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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="">1.8.2.9092</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</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 @@ the <code><a href="https://rdrr.io/r/utils/head.html" class="external-link">head
data set:</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">data</span><span class="op">)</span></span></code></pre></div>
<table style="width:100%;" class="table">
<table class="table">
<colgroup>
<col width="14%">
<col width="14%">
<col width="14%">
<col width="21%">
<col width="6%">
<col width="6%">
<col width="6%">
<col width="6%">
<col width="13%">
<col width="13%">
<col width="13%">
<col width="26%">
<col width="5%">
<col width="5%">
<col width="5%">
<col width="5%">
<col width="9%">
</colgroup>
<thead><tr class="header">
@ -400,8 +400,19 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2013-06-11</td>
<td align="center">R1</td>
<td align="center">2011-06-08</td>
<td align="center">B3</td>
<td align="center">Hospital D</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">2015-05-02</td>
<td align="center">T1</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -410,22 +421,33 @@ data set:</p>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2016-02-26</td>
<td align="center">G2</td>
<td align="center">Hospital C</td>
<tr class="odd">
<td align="center">2015-10-18</td>
<td align="center">M10</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">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2016-05-15</td>
<td align="center">B2</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2014-06-18</td>
<td align="center">D2</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia coli</td>
<td align="center">2012-07-12</td>
<td align="center">B1</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">S</td>
@ -433,20 +455,9 @@ data set:</p>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2014-05-13</td>
<td align="center">L4</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2010-05-08</td>
<td align="center">G4</td>
<td align="center">Hospital B</td>
<td align="center">2013-06-19</td>
<td align="center">M2</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
@ -454,17 +465,6 @@ data set:</p>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2011-04-08</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">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
</tbody>
</table>
<p>Now, let’s start the cleaning and the analysis!</p>
@ -499,16 +499,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,445</td>
<td align="right">52.23%</td>
<td align="right">10,445</td>
<td align="right">52.23%</td>
<td align="right">10,455</td>
<td align="right">52.28%</td>
<td align="right">10,455</td>
<td align="right">52.28%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,555</td>
<td align="right">47.78%</td>
<td align="right">9,545</td>
<td align="right">47.73%</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 10,661 'phenotype-based' first isolates (53.3% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,550 'phenotype-based' first isolates (52.8% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 53.3% is suitable for resistance analysis! We can now filter
<p>So only 52.8% 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">
@ -634,7 +634,7 @@ on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html"
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="co"># Including isolates from ICU.</span></span></code></pre></div>
<p>So we end up with 10,661 isolates for analysis. Now our data looks
<p>So we end up with 10,550 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>
@ -651,8 +651,8 @@ 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">
@ -673,15 +673,15 @@ like:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">4</td>
<td align="center">2014-05-13</td>
<td align="center">L4</td>
<td align="center">Hospital B</td>
<td align="left">1</td>
<td align="center">2011-06-08</td>
<td align="center">B3</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
@ -689,10 +689,10 @@ like:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">5</td>
<td align="center">2010-05-08</td>
<td align="center">G4</td>
<td align="center">Hospital B</td>
<td align="left">6</td>
<td align="center">2013-06-19</td>
<td align="center">M2</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -705,67 +705,67 @@ like:</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">6</td>
<td align="center">2011-04-08</td>
<td align="center">G7</td>
<td align="center">Hospital A</td>
<td align="left">7</td>
<td align="center">2017-08-21</td>
<td align="center">W8</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">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">7</td>
<td align="center">2015-06-18</td>
<td align="center">F7</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="left">8</td>
<td align="center">2011-06-07</td>
<td align="center">D4</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">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">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">9</td>
<td align="center">2013-04-22</td>
<td align="center">O4</td>
