P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-15 01:04:00 +02:00
Code Releases Activity

(v1.8.0) prerelease 1.8.0

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2021-12-23 18:56:28 +01:00
parent 3f4ff260d2
commit 25cef46c59
200 changed files with 585 additions and 588 deletions
Download Patch File Download Diff File Expand all files Collapse all files

588
docs/articles/AMR.html
View File

@ -44,7 +44,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9068</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
</span>
</div>
@ -191,7 +191,7 @@
<h1 data-toc-skip>How to conduct AMR data analysis</h1>
<h4 data-toc-skip class="author">Dr. Matthijs Berends</h4>
<h4 data-toc-skip class="date">12 December 2021</h4>
<h4 data-toc-skip class="date">23 December 2021</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="hidden name"><code>AMR.Rmd</code></div>
@ -200,7 +200,7 @@
<p><strong>Note:</strong> values on this page will change with every 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 December 2021.</p>
<p><strong>Note:</strong> values on this page will change with every 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 23 December 2021.</p>
<div class="section level1">
<h1 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h1>
@ -231,21 +231,21 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2021-12-12</td>
<td align="center">2021-12-23</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">2021-12-12</td>
<td align="center">2021-12-23</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">2021-12-12</td>
<td align="center">2021-12-23</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -342,71 +342,71 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2014-11-21</td>
<td align="center">L5</td>
<td align="center">Hospital C</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">M</td>
</tr>
<tr class="even">
<td align="center">2015-03-18</td>
<td align="center">G9</td>
<td align="center">Hospital D</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">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2011-10-31</td>
<td align="center">Z3</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">F</td>
</tr>
<tr class="even">
<td align="center">2017-05-24</td>
<td align="center">A3</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2013-01-31</td>
<td align="center">Y10</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">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2013-04-13</td>
<td align="center">L6</td>
<td align="center">2010-03-07</td>
<td align="center">U8</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">2015-08-15</td>
<td align="center">A4</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">M</td>
</tr>
<tr class="odd">
<td align="center">2012-02-22</td>
<td align="center">T7</td>
<td align="center">Hospital A</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">F</td>
</tr>
<tr class="even">
<td align="center">2017-04-28</td>
<td align="center">J10</td>
<td align="center">Hospital A</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2013-05-14</td>
<td align="center">X5</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2011-09-09</td>
<td align="center">Z1</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia 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">F</td>
</tr>
</tbody>
</table>
<p>Now, let’s start the cleaning and the analysis!</p>
@ -439,16 +439,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,451</td>
<td align="right">52.26%</td>
<td align="right">10,451</td>
<td align="right">52.26%</td>
<td align="right">10,513</td>
<td align="right">52.56%</td>
<td align="right">10,513</td>
<td align="right">52.56%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,549</td>
<td align="right">47.75%</td>
<td align="right">9,487</td>
<td align="right">47.44%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -502,7 +502,7 @@ Longest: 1</p>
<span class="co"># ℹ Using column 'patient_id' as input for `col_patient_id`.</span>
<span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span>
<span class="co"># 2</span>
<span class="co"># =&gt; Found 10,684 'phenotype-based' first isolates (53.4% of total where a</span>
<span class="co"># =&gt; Found 10,677 'phenotype-based' first isolates (53.4% of total where a</span>
<span class="co"># microbial ID was available)</span></code></pre></div>
<p>So only 53.4% 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">
@ -512,10 +512,10 @@ Longest: 1</p>
<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
<code class="sourceCode R"><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 class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
<p>So we end up with 10,684 isolates for analysis. Now our data looks like:</p>
<p>So we end up with 10,677 isolates for analysis. Now our data looks like:</p>
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
<code class="sourceCode R"><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></code></pre></div>
<table style="width:100%;" class="table">
<table class="table">
