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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="">1.8.2.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9084</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="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>
@@ -400,67 +400,67 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2017-09-27</td>
<td align="center">K9</td>
<td align="center">2010-02-03</td>
<td align="center">J4</td>
<td align="center">Hospital A</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">2012-09-19</td>
<td align="center">M7</td>
<td align="center">Hospital A</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2010-01-21</td>
<td align="center">Q3</td>
<tr class="even">
<td align="center">2011-05-02</td>
<td align="center">Z10</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">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">F</td>
</tr>
<tr class="even">
<td align="center">2016-11-24</td>
<td align="center">N1</td>
<tr class="odd">
<td align="center">2016-05-03</td>
<td align="center">N2</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</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">2016-03-05</td>
<td align="center">C5</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2016-07-29</td>
<td align="center">J7</td>
<td align="center">2010-06-18</td>
<td align="center">X9</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2012-04-30</td>
<td align="center">G8</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2016-06-19</td>
<td align="center">E7</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
@@ -499,16 +499,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,357</td>
<td align="right">51.79%</td>
<td align="right">10,357</td>
<td align="right">51.79%</td>
<td align="right">10,423</td>
<td align="right">52.12%</td>
<td align="right">10,423</td>
<td align="right">52.12%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,643</td>
<td align="right">48.22%</td>
<td align="right">9,577</td>
<td align="right">47.89%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@@ -621,7 +621,7 @@ 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 10,726 'phenotype-based' first isolates (53.6% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,719 'phenotype-based' first isolates (53.6% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 53.6% 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
@@ -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 10,726 isolates for analysis. Now our data looks
<p>So we end up with 10,719 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>
@@ -673,30 +673,30 @@ like:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">2</td>
<td align="center">2012-09-19</td>
<td align="center">M7</td>
<td align="left">1</td>
<td align="center">2010-02-03</td>
<td align="center">J4</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</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">R</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">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">4</td>
<td align="center">2016-11-24</td>
<td align="center">N1</td>
<td align="center">Hospital D</td>
<td align="center">2016-03-05</td>
<td align="center">C5</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">R</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
@@ -705,11 +705,43 @@ like:</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">10</td>
<td align="center">2013-06-30</td>
<td align="center">M8</td>
<td align="left">5</td>
<td align="center">2010-06-18</td>
<td align="center">X9</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">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">2013-12-21</td>
<td align="center">Q1</td>
<td align="center">Hospital D</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">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">9</td>
<td align="center">2016-02-01</td>
<td align="center">F7</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>
@@ -722,50 +754,18 @@ like:</p>
</tr>
<tr class="even">
<td align="left">11</td>
<td align="center">2017-03-10</td>
<td align="center">N8</td>
<td align="center">2017-03-22</td>
<td align="center">U3</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</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">S</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">12</td>
<td align="center">2016-12-09</td>
<td align="center">T3</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">14</td>
<td align="center">2014-04-02</td>
<td align="center">I2</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">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">Klebsiella</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: 10,726<br>
Available: 10,726 (100%, NA: 0 = 0%)<br>
Length: 10,719<br>
Available: 10,719 (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">4,697</td>
<td align="right">43.79%</td>
<td align="right">4,697</td>
<td align="right">43.79%</td>
<td align="right">4,696</td>
<td align="right">43.81%</td>
<td align="right">4,696</td>
<td align="right">43.81%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,746</td>
<td align="right">25.60%</td>
<td align="right">7,443</td>
<td align="right">69.39%</td>
