P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-27 14:27:53 +02:00
Code Releases Activity

Built site for AMR: 1.8.2.9138@dad2530

Browse Source
This commit is contained in:
github-actions
2023-02-22 13:47:35 +00:00
parent 8685119254
commit 69dc8795ae
104 changed files with 827 additions and 856 deletions
Download Patch File Download Diff File Expand all files Collapse all files

569
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="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</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">
@ -187,7 +187,7 @@
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 18 February 2023.</p>
generated on 22 February 2023.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@ -243,21 +243,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2023-02-18</td>
<td align="center">2023-02-22</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">2023-02-18</td>
<td align="center">2023-02-22</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">2023-02-18</td>
<td align="center">2023-02-22</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -408,69 +408,69 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2015-08-25</td>
<td align="center">Z2</td>
<td align="center">Hospital B</td>
<td align="center">2014-12-01</td>
<td align="center">V4</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">I</td>
<td align="center">R</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2010-08-12</td>
<td align="center">I7</td>
<td align="center">Hospital C</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">2012-07-28</td>
<td align="center">V1</td>
<td align="center">Hospital B</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2011-07-03</td>
<td align="center">F3</td>
<td align="center">2012-09-30</td>
<td align="center">D9</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2015-06-20</td>
<td align="center">R4</td>
<td align="center">Hospital B</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">2011-08-02</td>
<td align="center">M4</td>
<td align="center">Hospital D</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">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2012-08-20</td>
<td align="center">U4</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">I</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2014-04-29</td>
<td align="center">J7</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2015-10-22</td>
<td align="center">H6</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">2015-05-14</td>
<td align="center">N5</td>
<td align="center">Hospital C</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
</tbody>
@ -507,16 +507,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,346</td>
<td align="right">51.73%</td>
<td align="right">10,346</td>
<td align="right">51.73%</td>
<td align="right">10,361</td>
<td align="right">51.81%</td>
<td align="right">10,361</td>
<td align="right">51.81%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,654</td>
<td align="right">48.27%</td>
<td align="right">9,639</td>
<td align="right">48.20%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -629,9 +629,9 @@ takes into account the antimicrobial susceptibility test results using
<span><span class="co">#&gt; Basing inclusion on all antimicrobial results, using a points threshold of</span></span>
<span><span class="co">#&gt; 2</span></span>
<span><span class="co">#&gt; Including isolates from ICU.</span></span>
<span><span class="co">#&gt; =&gt; Found 12,322 'phenotype-based' first isolates (61.6% of total where a</span></span>
<span><span class="co">#&gt; =&gt; Found 12,431 'phenotype-based' first isolates (62.2% of total where a</span></span>
<span><span class="co">#&gt; microbial ID was available)</span></span></code></pre></div>
<p>So only 61.6% is suitable for resistance analysis! We can now filter
<p>So only 62.2% 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">
@ -641,7 +641,7 @@ on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html"
<div class="sourceCode" id="cb16"><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>
<span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<p>So we end up with 12 322 isolates for analysis. Now our data looks
<p>So we end up with 12 431 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>
@ -680,78 +680,30 @@ like:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2014-12-01</td>
<td align="center">V4</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">I</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">2</td>
<td align="center">2011-07-03</td>
<td align="center">F3</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">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">3</td>
<td align="center">2015-06-20</td>
<td align="center">R4</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">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="odd">
<td align="left">4</td>
<td align="center">2012-08-20</td>