<colgroup>
<col width="2%">
<col width="9%">
@ -528,7 +528,7 @@ Longest: 1</p>
<col width="3%">
<col width="6%">
<col width="11%">
<col width="12%">
<col width="10%">
<col width="9%">
<col width="5%">
</colgroup>
@ -550,46 +550,14 @@ Longest: 1</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">2</td>
<td align="center">2015-03-18</td>
<td align="center">G9</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">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">4</td>
<td align="center">2017-05-24</td>
<td align="center">A3</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">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">5</td>
<td align="center">2013-01-31</td>
<td align="center">Y10</td>
<td align="center">Hospital C</td>
<td align="left">1</td>
<td align="center">2010-03-07</td>
<td align="center">U8</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">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
@ -598,29 +566,13 @@ Longest: 1</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">10</td>
<td align="center">2014-07-29</td>
<td align="center">G3</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">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="left">11</td>
<td align="center">2010-12-28</td>
<td align="center">G5</td>
<td align="center">Hospital B</td>
<td align="left">2</td>
<td align="center">2015-08-15</td>
<td align="center">A4</td>
<td align="center">Hospital C</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">S</td>
<td align="center">S</td>
<td align="center">M</td>
@ -629,20 +581,68 @@ Longest: 1</p>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">14</td>
<td align="center">2015-01-05</td>
<td align="center">A8</td>
<tr class="odd">
<td align="left">4</td>
<td align="center">2017-04-28</td>
<td align="center">J10</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</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="left">6</td>
<td align="center">2011-09-09</td>
<td align="center">Z1</td>
<td align="center">Hospital A</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">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">7</td>
<td align="center">2017-04-11</td>
<td align="center">I3</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">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">10</td>
<td align="center">2011-06-22</td>
<td align="center">D10</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">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>
</tbody>
@ -666,8 +666,8 @@ Longest: 1</p>
<code class="sourceCode R"><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://rdrr.io/pkg/cleaner/man/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></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 10,684<br>
Available: 10,684 (100.0%, NA: 0 = 0.0%)<br>
Length: 10,677<br>
Available: 10,677 (100.0%, NA: 0 = 0.0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -684,33 +684,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">4,660</td>
<td align="right">43.62%</td>
<td align="right">4,660</td>
<td align="right">43.62%</td>
<td align="right">4,609</td>
<td align="right">43.17%</td>
<td align="right">4,609</td>
<td align="right">43.17%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,727</td>
<td align="right">25.52%</td>
<td align="right">7,387</td>
<td align="right">2,773</td>
<td align="right">25.97%</td>
<td align="right">7,382</td>
<td align="right">69.14%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,106</td>
<td align="right">19.71%</td>
<td align="right">9,493</td>
<td align="right">88.85%</td>
<td align="right">2,087</td>
<td align="right">19.55%</td>
<td align="right">9,469</td>
<td align="right">88.69%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,191</td>
<td align="right">11.15%</td>
<td align="right">10,684</td>
<td align="right">1,208</td>
<td align="right">11.31%</td>
<td align="right">10,677</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -757,53 +757,23 @@ Longest: 24</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2017-05-24</td>
<td align="center">A3</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">2017-04-11</td>
<td align="center">I3</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">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</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">2014-07-29</td>
<td align="center">G3</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">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">2014-10-24</td>
<td align="center">S9</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">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">2012-08-31</td>
<td align="center">A1</td>
<td align="center">2013-07-04</td>
<td align="center">C4</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
@ -817,27 +787,12 @@ Longest: 24</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2016-04-25</td>
<td align="center">Z10</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">S</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">2011-04-30</td>
