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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="">1.8.2.9049</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9050</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">
@ -380,12 +380,12 @@ data set:</p>
<col width="13%">
<col width="13%">
<col width="13%">
<col width="26%">
<col width="28%">
<col width="5%">
<col width="5%">
<col width="5%">
<col width="5%">
<col width="9%">
<col width="8%">
</colgroup>
<thead><tr class="header">
<th align="center">date</th>
@ -400,68 +400,68 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2012-05-17</td>
<td align="center">I10</td>
<td align="center">Hospital D</td>
<td align="center">2013-01-01</td>
<td align="center">Z8</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">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2010-04-10</td>
<td align="center">I9</td>
<td align="center">Hospital B</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2017-06-19</td>
<td align="center">I1</td>
<td align="center">Hospital A</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">2013-12-12</td>
<td align="center">C4</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">2014-01-26</td>
<td align="center">L2</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">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2015-05-08</td>
<td align="center">S6</td>
<td align="center">Hospital A</td>
<td align="center">2011-03-14</td>
<td align="center">T1</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">I</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>
</tr>
<tr class="even">
<td align="center">2012-02-06</td>
<td align="center">L4</td>
<td align="center">Hospital C</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">R</td>
<td align="center">2010-11-28</td>
<td align="center">E3</td>
<td align="center">Hospital B</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2017-11-15</td>
<td align="center">J6</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2017-09-22</td>
<td align="center">G7</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
@ -499,16 +499,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,335</td>
<td align="right">51.68%</td>
<td align="right">10,335</td>
<td align="right">51.68%</td>
<td align="right">10,557</td>
<td align="right">52.79%</td>
<td align="right">10,557</td>
<td align="right">52.79%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,665</td>
<td align="right">48.33%</td>
<td align="right">9,443</td>
<td align="right">47.22%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -621,9 +621,9 @@ 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 10,583 'phenotype-based' first isolates (52.9% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,739 'phenotype-based' first isolates (53.7% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 52.9% is suitable for resistance analysis! We can now filter
<p>So only 53.7% 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">
@ -634,11 +634,11 @@ 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 10,583 isolates for analysis. Now our data looks
<p>So we end up with 10,739 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>
<table class="table">
<table style="width:100%;" class="table">
<colgroup>
<col width="2%">
<col width="9%">
@ -652,7 +652,7 @@ like:</p>
<col width="6%">
<col width="11%">
<col width="12%">
<col width="7%">
<col width="9%">
<col width="5%">
</colgroup>
<thead><tr class="header">
@ -674,27 +674,27 @@ like:</p>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2012-05-17</td>
<td align="center">I10</td>
<td align="center">Hospital D</td>
<td align="center">2013-01-01</td>
<td align="center">Z8</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">R</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="center">2013-12-12</td>
<td align="center">C4</td>
<td align="left">3</td>
<td align="center">2017-06-19</td>
<td align="center">I1</td>
<td align="center">Hospital A</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">S</td>
@ -705,15 +705,15 @@ like:</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="center">2015-05-08</td>
<td align="center">S6</td>
<td align="center">Hospital A</td>
<td align="left">5</td>
<td align="center">2011-03-14</td>
<td align="center">T1</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</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>
@ -721,51 +721,51 @@ like:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">5</td>
<td align="center">2017-11-15</td>
<td align="center">J6</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</td>
<td align="left">6</td>
<td align="center">2010-11-28</td>
<td align="center">E3</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">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">7</td>
<td align="center">2011-04-08</td>
<td align="center">D2</td>
<td align="center">Hospital B</td>
<td align="center">2015-07-19</td>
<td align="center">Y3</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
<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">8</td>
<td align="center">2016-01-21</td>
<td align="center">F1</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="left">9</td>
<td align="center">2014-02-08</td>
<td align="center">U4</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">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</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>
</tbody>
