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10
articles/AMR.html
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@@ -30,7 +30,7 @@
<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="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</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">
@@ -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 03 July 2026.</p>
generated on 09 July 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">2026-07-03</td>
<td align="center">2026-07-09</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">2026-07-03</td>
<td align="center">2026-07-09</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">2026-07-03</td>
<td align="center">2026-07-09</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>

8
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 03 July 2026.
methodology remains unchanged. This page was generated on 09 July 2026.
## Introduction
@@ -51,9 +51,9 @@ structure of your data generally look like this:
| date | patient_id | mo | AMX | CIP |
|:----------:|:----------:|:----------------:|:---:|:---:|
| 2026-07-03 | abcd | Escherichia coli | S | S |
| 2026-07-03 | abcd | Escherichia coli | S | R |
| 2026-07-03 | efgh | Escherichia coli | R | S |
| 2026-07-09 | abcd | Escherichia coli | S | S |
| 2026-07-09 | abcd | Escherichia coli | S | R |
| 2026-07-09 | efgh | Escherichia coli | R | S |
### Needed R packages

2
articles/AMR_for_Python.html
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@@ -30,7 +30,7 @@
<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="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</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">

2
articles/AMR_with_tidymodels.html
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@@ -30,7 +30,7 @@
<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="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</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">

2
articles/EUCAST.html
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@@ -30,7 +30,7 @@
<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="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</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">

4
articles/PCA.html
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@@ -30,7 +30,7 @@
<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="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</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">
@@ -196,7 +196,7 @@ function:</p>
<span><span class="co">#&gt; [1] "Caryophanales" "Enterobacterales" "Lactobacillales" "Pseudomonadales"</span></span>
<span><span class="co">#&gt; Importance of components:</span></span>
<span><span class="co">#&gt; PC1 PC2 PC3 PC4 PC5 PC6 PC7</span></span>
<span><span class="co">#&gt; Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 1.232e-16</span></span>
<span><span class="co">#&gt; Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 9.577e-17</span></span>
<span><span class="co">#&gt; Proportion of Variance 0.5799 0.3531 0.0471 0.01435 0.00541 0.00012 0.000e+00</span></span>
<span><span class="co">#&gt; Cumulative Proportion 0.5799 0.9330 0.9801 0.99446 0.99988 1.00000 1.000e+00</span></span></code></pre></div>
<pre><code><span><span class="co">#&gt; Groups (n=4, named as 'order'):</span></span>

2
articles/PCA.md
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@@ -119,7 +119,7 @@ summary(pca_result)
#> [1] "Caryophanales" "Enterobacterales" "Lactobacillales" "Pseudomonadales"
#> Importance of components:
#> PC1 PC2 PC3 PC4 PC5 PC6 PC7
#> Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 1.232e-16
#> Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 9.577e-17
#> Proportion of Variance 0.5799 0.3531 0.0471 0.01435 0.00541 0.00012 0.000e+00
#> Cumulative Proportion 0.5799 0.9330 0.9801 0.99446 0.99988 1.00000 1.000e+00
```

2
articles/WHONET.html
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@@ -30,7 +30,7 @@
<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="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</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">

2
articles/WISCA.html
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@@ -30,7 +30,7 @@
<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="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</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">

18
articles/datasets.html
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@@ -30,7 +30,7 @@
<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="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</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">
@@ -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">03 July 2026</h4>
<h4 data-toc-skip class="date">09 July 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>
@@ -441,8 +441,8 @@ column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>a
<em>iv_ddd</em>, <em>iv_units</em>, and <em>loinc</em>.</p>
<p>This data set is in R available as <code>antimicrobials</code>, after
you load the <code>AMR</code> package.</p>
<p>It was last updated on 27 June 2026 12:31:58 UTC. Find more info
about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/antimicrobials.html">data set
<p>It was last updated on 9 July 2026 15:14:59 UTC. Find more info about
the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/antimicrobials.html">data set
here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
@@ -612,20 +612,20 @@ inhibitors</td>
<code>clinical_breakpoints</code>: Interpretation from MIC values
&amp; disk diameters to SIR<a class="anchor" aria-label="anchor" href="#clinical_breakpoints-interpretation-from-mic-values-disk-diameters-to-sir"></a>
</h2>
<p>A data set with 45 555 rows and 14 columns, containing the following
<p>A data set with 45 735 rows and 14 columns, containing the following
column names:<br><em>guideline</em>, <em>type</em>, <em>host</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>, <em>uti</em>, and <em>is_SDD</em>.</p>
<p>This data set is in R available as <code>clinical_breakpoints</code>,
after you load the <code>AMR</code> package.</p>
<p>It was last updated on 22 June 2026 23:38:13 UTC. Find more info
about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/clinical_breakpoints.html">data
<p>It was last updated on 9 July 2026 15:14:59 UTC. Find more info about
the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/clinical_breakpoints.html">data
set 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/datasets/clinical_breakpoints.rds" class="external-link">original
R Data Structure (RDS) file</a> (92 kB)<br>
R Data Structure (RDS) file</a> (93 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.txt" class="external-link">tab-separated
text file</a> (4.2 MB)<br>
@@ -637,7 +637,7 @@ Excel workbook</a> (2.7 MB)<br>
Feather file</a> (2 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.parquet" class="external-link">Apache
Parquet file</a> (0.1 MB)<br>
Parquet file</a> (0.2 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.sav" class="external-link">IBM
SPSS Statistics data file</a> (7.5 MB)<br>

10
articles/datasets.md
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@@ -100,7 +100,7 @@ names:
This data set is in R available as `antimicrobials`, after you load the
`AMR` package.
It was last updated on 27 June 2026 12:31:58 UTC. Find more info about
It was last updated on 9 July 2026 15:14:59 UTC. Find more info about
the contents, (scientific) source, and structure of this [data set
here](https://amr-for-r.org/reference/antimicrobials.html).
@@ -147,7 +147,7 @@ as comma separated values.
## `clinical_breakpoints`: Interpretation from MIC values & disk diameters to SIR
A data set with 45 555 rows and 14 columns, containing the following
A data set with 45 735 rows and 14 columns, containing the following
column names:
*guideline*, *type*, *host*, *method*, *site*, *mo*, *rank_index*, *ab*,
*ref_tbl*, *disk_dose*, *breakpoint_S*, *breakpoint_R*, *uti*, and
@@ -156,7 +156,7 @@ column names:
This data set is in R available as `clinical_breakpoints`, after you
load the `AMR` package.
It was last updated on 22 June 2026 23:38:13 UTC. Find more info about
It was last updated on 9 July 2026 15:14:59 UTC. Find more info about
the contents, (scientific) source, and structure of this [data set
here](https://amr-for-r.org/reference/clinical_breakpoints.html).
@@ -164,7 +164,7 @@ here](https://amr-for-r.org/reference/clinical_breakpoints.html).
- Download as [original R Data Structure (RDS)
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.rds)
(92 kB)
(93 kB)
- Download as [tab-separated text
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.txt)
(4.2 MB)
@@ -176,7 +176,7 @@ here](https://amr-for-r.org/reference/clinical_breakpoints.html).
(2 MB)
- Download as [Apache Parquet
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.parquet)
(0.1 MB)
(0.2 MB)
- Download as [IBM SPSS Statistics data
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.sav)
(7.5 MB)

2
articles/index.html
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@@ -7,7 +7,7 @@
<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="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</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">