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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="">1.8.2.9041</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</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">
@@ -163,7 +163,7 @@
<h4 data-toc-skip class="author">Dr. Matthijs
Berends</h4>
<h4 data-toc-skip class="date">31 October 2022</h4>
<h4 data-toc-skip class="date">05 November 2022</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/AMR.Rmd" class="external-link"><code>vignettes/AMR.Rmd</code></a></small>
<div class="d-none name"><code>AMR.Rmd</code></div>
@@ -175,7 +175,7 @@ Berends</h4>
website update since they are based on randomly created values and the
page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
Markdown</a>. However, the methodology remains unchanged. This page was
generated on 31 October 2022.</p>
generated on 05 November 2022.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@@ -231,21 +231,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2022-10-31</td>
<td align="center">2022-11-05</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="center">2022-10-31</td>
<td align="center">2022-11-05</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<tr class="odd">
<td align="center">2022-10-31</td>
<td align="center">2022-11-05</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@@ -395,70 +395,70 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2010-04-13</td>
<td align="center">B10</td>
<td align="center">2017-05-11</td>
<td align="center">P2</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">F</td>
</tr>
<tr class="even">
<td align="center">2014-09-24</td>
<td align="center">W9</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">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2014-01-20</td>
<td align="center">K9</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>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2016-01-31</td>
<td align="center">N7</td>
<td align="center">2015-03-26</td>
<td align="center">P5</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">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2010-10-29</td>
<td align="center">B9</td>
<td align="center">Hospital D</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2012-03-04</td>
<td align="center">E5</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">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2011-08-21</td>
<td align="center">N6</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">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2011-10-21</td>
<td align="center">F6</td>
<td align="center">2013-04-29</td>
<td align="center">U9</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">I</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">F</td>
</tr>
<tr class="even">
<td align="center">2010-07-12</td>
<td align="center">U6</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">F</td>
</tr>
</tbody>
</table>
@@ -494,16 +494,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,278</td>
<td align="right">51.39%</td>
<td align="right">10,278</td>
<td align="right">51.39%</td>
<td align="right">10,235</td>
<td align="right">51.18%</td>
<td align="right">10,235</td>
<td align="right">51.18%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,722</td>
<td align="right">48.61%</td>
<td align="right">9,765</td>
<td align="right">48.83%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@@ -616,10 +616,10 @@ 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 10,616 'phenotype-based' first isolates (53.1% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,603 'phenotype-based' first isolates (53.0% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 53.1% 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
<p>So only 53% 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">
<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>
@@ -629,7 +629,7 @@ 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 10,616 isolates for analysis. Now our data looks
<p>So we end up with 10,603 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>
@@ -669,45 +669,29 @@ like:</p>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2010-04-13</td>
<td align="center">B10</td>
<td align="center">2017-05-11</td>
<td align="center">P2</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="left">2</td>
<td align="center">2014-01-20</td>
<td align="center">K9</td>
<td align="center">Hospital A</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="odd">
<td align="left">3</td>
<td align="center">2016-01-31</td>
<td align="center">N7</td>
<td align="center">Hospital D</td>
<tr class="even">
<td align="left">2</td>
<td align="center">2014-09-24</td>
<td align="center">W9</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>
@@ -715,47 +699,63 @@ like:</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="center">2012-03-04</td>
<td align="center">E5</td>
<tr class="odd">
<td align="left">3</td>
<td align="center">2015-03-26</td>
<td align="center">P5</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">R</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">6</td>
<td align="center">2011-10-21</td>
<td align="center">F6</td>
<tr class="even">
<td align="left">5</td>
<td align="center">2013-04-29</td>
<td align="center">U9</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">I</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">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="left">7</td>
<td align="center">2014-06-01</td>
<td align="center">G3</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<tr class="odd">
<td align="left">6</td>
<td align="center">2010-07-12</td>
<td align="center">U6</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">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">10</td>
<td align="center">2015-03-25</td>
<td align="center">B1</td>