<td align="right">2,753</td>
<td align="right">25.68%</td>
<td align="right">7,449</td>
<td align="right">69.49%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,106</td>
<td align="right">19.63%</td>
<td align="right">9,549</td>
<td align="right">89.03%</td>
<td align="right">2,070</td>
<td align="right">19.31%</td>
<td align="right">9,519</td>
<td align="right">88.80%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,177</td>
<td align="right">10.97%</td>
<td align="right">10,726</td>
<td align="right">1,200</td>
<td align="right">11.20%</td>
<td align="right">10,719</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@@ -902,38 +902,23 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2012-09-19</td>
<td align="center">M7</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">2010-06-18</td>
<td align="center">X9</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</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">2010-02-14</td>
<td align="center">B5</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2016-09-23</td>
<td align="center">O10</td>
<td align="center">2013-12-21</td>
<td align="center">Q1</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
@@ -946,13 +931,13 @@ antibiotic class they are in:</p>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2015-05-01</td>
<td align="center">W1</td>
<td align="center">Hospital A</td>
<tr class="odd">
<td align="center">2012-03-21</td>
<td align="center">Q5</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">R</td>
<td align="center">F</td>
@@ -961,28 +946,28 @@ antibiotic class they are in:</p>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2017-08-13</td>
<td align="center">I9</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<tr class="even">
<td align="center">2016-10-25</td>
<td align="center">M2</td>
<td align="center">Hospital D</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-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="even">
<td align="center">2014-05-21</td>
<td align="center">O10</td>
<td align="center">Hospital A</td>
<tr class="odd">
<td align="center">2013-07-04</td>
<td align="center">T3</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
@@ -991,6 +976,21 @@ antibiotic class they are in:</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2015-12-29</td>
<td align="center">K1</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
<p>If you want to get a quick glance of the number of isolates in
@@ -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">2194</td>
<td align="center">130</td>
<td align="center">2373</td>
<td align="center">4697</td>
<td align="center">2212</td>
<td align="center">133</td>
<td align="center">2351</td>
<td align="center">4696</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3459</td>
<td align="center">3440</td>
<td align="center">180</td>
<td align="center">1058</td>
<td align="center">4697</td>
<td align="center">1076</td>
<td align="center">4696</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3421</td>
<td align="center">3409</td>
<td align="center">0</td>
<td align="center">1276</td>
<td align="center">4697</td>
<td align="center">1287</td>
<td align="center">4696</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4111</td>
<td align="center">4091</td>
<td align="center">0</td>
<td align="center">586</td>
<td align="center">4697</td>
<td align="center">605</td>
<td align="center">4696</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">1177</td>
<td align="center">1177</td>
<td align="center">1200</td>
<td align="center">1200</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">938</td>
<td align="center">48</td>
<td align="center">191</td>
<td align="center">1177</td>
<td align="center">950</td>
<td align="center">50</td>
<td align="center">200</td>
<td align="center">1200</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">4111</td>
<td align="center">4091</td>
<td align="center">0</td>
<td align="center">586</td>
<td align="center">4697</td>
<td align="center">605</td>
<td align="center">4696</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1045</td>
<td align="center">1083</td>
<td align="center">0</td>
<td align="center">132</td>
<td align="center">1177</td>
<td align="center">117</td>
<td align="center">1200</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2430</td>
<td align="center">2450</td>
<td align="center">0</td>
<td align="center">316</td>
<td align="center">2746</td>
<td align="center">303</td>
<td align="center">2753</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">2106</td>
<td align="center">2106</td>
<td align="center">2070</td>
<td align="center">2070</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] 0.5466157</span></span></code></pre></div>
<span><span class="co"># [1] 0.5435209</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">0.5586592</td>
<td align="center">0.5481644</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5431104</td>
<td align="center">0.5404344</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5266836</td>
<td align="center">0.5331288</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5491618</td>
<td align="center">0.5502162</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">0.5586592</td>
