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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="">1.8.2.9047</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9049</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">
@@ -111,6 +111,11 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../reference/av_property.html">
<span class="fa fa-capsules"></span>
Get properties of an antiviral agent
</a>
</div>
</li>
<li class="nav-item">
@@ -163,7 +168,7 @@
<h4 data-toc-skip class="author">Dr. Matthijs
Berends</h4>
<h4 data-toc-skip class="date">12 November 2022</h4>
<h4 data-toc-skip class="date">13 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 +180,7 @@ 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 12 November 2022.</p>
generated on 13 November 2022.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@@ -231,21 +236,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2022-11-12</td>
<td align="center">2022-11-13</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">2022-11-12</td>
<td align="center">2022-11-13</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">2022-11-12</td>
<td align="center">2022-11-13</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@@ -395,64 +400,53 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2012-03-28</td>
<td align="center">G1</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">2010-09-12</td>
<td align="center">E1</td>
<td align="center">Hospital A</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="odd">
<td align="center">2015-07-10</td>
<td align="center">N9</td>
<td align="center">2012-05-17</td>
<td align="center">I10</td>
<td align="center">Hospital D</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">Escherichia coli</td>
<td align="center">S</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">F</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2016-02-13</td>
<td align="center">B8</td>
<td align="center">Hospital B</td>
<td align="center">2013-12-12</td>
<td align="center">C4</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">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">2016-12-26</td>
<td align="center">X3</td>
<td align="center">2015-05-08</td>
<td align="center">S6</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">Escherichia coli</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2014-04-05</td>
<td align="center">K5</td>
<td align="center">Hospital B</td>
<td align="center">2012-02-06</td>
<td align="center">L4</td>
<td align="center">Hospital C</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2017-11-15</td>
<td align="center">J6</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
@@ -460,6 +454,17 @@ data set:</p>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2017-09-22</td>
<td align="center">G7</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
</tbody>
</table>
<p>Now, let’s start the cleaning and the analysis!</p>
@@ -494,16 +499,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,517</td>
<td align="right">52.59%</td>
<td align="right">10,517</td>
<td align="right">52.59%</td>
<td align="right">10,335</td>
<td align="right">51.68%</td>
<td align="right">10,335</td>
<td align="right">51.68%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,483</td>
<td align="right">47.42%</td>
<td align="right">9,665</td>
<td align="right">48.33%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@@ -616,10 +621,10 @@ 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 10,603 'phenotype-based' first isolates (53.0% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,583 'phenotype-based' first isolates (52.9% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<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
<p>So only 52.9% 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 +634,7 @@ it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" cl
<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 10,603 isolates for analysis. Now our data looks
<p>So we end up with 10,583 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>
@@ -646,8 +651,8 @@ like:</p>
<col width="3%">
<col width="6%">
<col width="11%">
<col width="10%">
<col width="9%">
<col width="12%">
<col width="7%">
<col width="5%">
</colgroup>
<thead><tr class="header">
@@ -668,73 +673,89 @@ like:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">3</td>
<td align="center">2015-07-10</td>
<td align="center">N9</td>
<td align="left">1</td>
<td align="center">2012-05-17</td>
<td align="center">I10</td>
<td align="center">Hospital D</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="center">2013-12-12</td>
<td align="center">C4</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</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">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">3</td>
<td align="center">2015-05-08</td>
<td align="center">S6</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">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">5</td>
<td align="center">2017-11-15</td>
<td align="center">J6</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</td>
<td align="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">M</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">7</td>
<td align="center">2011-04-08</td>
<td align="center">D2</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">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">TRUE</td>
</tr>
<tr class="even">
<td align="left">8</td>
<td align="center">2013-12-26</td>
<td align="center">K2</td>
<td align="center">Hospital D</td>
<td align="center">B_KLBSL_PNMN</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>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">11</td>
<td align="center">2017-12-04</td>
<td align="center">B10</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">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">12</td>
<td align="center">2010-03-06</td>
<td align="center">X9</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">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">14</td>
<td align="center">2017-11-16</td>
<td align="center">K5</td>
<td align="center">2016-01-21</td>
