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50
articles/AMR.html
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@@ -91,7 +91,7 @@
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 24 April 2026.</p>
generated on 25 April 2026.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@@ -147,21 +147,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2026-04-24</td>
<td align="center">2026-04-25</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">2026-04-24</td>
<td align="center">2026-04-25</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">2026-04-24</td>
<td align="center">2026-04-25</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@@ -442,27 +442,27 @@ impression, as it comes with support for the new <code>mo</code> and
<code>sir</code> classes that we now have in our data set:</p>
<div class="sourceCode" id="cb12"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">our_data_1st</span><span class="op">)</span></span>
<span><span class="co">#&gt; patient_id hospital date </span></span>
<span><span class="co">#&gt; Length:2724 Length:2724 Min. :2011-01-01 </span></span>
<span><span class="co">#&gt; Class :character Class :character 1st Qu.:2013-04-07 </span></span>
<span><span class="co">#&gt; Mode :character Mode :character Median :2015-06-03 </span></span>
<span><span class="co">#&gt; Mean :2015-06-09 </span></span>
<span><span class="co">#&gt; 3rd Qu.:2017-08-11 </span></span>
<span><span class="co">#&gt; Max. :2019-12-27 </span></span>
<span><span class="co">#&gt; bacteria AMX AMC </span></span>
<span><span class="co">#&gt; Class :mo Class:sir Class:sir </span></span>
<span><span class="co">#&gt; &lt;NA&gt; :0 %S :41.6% (n=1133) %S :52.6% (n=1432) </span></span>
<span><span class="co">#&gt; Unique:4 %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span></span>
<span><span class="co">#&gt; #1 :B_ESCHR_COLI %I :16.4% (n=446) %I :12.2% (n=333) </span></span>
<span><span class="co">#&gt; #2 :B_STPHY_AURS %R :42.0% (n=1145) %R :35.2% (n=959) </span></span>
<span><span class="co">#&gt; #3 :B_STRPT_PNMN %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span></span>
<span><span class="co">#&gt; CIP GEN first </span></span>
<span><span class="co">#&gt; Class:sir Class:sir Mode:logical </span></span>
<span><span class="co">#&gt; %S :52.5% (n=1431) %S :61.0% (n=1661) TRUE:2724 </span></span>
<span><span class="co">#&gt; %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span></span>
<span><span class="co">#&gt; %I : 6.5% (n=176) %I : 3.0% (n=82) </span></span>
<span><span class="co">#&gt; %R :41.0% (n=1117) %R :36.0% (n=981) </span></span>
<span><span class="co">#&gt; %NI : 0.0% (n=0) %NI : 0.0% (n=0)</span></span>
<span><span class="co">#&gt; patient_id hospital date bacteria </span></span>
<span><span class="co">#&gt; Length :2724 Length :2724 Min. :2011-01-01 Class :mo </span></span>
<span><span class="co">#&gt; N.unique : 260 N.unique : 3 1st Qu.:2013-04-07 &lt;NA&gt; :0 </span></span>
<span><span class="co">#&gt; N.blank : 0 N.blank : 0 Median :2015-06-03 Unique:4 </span></span>
<span><span class="co">#&gt; Min.nchar: 2 Min.nchar: 1 Mean :2015-06-09 #1 :B_ESCHR_COLI </span></span>
<span><span class="co">#&gt; Max.nchar: 3 Max.nchar: 1 3rd Qu.:2017-08-11 #2 :B_STPHY_AURS </span></span>
<span><span class="co">#&gt; Max. :2019-12-27 #3 :B_STRPT_PNMN </span></span>
<span><span class="co">#&gt; AMX AMC CIP </span></span>
<span><span class="co">#&gt; Class:sir Class:sir Class:sir </span></span>
<span><span class="co">#&gt; %S :41.6% (n=1133) %S :52.6% (n=1432) %S :52.5% (n=1431) </span></span>
<span><span class="co">#&gt; %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span></span>
<span><span class="co">#&gt; %I :16.4% (n=446) %I :12.2% (n=333) %I : 6.5% (n=176) </span></span>
<span><span class="co">#&gt; %R :42.0% (n=1145) %R :35.2% (n=959) %R :41.0% (n=1117) </span></span>
<span><span class="co">#&gt; %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span></span>
<span><span class="co">#&gt; GEN first </span></span>
<span><span class="co">#&gt; Class:sir Mode:logical </span></span>
<span><span class="co">#&gt; %S :61.0% (n=1661) TRUE:2724 </span></span>
<span><span class="co">#&gt; %SDD : 0.0% (n=0) </span></span>
<span><span class="co">#&gt; %I : 3.0% (n=82) </span></span>
<span><span class="co">#&gt; %R :36.0% (n=981) </span></span>
<span><span class="co">#&gt; %NI : 0.0% (n=0)</span></span>
<span></span>
<span><span class="fu"><a href="https://pillar.r-lib.org/reference/glimpse.html" class="external-link">glimpse</a></span><span class="op">(</span><span class="va">our_data_1st</span><span class="op">)</span></span>
<span><span class="co">#&gt; Rows: 2,724</span></span>

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articles/AMR.md
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@@ -3,7 +3,7 @@
**Note:** values on this page will change with every website update
since they are based on randomly created values and the page was written
in [R Markdown](https://rmarkdown.rstudio.com/). However, the
methodology remains unchanged. This page was generated on 24 April 2026.
