-12-13</td>
<td align="center">N3</td>
<td align="center">Hospital C</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">R</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">F</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>
<tr class="even">
<td align="left">6</td>
<td align="center">2017-10-13</td>
<td align="center">F8</td>
<td align="center">Hospital D</td>
<td align="left">4</td>
<td align="center">2015-01-26</td>
<td align="center">S8</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</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="odd">
<td align="left">7</td>
<td align="center">2013-03-22</td>
<td align="center">H3</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="left">6</td>
<td align="center">2011-08-06</td>
<td align="center">N5</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">I</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">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">8</td>
<td align="center">2014-11-05</td>
<td align="center">Y10</td>
<td align="center">Hospital D</td>
<td align="left">7</td>
<td align="center">2014-05-14</td>
<td align="center">C6</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">R</td>
<td align="center">F</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>
@ -808,8 +808,8 @@ 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: 12,293<br>
Available: 12,293 (100%, NA: 0 = 0%)<br>
Length: 12,307<br>
Available: 12,307 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -834,33 +834,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">5,873</td>
<td align="right">47.78%</td>
<td align="right">5,873</td>
<td align="right">47.78%</td>
<td align="right">5,867</td>
<td align="right">47.67%</td>
<td align="right">5,867</td>
<td align="right">47.67%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,225</td>
<td align="right">26.23%</td>
<td align="right">9,098</td>
<td align="right">74.01%</td>
<td align="right">3,275</td>
<td align="right">26.61%</td>
<td align="right">9,142</td>
<td align="right">74.28%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">1,844</td>
<td align="right">15.00%</td>
<td align="right">10,942</td>
<td align="right">89.01%</td>
<td align="right">1,823</td>
<td align="right">14.81%</td>
<td align="right">10,965</td>
<td align="right">89.10%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,351</td>
<td align="right">10.99%</td>
<td align="right">12,293</td>
<td align="right">1,342</td>
<td align="right">10.90%</td>
<td align="right">12,307</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -909,39 +909,9 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2011-02-12</td>
<td align="center">O4</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">I</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">2013-03-22</td>
<td align="center">H3</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">I</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">2014-11-05</td>
<td align="center">Y10</td>
<td align="center">Hospital D</td>
<td align="center">2015-01-26</td>
<td align="center">S8</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
@ -954,50 +924,80 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2013-09-13</td>
<td align="center">A8</td>
<td align="center">2011-08-06</td>
<td align="center">N5</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</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">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2016-08-04</td>
<td align="center">S3</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2013-05-16</td>
<td align="center">K6</td>
<td align="center">Hospital C</td>
<tr class="odd">
<td align="center">2015-06-03</td>
<td align="center">Z9</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</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">M</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">2010-03-15</td>
<td align="center">V2</td>
<td align="center">Hospital C</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">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">2015-07-13</td>
<td align="center">Y7</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">I</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">2010-06-03</td>
<td align="center">A1</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">I</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
@ -1020,50 +1020,50 @@ different bug/drug combinations, you can use the
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">2744</td>
<td align="center">1216</td>
<td align="center">1913</td>
<td align="center">5873</td>
<td align="center">2775</td>
<td align="center">1160</td>
<td align="center">1932</td>
<td align="center">5867</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">1504</td>
<td align="center">1272</td>
<td align="center">3097</td>
<td align="center">5873</td>
<td align="center">1509</td>
<td align="center">1274</td>
<td align="center">3084</td>
<td align="center">5867</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">2018</td>
<td align="center">1818</td>
<td align="center">2037</td>
<td align="center">5873</td>
<td align="center">2087</td>
<td align="center">1786</td>
<td align="center">1994</td>
<td align="center">5867</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">2067</td>
<td align="center">1812</td>
<td align="center">1994</td>
<td align="center">5873</td>
<td align="center">2011</td>
<td align="center">1802</td>
<td align="center">2054</td>
<td align="center">5867</td>
</tr>
<tr class="odd">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">599</td>
