P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-27 17:07:54 +02:00
Code Releases Activity

Built site for AMR: 1.8.1.9026@e05d036

Browse Source
This commit is contained in:
github-actions
2022-08-25 17:30:35 +00:00
parent bcd6e333f0
commit f08c645b0c
92 changed files with 445 additions and 843 deletions
Download Patch File Download Diff File Expand all files Collapse all files

565
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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -111,11 +111,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
</li>
<li class="nav-item">
@ -167,7 +162,7 @@
<img src="../logo.svg" class="logo" alt=""><h1>How to conduct AMR data analysis</h1>
<h4 data-toc-skip class="author">Dr. Matthijs Berends</h4>
<h4 data-toc-skip class="date">21 August 2022</h4>
<h4 data-toc-skip class="date">25 August 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 +170,7 @@
<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 21 August 2022.</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 25 August 2022.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@ -206,21 +201,21 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2022-08-21</td>
<td align="center">2022-08-25</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">2022-08-21</td>
<td align="center">2022-08-25</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">2022-08-21</td>
<td align="center">2022-08-25</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -317,71 +312,71 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2011-06-19</td>
<td align="center">N8</td>
<td align="center">2010-03-22</td>
<td align="center">I8</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2012-04-13</td>
<td align="center">G1</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">R</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2014-11-21</td>
<td align="center">D5</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia 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">F</td>
</tr>
<tr class="even">
<td align="center">2013-07-08</td>
<td align="center">U10</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="odd">
<td align="center">2015-07-14</td>
<td align="center">N3</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">M</td>
</tr>
<tr class="even">
<td align="center">2014-07-29</td>
<td align="center">J1</td>
<td align="center">Hospital B</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2015-03-05</td>
<td align="center">A9</td>
<td align="center">Hospital C</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">M</td>
</tr>
<tr class="even">
<td align="center">2017-10-20</td>
<td align="center">P10</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">M</td>
</tr>
<tr class="even">
<td align="center">2010-01-18</td>
<td align="center">T4</td>
<td align="center">Hospital C</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2012-07-14</td>
<td align="center">M9</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="even">
<td align="center">2010-02-17</td>
<td align="center">H3</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia 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>
</tr>
</tbody>
</table>
<p>Now, let’s start the cleaning and the analysis!</p>
@ -414,16 +409,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,328</td>
<td align="right">51.64%</td>
<td align="right">10,328</td>
<td align="right">51.64%</td>
<td align="right">10,334</td>
<td align="right">51.67%</td>
<td align="right">10,334</td>
<td align="right">51.67%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,672</td>
<td align="right">48.36%</td>
<td align="right">9,666</td>
<td align="right">48.33%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -477,9 +472,9 @@ Longest: 1</p>
<span><span class="co"># ℹ Using column 'patient_id' as input for `col_patient_id`.</span></span>
<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"># =&gt; Found 10,619 'phenotype-based' first isolates (53.1% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,754 'phenotype-based' first isolates (53.8% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 53.1% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
<p>So only 53.8% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">first</span> <span class="op">==</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
@ -487,10 +482,10 @@ Longest: 1</p>
<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 10,619 isolates for analysis. Now our data looks like:</p>
<p>So we end up with 10,754 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 style="width:100%;" class="table">
<table class="table">
<colgroup>
<col width="2%">
<col width="9%">
@ -503,7 +498,7 @@ Longest: 1</p>
<col width="3%">
<col width="6%">
<col width="11%">
<col width="12%">
<col width="11%">
<col width="9%">
<col width="5%">
</colgroup>
@ -525,74 +520,26 @@ Longest: 1</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">5</td>
<td align="center">2015-03-05</td>
<td align="center">A9</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">6</td>
<td align="center">2017-10-20</td>
<td align="center">P10</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">S</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="left">8</td>
<td align="center">2013-03-11</td>
<td align="center">S7</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">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="even">
<td align="left">9</td>
<td align="center">2012-06-14</td>
<td align="center">I1</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">10</td>
<td align="center">2010-11-23</td>
<td align="center">V10</td>
<td align="left">2</td>
<td align="center">2012-04-13</td>
<td align="center">G1</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">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">4</td>
<td align="center">2010-01-18</td>
<td align="center">T4</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
@ -604,17 +551,65 @@ Longest: 1</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">6</td>
<td align="center">2010-02-17</td>
<td align="center">H3</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="even">
<td align="left">13</td>
<td align="center">2012-03-06</td>