@ -801,8 +801,8 @@ 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: 10,583<br>
Available: 10,583 (100%, NA: 0 = 0%)<br>
Length: 10,739<br>
Available: 10,739 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -827,33 +827,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">4,553</td>
<td align="right">43.02%</td>
<td align="right">4,553</td>
<td align="right">43.02%</td>
<td align="right">4,749</td>
<td align="right">44.22%</td>
<td align="right">4,749</td>
<td align="right">44.22%</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">25.98%</td>
<td align="right">7,302</td>
<td align="right">69.00%</td>
<td align="right">2,673</td>
<td align="right">24.89%</td>
<td align="right">7,422</td>
<td align="right">69.11%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,123</td>
<td align="right">20.06%</td>
<td align="right">9,425</td>
<td align="right">89.06%</td>
<td align="right">2,118</td>
<td align="right">19.72%</td>
<td align="right">9,540</td>
<td align="right">88.84%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,158</td>
<td align="right">10.94%</td>
<td align="right">10,583</td>
<td align="right">1,199</td>
<td align="right">11.16%</td>
<td align="right">10,739</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -874,14 +874,14 @@ antibiotic class they are in:</p>
<col width="9%">
<col width="9%">
<col width="9%">
<col width="10%">
<col width="11%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="6%">
<col width="11%">
<col width="12%">
<col width="11%">
<col width="9%">
<col width="5%">
</colgroup>
@ -902,14 +902,14 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2015-05-08</td>
<td align="center">S6</td>
<td align="center">Hospital A</td>
<td align="center">2011-03-14</td>
<td align="center">T1</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</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>
@ -917,43 +917,28 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2014-04-13</td>
<td align="center">Y5</td>
<td align="center">Hospital C</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">2010-11-28</td>
<td align="center">E3</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">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="center">2010-08-29</td>
<td align="center">R6</td>
<td align="center">2014-02-08</td>
<td align="center">U4</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2013-06-25</td>
<td align="center">O8</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">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
@ -961,14 +946,29 @@ antibiotic class they are in:</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2017-10-23</td>
<td align="center">Q3</td>
<td align="center">Hospital C</td>
<td align="center">B_KLBSL_PNMN</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">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2016-02-06</td>
<td align="center">2017-05-27</td>
<td align="center">W10</td>
<td align="center">Hospital D</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">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>
@ -977,18 +977,18 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2016-03-30</td>
<td align="center">O7</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">2016-10-31</td>
<td align="center">L4</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">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">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>
@ -1014,50 +1014,50 @@ 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">2155</td>
<td align="center">146</td>
<td align="center">2252</td>
<td align="center">4553</td>
<td align="center">2232</td>
<td align="center">132</td>
<td align="center">2385</td>
<td align="center">4749</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3346</td>
<td align="center">152</td>
<td align="center">1055</td>
<td align="center">4553</td>
<td align="center">3526</td>
<td align="center">160</td>
<td align="center">1063</td>
<td align="center">4749</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3368</td>
<td align="center">3417</td>
<td align="center">0</td>
<td align="center">1185</td>
<td align="center">4553</td>
<td align="center">1332</td>
<td align="center">4749</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">3965</td>
<td align="center">4139</td>
<td align="center">0</td>
<td align="center">588</td>
<td align="center">4553</td>
<td align="center">610</td>
<td align="center">4749</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">1158</td>
<td align="center">1158</td>
<td align="center">1199</td>
<td align="center">1199</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">926</td>
<td align="center">43</td>
<td align="center">189</td>
<td align="center">1158</td>
<td align="center">933</td>
<td align="center">44</td>
<td align="center">222</td>
<td align="center">1199</td>
</tr>
</tbody>
</table>
@ -1080,34 +1080,34 @@ 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">3965</td>
<td align="center">4139</td>
<td align="center">0</td>
<td align="center">588</td>
<td align="center">4553</td>
<td align="center">610</td>
<td align="center">4749</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1041</td>
<td align="center">1089</td>
<td align="center">0</td>
<td align="center">117</td>
<td align="center">1158</td>
<td align="center">110</td>
<td align="center">1199</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2425</td>