<td align="center">2014-05-22</td>
<td align="center">G4</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">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">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">13</td>
<td align="center">2014-07-04</td>
<td align="center">H10</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="left">10</td>
<td align="center">2017-10-08</td>
<td align="center">Y10</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">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">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</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: 10,661<br>
Available: 10,661 (100%, NA: 0 = 0%)<br>
Length: 10,550<br>
Available: 10,550 (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">4,638</td>
<td align="right">43.50%</td>
<td align="right">4,638</td>
<td align="right">43.50%</td>
<td align="right">4,580</td>
<td align="right">43.41%</td>
<td align="right">4,580</td>
<td align="right">43.41%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,699</td>
<td align="right">25.32%</td>
<td align="right">7,337</td>
<td align="right">68.82%</td>
<td align="right">2,689</td>
<td align="right">25.49%</td>
<td align="right">7,269</td>
<td align="right">68.90%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,127</td>
<td align="right">19.95%</td>
<td align="right">9,464</td>
<td align="right">88.77%</td>
<td align="right">2,098</td>
<td align="right">19.89%</td>
<td align="right">9,367</td>
<td align="right">88.79%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,197</td>
<td align="right">11.23%</td>
<td align="right">10,661</td>
<td align="right">1,183</td>
<td align="right">11.21%</td>
<td align="right">10,550</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>
@ -902,8 +902,23 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2013-04-22</td>
<td align="center">O4</td>
<td align="center">2014-02-15</td>
<td align="center">F2</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2013-04-24</td>
<td align="center">U2</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
@ -916,10 +931,25 @@ antibiotic class they are in:</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2017-05-20</td>
<tr class="odd">
<td align="center">2016-10-17</td>
<td align="center">J4</td>
<td align="center">Hospital C</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="even">
<td align="center">2016-08-24</td>
<td align="center">B10</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
@ -932,38 +962,8 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2010-01-06</td>
<td align="center">Z7</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2013-04-07</td>
<td align="center">R8</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">R</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="odd">
<td align="center">2010-04-24</td>
<td align="center">G2</td>
<td align="center">2014-02-03</td>
<td align="center">F6</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
@ -977,17 +977,17 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2017-10-15</td>
<td align="center">U1</td>
<td align="center">2010-06-12</td>
<td align="center">J7</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
@ -1013,50 +1013,50 @@ 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">2172</td>
<td align="center">141</td>
<td align="center">2325</td>
<td align="center">4638</td>
<td align="center">2132</td>
<td align="center">111</td>
<td align="center">2337</td>
<td align="center">4580</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3409</td>
<td align="center">162</td>
<td align="center">1067</td>
<td align="center">4638</td>
<td align="center">3342</td>
<td align="center">182</td>
<td align="center">1056</td>
<td align="center">4580</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3344</td>
<td align="center">3363</td>
<td align="center">0</td>
<td align="center">1294</td>
<td align="center">4638</td>
<td align="center">1217</td>
<td align="center">4580</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4074</td>
<td align="center">4007</td>
<td align="center">0</td>
<td align="center">564</td>
<td align="center">4638</td>
<td align="center">573</td>
<td align="center">4580</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">1197</td>
<td align="center">1197</td>
<td align="center">1183</td>
<td align="center">1183</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">926</td>
<td align="center">62</td>
<td align="center">209</td>
<td align="center">1197</td>
<td align="center">909</td>
<td align="center">59</td>
<td align="center">215</td>
<td align="center">1183</td>
</tr>
</tbody>
</table>
@ -1078,34 +1078,34 @@ 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">4074</td>
<td align="center">4007</td>
<td align="center">0</td>
<td align="center">564</td>
<td align="center">4638</td>
<td align="center">573</td>
<td align="center">4580</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1080</td>
<td align="center">1071</td>
<td align="center">0</td>
<td align="center">117</td>
<td align="center">1197</td>
<td align="center">112</td>
<td align="center">1183</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2419</td>