<td align="center">R5</td>
<td align="left">7</td>
<td align="center">2013-01-04</td>
<td align="center">C5</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">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">10</td>
<td align="center">2014-12-10</td>
<td align="center">G7</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">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="left">11</td>
<td align="center">2015-10-09</td>
<td align="center">B3</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
@ -641,8 +636,8 @@ Longest: 1</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://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></span></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 10,619<br>
Available: 10,619 (100.0%, NA: 0 = 0.0%)<br>
Length: 10,754<br>
Available: 10,754 (100.0%, NA: 0 = 0.0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -659,33 +654,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">4,632</td>
<td align="right">43.62%</td>
<td align="right">4,632</td>
<td align="right">43.62%</td>
<td align="right">4,654</td>
<td align="right">43.28%</td>
<td align="right">4,654</td>
<td align="right">43.28%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,742</td>
<td align="right">25.82%</td>
<td align="right">7,374</td>
<td align="right">69.44%</td>
<td align="right">2,782</td>
<td align="right">25.87%</td>
<td align="right">7,436</td>
<td align="right">69.15%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,062</td>
<td align="right">19.42%</td>
<td align="right">9,436</td>
<td align="right">88.86%</td>
<td align="right">2,109</td>
<td align="right">19.61%</td>
<td align="right">9,545</td>
<td align="right">88.76%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,183</td>
<td align="right">11.14%</td>
<td align="right">10,619</td>
<td align="right">1,209</td>
<td align="right">11.24%</td>
<td align="right">10,754</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -704,14 +699,14 @@ Longest: 24</p>
<col width="9%">
<col width="9%">
<col width="9%">
<col width="10%">
<col width="11%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="6%">
<col width="11%">
<col width="12%">
<col width="11%">
<col width="9%">
<col width="5%">
</colgroup>
@ -732,9 +727,24 @@ Longest: 24</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2010-11-23</td>
<td align="center">V10</td>
<td align="center">2012-04-13</td>
<td align="center">G1</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">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="center">2010-01-18</td>
<td align="center">T4</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
@ -746,24 +756,24 @@ Longest: 24</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2011-11-01</td>
<td align="center">B1</td>
<tr class="odd">
<td align="center">2014-06-06</td>
<td align="center">Y10</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">R</td>
<td align="center">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">2017-01-30</td>
<td align="center">H5</td>
<tr class="even">
<td align="center">2011-12-29</td>
<td align="center">J7</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
@ -776,43 +786,28 @@ Longest: 24</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2015-12-11</td>
<td align="center">I5</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<tr class="odd">
<td align="center">2010-05-28</td>
<td align="center">C3</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">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">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2017-08-04</td>
<td align="center">O3</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">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2014-10-06</td>
<td align="center">V8</td>
<td align="center">Hospital A</td>
<td align="center">2012-12-04</td>
<td align="center">V6</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">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
@ -842,50 +837,50 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">2203</td>
<td align="center">123</td>
<td align="center">2306</td>
<td align="center">4632</td>
<td align="center">2225</td>
<td align="center">122</td>
<td align="center">2307</td>
<td align="center">4654</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3385</td>
<td align="center">145</td>
<td align="center">1102</td>
<td align="center">4632</td>
<td align="center">3423</td>
<td align="center">151</td>
<td align="center">1080</td>
<td align="center">4654</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3390</td>
<td align="center">3411</td>
<td align="center">0</td>
<td align="center">1242</td>
<td align="center">4632</td>
<td align="center">1243</td>
<td align="center">4654</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4049</td>
<td align="center">4041</td>
<td align="center">0</td>
<td align="center">583</td>
<td align="center">4632</td>
<td align="center">613</td>
<td align="center">4654</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">1183</td>
<td align="center">1183</td>
<td align="center">1209</td>
<td align="center">1209</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">929</td>
<td align="center">948</td>
<td align="center">54</td>
<td align="center">200</td>
<td align="center">1183</td>
<td align="center">207</td>
<td align="center">1209</td>
</tr>
</tbody>
</table>
@ -908,34 +903,34 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4049</td>
<td align="center">4041</td>
<td align="center">0</td>
<td align="center">583</td>
<td align="center">4632</td>
<td align="center">613</td>
<td align="center">4654</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1078</td>
<td align="center">1069</td>
<td align="center">0</td>
<td align="center">105</td>
<td align="center">1183</td>
<td align="center">140</td>
<td align="center">1209</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2430</td>
<td align="center">2474</td>
<td align="center">0</td>
<td align="center">312</td>
<td align="center">2742</td>
<td align="center">308</td>
<td align="center">2782</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">2062</td>
<td align="center">2062</td>
<td align="center">2109</td>
