P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2026-03-16 02:47:52 +01:00
Code Releases Activity

Built site for AMR@3.0.1.9033: 353eaa3

Browse Source
This commit is contained in:
github-actions
2026-03-09 11:08:33 +00:00
parent e7e8aa636e
commit 86a53a0901
94 changed files with 188 additions and 159 deletions
Download Patch File Download Diff File Expand all files Collapse all files

10
articles/AMR.html
View File

@@ -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="">3.0.1.9032</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</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 08 March 2026.</p>
generated on 09 March 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">2026-03-08</td>
<td align="center">2026-03-09</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">2026-03-08</td>
<td align="center">2026-03-09</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">2026-03-08</td>
<td align="center">2026-03-09</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>

8
articles/AMR.md
View File

@@ -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 08 March 2026.
methodology remains unchanged. This page was generated on 09 March 2026.
## Introduction
@@ -51,9 +51,9 @@ structure of your data generally look like this:
| date | patient_id | mo | AMX | CIP |
|:----------:|:----------:|:----------------:|:---:|:---:|
| 2026-03-08 | abcd | Escherichia coli | S | S |
| 2026-03-08 | abcd | Escherichia coli | S | R |
| 2026-03-08 | efgh | Escherichia coli | R | S |
| 2026-03-09 | abcd | Escherichia coli | S | S |
| 2026-03-09 | abcd | Escherichia coli | S | R |
| 2026-03-09 | efgh | Escherichia coli | R | S |
### Needed R packages

2
articles/AMR_for_Python.html
View File

@@ -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="">3.0.1.9032</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</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
View File

@@ -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="">3.0.1.9032</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</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
View File

@@ -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="">3.0.1.9032</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</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/PCA.html
View File

@@ -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="">3.0.1.9032</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</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/WHONET.html
View File

@@ -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="">3.0.1.9032</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</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
View File

@@ -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="">3.0.1.9032</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</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">

12
articles/datasets.html
View File

@@ -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="">3.0.1.9032</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</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">08 March 2026</h4>
<h4 data-toc-skip class="date">09 March 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>
@@ -417,20 +417,20 @@ all SNOMED codes as comma separated values.</p>
<h2 id="antimicrobials-antibiotic-and-antifungal-drugs">
<code>antimicrobials</code>: Antibiotic and Antifungal Drugs<a class="anchor" aria-label="anchor" href="#antimicrobials-antibiotic-and-antifungal-drugs"></a>
</h2>
<p>A data set with 504 rows and 14 columns, containing the following
<p>A data set with 505 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>antimicrobials</code>, after
you load the <code>AMR</code> package.</p>
<p>It was last updated on 6 March 2026 17:53:42 UTC. Find more info
<p>It was last updated on 9 March 2026 10:57:36 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>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/antimicrobials.rds" class="external-link">original
R Data Structure (RDS) file</a> (46 kB)<br>
R Data Structure (RDS) file</a> (44 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/antimicrobials.txt" class="external-link">tab-separated
text file</a> (0.1 MB)<br>
@@ -442,7 +442,7 @@ Excel workbook</a> (79 kB)<br>
Feather file</a> (0.1 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/antimicrobials.parquet" class="external-link">Apache
Parquet file</a> (0.1 MB)<br>
Parquet file</a> (94 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/antimicrobials.sav" class="external-link">IBM
SPSS Statistics data file</a> (0.4 MB)<br>

8
articles/datasets.md
View File

@@ -91,7 +91,7 @@ First 6 rows when filtering on genus *Escherichia*:
## `antimicrobials`: Antibiotic and Antifungal Drugs
A data set with 504 rows and 14 columns, containing the following column
A data set with 505 rows and 14 columns, containing the following column
names:
*ab*, *cid*, *name*, *group*, *atc*, *atc_group1*, *atc_group2*,
*abbreviations*, *synonyms*, *oral_ddd*, *oral_units*, *iv_ddd*,
@@ -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 6 March 2026 17:53:42 UTC. Find more info about
It was last updated on 9 March 2026 10:57:36 UTC. Find more info about
the contents, (scientific) source, and structure of this [data set
here](https://amr-for-r.org/reference/antimicrobials.html).
@@ -108,7 +108,7 @@ here](https://amr-for-r.org/reference/antimicrobials.html).
- Download as [original R Data Structure (RDS)
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/antimicrobials.rds)
(46 kB)
(44 kB)
- Download as [tab-separated text
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/antimicrobials.txt)
(0.1 MB)
@@ -120,7 +120,7 @@ here](https://amr-for-r.org/reference/antimicrobials.html).
(0.1 MB)
- Download as [Apache Parquet
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/antimicrobials.parquet)
(0.1 MB)
(94 kB)
- Download as [IBM SPSS Statistics data
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/antimicrobials.sav)
(0.4 MB)

2
articles/index.html
View File

@@ -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="">3.0.1.9032</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</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">