<td align="center">J10</td>
<td align="center">Hospital D</td>
<td align="center">2010-11-18</td>
<td align="center">F8</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
@ -846,6 +801,51 @@ Longest: 24</p>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2017-06-06</td>
<td align="center">H4</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">R</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2014-02-16</td>
<td align="center">V2</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">2013-02-16</td>
<td align="center">M1</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
<p>If you want to get a quick glance of the number of isolates in different bug/drug combinations, you can use the <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> function:</p>
@ -867,50 +867,50 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">2148</td>
<td align="center">144</td>
<td align="center">2368</td>
<td align="center">4660</td>
<td align="center">2190</td>
<td align="center">112</td>
<td align="center">2307</td>
<td align="center">4609</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3418</td>
<td align="center">162</td>
<td align="center">3359</td>
<td align="center">170</td>
<td align="center">1080</td>
<td align="center">4660</td>
<td align="center">4609</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3376</td>
<td align="center">3366</td>
<td align="center">0</td>
<td align="center">1284</td>
<td align="center">4660</td>
<td align="center">1243</td>
<td align="center">4609</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4068</td>
<td align="center">4002</td>
<td align="center">0</td>
<td align="center">592</td>
<td align="center">4660</td>
<td align="center">607</td>
<td align="center">4609</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">1191</td>
<td align="center">1191</td>
<td align="center">1208</td>
<td align="center">1208</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">947</td>
<td align="center">46</td>
<td align="center">198</td>
<td align="center">1191</td>
<td align="center">951</td>
<td align="center">35</td>
<td align="center">222</td>
<td align="center">1208</td>
</tr>
</tbody>
</table>
@ -933,34 +933,34 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4068</td>
<td align="center">4002</td>
<td align="center">0</td>
<td align="center">592</td>
<td align="center">4660</td>
<td align="center">607</td>
<td align="center">4609</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1062</td>
<td align="center">1063</td>
<td align="center">0</td>
<td align="center">129</td>
<td align="center">1191</td>
<td align="center">145</td>
<td align="center">1208</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2401</td>
<td align="center">2446</td>
<td align="center">0</td>
<td align="center">326</td>
<td align="center">2727</td>
<td align="center">327</td>
<td align="center">2773</td>
</tr>
<tr class="even">
<td align="center">S. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">0</td>
<td align="center">0</td>
<td align="center">2106</td>
<td align="center">2106</td>
<td align="center">2087</td>
<td align="center">2087</td>
</tr>
</tbody>
</table>
@ -974,7 +974,7 @@ Longest: 24</p>
<p>As per the EUCAST guideline of 2019, we calculate resistance as the proportion of R (<code><a href="../reference/proportion.html">proportion_R()</a></code>, equal to <code><a href="../reference/proportion.html">resistance()</a></code>) and susceptibility as the proportion of S and I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equal to <code><a href="../reference/proportion.html">susceptibility()</a></code>). These functions can be used on their own:</p>
<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
<code class="sourceCode R"><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 class="co"># [1] 0.5497005</span></code></pre></div>
<span class="co"># [1] 0.544254</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">
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
@ -988,19 +988,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5528455</td>
<td align="center">0.5349716</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5463890</td>
<td align="center">0.5482514</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5533333</td>
<td align="center">0.5800508</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5482679</td>
<td align="center">0.5244591</td>
</tr>
</tbody>
</table>
@ -1019,23 +1019,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5528455</td>
<td align="center">3075</td>
<td align="center">0.5349716</td>
<td align="center">3174</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5463890</td>
<td align="center">3794</td>
<td align="center">0.5482514</td>
<td align="center">3803</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5533333</td>
<td align="center">1650</td>
<td align="center">0.5800508</td>
<td align="center">1574</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5482679</td>
<td align="center">2165</td>
<td align="center">0.5244591</td>