methodology remains unchanged. This page was generated on 25 April 2026.
## Introduction
@@ -51,9 +51,9 @@ structure of your data generally look like this:
| date | patient_id | mo | AMX | CIP |
|:----------:|:----------:|:----------------:|:---:|:---:|
| 2026-04-24 | abcd | Escherichia coli | S | S |
| 2026-04-24 | abcd | Escherichia coli | S | R |
| 2026-04-24 | efgh | Escherichia coli | R | S |
| 2026-04-25 | abcd | Escherichia coli | S | S |
| 2026-04-25 | abcd | Escherichia coli | S | R |
| 2026-04-25 | efgh | Escherichia coli | R | S |
### Needed R packages
@@ -367,27 +367,27 @@ and `sir` classes that we now have in our data set:
``` r
summary(our_data_1st)
#> patient_id hospital date
#> Length:2724 Length:2724 Min. :2011-01-01
#> Class :character Class :character 1st Qu.:2013-04-07
#> Mode :character Mode :character Median :2015-06-03
#> Mean :2015-06-09
#> 3rd Qu.:2017-08-11
#> Max. :2019-12-27
#> bacteria AMX AMC
#> Class :mo Class:sir Class:sir
#> <NA> :0 %S :41.6% (n=1133) %S :52.6% (n=1432)
#> Unique:4 %SDD : 0.0% (n=0) %SDD : 0.0% (n=0)
#> #1 :B_ESCHR_COLI %I :16.4% (n=446) %I :12.2% (n=333)
#> #2 :B_STPHY_AURS %R :42.0% (n=1145) %R :35.2% (n=959)
#> #3 :B_STRPT_PNMN %NI : 0.0% (n=0) %NI : 0.0% (n=0)
#> CIP GEN first
#> Class:sir Class:sir Mode:logical
#> %S :52.5% (n=1431) %S :61.0% (n=1661) TRUE:2724
#> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0)
#> %I : 6.5% (n=176) %I : 3.0% (n=82)
#> %R :41.0% (n=1117) %R :36.0% (n=981)
#> %NI : 0.0% (n=0) %NI : 0.0% (n=0)
#> patient_id hospital date bacteria
#> Length :2724 Length :2724 Min. :2011-01-01 Class :mo
#> N.unique : 260 N.unique : 3 1st Qu.:2013-04-07 <NA> :0
#> N.blank : 0 N.blank : 0 Median :2015-06-03 Unique:4
#> Min.nchar: 2 Min.nchar: 1 Mean :2015-06-09 #1 :B_ESCHR_COLI
#> Max.nchar: 3 Max.nchar: 1 3rd Qu.:2017-08-11 #2 :B_STPHY_AURS
#> Max. :2019-12-27 #3 :B_STRPT_PNMN
#> AMX AMC CIP
#> Class:sir Class:sir Class:sir
#> %S :41.6% (n=1133) %S :52.6% (n=1432) %S :52.5% (n=1431)
#> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0)
#> %I :16.4% (n=446) %I :12.2% (n=333) %I : 6.5% (n=176)
#> %R :42.0% (n=1145) %R :35.2% (n=959) %R :41.0% (n=1117)
#> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0)
#> GEN first
#> Class:sir Mode:logical
#> %S :61.0% (n=1661) TRUE:2724
#> %SDD : 0.0% (n=0)
#> %I : 3.0% (n=82)
#> %R :36.0% (n=981)
#> %NI : 0.0% (n=0)
glimpse(our_data_1st)
#> Rows: 2,724

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@@ -80,7 +80,7 @@
<main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Download data sets for download / own use</h1>
<h4 data-toc-skip class="date">24 April 2026</h4>
<h4 data-toc-skip class="date">25 April 2026</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<div class="d-none name"><code>datasets.Rmd</code></div>