<td align="center">2109</td>
</tr>
</tbody>
</table>
@ -949,7 +944,7 @@ 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><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] 0.5432715</span></span></code></pre></div>
<span><span class="co"># [1] 0.5432397</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">
<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>
@ -963,19 +958,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5382868</td>
<td align="center">0.5458167</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5447543</td>
<td align="center">0.5334954</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5595602</td>
<td align="center">0.5404571</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5353630</td>
<td align="center">0.5580645</td>
</tr>
</tbody>
</table>
@ -994,23 +989,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5382868</td>
<td align="center">3082</td>
<td align="center">0.5458167</td>
<td align="center">3263</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5447543</td>
<td align="center">3765</td>
<td align="center">0.5334954</td>
<td align="center">3702</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5595602</td>
<td align="center">1637</td>
<td align="center">0.5404571</td>
<td align="center">1619</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5353630</td>
<td align="center">2135</td>
<td align="center">0.5580645</td>
<td align="center">2170</td>
</tr>
</tbody>
</table>
@ -1031,27 +1026,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7620898</td>
<td align="center">0.8741364</td>
<td align="center">0.9771157</td>
<td align="center">0.7679416</td>
<td align="center">0.8682853</td>
<td align="center">0.9735711</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8309383</td>
<td align="center">0.9112426</td>
<td align="center">0.9805579</td>
<td align="center">0.8287841</td>
<td align="center">0.8842018</td>
<td align="center">0.9809760</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7884756</td>
<td align="center">0.8862144</td>
<td align="center">0.9817651</td>
<td align="center">0.7890007</td>
<td align="center">0.8892883</td>
<td align="center">0.9780733</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5354025</td>
<td align="center">0.5372214</td>
<td align="center">0.0000000</td>
<td align="center">0.5354025</td>
<td align="center">0.5372214</td>
</tr>
</tbody>
</table>
@ -1076,23 +1071,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">53.8%</td>
<td align="right">26.2%</td>
<td align="right">54.6%</td>
<td align="right">26.9%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">54.5%</td>
<td align="right">27.0%</td>
<td align="right">53.3%</td>
<td align="right">25.9%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">56.0%</td>
<td align="right">27.9%</td>
<td align="right">54.0%</td>
<td align="right">25.6%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">53.5%</td>
<td align="right">26.1%</td>
<td align="right">55.8%</td>
<td align="right">27.5%</td>
</tr>
</tbody>
</table>
@ -1176,16 +1171,16 @@ Longest: 24</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 &lt;mic&gt;</span></span>
<span><span class="co"># [1] 256 16 0.002 0.025 8 0.025 32 0.025 0.01 256 </span></span>
<span><span class="co"># [11] 16 0.01 32 0.025 0.01 0.0625 2 0.25 128 0.005 </span></span>
<span><span class="co"># [21] 0.01 16 0.125 0.25 0.01 0.001 8 0.025 8 1 </span></span>
<span><span class="co"># [31] 0.025 0.25 0.0625 256 0.001 0.025 0.001 8 0.01 0.025 </span></span>
<span><span class="co"># [41] 0.25 8 64 8 0.25 4 1 0.0625 0.0625 0.5 </span></span>
<span><span class="co"># [51] 2 0.002 16 0.002 0.01 16 0.25 64 8 256 </span></span>
<span><span class="co"># [61] 0.005 0.0625 1 64 64 0.5 128 0.002 32 0.002 </span></span>
<span><span class="co"># [71] 128 128 0.5 0.002 0.25 0.5 0.125 1 16 64 </span></span>
<span><span class="co"># [81] 128 32 0.025 128 16 32 32 32 0.002 0.125 </span></span>
<span><span class="co"># [91] 0.5 0.0625 0.5 128 0.125 128 8 0.25 128 0.25</span></span></code></pre></div>
<span><span class="co"># [1] 2 0.01 128 2 128 0.001 0.025 0.5 2 0.025 </span></span>
<span><span class="co"># [11] 0.0625 0.125 256 0.125 4 256 4 4 0.0625 256 </span></span>
<span><span class="co"># [21] 0.125 2 64 16 0.5 0.5 0.0625 4 256 1 </span></span>
<span><span class="co"># [31] 0.005 0.125 0.002 4 32 0.01 0.01 0.002 0.25 0.125 </span></span>
<span><span class="co"># [41] 0.025 0.01 64 32 0.001 0.5 16 32 0.5 0.01 </span></span>
<span><span class="co"># [51] 0.001 4 0.001 16 8 0.001 4 0.25 64 0.002 </span></span>
<span><span class="co"># [61] 0.01 32 0.005 0.25 4 0.002 0.002 16 32 1 </span></span>
<span><span class="co"># [71] 0.0625 32 0.001 256 0.25 2 0.025 4 0.0625 16 </span></span>
<span><span class="co"># [81] 0.002 32 256 0.0625 0.125 0.001 128 0.001 0.01 64 </span></span>
<span><span class="co"># [91] 2 64 1 256 0.01 8 32 8 128 0.002</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>
@ -1214,10 +1209,10 @@ Longest: 24</p>
<span><span class="co"># coli). Run `mo_uncertainties()` to review this.</span></span>
<span><span class="va">disk_values</span></span>
<span><span class="co"># Class &lt;disk&gt;</span></span>
<span><span class="co"># [1] 23 21 25 21 18 21 18 19 23 26 28 30 20 21 17 17 27 26 31 30 25 17 27 27 19</span></span>
<span><span class="co"># [26] 31 23 23 23 22 20 26 17 24 29 26 24 25 29 22 22 29 26 22 24 25 26 18 31 24</span></span>
<span><span class="co"># [51] 25 28 26 27 19 21 21 29 27 21 27 21 18 17 20 20 17 25 30 20 19 20 23 27 31</span></span>
<span><span class="co"># [76] 24 31 24 22 26 19 19 20 20 25 17 21 22 30 25 23 26 31 20 30 18 29 18 29 17</span></span></code></pre></div>
<span><span class="co"># [1] 25 31 18 30 19 28 18 31 17 30 31 30 20 20 25 18 30 28 18 22 25 28 17 21 22</span></span>
<span><span class="co"># [26] 22 29 30 28 29 19 21 21 30 21 28 22 19 27 26 31 21 22 31 31 29 28 31 27 28</span></span>
<span><span class="co"># [51] 28 30 24 27 21 23 26 23 22 19 25 21 30 25 26 29 31 18 18 21 26 23 19 18 24</span></span>
<span><span class="co"># [76] 20 30 28 22 31 21 28 28 24 23 21 24 17 28 18 29 28 31 21 23 24 19 17 29 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>