<td align="center">2383</td>
<td align="center">0</td>
<td align="center">280</td>
<td align="center">2699</td>
<td align="center">306</td>
<td align="center">2689</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">2127</td>
<td align="center">2127</td>
<td align="center">2098</td>
<td align="center">2098</td>
</tr>
</tbody>
</table>
@ -1137,7 +1137,7 @@ 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] 0.5433824</span></span></code></pre></div>
<span><span class="co"># [1] 0.5512796</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">
@ -1152,19 +1152,19 @@ own:</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5447360</td>
<td align="center">0.5525129</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5379915</td>
<td align="center">0.5444295</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5309842</td>
<td align="center">0.5600751</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5608238</td>
<td align="center">0.5548752</td>
</tr>
</tbody>
</table>
@ -1189,23 +1189,23 @@ 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">0.5447360</td>
<td align="center">3163</td>
<td align="center">0.5525129</td>
<td align="center">3104</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5379915</td>
<td align="center">3764</td>
<td align="center">0.5444295</td>
<td align="center">3725</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5309842</td>
<td align="center">1646</td>
<td align="center">0.5600751</td>
<td align="center">1598</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5608238</td>
<td align="center">2088</td>
<td align="center">0.5548752</td>
<td align="center">2123</td>
</tr>
</tbody>
</table>
@ -1230,27 +1230,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7699439</td>
<td align="center">0.8783959</td>
<td align="center">0.9762829</td>
<td align="center">0.7694323</td>
<td align="center">0.8748908</td>
<td align="center">0.9772926</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8253968</td>
<td align="center">0.9022556</td>
<td align="center">0.9841270</td>
<td align="center">0.8182587</td>
<td align="center">0.9053254</td>
<td align="center">0.9822485</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7899222</td>
<td align="center">0.8962579</td>
<td align="center">0.9818451</td>
<td align="center">0.7746374</td>
<td align="center">0.8862030</td>
<td align="center">0.9750837</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5514810</td>
<td align="center">0.5424214</td>
<td align="center">0.0000000</td>
<td align="center">0.5514810</td>
<td align="center">0.5424214</td>
</tr>
</tbody>
</table>
@ -1278,23 +1278,23 @@ classes, use a antibiotic class selector such as
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">54.5%</td>
<td align="right">26.8%</td>
<td align="right">55.3%</td>
<td align="right">26.3%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">53.8%</td>
<td align="right">25.7%</td>
<td align="right">54.4%</td>
<td align="right">26.6%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">53.1%</td>
<td align="right">26.5%</td>
<td align="right">56.0%</td>
<td align="right">27.7%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">56.1%</td>
<td align="right">26.0%</td>
<td align="right">55.5%</td>
<td align="right">27.7%</td>
</tr>
</tbody>
</table>
@ -1410,17 +1410,17 @@ 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] 8 1 8 128 0.125 0.025 0.125 0.25 0.01 </span></span>
<span><span class="co"># [10] 0.002 0.025 0.125 &lt;=0.001 0.125 0.01 32 0.025 64 </span></span>
<span><span class="co"># [19] 0.025 16 0.125 0.5 8 0.005 256 256 256 </span></span>
<span><span class="co"># [28] 8 0.5 0.005 32 256 0.01 &lt;=0.001 0.01 0.002 </span></span>
<span><span class="co"># [37] 64 64 0.0625 2 256 2 0.005 0.005 8 </span></span>
<span><span class="co"># [46] &lt;=0.001 4 64 0.025 128 256 0.0625 &lt;=0.001 8 </span></span>
<span><span class="co"># [55] 0.5 0.002 1 &lt;=0.001 4 0.5 32 2 256 </span></span>
<span><span class="co"># [64] 0.01 0.002 0.25 4 8 128 128 0.0625 16 </span></span>
<span><span class="co"># [73] 2 0.01 0.002 4 0.5 0.5 256 0.005 64 </span></span>
<span><span class="co"># [82] 16 0.125 128 0.005 4 1 1 256 0.01 </span></span>
<span><span class="co"># [91] 0.002 4 1 0.0625 0.125 32 256 2 0.002 </span></span>
<span><span class="co"># [1] 128 4 8 0.002 0.005 0.25 0.002 1 2 </span></span>
<span><span class="co"># [10] 128 0.025 64 0.5 2 1 0.025 0.025 64 </span></span>
<span><span class="co"># [19] 8 0.025 0.005 128 0.002 64 32 0.002 &gt;=256 </span></span>
<span><span class="co"># [28] 0.5 0.5 1 4 0.005 0.005 0.005 16 &lt;=0.001</span></span>
<span><span class="co"># [37] 16 0.01 64 2 128 0.25 2 &gt;=256 16 </span></span>
<span><span class="co"># [46] 0.002 0.25 0.0625 0.5 16 128 0.125 32 0.005 </span></span>
<span><span class="co"># [55] 128 32 32 8 0.002 16 0.002 128 2 </span></span>
<span><span class="co"># [64] 0.0625 2 4 0.005 0.25 16 1 8 0.025 </span></span>
<span><span class="co"># [73] 16 8 0.01 32 0.125 8 1 0.01 0.0625 </span></span>
<span><span class="co"># [82] &gt;=256 0.01 0.005 0.002 2 0.125 128 64 0.5 </span></span>
<span><span class="co"># [91] 0.01 8 64 64 1 0.025 &gt;=256 8 4 </span></span>