<td align="center">3222</td>
<td align="center">0.5481644</td>
<td align="center">3187</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5431104</td>
<td align="center">3723</td>
<td align="center">0.5404344</td>
<td align="center">3821</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5266836</td>
<td align="center">1574</td>
<td align="center">0.5331288</td>
<td align="center">1630</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5491618</td>
<td align="center">2207</td>
<td align="center">0.5502162</td>
<td align="center">2081</td>
</tr>
</tbody>
</table>
@@ -1230,27 +1230,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7747498</td>
<td align="center">0.8752395</td>
<td align="center">0.9774324</td>
<td align="center">0.7708688</td>
<td align="center">0.8711670</td>
<td align="center">0.9795571</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8377230</td>
<td align="center">0.8878505</td>
<td align="center">0.9770603</td>
<td align="center">0.8333333</td>
<td align="center">0.9025000</td>
<td align="center">0.9900000</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7760379</td>
<td align="center">0.8849235</td>
<td align="center">0.9756009</td>
<td align="center">0.7976753</td>
<td align="center">0.8899382</td>
<td align="center">0.9771159</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5394112</td>
<td align="center">0.5521739</td>
<td align="center">0.0000000</td>
<td align="center">0.5394112</td>
<td align="center">0.5521739</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">55.9%</td>
<td align="right">26.0%</td>
<td align="right">54.8%</td>
<td align="right">26.2%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">54.3%</td>
<td align="right">25.9%</td>
<td align="right">54.0%</td>
<td align="right">24.9%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">52.7%</td>
<td align="right">25.9%</td>
<td align="right">53.3%</td>
<td align="right">26.4%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">54.9%</td>
<td align="right">28.3%</td>
<td align="right">55.0%</td>
<td align="right">26.0%</td>
</tr>
</tbody>
</table>
@@ -1410,18 +1410,16 @@ 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] 0.0625 0.005 16 0.005 0.0625 8 1 0.25 0.01 </span></span>
<span><span class="co"># [10] &gt;=256 0.01 0.0625 0.0625 128 0.025 0.01 1 4 </span></span>
<span><span class="co"># [19] 0.01 128 0.125 0.025 16 &lt;=0.001 &lt;=0.001 8 0.125 </span></span>
<span><span class="co"># [28] 0.25 0.25 0.125 0.025 0.01 0.0625 16 0.002 8 </span></span>
<span><span class="co"># [37] 2 128 128 &lt;=0.001 0.0625 0.125 0.002 &lt;=0.001 0.025 </span></span>
<span><span class="co"># [46] 0.5 0.0625 128 0.5 64 0.5 0.005 0.5 16 </span></span>
<span><span class="co"># [55] 0.125 0.002 0.5 2 &gt;=256 &gt;=256 0.125 64 0.005 </span></span>
<span><span class="co"># [64] 64 32 16 4 16 8 8 0.125 0.5 </span></span>
<span><span class="co"># [73] 32 0.025 1 64 1 0.125 0.125 0.025 32 </span></span>
<span><span class="co"># [82] 64 0.01 0.25 2 0.125 0.0625 8 2 0.01 </span></span>
<span><span class="co"># [91] 64 0.005 8 0.25 0.125 8 128 0.5 &lt;=0.001</span></span>
<span><span class="co"># [100] 0.0625</span></span></code></pre></div>
<span><span class="co"># [1] 0.25 0.002 0.001 1 0.5 0.025 0.25 0.005 1 0.5 </span></span>
<span><span class="co"># [11] 8 0.025 0.025 0.01 0.005 2 2 8 0.5 1 </span></span>
<span><span class="co"># [21] 0.01 0.5 0.001 128 0.005 0.025 128 4 0.25 16 </span></span>
<span><span class="co"># [31] 16 0.25 0.005 0.01 4 0.25 8 0.01 0.125 256 </span></span>
<span><span class="co"># [41] 0.002 2 0.5 16 0.125 1 0.0625 0.0625 0.025 2 </span></span>
<span><span class="co"># [51] 0.01 2 32 0.005 0.025 0.025 4 128 0.001 4 </span></span>
<span><span class="co"># [61] 0.01 4 64 0.125 0.0625 0.0625 2 256 0.125 0.025 </span></span>
<span><span class="co"># [71] 8 0.5 64 0.0625 8 0.005 0.25 0.001 256 16 </span></span>
<span><span class="co"># [81] 128 64 0.125 0.025 0.5 2 0.005 0.0625 32 16 </span></span>
<span><span class="co"># [91] 1 8 128 0.25 0.0625 64 0.002 4 0.025 64</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>
@@ -1455,10 +1453,10 @@ 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 19 29 18 21 24 23 21 17 28 17 27 23 22 23 18 30 30 22 24 22 22 20 26 17</span></span>
<span><span class="co"># [26] 17 29 22 23 19 24 28 27 28 17 17 27 28 17 23 28 18 28 23 21 22 22 19 29 27</span></span>
<span><span class="co"># [51] 17 18 22 22 24 19 30 24 31 29 26 17 28 26 27 17 17 27 22 20 28 25 17 20 30</span></span>
<span><span class="co"># [76] 25 31 25 28 27 27 20 31 25 23 24 22 20 18 26 29 18 25 31 20 22 26 29 20 31</span></span></code></pre></div>
<span><span class="co"># [1] 24 18 27 18 24 19 22 17 18 31 24 25 28 21 25 22 21 21 20 25 23 28 31 24 24</span></span>
<span><span class="co"># [26] 23 22 18 17 23 30 26 20 23 19 20 17 19 29 24 20 31 29 29 30 20 30 20 30 25</span></span>
<span><span class="co"># [51] 19 27 22 21 29 29 23 28 21 31 29 20 20 18 17 22 23 29 25 23 23 30 28 30 30</span></span>
<span><span class="co"># [76] 28 19 20 29 30 30 20 20 19 22 20 24 25 26 31 23 23 20 24 17 28 24 28 19 26</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>