<td align="center">Hospital D</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">S</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
@@ -796,8 +796,8 @@ 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: 10,616<br>
Available: 10,616 (100%, NA: 0 = 0%)<br>
Length: 10,603<br>
Available: 10,603 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@@ -822,33 +822,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">4,668</td>
<td align="right">43.97%</td>
<td align="right">4,668</td>
<td align="right">43.97%</td>
<td align="right">4,603</td>
<td align="right">43.41%</td>
<td align="right">4,603</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">2,697</td>
<td align="right">25.41%</td>
<td align="right">7,365</td>
<td align="right">69.38%</td>
<td align="right">2,709</td>
<td align="right">25.55%</td>
<td align="right">7,312</td>
<td align="right">68.96%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,067</td>
<td align="right">19.47%</td>
<td align="right">9,432</td>
<td align="right">88.85%</td>
<td align="right">2,106</td>
<td align="right">19.86%</td>
<td align="right">9,418</td>
<td align="right">88.82%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,184</td>
<td align="right">11.15%</td>
<td align="right">10,616</td>
<td align="right">1,185</td>
<td align="right">11.18%</td>
<td align="right">10,603</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@@ -869,14 +869,14 @@ antibiotic class they are in:</p>
<col width="9%">
<col width="9%">
<col width="9%">
<col width="11%">
<col width="10%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="6%">
<col width="11%">
<col width="11%">
<col width="12%">
<col width="9%">
<col width="5%">
</colgroup>
@@ -897,14 +897,44 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2010-04-13</td>
<td align="center">B10</td>
<td align="center">2014-09-24</td>
<td align="center">W9</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">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">2014-11-16</td>
<td align="center">M1</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">2016-07-19</td>
<td align="center">G10</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">R</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
@@ -912,77 +942,47 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2016-01-31</td>
<td align="center">N7</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2016-12-09</td>
<td align="center">H8</td>
<td align="center">Hospital B</td>
<td align="center">2015-01-12</td>
<td align="center">W8</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">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2016-05-21</td>
<td align="center">O5</td>
<tr class="odd">
<td align="center">2014-10-02</td>
<td align="center">X5</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">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">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="odd">
<td align="center">2011-03-11</td>
<td align="center">A3</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<tr class="even">
<td align="center">2010-11-15</td>
<td align="center">M5</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">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">2017-02-09</td>
<td align="center">Q3</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">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
@@ -1009,50 +1009,50 @@ 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">2238</td>
<td align="center">132</td>
<td align="center">2298</td>
<td align="center">4668</td>
<td align="center">2197</td>
<td align="center">137</td>
<td align="center">2269</td>
<td align="center">4603</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3403</td>
<td align="center">152</td>
<td align="center">1113</td>
<td align="center">4668</td>
<td align="center">3391</td>
<td align="center">167</td>
<td align="center">1045</td>
<td align="center">4603</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3452</td>
<td align="center">3413</td>
<td align="center">0</td>
<td align="center">1216</td>
<td align="center">4668</td>
<td align="center">1190</td>
<td align="center">4603</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4097</td>
<td align="center">3980</td>
<td align="center">0</td>
<td align="center">571</td>
<td align="center">4668</td>
<td align="center">623</td>
<td align="center">4603</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">1184</td>
<td align="center">1184</td>
<td align="center">1185</td>
<td align="center">1185</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">926</td>
<td align="center">58</td>
<td align="center">942</td>
<td align="center">43</td>
<td align="center">200</td>
<td align="center">1184</td>
<td align="center">1185</td>
</tr>
</tbody>
</table>
@@ -1075,34 +1075,34 @@ 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">4097</td>
<td align="center">3980</td>
<td align="center">0</td>
<td align="center">571</td>
<td align="center">4668</td>
<td align="center">623</td>
<td align="center">4603</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1055</td>
<td align="center">1060</td>
<td align="center">0</td>
<td align="center">129</td>
<td align="center">1184</td>
<td align="center">125</td>
<td align="center">1185</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2375</td>
<td align="center">2422</td>
<td align="center">0</td>
<td align="center">322</td>
<td align="center">2697</td>
<td align="center">287</td>
<td align="center">2709</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">2067</td>
<td align="center">2067</td>
<td align="center">2106</td>
<td align="center">2106</td>
</tr>
</tbody>
</table>
@@ -1134,7 +1134,7 @@ 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] 0.5417295</span></span></code></pre></div>
<span><span class="co"># [1] 0.5352259</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">