BIN
articles/AMR_files/figure-html/disk_plots-1.png
View File

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 38 KiB

After

Width:  |  Height:  |  Size: 38 KiB

BIN
articles/AMR_files/figure-html/disk_plots_mo_ab-1.png
View File

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 52 KiB

After

Width:  |  Height:  |  Size: 50 KiB

BIN
articles/AMR_files/figure-html/mic_plots-1.png
View File

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 27 KiB

After

Width:  |  Height:  |  Size: 27 KiB

BIN
articles/AMR_files/figure-html/mic_plots-2.png
View File

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 36 KiB

After

Width:  |  Height:  |  Size: 36 KiB

BIN
articles/AMR_files/figure-html/mic_plots_mo_ab-1.png
View File

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 38 KiB

After

Width:  |  Height:  |  Size: 37 KiB

BIN
articles/AMR_files/figure-html/mic_plots_mo_ab-2.png
View File

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 49 KiB

After

Width:  |  Height:  |  Size: 50 KiB

BIN
articles/AMR_files/figure-html/plot 1-1.png
View File

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 42 KiB

After

Width:  |  Height:  |  Size: 42 KiB

BIN
articles/AMR_files/figure-html/plot 3-1.png
View File

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 28 KiB

After

Width:  |  Height:  |  Size: 28 KiB

BIN
articles/AMR_files/figure-html/plot 4-1.png
View File

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 76 KiB

After

Width:  |  Height:  |  Size: 76 KiB

BIN
articles/AMR_files/figure-html/plot 5-1.png
View File

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 49 KiB

After

Width:  |  Height:  |  Size: 49 KiB

7
articles/EUCAST.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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -111,11 +111,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
</li>
<li class="nav-item">

