P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-09-11 05:29:40 +02:00
Code Releases Activity

Built site for AMR: 1.8.2.9045@d2ceebe

Browse Source
This commit is contained in:
github-actions
2022-11-07 17:57:12 +00:00
parent f74da6c86a
commit 7fe29a8401
95 changed files with 533 additions and 538 deletions
Download Patch File Download Diff File Expand all files Collapse all files

548
articles/AMR.html
View File

@@ -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="">1.8.2.9044</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9045</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">05 November 2022</h4>
<h4 data-toc-skip class="date">07 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 05 November 2022.</p>
generated on 07 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">2022-11-05</td>
<td align="center">2022-11-07</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">2022-11-05</td>
<td align="center">2022-11-07</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">2022-11-05</td>
<td align="center">2022-11-07</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@@ -375,12 +375,12 @@ data set:</p>
<col width="13%">
<col width="13%">
<col width="13%">
<col width="26%">
<col width="28%">
<col width="5%">
<col width="5%">
<col width="5%">
<col width="5%">
<col width="9%">
<col width="8%">
</colgroup>
<thead><tr class="header">
<th align="center">date</th>
@@ -395,66 +395,66 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2016-09-06</td>
<td align="center">Z8</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2015-06-24</td>
<td align="center">I6</td>
<td align="center">2015-05-10</td>
<td align="center">P6</td>
<td align="center">Hospital B</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2016-06-01</td>
<td align="center">N5</td>
<td align="center">Hospital B</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>
<tr class="odd">
<td align="center">2012-04-02</td>
<td align="center">O6</td>
<td align="center">2016-09-10</td>
<td align="center">H3</td>
<td align="center">Hospital C</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">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2016-04-25</td>
<td align="center">K7</td>
<td align="center">Hospital B</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>
<tr class="odd">
<td align="center">2016-10-17</td>
<td align="center">I6</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2017-10-02</td>
<td align="center">S7</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2010-02-16</td>
<td align="center">U10</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">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2017-07-07</td>
<td align="center">F7</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">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2010-02-03</td>
<td align="center">Q9</td>
<td align="center">Hospital A</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">S</td>
@@ -494,16 +494,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,514</td>
<td align="right">52.57%</td>
<td align="right">10,514</td>
<td align="right">52.57%</td>
<td align="right">10,394</td>
<td align="right">51.97%</td>
<td align="right">10,394</td>
<td align="right">51.97%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,486</td>
<td align="right">47.43%</td>
<td align="right">9,606</td>
<td align="right">48.03%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@@ -616,9 +616,9 @@ 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 10,720 'phenotype-based' first isolates (53.6% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,650 'phenotype-based' first isolates (53.3% 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
<p>So only 53.3% 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">
@@ -629,25 +629,25 @@ 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 10,720 isolates for analysis. Now our data looks
<p>So we end up with 10,650 isolates for analysis. Now our data looks
like:</p>
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">data_1st</span><span class="op">)</span></span></code></pre></div>
<table class="table">
<table style="width:100%;" class="table">
<colgroup>
<col width="2%">
<col width="9%">
<col width="9%">
<col width="9%">
<col width="11%">
<col width="4%">
<col width="4%">
<col width="4%">
<col width="4%">
<col width="6%">
<col width="12%">
<col width="10%">
<col width="7%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="6%">
<col width="11%">
<col width="12%">
<col width="9%">
<col width="5%">
</colgroup>
<thead><tr class="header">
@@ -669,98 +669,98 @@ like:</p>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2016-09-06</td>
<td align="center">Z8</td>
<td align="center">2015-05-10</td>
<td align="center">P6</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</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">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">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">3</td>
<td align="center">2012-04-02</td>
<td align="center">O6</td>
<td align="center">Hospital C</td>
<td align="left">2</td>
<td align="center">2016-06-01</td>
<td align="center">N5</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">S</td>
<td align="center">F</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="odd">
<td align="left">6</td>
<td align="center">2010-02-03</td>
<td align="center">Q9</td>
<td align="center">Hospital A</td>
<td align="left">3</td>
<td align="center">2016-09-10</td>
<td align="center">H3</td>
<td align="center">Hospital C</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="left">5</td>
<td align="center">2016-10-17</td>
<td align="center">I6</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">F</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="odd">
<td align="left">8</td>
<td align="center">2012-01-16</td>
