P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-27 13:47:56 +02:00
Code Releases Activity

Built site for AMR@2.1.1.9239: ec937e8

Browse Source
This commit is contained in:
github-actions
2025-04-14 07:59:20 +00:00
parent cfc9269348
commit 80b584cd20
80 changed files with 125 additions and 114 deletions
Download Patch File Download Diff File Expand all files Collapse all files

10
articles/AMR.html
View File

@ -31,7 +31,7 @@
<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="">2.1.1.9237</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9239</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">
@ -92,7 +92,7 @@
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 13 April 2025.</p>
generated on 14 April 2025.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@ -148,21 +148,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2025-04-13</td>
<td align="center">2025-04-14</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">2025-04-13</td>
<td align="center">2025-04-14</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">2025-04-13</td>
<td align="center">2025-04-14</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>

2
articles/AMR_for_Python.html
View File

@ -31,7 +31,7 @@
<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="">2.1.1.9237</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9239</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">

6
articles/AMR_with_tidymodels.html
View File

@ -31,7 +31,7 @@
<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="">2.1.1.9237</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9239</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">
@ -286,7 +286,7 @@ engine.</li>
<h4 id="building-the-workflow">3. Building the Workflow<a class="anchor" aria-label="anchor" href="#building-the-workflow"></a>
</h4>
<p>We bundle the recipe and model together into a <code>workflow</code>,
which organises the entire modeling process.</p>
which organises the entire modelling process.</p>
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># Combine the recipe and model into a workflow</span></span>
<span><span class="va">resistance_workflow</span> <span class="op">&lt;-</span> <span class="fu">workflow</span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
@ -503,7 +503,7 @@ rates by year and ward.</li>
<h3 id="defining-the-workflow-1">
<strong>Defining the Workflow</strong><a class="anchor" aria-label="anchor" href="#defining-the-workflow-1"></a>
</h3>
<p>We now define the modeling workflow, which consists of a
<p>We now define the modelling workflow, which consists of a
preprocessing step, a model specification, and the fitting process.</p>
<div class="section level4">
<h4 id="preprocessing-with-a-recipe-1">1. Preprocessing with a Recipe<a class="anchor" aria-label="anchor" href="#preprocessing-with-a-recipe-1"></a>

2
articles/EUCAST.html
View File

@ -31,7 +31,7 @@
<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="">2.1.1.9237</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9239</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/MDR.html
View File

@ -31,7 +31,7 @@
<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="">2.1.1.9237</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9239</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

@ -31,7 +31,7 @@
<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="">2.1.1.9237</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9239</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

@ -31,7 +31,7 @@
<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="">2.1.1.9237</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9239</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">

13
articles/datasets.html
View File

@ -31,7 +31,7 @@
<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="">2.1.1.9237</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9239</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">
@ -81,7 +81,7 @@
<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">13 April 2025</h4>
<h4 data-toc-skip class="date">14 April 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>
@ -412,6 +412,7 @@ all SNOMED codes as comma separated values.</p>
</tr>
</tbody>
</table>
<hr>
</div>
<div class="section level2">
<h2 id="antimicrobials-antibiotic-and-antifungal-drugs">
@ -588,6 +589,7 @@ inhibitors</td>
</tr>
</tbody>
</table>
<hr>
</div>
<div class="section level2">
<h2 id="clinical_breakpoints-interpretation-from-mic-values-disk-diameters-to-sir">
@ -776,6 +778,7 @@ DTA file</a> (9.6 MB)</li>
</tr>
</tbody>
</table>
<hr>
</div>
<div class="section level2">
<h2 id="microorganisms-groups-species-groups-and-microbiological-complexes">
@ -867,6 +870,7 @@ DTA file</a> (83 kB)</li>
</tr>
</tbody>
</table>
<hr>
</div>
<div class="section level2">
<h2 id="intrinsic_resistant-intrinsic-bacterial-resistance">
@ -1141,6 +1145,7 @@ DTA file</a> (22.6 MB)</li>
</tr>
</tbody>
</table>
<hr>
</div>
<div class="section level2">
<h2 id="dosage-dosage-guidelines-from-eucast">
@ -1271,6 +1276,7 @@ DTA file</a> (0.1 MB)</li>
</tr>
</tbody>
</table>
<hr>
</div>
<div class="section level2">
<h2 id="example_isolates-example-data-for-practice">
@ -1681,6 +1687,7 @@ here</a>.</p>
</tr>
</tbody>
</table>
<hr>
</div>
<div class="section level2">
<h2 id="example_isolates_unclean-example-data-for-practice">
@ -1782,6 +1789,7 @@ set here</a>.</p>
</tr>
</tbody>
</table>
<hr>
</div>
<div class="section level2">
<h2 id="microorganisms-codes-common-laboratory-codes">
@ -1850,6 +1858,7 @@ DTA file</a> (0.1 MB)</li>
</tr>
</tbody>
</table>
<hr>
</div>
<div class="section level2">
<h2 id="antivirals-antiviral-drugs">

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="">2.1.1.9237</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9239</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/welcome_to_AMR.html
View File

@ -31,7 +31,7 @@
<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="">2.1.1.9237</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9239</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">