59
articles/MDR.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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -111,11 +111,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
</li>
<li class="nav-item">
@ -313,19 +308,19 @@ Unique: 2</p>
<div class="sourceCode" id="cb8"><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">my_TB_data</span><span class="op">)</span></span>
<span><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
<span><span class="co"># 1 S S R I R I</span></span>
<span><span class="co"># 2 I R S S S S</span></span>
<span><span class="co"># 3 I R S I S S</span></span>
<span><span class="co"># 4 R I S I S R</span></span>
<span><span class="co"># 5 I I S R S R</span></span>
<span><span class="co"># 6 S I S S R R</span></span>
<span><span class="co"># 1 R S I R I I</span></span>
<span><span class="co"># 2 S R R S R S</span></span>
<span><span class="co"># 3 R R S R S S</span></span>
<span><span class="co"># 4 I R S R I I</span></span>
<span><span class="co"># 5 S R S I S I</span></span>
<span><span class="co"># 6 R S R R S R</span></span>
<span><span class="co"># kanamycin</span></span>
<span><span class="co"># 1 S</span></span>
<span><span class="co"># 1 R</span></span>
<span><span class="co"># 2 S</span></span>
<span><span class="co"># 3 I</span></span>
<span><span class="co"># 4 R</span></span>
<span><span class="co"># 5 I</span></span>
<span><span class="co"># 6 S</span></span></code></pre></div>
<span><span class="co"># 6 R</span></span></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can use:</p>
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/mdro.html">mdro</a></span><span class="op">(</span><span class="va">my_TB_data</span>, guideline <span class="op">=</span> <span class="st">"TB"</span><span class="op">)</span></span></code></pre></div>
@ -356,40 +351,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3182</td>
<td align="right">63.64%</td>
<td align="right">3182</td>
<td align="right">63.64%</td>
<td align="right">3214</td>
<td align="right">64.28%</td>
<td align="right">3214</td>
<td align="right">64.28%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">993</td>
<td align="right">19.86%</td>
<td align="right">4175</td>
<td align="right">83.50%</td>
<td align="right">977</td>
<td align="right">19.54%</td>
<td align="right">4191</td>
<td align="right">83.82%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">477</td>
<td align="right">9.54%</td>
<td align="right">4652</td>
<td align="right">93.04%</td>
<td align="right">450</td>
<td align="right">9.00%</td>
<td align="right">4641</td>
<td align="right">92.82%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">250</td>
<td align="right">5.00%</td>
<td align="right">4902</td>
<td align="right">98.04%</td>
<td align="right">255</td>
<td align="right">5.10%</td>
<td align="right">4896</td>
<td align="right">97.92%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">98</td>
<td align="right">1.96%</td>
<td align="right">104</td>
<td align="right">2.08%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

7
articles/PCA.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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -111,11 +111,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
</li>
<li class="nav-item">

9
articles/SPSS.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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -111,11 +111,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
</li>
<li class="nav-item">
@ -167,7 +162,7 @@
<img src="../logo.svg" class="logo" alt=""><h1>How to import data from SPSS / SAS / Stata</h1>
<h4 data-toc-skip class="author">Dr. Matthijs Berends</h4>
<h4 data-toc-skip class="date">21 August 2022</h4>
<h4 data-toc-skip class="date">25 August 2022</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/SPSS.Rmd" class="external-link"><code>vignettes/SPSS.Rmd</code></a></small>
<div class="d-none name"><code>SPSS.Rmd</code></div>

7
articles/WHONET.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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -111,11 +111,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
</li>
<li class="nav-item">