<td align="center">M3</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</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-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">10</td>
<td align="center">2010-09-27</td>
<td align="center">K3</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">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="odd">
<td align="left">12</td>
<td align="center">2016-06-26</td>
<td align="center">B2</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">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">13</td>
<td align="center">2013-06-06</td>
<td align="center">P10</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">2010-08-25</td>
<td align="center">U3</td>
<td align="center">Hospital C</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-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>
</tbody>
@@ -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: 10,720<br>
Available: 10,720 (100%, NA: 0 = 0%)<br>
Length: 10,650<br>
Available: 10,650 (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">4,594</td>
<td align="right">42.85%</td>
<td align="right">4,594</td>
<td align="right">42.85%</td>
<td align="right">4,676</td>
<td align="right">43.91%</td>
<td align="right">4,676</td>
<td align="right">43.91%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,791</td>
<td align="right">26.04%</td>
<td align="right">7,385</td>
<td align="right">68.89%</td>
<td align="right">2,721</td>
<td align="right">25.55%</td>
<td align="right">7,397</td>
<td align="right">69.46%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,113</td>
<td align="right">19.71%</td>
<td align="right">9,498</td>
<td align="right">88.60%</td>
<td align="right">2,087</td>
<td align="right">19.60%</td>
<td align="right">9,484</td>
<td align="right">89.05%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,222</td>
<td align="right">11.40%</td>
<td align="right">10,720</td>
<td align="right">1,166</td>
<td align="right">10.95%</td>
<td align="right">10,650</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@@ -897,42 +897,72 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2013-06-06</td>
<td align="center">P10</td>
<td align="center">2015-05-10</td>
<td align="center">P6</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</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-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>
<tr class="even">
<td align="center">2011-03-14</td>
<td align="center">R6</td>
<td align="center">2016-09-10</td>
<td align="center">H3</td>
<td align="center">Hospital C</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">2010-08-25</td>
<td align="center">U3</td>
<td align="center">Hospital C</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">2016-11-19</td>
<td align="center">M8</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">F</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="odd">
<td align="center">2014-10-08</td>
<td align="center">G5</td>
<td align="center">Hospital A</td>
<td align="center">2011-04-24</td>
<td align="center">H4</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">S</td>
<td align="center">R</td>
<td align="center">M</td>
@@ -942,45 +972,15 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2012-05-12</td>
<td align="center">K6</td>
<td align="center">Hospital A</td>
<td align="center">2017-11-30</td>
<td align="center">Z6</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">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">2015-11-05</td>
<td align="center">J2</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-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2015-03-24</td>
<td align="center">J7</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">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
@@ -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">2171</td>
<td align="center">107</td>
<td align="center">2316</td>
<td align="center">4594</td>
<td align="center">2239</td>
<td align="center">111</td>
<td align="center">2326</td>
<td align="center">4676</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3346</td>
<td align="center">170</td>
<td align="center">1078</td>
<td align="center">4594</td>
<td align="center">3433</td>
<td align="center">145</td>
<td align="center">1098</td>
<td align="center">4676</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3400</td>
<td align="center">3431</td>
<td align="center">0</td>
<td align="center">1194</td>
<td align="center">4594</td>
<td align="center">1245</td>
<td align="center">4676</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4025</td>
<td align="center">4066</td>
<td align="center">0</td>
<td align="center">569</td>
<td align="center">4594</td>
<td align="center">610</td>
<td align="center">4676</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">1222</td>
<td align="center">1222</td>
<td align="center">1166</td>
<td align="center">1166</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">959</td>
<td align="center">32</td>
<td align="center">231</td>
<td align="center">1222</td>
<td align="center">907</td>
<td align="center">49</td>
<td align="center">210</td>
<td align="center">1166</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">4025</td>
<td align="center">4066</td>
<td align="center">0</td>
<td align="center">569</td>
<td align="center">4594</td>
<td align="center">610</td>
<td align="center">4676</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1099</td>
<td align="center">1048</td>
<td align="center">0</td>
<td align="center">123</td>
<td align="center">1222</td>
<td align="center">118</td>
<td align="center">1166</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2456</td>
<td align="center">2385</td>
<td align="center">0</td>
<td align="center">335</td>
<td align="center">2791</td>
<td align="center">336</td>
<td align="center">2721</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">2113</td>