<td align="center">275</td>
<td align="center">477</td>
<td align="center">1351</td>
<td align="center">576</td>
<td align="center">312</td>
<td align="center">454</td>
<td align="center">1342</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMX</td>
<td align="center">0</td>
<td align="center">0</td>
<td align="center">1351</td>
<td align="center">1351</td>
<td align="center">1342</td>
<td align="center">1342</td>
</tr>
</tbody>
</table>
@ -1085,34 +1085,34 @@ 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">2067</td>
<td align="center">1812</td>
<td align="center">1994</td>
<td align="center">5873</td>
<td align="center">2011</td>
<td align="center">1802</td>
<td align="center">2054</td>
<td align="center">5867</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">450</td>
<td align="center">437</td>
<td align="center">464</td>
<td align="center">1351</td>
<td align="center">472</td>
<td align="center">430</td>
<td align="center">440</td>
<td align="center">1342</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">1128</td>
<td align="center">980</td>
<td align="center">1117</td>
<td align="center">3225</td>
<td align="center">1132</td>
<td align="center">1037</td>
<td align="center">1106</td>
<td align="center">3275</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">1844</td>
<td align="center">1844</td>
<td align="center">1823</td>
<td align="center">1823</td>
</tr>
</tbody>
</table>
@ -1144,7 +1144,7 @@ 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">#&gt; [1] 0.5805743</span></span></code></pre></div>
<span><span class="co">#&gt; [1] 0.5778013</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">
@ -1159,19 +1159,19 @@ own:</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5836502</td>
<td align="center">0.5752970</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5788257</td>
<td align="center">0.5688009</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5675105</td>
<td align="center">0.5894074</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5893679</td>
<td align="center">0.5880933</td>
</tr>
</tbody>
</table>
@ -1196,23 +1196,23 @@ 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">0.5836502</td>
<td align="center">3682</td>
<td align="center">0.5752970</td>
<td align="center">3619</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5788257</td>
<td align="center">4326</td>
<td align="center">0.5688009</td>
<td align="center">4295</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5675105</td>
<td align="center">1896</td>
<td align="center">0.5894074</td>
<td align="center">1907</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5893679</td>
<td align="center">2389</td>
<td align="center">0.5880933</td>
<td align="center">2486</td>
</tr>
</tbody>
</table>
@ -1237,27 +1237,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.6742721</td>
<td align="center">0.6604802</td>
<td align="center">0.8923889</td>
<td align="center">0.6707005</td>
<td align="center">0.6499063</td>
<td align="center">0.8813704</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.6469282</td>
<td align="center">0.6565507</td>
<td align="center">0.8793486</td>
<td align="center">0.6616990</td>
<td align="center">0.6721311</td>
<td align="center">0.8964232</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.6731783</td>
<td align="center">0.6536434</td>
<td align="center">0.8862016</td>
<td align="center">0.6726718</td>
<td align="center">0.6622901</td>
<td align="center">0.8934351</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.4766811</td>
<td align="center">0.4816237</td>
<td align="center">0.0000000</td>
<td align="center">0.4766811</td>
<td align="center">0.4816237</td>
</tr>
</tbody>
</table>
@ -1285,23 +1285,23 @@ classes, use a antibiotic class selector such as
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">58.4%</td>
<td align="right">36.1%</td>
<td align="right">57.5%</td>
<td align="right">35.3%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">57.9%</td>
<td align="right">36.2%</td>
<td align="right">56.9%</td>
<td align="right">35.1%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">56.8%</td>
<td align="right">34.6%</td>
<td align="right">58.9%</td>
<td align="right">36.8%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">58.9%</td>
<td align="right">35.8%</td>
<td align="right">58.8%</td>
<td align="right">36.8%</td>
</tr>
</tbody>
</table>
@ -1417,18 +1417,18 @@ 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">#&gt; Class 'mic'</span></span>
<span><span class="co">#&gt; [1] &lt;=0.001 0.5 0.002 0.0625 32 &lt;=0.001 0.125 0.002 0.0625 </span></span>
<span><span class="co">#&gt; [10] 1 0.01 16 0.5 0.25 4 8 2 0.002 </span></span>
<span><span class="co">#&gt; [19] 0.125 8 0.002 1 16 1 2 0.025 &lt;=0.001</span></span>
<span><span class="co">#&gt; [28] 32 16 &lt;=0.001 1 4 0.01 &lt;=0.001 0.002 &gt;=128 </span></span>
<span><span class="co">#&gt; [37] 0.005 2 &lt;=0.001 2 0.002 16 32 4 0.025 </span></span>
<span><span class="co">#&gt; [46] 1 0.01 0.005 0.002 4 2 0.0625 &gt;=128 0.01 </span></span>
<span><span class="co">#&gt; [55] 0.25 32 &gt;=128 0.0625 1 0.5 4 &lt;=0.001 0.005 </span></span>
<span><span class="co">#&gt; [64] 2 16 &lt;=0.001 4 0.25 &gt;=128 64 &lt;=0.001 &gt;=128 </span></span>
<span><span class="co">#&gt; [73] 0.0625 4 0.5 0.025 &gt;=128 &gt;=128 64 32 &gt;=128 </span></span>
<span><span class="co">#&gt; [82] 1 0.0625 0.25 1 0.25 0.0625 8 0.025 2 </span></span>
<span><span class="co">#&gt; [91] 1 0.025 0.002 8 32 2 2 4 16 </span></span>
<span><span class="co">#&gt; [100] 64</span></span></code></pre></div>