<td align="center">F1</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
@@ -747,22 +768,6 @@ like:</p>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">15</td>
<td align="center">2012-05-28</td>
<td align="center">X4</td>
<td align="center">Hospital B</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
<p>Time for the analysis!</p>
@@ -796,8 +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: 10,603<br>
Available: 10,603 (100%, NA: 0 = 0%)<br>
Length: 10,583<br>
Available: 10,583 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@@ -822,33 +827,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">4,605</td>
<td align="right">43.43%</td>
<td align="right">4,605</td>
<td align="right">43.43%</td>
<td align="right">4,553</td>
<td align="right">43.02%</td>
<td align="right">4,553</td>
<td align="right">43.02%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,704</td>
<td align="right">25.50%</td>
<td align="right">7,309</td>
<td align="right">68.93%</td>
<td align="right">2,749</td>
<td align="right">25.98%</td>
<td align="right">7,302</td>
<td align="right">69.00%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,080</td>
<td align="right">19.62%</td>
<td align="right">9,389</td>
<td align="right">88.55%</td>
<td align="right">2,123</td>
<td align="right">20.06%</td>
<td align="right">9,425</td>
<td align="right">89.06%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,214</td>
<td align="right">11.45%</td>
<td align="right">10,603</td>
<td align="right">1,158</td>
<td align="right">10.94%</td>
<td align="right">10,583</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@@ -897,26 +902,11 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2012-05-28</td>
<td align="center">X4</td>
<td align="center">Hospital B</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2013-02-21</td>
<td align="center">Q4</td>
<td align="center">2015-05-08</td>
<td align="center">S6</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_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">R</td>
@@ -926,61 +916,76 @@ antibiotic class they are in:</p>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2014-12-17</td>
<td align="center">V4</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">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="center">2012-01-20</td>
<td align="center">E6</td>
<td align="center">2014-04-13</td>
<td align="center">Y5</td>
<td align="center">Hospital C</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</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">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">2014-01-15</td>
<td align="center">Y1</td>
<td align="center">2010-08-29</td>
<td align="center">R6</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2013-06-25</td>
<td align="center">O8</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">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">2016-02-06</td>
<td align="center">W10</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</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-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">2015-02-24</td>
<td align="center">I1</td>
<td align="center">Hospital A</td>
<td align="center">2016-03-30</td>
<td align="center">O7</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">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">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
@@ -1009,50 +1014,50 @@ different bug/drug combinations, you can use the
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">2153</td>
<td align="center">133</td>
<td align="center">2319</td>
<td align="center">4605</td>
<td align="center">2155</td>
<td align="center">146</td>
<td align="center">2252</td>
<td align="center">4553</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3353</td>
<td align="center">146</td>
<td align="center">1106</td>
<td align="center">4605</td>
<td align="center">3346</td>
<td align="center">152</td>
<td align="center">1055</td>
<td align="center">4553</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3357</td>
<td align="center">3368</td>
<td align="center">0</td>
<td align="center">1248</td>
<td align="center">4605</td>
<td align="center">1185</td>
<td align="center">4553</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4032</td>
<td align="center">3965</td>
<td align="center">0</td>
<td align="center">573</td>
<td align="center">4605</td>
<td align="center">588</td>
<td align="center">4553</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">1214</td>
<td align="center">1214</td>
<td align="center">1158</td>
<td align="center">1158</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">228</td>
<td align="center">1214</td>
<td align="center">926</td>
<td align="center">43</td>
<td align="center">189</td>
<td align="center">1158</td>
</tr>
</tbody>
</table>
@@ -1075,34 +1080,34 @@ different bug/drug combinations, you can use the
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4032</td>
<td align="center">3965</td>
<td align="center">0</td>
<td align="center">573</td>
<td align="center">4605</td>
<td align="center">588</td>
<td align="center">4553</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1077</td>
<td align="center">1041</td>
<td align="center">0</td>
<td align="center">137</td>
<td align="center">1214</td>
<td align="center">117</td>
<td align="center">1158</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2407</td>
<td align="center">2425</td>
<td align="center">0</td>
<td align="center">297</td>
<td align="center">2704</td>
<td align="center">324</td>
<td align="center">2749</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">2080</td>
<td align="center">2080</td>
<td align="center">2123</td>
<td align="center">2123</td>
</tr>
</tbody>
</table>
@@ -1134,7 +1139,7 @@ I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equa
own:</p>
<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span></span>
<span><span class="co"># [1] 0.5472036</span></span></code></pre></div>
<span><span class="co"># [1] 0.5406784</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 +1154,19 @@ own:</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5600486</td>