<td align="center">U4</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">I</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">7</td>
<td align="center">2017-10-28</td>
<td align="center">J6</td>
<td align="center">Hospital B</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">8</td>
<td align="center">2017-08-19</td>
<td align="center">I1</td>
<td align="center">Hospital D</td>
<td align="center">2010-08-12</td>
<td align="center">I7</td>
<td align="center">Hospital C</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">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
@ -759,22 +711,70 @@ like:</p>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">9</td>
<td align="center">2017-07-16</td>
<td align="center">S8</td>
<tr class="odd">
<td align="left">3</td>
<td align="center">2012-07-28</td>
<td align="center">V1</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</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="even">
<td align="left">6</td>
<td align="center">2015-05-14</td>
<td align="center">N5</td>
<td align="center">Hospital C</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">I</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">7</td>
<td align="center">2011-03-07</td>
<td align="center">X4</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">8</td>
<td align="center">2016-11-12</td>
<td align="center">T7</td>
<td align="center">Hospital A</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</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>
@ -808,8 +808,8 @@ 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: 12,322<br>
Available: 12,322 (100%, NA: 0 = 0%)<br>
Length: 12,431<br>
Available: 12,431 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -834,33 +834,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">5,843</td>
<td align="right">47.42%</td>
<td align="right">5,843</td>
<td align="right">47.42%</td>
<td align="right">5,970</td>
<td align="right">48.03%</td>
<td align="right">5,970</td>
<td align="right">48.03%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,319</td>
<td align="right">26.94%</td>
<td align="right">9,162</td>
<td align="right">74.35%</td>
<td align="right">3,335</td>
<td align="right">26.83%</td>
<td align="right">9,305</td>
<td align="right">74.85%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">1,857</td>
<td align="right">15.07%</td>
<td align="right">11,019</td>
<td align="right">89.43%</td>
<td align="right">1,817</td>
<td align="right">14.62%</td>
<td align="right">11,122</td>
<td align="right">89.47%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,303</td>
<td align="right">10.57%</td>
<td align="right">12,322</td>
<td align="right">1,309</td>
<td align="right">10.53%</td>
<td align="right">12,431</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -909,41 +909,11 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2015-06-20</td>
<td align="center">R4</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2014-01-08</td>
<td align="center">V3</td>
<td align="center">Hospital C</td>
<td align="center">B_STPHY_AURS</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">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2013-07-30</td>
<td align="center">Y4</td>
<td align="center">Hospital B</td>
<td align="center">2014-12-01</td>
<td align="center">V4</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">R</td>
@ -954,13 +924,58 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2013-03-23</td>
<td align="center">E6</td>
<td align="center">Hospital A</td>
<td align="center">2012-07-28</td>
<td align="center">V1</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">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">2016-08-30</td>
<td align="center">Q3</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2013-03-03</td>
<td align="center">F7</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">I</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="center">2010-10-30</td>
<td align="center">H10</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
@ -968,36 +983,21 @@ antibiotic class they are in:</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2013-12-04</td>
<td align="center">S8</td>
<td align="center">Hospital B</td>
<tr class="even">
<td align="center">2011-04-07</td>
<td align="center">D8</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">R</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="even">
<td align="center">2013-02-27</td>
<td align="center">Z2</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">I</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>
</tbody>
</table>
<p>If you want to get a quick glance of the number of isolates in
@ -1020,50 +1020,50 @@ different bug/drug combinations, you can use the
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">2759</td>
<td align="center">1167</td>
<td align="center">1917</td>
<td align="center">5843</td>
<td align="center">2855</td>