<td align="center">2352</td>
<td align="center">0</td>
<td align="center">324</td>
<td align="center">2749</td>
<td align="center">321</td>
<td align="center">2673</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">2123</td>
<td align="center">2123</td>
<td align="center">2118</td>
<td align="center">2118</td>
</tr>
</tbody>
</table>
@ -1139,7 +1139,7 @@ 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] 0.5406784</span></span></code></pre></div>
<span><span class="co"># [1] 0.5423224</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">
@ -1154,19 +1154,19 @@ own:</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5424045</td>
<td align="center">0.5322120</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5265943</td>
<td align="center">0.5366357</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5560626</td>
<td align="center">0.5579757</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5524135</td>
<td align="center">0.5560205</td>
</tr>
</tbody>
</table>
@ -1191,23 +1191,23 @@ 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">0.5424045</td>
<td align="center">3219</td>
<td align="center">0.5322120</td>
<td align="center">3151</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5265943</td>
<td align="center">3779</td>
<td align="center">0.5366357</td>
<td align="center">3876</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5560626</td>
<td align="center">1534</td>
<td align="center">0.5579757</td>
<td align="center">1561</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5524135</td>
<td align="center">2051</td>
<td align="center">0.5560205</td>
<td align="center">2151</td>
</tr>
</tbody>
</table>
@ -1232,27 +1232,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7682846</td>
<td align="center">0.8708544</td>
<td align="center">0.9745223</td>
<td align="center">0.7761634</td>
<td align="center">0.8715519</td>
<td align="center">0.9816804</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8367876</td>
<td align="center">0.8989637</td>
<td align="center">0.9792746</td>
<td align="center">0.8148457</td>
<td align="center">0.9082569</td>
<td align="center">0.9824854</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7995635</td>
<td align="center">0.8821390</td>
<td align="center">0.9796290</td>
<td align="center">0.8017209</td>
<td align="center">0.8799102</td>
<td align="center">0.9816685</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5393311</td>
<td align="center">0.5325779</td>
<td align="center">0.0000000</td>
<td align="center">0.5393311</td>
<td align="center">0.5325779</td>
</tr>
</tbody>
</table>
@ -1280,23 +1280,23 @@ classes, use a antibiotic class selector such as
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">54.2%</td>
<td align="right">25.6%</td>
<td align="right">53.2%</td>
<td align="right">26.1%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">52.7%</td>
<td align="right">26.4%</td>
<td align="right">53.7%</td>
<td align="right">25.5%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">55.6%</td>
<td align="right">26.5%</td>
<td align="right">55.8%</td>
<td align="right">27.9%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">55.2%</td>
<td align="right">26.5%</td>
<td align="right">55.6%</td>
<td align="right">26.0%</td>
</tr>
</tbody>
</table>
@ -1412,16 +1412,16 @@ 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] 0.001 0.025 16 0.025 128 64 0.01 0.005 4 64 </span></span>
<span><span class="co"># [11] 1 0.5 0.0625 64 0.125 0.002 0.025 0.001 0.002 8 </span></span>
<span><span class="co"># [21] 16 16 0.25 1 1 2 16 0.001 2 2 </span></span>
<span><span class="co"># [31] 0.0625 4 16 0.002 0.025 2 64 4 16 4 </span></span>
<span><span class="co"># [41] 1 0.005 0.25 0.025 256 0.5 0.01 0.001 128 4 </span></span>
<span><span class="co"># [51] 32 0.5 2 256 1 64 1 0.005 1 4 </span></span>
<span><span class="co"># [61] 0.0625 0.0625 256 0.025 0.0625 64 0.01 0.0625 0.0625 32 </span></span>
<span><span class="co"># [71] 0.0625 0.5 256 4 4 0.0625 32 0.0625 0.005 256 </span></span>
<span><span class="co"># [81] 0.5 1 128 0.001 16 64 0.0625 0.002 0.125 0.125 </span></span>
<span><span class="co"># [91] 256 0.01 0.002 0.025 0.25 1 0.005 0.001 0.125 0.125</span></span></code></pre></div>
<span><span class="co"># [1] 0.0625 0.005 0.005 0.001 256 128 0.125 0.5 0.125 0.025 </span></span>
<span><span class="co"># [11] 8 64 0.0625 0.5 0.001 4 0.01 8 0.0625 4 </span></span>
<span><span class="co"># [21] 16 8 0.5 0.0625 0.01 0.001 0.01 8 8 0.01 </span></span>
<span><span class="co"># [31] 0.5 1 32 8 4 0.5 0.25 32 0.005 8 </span></span>
<span><span class="co"># [41] 128 32 0.001 128 8 0.025 64 8 16 0.0625</span></span>
<span><span class="co"># [51] 0.01 0.5 0.025 16 32 256 0.001 16 8 0.01 </span></span>
<span><span class="co"># [61] 0.5 8 8 0.0625 0.01 0.125 128 16 0.002 128 </span></span>
<span><span class="co"># [71] 64 128 64 32 32 16 64 0.01 64 2 </span></span>
<span><span class="co"># [81] 0.25 0.002 0.025 128 0.002 64 0.001 2 32 16 </span></span>
<span><span class="co"># [91] 0.005 8 0.25 0.002 16 32 1 0.25 16 0.005</span></span></code></pre></div>
<div class="sourceCode" id="cb37"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">mic_values</span><span class="op">)</span></span></code></pre></div>
@ -1455,10 +1455,10 @@ 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] 27 17 19 21 26 26 28 25 17 24 21 19 20 24 25 30 23 26 31 22 25 27 26 29 18</span></span>