<span><span class="co">#&gt; [1] 16 32 8 4 0.125 0.25 16 64 16 </span></span>
<span><span class="co">#&gt; [10] 4 4 &lt;=0.001 2 0.25 0.125 0.0625 128 0.01 </span></span>
<span><span class="co">#&gt; [19] 0.025 &gt;=256 1 0.025 128 0.125 128 0.25 0.005 </span></span>
<span><span class="co">#&gt; [28] &gt;=256 4 16 0.01 0.005 &gt;=256 8 0.002 64 </span></span>
<span><span class="co">#&gt; [37] 0.025 0.002 &lt;=0.001 1 0.25 4 0.005 0.01 0.005 </span></span>
<span><span class="co">#&gt; [46] 32 0.125 1 2 &gt;=256 0.01 0.025 0.5 64 </span></span>
<span><span class="co">#&gt; [55] 16 0.01 2 8 1 4 32 64 &gt;=256 </span></span>
<span><span class="co">#&gt; [64] 64 8 0.125 0.01 0.5 32 32 0.25 128 </span></span>
<span><span class="co">#&gt; [73] 0.01 0.01 4 0.125 64 32 0.002 32 32 </span></span>
<span><span class="co">#&gt; [82] 0.01 0.25 1 &lt;=0.001 32 0.01 0.025 0.25 64 </span></span>
<span><span class="co">#&gt; [91] 0.0625 0.005 0.01 0.25 &lt;=0.001 0.25 0.125 0.0625 0.01 </span></span>
<span><span class="co">#&gt; [100] 2</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>
@ -1462,10 +1462,10 @@ 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">#&gt; Class 'disk'</span></span>
<span><span class="co">#&gt; [1] 23 21 21 24 27 18 21 29 31 18 17 26 21 21 27 25 28 31 30 17 29 21 18 30 25</span></span>
<span><span class="co">#&gt; [26] 28 31 17 25 23 22 17 27 24 30 31 24 24 25 27 18 31 20 21 29 30 17 21 20 19</span></span>
<span><span class="co">#&gt; [51] 25 21 17 17 26 25 30 26 19 18 21 28 27 21 30 29 21 17 30 28 26 27 23 31 27</span></span>
<span><span class="co">#&gt; [76] 31 31 26 24 30 31 22 20 17 17 23 31 27 17 28 27 18 27 29 24 24 28 20 19 26</span></span></code></pre></div>
<span><span class="co">#&gt; [1] 19 18 19 22 17 21 31 27 23 29 26 25 28 19 30 27 20 23 20 21 21 21 29 17 26</span></span>
<span><span class="co">#&gt; [26] 21 24 27 24 25 25 29 26 23 23 20 30 23 30 24 20 22 19 18 23 24 25 22 23 22</span></span>
<span><span class="co">#&gt; [51] 17 17 25 22 31 19 20 28 21 28 24 22 23 17 28 30 28 27 22 27 27 17 30 31 17</span></span>
<span><span class="co">#&gt; [76] 27 25 23 17 27 25 28 18 18 29 26 22 22 20 30 20 29 25 26 29 20 28 30 24 27</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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@ -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="">1.8.2.9139</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9140</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="">1.8.2.9139</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9140</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">
@ -385,19 +385,19 @@ 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">#&gt; rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
<span><span class="co">#&gt; 1 R S S S I S</span></span>
<span><span class="co">#&gt; 2 I R S R I S</span></span>
<span><span class="co">#&gt; 3 I R R I S R</span></span>
<span><span class="co">#&gt; 4 R R S R S I</span></span>
<span><span class="co">#&gt; 5 S S S S I S</span></span>
<span><span class="co">#&gt; 6 R I I S S I</span></span>
<span><span class="co">#&gt; 1 R I R I I I</span></span>
<span><span class="co">#&gt; 2 I S S S R S</span></span>
<span><span class="co">#&gt; 3 S R R S I S</span></span>
<span><span class="co">#&gt; 4 I S S I I R</span></span>
<span><span class="co">#&gt; 5 R I I I R I</span></span>
<span><span class="co">#&gt; 6 R R I S R S</span></span>
<span><span class="co">#&gt; kanamycin</span></span>
<span><span class="co">#&gt; 1 I</span></span>
<span><span class="co">#&gt; 1 S</span></span>
<span><span class="co">#&gt; 2 I</span></span>
<span><span class="co">#&gt; 3 S</span></span>
<span><span class="co">#&gt; 3 R</span></span>
<span><span class="co">#&gt; 4 S</span></span>
<span><span class="co">#&gt; 5 S</span></span>
<span><span class="co">#&gt; 6 I</span></span></code></pre></div>
<span><span class="co">#&gt; 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">
@ -438,40 +438,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3221</td>
<td align="right">64.42%</td>
<td align="right">3221</td>
<td align="right">64.42%</td>
<td align="right">3142</td>
<td align="right">62.84%</td>
<td align="right">3142</td>
<td align="right">62.84%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">985</td>
<td align="right">19.70%</td>
<td align="right">4206</td>
<td align="right">84.12%</td>
<td align="right">970</td>
<td align="right">19.40%</td>
<td align="right">4112</td>
<td align="right">82.24%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">437</td>
<td align="right">8.74%</td>
<td align="right">4643</td>
<td align="right">92.86%</td>
<td align="right">488</td>
<td align="right">9.76%</td>
<td align="right">4600</td>
<td align="right">92.00%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">252</td>
<td align="right">5.04%</td>
<td align="right">4895</td>
<td align="right">97.90%</td>
<td align="right">263</td>
<td align="right">5.26%</td>
<td align="right">4863</td>
<td align="right">97.26%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">105</td>
<td align="right">2.10%</td>
<td align="right">137</td>
<td align="right">2.74%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

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="">1.8.2.9139</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9140</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="">1.8.2.9139</small>
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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>
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