@@ -1149,19 +1149,19 @@ own:</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5468395</td>
<td align="center">0.5432099</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5509504</td>
<td align="center">0.5246981</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5332103</td>
<td align="center">0.5336856</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5243269</td>
<td align="center">0.5419501</td>
</tr>
</tbody>
</table>
@@ -1186,23 +1186,23 @@ 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">0.5468395</td>
<td align="center">3085</td>
<td align="center">0.5432099</td>
<td align="center">3240</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5509504</td>
<td align="center">3788</td>
<td align="center">0.5246981</td>
<td align="center">3644</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5332103</td>
<td align="center">1626</td>
<td align="center">0.5336856</td>
<td align="center">1514</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5243269</td>
<td align="center">2117</td>
<td align="center">0.5419501</td>
<td align="center">2205</td>
</tr>
</tbody>
</table>
@@ -1227,27 +1227,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7615681</td>
<td align="center">0.8776778</td>
<td align="center">0.9768638</td>
<td align="center">0.7729741</td>
<td align="center">0.8646535</td>
<td align="center">0.9761025</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8310811</td>
<td align="center">0.8910473</td>
<td align="center">0.9805743</td>
<td align="center">0.8312236</td>
<td align="center">0.8945148</td>
<td align="center">0.9746835</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7897664</td>
<td align="center">0.8806081</td>
<td align="center">0.9762699</td>
<td align="center">0.7958656</td>
<td align="center">0.8940568</td>
<td align="center">0.9778516</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5365264</td>
<td align="center">0.5413105</td>
<td align="center">0.0000000</td>
<td align="center">0.5365264</td>
<td align="center">0.5413105</td>
</tr>
</tbody>
</table>
@@ -1275,23 +1275,23 @@ classes, use a antibiotic class selector such as
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">54.7%</td>
<td align="right">26.2%</td>
<td align="right">54.3%</td>
<td align="right">26.5%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">55.1%</td>
<td align="right">27.6%</td>
<td align="right">52.5%</td>
<td align="right">25.0%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">53.3%</td>
<td align="right">26.8%</td>
<td align="right">53.4%</td>
<td align="right">26.4%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">52.4%</td>
<td align="right">25.9%</td>
<td align="right">54.2%</td>
<td align="right">27.0%</td>
</tr>
</tbody>
</table>
@@ -1407,16 +1407,16 @@ 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] 0.125 16 64 0.0625 0.01 4 0.5 1 0.5 1 </span></span>
<span><span class="co"># [11] 0.001 16 0.0625 0.025 0.5 0.025 0.025 16 0.5 32 </span></span>
<span><span class="co"># [21] 1 0.025 0.5 64 0.25 0.5 0.001 0.5 0.25 0.001 </span></span>
<span><span class="co"># [31] 0.0625 2 0.002 0.025 64 1 1 64 0.01 0.001 </span></span>
<span><span class="co"># [41] 0.025 0.002 0.01 64 0.01 1 0.005 16 64 0.0625</span></span>
<span><span class="co"># [51] 0.002 128 0.5 32 0.25 0.002 0.01 0.025 8 128 </span></span>
<span><span class="co"># [61] 0.025 64 0.25 2 4 0.025 2 16 0.25 0.25 </span></span>
<span><span class="co"># [71] 64 32 1 0.125 0.125 32 16 128 2 0.0625</span></span>
<span><span class="co"># [81] 0.01 0.125 0.01 16 32 0.01 2 16 4 0.002 </span></span>
<span><span class="co"># [91] 32 8 0.25 0.025 0.005 0.01 8 16 0.005 8</span></span></code></pre></div>
<span><span class="co"># [1] 0.125 64 32 0.01 0.25 0.01 1 0.005 4 8 </span></span>
<span><span class="co"># [11] 64 0.001 8 0.005 4 0.5 0.005 16 0.001 128 </span></span>
<span><span class="co"># [21] 64 16 64 8 2 2 0.25 128 0.001 &gt;=256 </span></span>
<span><span class="co"># [31] 4 4 8 2 4 16 0.5 2 0.25 0.025 </span></span>
<span><span class="co"># [41] 2 8 8 0.005 128 2 0.01 16 1 1 </span></span>
<span><span class="co"># [51] 0.002 64 16 32 1 0.025 0.0625 16 64 0.001 </span></span>
<span><span class="co"># [61] 0.001 0.002 2 0.002 0.025 0.01 0.025 0.01 16 16 </span></span>
<span><span class="co"># [71] &gt;=256 64 16 0.25 0.01 64 0.25 64 0.001 0.001 </span></span>
<span><span class="co"># [81] 64 16 &gt;=256 4 0.25 0.002 0.5 1 128 0.002 </span></span>
<span><span class="co"># [91] 0.025 0.125 0.025 0.025 0.002 0.25 0.025 64 4 8</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>
@@ -1450,10 +1450,10 @@ plotting:</p>
<code class="sourceCode R"><span><span class="va">disk_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_disk</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span>
<span><span class="va">disk_values</span></span>
<span><span class="co"># Class 'disk'</span></span>
<span><span class="co"># [1] 28 17 23 21 20 24 23 26 17 17 24 20 29 17 20 24 17 17 27 20 28 21 17 18 30</span></span>
<span><span class="co"># [26] 28 26 20 20 30 26 29 18 28 23 20 23 19 28 22 29 29 19 25 31 26 24 21 23 22</span></span>
<span><span class="co"># [51] 25 25 25 18 28 17 31 29 25 26 27 23 17 24 17 28 25 29 29 24 29 29 18 20 27</span></span>
<span><span class="co"># [76] 26 18 22 25 28 30 31 27 25 21 26 29 18 18 26 22 30 29 29 29 22 24 28 17 27</span></span></code></pre></div>
<span><span class="co"># [1] 21 22 20 24 22 19 26 17 18 29 25 23 23 30 27 29 23 27 17 26 28 17 23 22 24</span></span>
<span><span class="co"># [26] 19 17 18 21 18 19 26 23 28 20 26 29 20 29 21 30 23 31 22 31 22 27 20 25 22</span></span>
<span><span class="co"># [51] 19 24 26 29 21 21 23 22 24 31 24 20 17 18 20 21 29 20 18 23 18 17 30 21 18</span></span>
<span><span class="co"># [76] 18 17 23 21 26 29 25 26 30 30 29 29 18 18 23 26 19 29 28 24 28 24 23 17 20</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>