23
articles/datasets.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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -111,11 +111,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
</li>
<li class="nav-item">
@ -166,7 +161,7 @@
<main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
<h4 data-toc-skip class="date">21 August 2022</h4>
<h4 data-toc-skip class="date">25 August 2022</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<div class="d-none name"><code>datasets.Rmd</code></div>
@ -184,7 +179,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</h2>
<p>A data set with 70,764 rows and 16 columns, containing the following column names:<br><em>mo</em>, <em>fullname</em>, <em>kingdom</em>, <em>phylum</em>, <em>class</em>, <em>order</em>, <em>family</em>, <em>genus</em>, <em>species</em>, <em>subspecies</em>, <em>rank</em>, <em>ref</em>, <em>species_id</em>, <em>source</em>, <em>prevalence</em> and <em>snomed</em>.</p>
<p>This data set is in R available as <code>microorganisms</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 21 August 2022 15:23:37 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
<p>It was last updated on 25 August 2022 17:23:20 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.rds" class="external-link">R file</a> (1.3 MB)<br>
@ -405,7 +400,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
<p>A data set with 14,338 rows and 4 columns, containing the following column names:<br><em>fullname</em>, <em>fullname_new</em>, <em>ref</em> and <em>prevalence</em>.</p>
<p><strong>Note:</strong> remember that the ‘ref’ columns contains the scientific reference to the old taxonomic entries, i.e. of column <em>‘fullname’</em>. For the scientific reference of the new names, i.e. of column <em>‘fullname_new’</em>, see the <code>microorganisms</code> data set.</p>
<p>This data set is in R available as <code>microorganisms.old</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 21 August 2022 15:23:37 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.old.html">here</a>.</p>
<p>It was last updated on 25 August 2022 17:23:20 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.old.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.rds" class="external-link">R file</a> (0.2 MB)<br>
@ -470,7 +465,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</h2>
<p>A data set with 464 rows and 14 columns, containing the following column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>atc</em>, <em>atc_group1</em>, <em>atc_group2</em>, <em>abbreviations</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em>, <em>iv_units</em> and <em>loinc</em>.</p>
<p>This data set is in R available as <code>antibiotics</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 21 August 2022 15:23:37 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p>It was last updated on 25 August 2022 17:23:20 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.rds" class="external-link">R file</a> (33 kB)<br>
@ -638,7 +633,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</h2>
<p>A data set with 102 rows and 9 columns, containing the following column names:<br><em>atc</em>, <em>cid</em>, <em>name</em>, <em>atc_group</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em> and <em>iv_units</em>.</p>
<p>This data set is in R available as <code>antivirals</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 21 August 2022 15:23:37 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p>It was last updated on 25 August 2022 17:23:20 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.rds" class="external-link">R file</a> (5 kB)<br>
@ -765,7 +760,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</h2>
<p>A data set with 20,369 rows and 11 columns, containing the following column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>, <em>rank_index</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</em>, <em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
<p>This data set is in R available as <code>rsi_translation</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 21 August 2022 15:23:37 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
<p>It was last updated on 25 August 2022 17:23:20 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.rds" class="external-link">R file</a> (49 kB)<br>
@ -919,7 +914,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</h2>
<p>A data set with 134,956 rows and 2 columns, containing the following column names:<br><em>mo</em> and <em>ab</em>.</p>
<p>This data set is in R available as <code>intrinsic_resistant</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 21 August 2022 15:23:37 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
<p>It was last updated on 25 August 2022 17:23:20 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.rds" class="external-link">R file</a> (78 kB)<br>
@ -1186,7 +1181,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</h2>
<p>A data set with 169 rows and 9 columns, containing the following column names:<br><em>ab</em>, <em>name</em>, <em>type</em>, <em>dose</em>, <em>dose_times</em>, <em>administration</em>, <em>notes</em>, <em>original_txt</em> and <em>eucast_version</em>.</p>
<p>This data set is in R available as <code>dosage</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 21 August 2022 15:23:37 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
<p>It was last updated on 25 August 2022 17:23:20 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.rds" class="external-link">R file</a> (3 kB)<br>

7
articles/index.html
View File

@ -10,7 +10,7 @@
<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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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">
@ -82,11 +82,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
</li>
<li class="nav-item">

7
articles/resistance_predict.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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -111,11 +111,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
</li>
<li class="nav-item">

7
articles/welcome_to_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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -111,11 +111,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
</li>
<li class="nav-item">