<span><span class="co"># [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>
@ -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] 30 31 18 26 29 17 30 31 18 18 19 25 28 22 22 24 26 31 30 29 27 25 26 30 19</span></span>
<span><span class="co"># [26] 23 17 17 25 21 21 28 27 29 17 28 30 29 28 29 28 31 29 28 28 29 19 30 29 27</span></span>
<span><span class="co"># [51] 24 29 17 27 28 18 21 17 26 17 23 31 27 17 18 29 26 22 20 20 21 21 28 19 17</span></span>
<span><span class="co"># [76] 31 27 24 28 21 24 23 30 25 22 19 28 25 27 25 28 25 18 26 30 19 27 28 20 17</span></span></code></pre></div>
<span><span class="co"># [1] 31 25 30 30 21 26 27 26 22 21 30 31 22 29 22 30 30 28 21 19 31 31 30 20 25</span></span>
<span><span class="co"># [26] 24 17 20 27 24 20 22 28 31 20 25 30 25 21 31 21 22 29 18 23 19 23 19 19 19</span></span>
<span><span class="co"># [51] 25 22 22 29 22 17 21 19 21 26 17 27 23 28 27 20 18 24 29 26 23 27 27 19 20</span></span>
<span><span class="co"># [76] 28 24 22 31 22 28 22 27 31 30 25 27 18 22 18 17 25 20 20 25 22 24 20 23 22</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="">1.8.2.9092</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

58
articles/MDR.html
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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="">1.8.2.9092</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</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">
@ -375,19 +375,19 @@ names or codes, this would have worked exactly the same way:</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span>
<span><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
<span><span class="co"># 1 R S S S S R</span></span>
<span><span class="co"># 2 I R I R I I</span></span>
<span><span class="co"># 3 R S I S S R</span></span>
<span><span class="co"># 4 R S I S I S</span></span>
<span><span class="co"># 5 R R R I I R</span></span>
<span><span class="co"># 6 S R R S S S</span></span>
<span><span class="co"># 1 S S S R R S</span></span>
<span><span class="co"># 2 R R I R S I</span></span>
<span><span class="co"># 3 I R I S R I</span></span>
<span><span class="co"># 4 R I R S R S</span></span>
<span><span class="co"># 5 I I I S I R</span></span>
<span><span class="co"># 6 S S R S I I</span></span>
<span><span class="co"># kanamycin</span></span>
<span><span class="co"># 1 I</span></span>
<span><span class="co"># 2 R</span></span>
<span><span class="co"># 3 S</span></span>
<span><span class="co"># 4 S</span></span>
<span><span class="co"># 5 S</span></span>
<span><span class="co"># 6 R</span></span></code></pre></div>
<span><span class="co"># 3 R</span></span>
<span><span class="co"># 4 I</span></span>
<span><span class="co"># 5 R</span></span>
<span><span class="co"># 6 S</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">
@ -428,40 +428,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3163</td>
<td align="right">63.26%</td>
<td align="right">3163</td>
<td align="right">63.26%</td>
<td align="right">3198</td>
<td align="right">63.96%</td>
<td align="right">3198</td>
<td align="right">63.96%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">976</td>
<td align="right">19.52%</td>
<td align="right">4139</td>
<td align="right">82.78%</td>
<td align="right">1027</td>
<td align="right">20.54%</td>
<td align="right">4225</td>
<td align="right">84.50%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">504</td>
<td align="right">10.08%</td>
<td align="right">4643</td>
<td align="right">92.86%</td>
<td align="right">423</td>
<td align="right">8.46%</td>
<td align="right">4648</td>
<td align="right">92.96%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">259</td>
<td align="right">5.18%</td>
<td align="right">4902</td>
<td align="right">98.04%</td>
<td align="right">243</td>
<td align="right">4.86%</td>
<td align="right">4891</td>
<td align="right">97.82%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">98</td>
<td align="right">1.96%</td>
<td align="right">109</td>
<td align="right">2.18%</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="">1.8.2.9092</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</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
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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="">1.8.2.9092</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9092</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
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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="">1.8.2.9092</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
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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="">1.8.2.9092</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</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="">1.8.2.9092</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</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/welcome_to_AMR.html
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<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="">1.8.2.9092</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</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">