<td align="center">1161</td>
<td align="center">1954</td>
<td align="center">5970</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">1459</td>
<td align="center">1245</td>
<td align="center">3139</td>
<td align="center">5843</td>
<td align="center">1518</td>
<td align="center">1282</td>
<td align="center">3170</td>
<td align="center">5970</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">2071</td>
<td align="center">1788</td>
<td align="center">1984</td>
<td align="center">5843</td>
<td align="center">2087</td>
<td align="center">1796</td>
<td align="center">2087</td>
<td align="center">5970</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">2002</td>
<td align="center">1833</td>
<td align="center">2008</td>
<td align="center">5843</td>
<td align="center">2119</td>
<td align="center">1854</td>
<td align="center">1997</td>
<td align="center">5970</td>
</tr>
<tr class="odd">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">583</td>
<td align="center">292</td>
<td align="center">428</td>
<td align="center">1303</td>
<td align="center">615</td>
<td align="center">256</td>
<td align="center">438</td>
<td align="center">1309</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMX</td>
<td align="center">0</td>
<td align="center">0</td>
<td align="center">1303</td>
<td align="center">1303</td>
<td align="center">1309</td>
<td align="center">1309</td>
</tr>
</tbody>
</table>
@ -1085,34 +1085,34 @@ 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">2002</td>
<td align="center">1833</td>
<td align="center">2008</td>
<td align="center">5843</td>
<td align="center">2119</td>
<td align="center">1854</td>
<td align="center">1997</td>
<td align="center">5970</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">456</td>
<td align="center">423</td>
<td align="center">424</td>
<td align="center">1303</td>
<td align="center">409</td>
<td align="center">444</td>
<td align="center">1309</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">1144</td>
<td align="center">1045</td>
<td align="center">1130</td>
<td align="center">3319</td>
<td align="center">1122</td>
<td align="center">1075</td>
<td align="center">1138</td>
<td align="center">3335</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">1857</td>
<td align="center">1857</td>
<td align="center">1817</td>
<td align="center">1817</td>
</tr>
</tbody>
</table>
@ -1144,7 +1144,7 @@ I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equa
own:</p>
<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span></span>
<span><span class="co">#&gt; [1] 0.5842396</span></span></code></pre></div>
<span><span class="co">#&gt; [1] 0.5810474</span></span></code></pre></div>
<p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and
<code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
@ -1159,19 +1159,19 @@ own:</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5827676</td>
<td align="center">0.5871733</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5907183</td>
<td align="center">0.5822430</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5845813</td>
<td align="center">0.5788635</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5747605</td>
<td align="center">0.5717638</td>
</tr>
</tbody>
</table>
@ -1196,23 +1196,23 @@ 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">0.5827676</td>
<td align="center">3830</td>
<td align="center">0.5871733</td>
<td align="center">3711</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5907183</td>
<td align="center">4288</td>
<td align="center">0.5822430</td>
<td align="center">4280</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5845813</td>
<td align="center">1803</td>
<td align="center">0.5788635</td>
<td align="center">1883</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5747605</td>
<td align="center">2401</td>
<td align="center">0.5717638</td>
<td align="center">2557</td>
</tr>
</tbody>
</table>
@ -1237,27 +1237,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.6719151</td>
<td align="center">0.6563409</td>
<td align="center">0.8921787</td>
<td align="center">0.6726968</td>
<td align="center">0.6654941</td>
<td align="center">0.8934673</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.6715272</td>
<td align="center">0.6745971</td>
<td align="center">0.8879509</td>
<td align="center">0.6653934</td>
<td align="center">0.6608098</td>
<td align="center">0.8800611</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.6776137</td>
<td align="center">0.6595360</td>
<td align="center">0.8945466</td>
<td align="center">0.6773613</td>
<td align="center">0.6587706</td>
<td align="center">0.8917541</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.4717286</td>
<td align="center">0.4777105</td>
<td align="center">0.0000000</td>
<td align="center">0.4717286</td>
<td align="center">0.4777105</td>
</tr>
</tbody>
</table>
@ -1285,23 +1285,23 @@ classes, use a antibiotic class selector such as