<td align="center">2126</td>
</tr>
</tbody>
</table>
@ -1056,27 +1056,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7682403</td>
<td align="center">0.8729614</td>
<td align="center">0.9766094</td>
<td align="center">0.7656759</td>
<td align="center">0.8683011</td>
<td align="center">0.9709264</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8337531</td>
<td align="center">0.8916877</td>
<td align="center">0.9806885</td>
<td align="center">0.8162252</td>
<td align="center">0.8799669</td>
<td align="center">0.9726821</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7887789</td>
<td align="center">0.8804547</td>
<td align="center">0.9790979</td>
<td align="center">0.7991345</td>
<td align="center">0.8820772</td>
<td align="center">0.9772809</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5318139</td>
<td align="center">0.5462386</td>
<td align="center">0.0000000</td>
<td align="center">0.5318139</td>
<td align="center">0.5462386</td>
</tr>
</tbody>
</table>
@ -1101,23 +1101,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">55.3%</td>
<td align="right">26.3%</td>
<td align="right">53.5%</td>
<td align="right">26.0%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">54.6%</td>
<td align="right">27.2%</td>
<td align="right">54.8%</td>
<td align="right">26.1%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">55.3%</td>
<td align="right">25.7%</td>
<td align="right">58.0%</td>
<td align="right">28.5%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">54.8%</td>
<td align="right">26.5%</td>
<td align="right">52.4%</td>
<td align="right">25.4%</td>
</tr>
</tbody>
</table>
@ -1201,16 +1201,16 @@ Longest: 24</p>
<code class="sourceCode R"><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 class="va">mic_values</span>
<span class="co"># Class &lt;mic&gt;</span>
<span class="co"># [1] 0.0625 0.002 0.002 0.001 4 1 0.0625 32 0.5 0.5 </span>
<span class="co"># [11] 0.25 0.025 0.001 64 0.5 0.5 2 0.005 16 0.5 </span>
<span class="co"># [21] 0.25 64 4 0.002 128 0.01 64 0.25 0.01 0.005 </span>
<span class="co"># [31] 32 32 16 0.25 0.002 1 128 128 0.25 0.001 </span>
<span class="co"># [41] 0.0625 0.125 0.001 128 0.0625 0.001 1 0.25 2 0.001 </span>
<span class="co"># [51] 0.005 4 8 2 0.125 0.0625 16 0.25 64 8 </span>
<span class="co"># [61] 0.005 32 0.0625 0.01 0.002 32 8 64 16 2 </span>
<span class="co"># [71] 1 2 32 2 8 0.001 0.25 8 8 64 </span>
<span class="co"># [81] 128 0.01 0.0625 0.125 0.002 8 0.025 0.0625 0.0625 8 </span>
<span class="co"># [91] 0.005 16 4 8 0.25 0.025 8 0.002 0.25 0.25</span></code></pre></div>
<span class="co"># [1] 0.5 1 0.002 0.125 0.025 2 8 0.125 0.125 4 </span>
<span class="co"># [11] 0.0625 0.001 0.025 0.001 8 64 0.025 32 0.001 64 </span>
<span class="co"># [21] 8 0.001 16 0.5 0.0625 0.002 128 8 0.125 4 </span>
<span class="co"># [31] 0.125 64 32 0.001 0.0625 0.005 2 4 0.125 32 </span>
<span class="co"># [41] 0.125 0.5 0.0625 128 0.125 0.125 0.01 0.25 0.5 0.002 </span>
<span class="co"># [51] 8 8 0.002 0.002 0.25 256 1 8 2 2 </span>
<span class="co"># [61] 0.0625 0.005 0.005 16 0.5 0.025 16 8 8 0.0625</span>
<span class="co"># [71] 0.002 0.125 0.025 0.025 1 32 0.25 16 128 8 </span>
<span class="co"># [81] 0.0625 0.025 64 0.001 0.5 4 8 4 16 32 </span>
<span class="co"># [91] 0.005 8 0.125 256 64 0.001 1 32 0.005 0.025</span></code></pre></div>
<div class="sourceCode" id="cb37"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="co"># base R:</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></code></pre></div>
@ -1236,13 +1236,13 @@ Longest: 24</p>
<div class="sourceCode" id="cb42"><pre class="downlit sourceCode r">
<code class="sourceCode R"><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 class="co"># ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
<span class="co"># coli). Run `mo_uncertainties()` to review this uncertainty.</span>
<span class="co"># coli). Run `mo_uncertainties()` to review this.</span>
<span class="va">disk_values</span>
<span class="co"># Class &lt;disk&gt;</span>
<span class="co"># [1] 22 25 27 18 21 30 29 21 21 24 26 18 23 28 22 24 18 20 19 18 27 23 25 23 21</span>
<span class="co"># [26] 24 22 22 23 27 23 19 22 20 17 19 30 19 23 19 23 21 24 30 30 26 25 27 17 29</span>
<span class="co"># [51] 25 30 31 26 17 18 30 24 18 25 21 19 31 24 20 24 18 25 26 24 19 30 27 21 26</span>
<span class="co"># [76] 20 17 31 28 31 26 27 30 17 27 19 26 26 31 17 30 23 20 17 30 19 19 20 21 19</span></code></pre></div>
<span class="co"># [1] 29 17 17 18 17 29 28 25 21 24 30 29 20 26 21 28 22 21 28 25 25 22 29 29 27</span>
<span class="co"># [26] 19 30 19 25 28 27 26 19 16 29 20 19 25 16 27 25 19 30 23 20 20 25 23 25 17</span>
<span class="co"># [51] 19 21 20 25 19 25 22 16 29 25 25 21 29 29 28 24 30 23 22 22 31 26 20 19 30</span>
<span class="co"># [76] 30 28 26 25 26 27 16 25 27 21 29 17 31 16 27 22 19 26 20 21 19 27 21 24 27</span></code></pre></div>
<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="co"># base R:</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></code></pre></div>