<span><span class="co"># [26] 29 22 18 22 27 24 25 18 29 21 18 28 21 17 25 28 23 22 21 21 31 28 20 29 20</span></span>
<span><span class="co"># [51] 24 25 17 18 30 23 28 21 18 28 24 29 20 18 22 24 29 26 21 19 17 19 30 22 19</span></span>
<span><span class="co"># [76] 28 19 23 31 19 28 26 29 17 22 29 17 29 29 18 29 27 23 27 26 30 28 28 29 22</span></span></code></pre></div>
<span><span class="co"># [1] 25 31 26 31 24 31 27 17 28 25 21 28 20 20 17 17 26 20 20 29 26 31 30 20 25</span></span>
<span><span class="co"># [26] 25 27 29 29 21 17 27 20 20 17 25 17 20 27 29 19 27 18 28 31 21 23 26 26 27</span></span>
<span><span class="co"># [51] 23 23 21 18 22 23 19 17 22 23 29 28 19 29 20 31 18 25 21 17 18 31 20 21 17</span></span>
<span><span class="co"># [76] 21 28 25 31 24 30 24 17 20 26 31 25 20 30 18 21 29 19 30 20 24 29 23 23 22</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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@ -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="">1.8.2.9049</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9050</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="">1.8.2.9049</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9050</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">
@ -375,16 +375,16 @@ 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 S R I S I</span></span>
<span><span class="co"># 2 R R I S R I</span></span>
<span><span class="co"># 3 I I R R R R</span></span>
<span><span class="co"># 4 S S S I R I</span></span>
<span><span class="co"># 5 S I S R R I</span></span>
<span><span class="co"># 6 I R S R I I</span></span>
<span><span class="co"># 1 S S R R S S</span></span>
<span><span class="co"># 2 R R I S I R</span></span>
<span><span class="co"># 3 S I S R I S</span></span>
<span><span class="co"># 4 I S R R I I</span></span>
<span><span class="co"># 5 I I I I I R</span></span>
<span><span class="co"># 6 R S R R R S</span></span>
<span><span class="co"># kanamycin</span></span>
<span><span class="co"># 1 S</span></span>
<span><span class="co"># 2 S</span></span>
<span><span class="co"># 3 S</span></span>
<span><span class="co"># 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 R</span></span>
<span><span class="co"># 5 S</span></span>
<span><span class="co"># 6 R</span></span></code></pre></div>
@ -428,40 +428,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3191</td>
<td align="right">63.82%</td>
<td align="right">3191</td>
<td align="right">63.82%</td>
<td align="right">3261</td>
<td align="right">65.22%</td>
<td align="right">3261</td>
<td align="right">65.22%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">1008</td>
<td align="right">20.16%</td>
<td align="right">4199</td>
<td align="right">83.98%</td>
<td align="right">919</td>
<td align="right">18.38%</td>
<td align="right">4180</td>
<td align="right">83.60%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">495</td>
<td align="right">9.90%</td>
<td align="right">4694</td>
<td align="right">93.88%</td>
<td align="right">488</td>
<td align="right">9.76%</td>
<td align="right">4668</td>
<td align="right">93.36%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">216</td>
<td align="right">4.32%</td>
<td align="right">4910</td>
<td align="right">98.20%</td>
<td align="right">235</td>
<td align="right">4.70%</td>
<td align="right">4903</td>
<td align="right">98.06%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">90</td>
<td align="right">1.80%</td>
<td align="right">97</td>
<td align="right">1.94%</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="">1.8.2.9049</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9050</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">

4
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="">1.8.2.9049</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9050</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">
@ -247,7 +247,7 @@ data using a custom made website. The webdesign knowledge needed
<li>
<p><strong>R has a huge community.</strong></p>
<p>Many R users just ask questions on websites like <a href="https://stackoverflow.com" class="external-link">StackOverflow.com</a>, the largest
online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">469,596
online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">470,620
R-related questions</a> have already been asked on this platform (that
covers questions and answers for any programming language). In my own
experience, most questions are answered within a couple of

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="">1.8.2.9049</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9050</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/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="">1.8.2.9049</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9050</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/index.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9049</small>
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2
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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9049</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9050</small>
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articles/welcome_to_AMR.html
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9049</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9050</small>
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