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">58.3%</td>
<td align="right">35.1%</td>
<td align="right">58.7%</td>
<td align="right">36.2%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">59.1%</td>
<td align="right">35.8%</td>
<td align="right">58.2%</td>
<td align="right">35.9%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">58.5%</td>
<td align="right">37.4%</td>
<td align="right">57.9%</td>
<td align="right">34.9%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">57.5%</td>
<td align="right">34.9%</td>
<td align="right">57.2%</td>
<td align="right">34.5%</td>
</tr>
</tbody>
</table>
@ -1417,16 +1417,16 @@ 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">#&gt; Class 'mic'</span></span>
<span><span class="co">#&gt; [1] 0.25 0.5 0.125 0.125 16 32 0.002 &gt;=256 0.025 1 </span></span>
<span><span class="co">#&gt; [11] 64 128 32 0.25 0.5 0.0625 128 &gt;=256 8 0.002 </span></span>
<span><span class="co">#&gt; [21] 0.005 0.002 4 0.125 0.005 0.125 0.01 4 64 0.005 </span></span>
<span><span class="co">#&gt; [31] 32 0.002 0.25 0.002 0.0625 32 16 128 0.001 128 </span></span>
<span><span class="co">#&gt; [41] 0.001 0.5 0.025 0.5 128 4 0.005 0.25 0.125 0.002 </span></span>
<span><span class="co">#&gt; [51] 16 0.025 0.005 0.0625 4 32 0.005 4 0.025 0.001 </span></span>
<span><span class="co">#&gt; [61] 128 0.125 0.025 2 4 0.0625 0.001 8 0.25 0.025 </span></span>
<span><span class="co">#&gt; [71] 1 32 &gt;=256 1 16 8 0.0625 0.01 2 0.005 </span></span>
<span><span class="co">#&gt; [81] 16 0.025 1 0.002 128 0.002 0.5 8 8 64 </span></span>
<span><span class="co">#&gt; [91] 128 0.01 0.005 16 0.002 0.005 &gt;=256 8 0.002 0.25</span></span></code></pre></div>
<span><span class="co">#&gt; [1] 0.0625 0.125 16 0.025 0.005 128 8 4 0.002 32 </span></span>
<span><span class="co">#&gt; [11] 64 0.5 0.025 0.01 8 0.002 0.5 1 0.125 0.001 </span></span>
<span><span class="co">#&gt; [21] 0.005 0.025 0.005 0.125 0.001 128 0.01 2 64 128 </span></span>
<span><span class="co">#&gt; [31] 8 1 1 128 8 4 16 0.5 0.25 0.25 </span></span>
<span><span class="co">#&gt; [41] 16 256 0.002 8 0.025 0.5 128 8 256 64 </span></span>
<span><span class="co">#&gt; [51] 0.025 128 0.025 0.001 1 0.002 0.125 0.001 256 0.01 </span></span>
<span><span class="co">#&gt; [61] 64 0.0625 0.025 16 0.5 0.125 256 1 1 128 </span></span>
<span><span class="co">#&gt; [71] 32 0.01 0.01 0.0625 128 4 16 0.005 256 8 </span></span>
<span><span class="co">#&gt; [81] 8 0.005 0.01 0.025 32 64 1 0.005 128 0.25 </span></span>
<span><span class="co">#&gt; [91] 16 0.001 0.5 0.001 0.25 0.0625 2 2 0.001 0.125</span></span></code></pre></div>
<div class="sourceCode" id="cb36"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">mic_values</span><span class="op">)</span></span></code></pre></div>
@ -1438,7 +1438,8 @@ classes) <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code>:</p>
<p>But we could also be more specific, by generating MICs that are
likely to be found in <em>E. coli</em> for ciprofloxacin:</p>
<div class="sourceCode" id="cb38"><pre class="downlit sourceCode r">
<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>, 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>
<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>, 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="co">#&gt; [1] "here"</span></span></code></pre></div>
<p>For the <code><a href="../reference/plot.html">plot()</a></code> and <code><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot()</a></code> function, we
can define the microorganism and an antimicrobial agent the same way.
This will add the interpretation of those values according to a chosen
@ -1460,10 +1461,10 @@ 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">#&gt; Class 'disk'</span></span>
<span><span class="co">#&gt; [1] 28 18 29 27 31 26 27 30 31 18 30 25 17 20 20 31 22 22 30 26 24 26 23 28 28</span></span>
<span><span class="co">#&gt; [26] 24 27 29 20 30 25 25 25 22 23 27 27 23 29 27 23 20 19 23 23 18 29 21 31 29</span></span>
<span><span class="co">#&gt; [51] 19 31 27 27 31 20 22 28 31 19 21 30 28 21 24 21 20 20 19 27 26 30 19 24 29</span></span>
<span><span class="co">#&gt; [76] 17 26 18 27 23 19 29 24 27 27 20 25 28 17 21 29 29 17 22 20 26 24 23 17 25</span></span></code></pre></div>
<span><span class="co">#&gt; [1] 27 29 20 31 27 23 30 27 19 24 31 20 19 28 23 25 17 22 20 24 24 28 17 29 26</span></span>
<span><span class="co">#&gt; [26] 29 31 23 23 30 18 29 30 23 21 19 25 24 22 18 28 25 24 18 25 25 27 24 24 27</span></span>
<span><span class="co">#&gt; [51] 27 18 18 25 22 27 30 24 31 26 19 30 21 22 23 19 23 23 22 26 22 29 29 29 29</span></span>
<span><span class="co">#&gt; [76] 26 26 24 30 17 30 17 25 27 17 27 20 23 17 21 17 27 18 23 30 19 22 20 30 17</span></span></code></pre></div>
<div class="sourceCode" id="cb42"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">disk_values</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></code></pre></div>