<td align="center">0.5424045</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5391692</td>
<td align="center">0.5265943</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5552826</td>
<td align="center">0.5560626</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5345403</td>
<td align="center">0.5524135</td>
</tr>
</tbody>
</table>
@@ -1186,23 +1191,23 @@ all isolates available for every group (i.e. values S, I or R):</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5600486</td>
<td align="center">3289</td>
<td align="center">0.5424045</td>
<td align="center">3219</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5391692</td>
<td align="center">3587</td>
<td align="center">0.5265943</td>
<td align="center">3779</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5552826</td>
<td align="center">1628</td>
<td align="center">0.5560626</td>
<td align="center">1534</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5345403</td>
<td align="center">2099</td>
<td align="center">0.5524135</td>
<td align="center">2051</td>
</tr>
</tbody>
</table>
@@ -1227,27 +1232,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7598263</td>
<td align="center">0.8755700</td>
<td align="center">0.9774159</td>
<td align="center">0.7682846</td>
<td align="center">0.8708544</td>
<td align="center">0.9745223</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8121911</td>
<td align="center">0.8871499</td>
<td align="center">0.9728171</td>
<td align="center">0.8367876</td>
<td align="center">0.8989637</td>
<td align="center">0.9792746</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7917899</td>
<td align="center">0.8901627</td>
<td align="center">0.9822485</td>
<td align="center">0.7995635</td>
<td align="center">0.8821390</td>
<td align="center">0.9796290</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5423077</td>
<td align="center">0.5393311</td>
<td align="center">0.0000000</td>
<td align="center">0.5423077</td>
<td align="center">0.5393311</td>
</tr>
</tbody>
</table>
@@ -1275,23 +1280,23 @@ classes, use a antibiotic class selector such as
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">56.0%</td>
<td align="right">28.0%</td>
<td align="right">54.2%</td>
<td align="right">25.6%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">53.9%</td>
<td align="right">27.0%</td>
<td align="right">52.7%</td>
<td align="right">26.4%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">55.5%</td>
<td align="right">25.3%</td>
<td align="right">55.6%</td>
<td align="right">26.5%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">53.5%</td>
<td align="right">26.1%</td>
<td align="right">55.2%</td>
<td align="right">26.5%</td>
</tr>
</tbody>
</table>
@@ -1407,18 +1412,16 @@ classes) <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code>:</p>
<code class="sourceCode R"><span><span class="va">mic_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span></span>
<span><span class="va">mic_values</span></span>
<span><span class="co"># Class 'mic'</span></span>
<span><span class="co"># [1] 32 &lt;=0.001 16 16 0.5 0.5 0.0625 4 0.25 </span></span>
<span><span class="co"># [10] 0.01 128 256 0.01 &lt;=0.001 0.25 0.25 128 256 </span></span>
<span><span class="co"># [19] 8 64 256 256 1 32 0.0625 0.005 4 </span></span>
<span><span class="co"># [28] 0.005 0.125 0.025 0.125 8 64 &lt;=0.001 0.5 0.025 </span></span>
<span><span class="co"># [37] 0.002 0.5 0.002 4 &lt;=0.001 0.25 1 0.125 4 </span></span>
<span><span class="co"># [46] 128 256 0.01 0.002 0.01 32 32 0.005 4 </span></span>
<span><span class="co"># [55] 0.0625 256 0.25 2 32 0.01 &lt;=0.001 4 0.5 </span></span>
<span><span class="co"># [64] 8 0.125 0.005 &lt;=0.001 64 1 0.5 16 1 </span></span>
<span><span class="co"># [73] 2 0.005 0.25 64 32 16 &lt;=0.001 128 0.025 </span></span>
<span><span class="co"># [82] 4 256 16 0.125 2 0.005 &lt;=0.001 0.0625 0.005 </span></span>
<span><span class="co"># [91] 0.5 2 128 0.5 2 16 0.002 &lt;=0.001 0.125 </span></span>
<span><span class="co"># [100] 0.002</span></span></code></pre></div>
<span><span class="co"># [1] 0.001 0.025 16 0.025 128 64 0.01 0.005 4 64 </span></span>
<span><span class="co"># [11] 1 0.5 0.0625 64 0.125 0.002 0.025 0.001 0.002 8 </span></span>
<span><span class="co"># [21] 16 16 0.25 1 1 2 16 0.001 2 2 </span></span>
<span><span class="co"># [31] 0.0625 4 16 0.002 0.025 2 64 4 16 4 </span></span>
<span><span class="co"># [41] 1 0.005 0.25 0.025 256 0.5 0.01 0.001 128 4 </span></span>
<span><span class="co"># [51] 32 0.5 2 256 1 64 1 0.005 1 4 </span></span>
<span><span class="co"># [61] 0.0625 0.0625 256 0.025 0.0625 64 0.01 0.0625 0.0625 32 </span></span>
<span><span class="co"># [71] 0.0625 0.5 256 4 4 0.0625 32 0.0625 0.005 256 </span></span>
<span><span class="co"># [81] 0.5 1 128 0.001 16 64 0.0625 0.002 0.125 0.125 </span></span>
<span><span class="co"># [91] 256 0.01 0.002 0.025 0.25 1 0.005 0.001 0.125 0.125</span></span></code></pre></div>
<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>
@@ -1452,10 +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] 20 26 25 18 21 30 25 24 29 29 18 31 24 22 19 21 21 30 18 22 27 20 25 19 28</span></span>
<span><span class="co"># [26] 28 29 26 17 24 20 30 22 30 24 18 25 27 29 29 22 28 18 29 28 21 29 27 19 29</span></span>
<span><span class="co"># [51] 21 17 17 23 26 22 27 30 29 20 26 18 18 17 24 21 23 25 26 17 24 22 18 31 29</span></span>
<span><span class="co"># [76] 29 21 24 27 22 28 26 25 19 17 23 24 28 31 18 30 30 25 22 22 31 25 31 24 26</span></span></code></pre></div>
<span><span class="co"># [1] 27 17 19 21 26 26 28 25 17 24 21 19 20 24 25 30 23 26 31 22 25 27 26 29 18</span></span>
<span><span class="co"># [26] 29 22 18 22 27 24 25 18 29 21 18 28 21 17 25 28 23 22 21 21 31 28 20 29 20</span></span>
<span><span class="co"># [51] 24 25 17 18 30 23 28 21 18 28 24 29 20 18 22 24 29 26 21 19 17 19 30 22 19</span></span>
<span><span class="co"># [76] 28 19 23 31 19 28 26 29 17 22 29 17 29 29 18 29 27 23 27 26 30 28 28 29 22</span></span></code></pre></div>
<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>