<td align="center">2113</td>
<td align="center">2087</td>
<td align="center">2087</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] 0.5489739</span></span></code></pre></div>
<span><span class="co"># [1] 0.544507</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">0.5351351</td>
<td align="center">0.5551767</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5533618</td>
<td align="center">0.5362818</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5506899</td>
<td align="center">0.5477707</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5601852</td>
<td align="center">0.5404235</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">0.5351351</td>
<td align="center">3145</td>
<td align="center">0.5551767</td>
<td align="center">3226</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5533618</td>
<td align="center">3748</td>
<td align="center">0.5362818</td>
<td align="center">3776</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5506899</td>
<td align="center">1667</td>
<td align="center">0.5477707</td>
<td align="center">1570</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5601852</td>
<td align="center">2160</td>
<td align="center">0.5404235</td>
<td align="center">2078</td>
</tr>
</tbody>
</table>
@@ -1227,27 +1227,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7653461</td>
<td align="center">0.8761428</td>
<td align="center">0.9775795</td>
<td align="center">0.7651839</td>
<td align="center">0.8695466</td>
<td align="center">0.9773311</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8109656</td>
<td align="center">0.8993453</td>
<td align="center">0.9836334</td>
<td align="center">0.8198971</td>
<td align="center">0.8987993</td>
<td align="center">0.9785592</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7864565</td>
<td align="center">0.8799713</td>
<td align="center">0.9774274</td>
<td align="center">0.7897832</td>
<td align="center">0.8765160</td>
<td align="center">0.9816244</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5428301</td>
<td align="center">0.5433637</td>
<td align="center">0.0000000</td>
<td align="center">0.5428301</td>
<td align="center">0.5433637</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">53.5%</td>
<td align="right">25.5%</td>
<td align="right">55.5%</td>
<td align="right">26.2%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">55.3%</td>
<td align="right">26.7%</td>
<td align="right">53.6%</td>
<td align="right">26.6%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">55.1%</td>
<td align="right">27.5%</td>
<td align="right">54.8%</td>
<td align="right">25.7%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">56.0%</td>
<td align="right">28.1%</td>
<td align="right">54.0%</td>
<td align="right">27.8%</td>
</tr>
</tbody>
</table>
@@ -1407,18 +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] &lt;=0.001 0.005 16 32 0.002 64 0.125 2 0.005 </span></span>
<span><span class="co"># [10] 8 0.002 128 0.025 &gt;=256 1 16 &gt;=256 &lt;=0.001</span></span>
<span><span class="co"># [19] 0.0625 16 0.125 16 4 0.0625 8 64 4 </span></span>
<span><span class="co"># [28] &gt;=256 0.025 &lt;=0.001 128 &gt;=256 0.125 0.002 0.125 0.0625 </span></span>
<span><span class="co"># [37] 0.005 4 0.5 128 16 0.25 &gt;=256 0.025 &gt;=256 </span></span>
<span><span class="co"># [46] 0.5 8 0.01 0.0625 0.125 0.002 2 0.01 1 </span></span>
<span><span class="co"># [55] 32 0.002 0.025 0.002 0.025 64 &lt;=0.001 0.25 0.005 </span></span>
<span><span class="co"># [64] 0.002 0.005 0.025 128 0.025 8 2 0.5 128 </span></span>
<span><span class="co"># [73] 16 0.002 &gt;=256 0.005 2 0.002 0.0625 32 &gt;=256 </span></span>
<span><span class="co"># [82] 0.5 128 4 &lt;=0.001 0.0625 16 0.0625 0.01 1 </span></span>
<span><span class="co"># [91] 64 &gt;=256 0.125 0.002 0.005 0.002 128 0.025 0.125 </span></span>
<span><span class="co"># [100] 0.005</span></span></code></pre></div>
<span><span class="co"># [1] 16 64 0.0625 4 0.025 256 0.005 128 64 0.5 </span></span>
<span><span class="co"># [11] 1 64 0.25 4 0.5 0.25 0.25 0.25 4 0.002 </span></span>
<span><span class="co"># [21] 256 1 0.125 64 0.01 1 0.002 0.002 32 0.005 </span></span>
<span><span class="co"># [31] 4 0.025 128 0.01 0.0625 0.25 0.0625 0.125 2 0.125 </span></span>
<span><span class="co"># [41] 0.005 8 0.005 8 4 0.025 128 0.25 16 1 </span></span>
<span><span class="co"># [51] 0.005 16 0.005 0.002 1 0.125 0.125 128 0.0625 0.125 </span></span>
<span><span class="co"># [61] 0.025 0.002 256 0.01 0.25 0.002 0.002 0.002 0.005 256 </span></span>
<span><span class="co"># [71] 0.0625 0.125 0.25 0.001 0.0625 4 0.025 64 0.01 8 </span></span>
<span><span class="co"># [81] 0.25 32 0.005 0.005 0.001 128 128 8 256 0.0625</span></span>
<span><span class="co"># [91] 0.005 64 0.5 0.005 2 1 0.01 4 0.5 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>
@@ -1452,10 +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] 22 28 30 31 29 30 18 29 17 21 29 22 17 19 25 23 23 30 28 31 21 17 26 26 22</span></span>
<span><span class="co"># [26] 26 31 22 25 31 28 18 27 19 18 17 29 26 23 18 27 31 18 30 17 17 19 22 28 30</span></span>
<span><span class="co"># [51] 18 21 17 24 29 29 17 26 20 26 20 22 29 21 18 30 28 17 17 21 26 29 24 30 17</span></span>
<span><span class="co"># [76] 23 27 30 25 31 27 31 19 30 30 22 27 20 31 24 25 29 30 26 22 30 26 20 30 29</span></span></code></pre></div>
<span><span class="co"># [1] 20 25 21 31 30 18 20 19 29 26 26 18 21 29 19 17 17 25 17 26 29 27 23 22 29</span></span>
<span><span class="co"># [26] 30 22 29 18 30 20 20 25 17 25 29 17 23 24 23 28 27 29 29 27 17 30 27 22 30</span></span>
<span><span class="co"># [51] 19 29 31 29 28 31 22 20 25 18 29 22 19 19 17 19 28 28 26 20 30 31 26 30 17</span></span>
<span><span class="co"># [76] 24 17 21 26 23 29 22 18 19 28 24 24 18 23 24 22 31 23 31 17 30 26 18 19 17</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>