P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-10-31 03:28:12 +01:00
Code Releases Activity

Built site for AMR@3.0.0.9019: eca6385

Browse Source
This commit is contained in:
github-actions
2025-09-03 09:56:20 +00:00
parent 43285cb936
commit 75b8c2485a
8 changed files with 49 additions and 3922 deletions
Download Patch File Download Diff File Expand all files Collapse all files

8
articles/AMR.html
View File

@@ -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 01 September 2025.</p>
generated on 03 September 2025.</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">2025-09-01</td>
<td align="center">2025-09-03</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">2025-09-01</td>
<td align="center">2025-09-03</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">2025-09-01</td>
<td align="center">2025-09-03</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>

22
articles/datasets.html
View File

@@ -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">01 September 2025</h4>
<h4 data-toc-skip class="date">03 September 2025</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>
@@ -115,7 +115,7 @@ column names:<br><em>mo</em>, <em>fullname</em>, <em>status</em>, <em>kingdom</e
<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 1 September 2025 15:00:00 UTC. Find more info
<p>It was last updated on 3 September 2025 09:50:16 UTC. Find more info
about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/microorganisms.html">data set
here</a>.</p>
<p><strong>Direct download links:</strong></p>
@@ -424,7 +424,7 @@ 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 1 September 2025 15:00:00 UTC. Find more info
<p>It was last updated on 3 September 2025 09:50:16 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>
@@ -602,7 +602,7 @@ column names:<br><em>guideline</em>, <em>type</em>, <em>host</em>, <em>method</e
<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 1 September 2025 15:00:00 UTC. Find more info
<p>It was last updated on 3 September 2025 09:50:16 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>
@@ -790,7 +790,7 @@ column names:<br><em>mo_group</em>, <em>mo</em>, <em>mo_group_name</em>, and
<p>This data set is in R available as
<code>microorganisms.groups</code>, after you load the <code>AMR</code>
package.</p>
<p>It was last updated on 1 September 2025 15:00:00 UTC. Find more info
<p>It was last updated on 3 September 2025 09:50:16 UTC. Find more info
about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/microorganisms.groups.html">data
set here</a>.</p>
<p><strong>Direct download links:</strong></p>
@@ -880,7 +880,7 @@ Resistance<a class="anchor" aria-label="anchor" href="#intrinsic_resistant-intri
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 1 September 2025 15:00:00 UTC. Find more info
<p>It was last updated on 3 September 2025 09:50:16 UTC. Find more info
about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/intrinsic_resistant.html">data set
here</a>.</p>
<p><strong>Direct download links:</strong></p>
@@ -1156,7 +1156,7 @@ column names:<br><em>ab</em>, <em>name</em>, <em>type</em>, <em>dose</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 1 September 2025 15:00:00 UTC. Find more info
<p>It was last updated on 3 September 2025 09:50:16 UTC. Find more info
about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/dosage.html">data set
here</a>.</p>
<p><strong>Direct download links:</strong></p>
@@ -1294,7 +1294,7 @@ column names:<br><em>date</em>, <em>patient</em>, <em>age</em>, <em>gender</em>,
<em>MUP</em>, and <em>RIF</em>.</p>
<p>This data set is in R available as <code>example_isolates</code>,
after you load the <code>AMR</code> package.</p>
<p>It was last updated on 1 September 2025 15:00:00 UTC. Find more info
<p>It was last updated on 3 September 2025 09:50:16 UTC. Find more info
about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/example_isolates.html">data set
here</a>.</p>
<p><strong>Example content</strong></p>
@@ -1700,7 +1700,7 @@ column names:<br><em>patient_id</em>, <em>hospital</em>, <em>date</em>,
<p>This data set is in R available as
<code>example_isolates_unclean</code>, after you load the
<code>AMR</code> package.</p>
<p>It was last updated on 1 September 2025 15:00:00 UTC. Find more info
<p>It was last updated on 3 September 2025 09:50:16 UTC. Find more info
about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/example_isolates_unclean.html">data
set here</a>.</p>
<p><strong>Example content</strong></p>
@@ -1798,7 +1798,7 @@ set here</a>.</p>
column names:<br><em>code</em> and <em>mo</em>.</p>
<p>This data set is in R available as <code>microorganisms.codes</code>,
after you load the <code>AMR</code> package.</p>
<p>It was last updated on 1 September 2025 15:00:00 UTC. Find more info
<p>It was last updated on 3 September 2025 09:50:16 UTC. Find more info
about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/microorganisms.codes.html">data
set here</a>.</p>
<p><strong>Direct download links:</strong></p>
@@ -1870,7 +1870,7 @@ column names:<br><em>av</em>, <em>name</em>, <em>atc</em>, <em>cid</em>,
<em>loinc</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 1 September 2025 15:00:00 UTC. Find more info
<p>It was last updated on 3 September 2025 09:50:16 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>