Built site for AMR@3.0.1.9019: ba4c159

2026-10-01 04:13:33 +02:00 · 2026-02-08 22:40:23 +00:00
1 parent 0551ea51cb
commit 8b71d0eb99
@@ -31,7 +31,7 @@
    <a class="navbar-brand me-2" href="https://amr-for-r.org/index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9019</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">
@@ -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="">3.0.1.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9019</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">
@@ -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="">3.0.1.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9019</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 16 January 2026.</p>
+generated on 08 February 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">2026-01-16</td>
+<td align="center">2026-02-08</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">2026-01-16</td>
+<td align="center">2026-02-08</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">2026-01-16</td>
+<td align="center">2026-02-08</td>
 <td align="center">efgh</td>
 <td align="center">Escherichia coli</td>
 <td align="center">R</td>
@@ -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 16 January
+methodology remains unchanged. This page was generated on 08 February
 2026.
 ## Introduction
@@ -52,9 +52,9 @@ structure of your data generally look like this:
 |    date    | patient_id |        mo        | AMX | CIP |
 |:----------:|:----------:|:----------------:|:---:|:---:|
-| 2026-01-16 |    abcd    | Escherichia coli |  S  |  S  |
+| 2026-02-08 |    abcd    | Escherichia coli |  S  |  S  |
-| 2026-01-16 |    abcd    | Escherichia coli |  S  |  R  |
+| 2026-02-08 |    abcd    | Escherichia coli |  S  |  R  |
-| 2026-01-16 |    efgh    | Escherichia coli |  R  |  S  |
+| 2026-02-08 |    efgh    | Escherichia coli |  R  |  S  |
 ### Needed R packages
@@ -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="">3.0.1.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9019</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">
@@ -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="">3.0.1.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9019</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">
@@ -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="">3.0.1.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9019</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">
@@ -118,7 +118,7 @@ resistant to ampicillin.</p>
 <em>Klebsiella</em> being susceptible to ampicillin. This could be
 because an antibiogram is available before an identification is
 available, and the antibiogram is then not re-interpreted based on the
-identification. The <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function resolves this,
+identification. The <code><a href="../reference/interpretive_rules.html">eucast_rules()</a></code> function resolves this,
 by applying the latest ‘EUCAST Expected Resistant Phenotypes’
 guideline:</p>
 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
@@ -136,7 +136,7 @@ guideline:</p>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;">1</span> Klebsiella pneumoniae <span style="color: #080808; background-color: #5FD7AF;">  S  </span>     </span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;">2</span> Escherichia coli      <span style="color: #080808; background-color: #5FD7AF;">  S  </span></span></span>
 <span></span>
-<span><span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span><span class="op">(</span><span class="va">oops</span>, info <span class="op">=</span> <span class="cn">FALSE</span>, overwrite <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
+<span><span class="fu"><a href="../reference/interpretive_rules.html">eucast_rules</a></span><span class="op">(</span><span class="va">oops</span>, info <span class="op">=</span> <span class="cn">FALSE</span>, overwrite <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
 <span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2 × 2</span></span></span>
 <span><span class="co">#&gt;   mo                    ampicillin</span></span>
 <span><span class="co">#&gt;   <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>                 <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span>     </span></span>
@@ -246,7 +246,7 @@ reading</em>, and is basically a form of imputation:</p>
 </tbody>
 </table>
 <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span><span class="op">(</span><span class="va">data</span>, overwrite <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
+<code class="sourceCode R"><span><span class="fu"><a href="../reference/interpretive_rules.html">eucast_rules</a></span><span class="op">(</span><span class="va">data</span>, overwrite <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
 <table class="table">
 <thead><tr class="header">
 <th align="left">mo</th>
@@ -31,7 +31,7 @@ Sometimes, laboratory data can still contain such strains with
 *Klebsiella* being susceptible to ampicillin. This could be because an
 antibiogram is available before an identification is available, and the
 antibiogram is then not re-interpreted based on the identification. The
-[`eucast_rules()`](https://amr-for-r.org/reference/eucast_rules.md)
+[`eucast_rules()`](https://amr-for-r.org/reference/interpretive_rules.md)
 function resolves this, by applying the latest ‘EUCAST Expected
 Resistant Phenotypes’ guideline:
@@ -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="">3.0.1.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9019</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">
@@ -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="">3.0.1.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9019</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">
@@ -258,7 +258,8 @@ Longest: 40</p>
 <p><strong>Frequency table</strong></p>
 <p>Class: factor &gt; ordered &gt; sir (numeric)<br>
 Length: 500<br>
-Levels: 5: S &lt; SDD &lt; I &lt; R &lt; NI<br>
+Levels: 8: S &lt; SDD &lt; I &lt; R &lt; NI &lt; WT &lt; NWT &lt;
 NS<br>
 Available: 481 (96.2%, NA: 19 = 3.8%)<br>
 Unique: 3</p>
 <p>Drug: Amoxicillin/clavulanic acid (AMC, J01CR02/QJ01CR02)<br>
@@ -107,7 +107,7 @@ data %>% freq(AMC_ND2)
 Class: factor \> ordered \> sir (numeric)  
 Length: 500  
-Levels: 5: S \< SDD \< I \< R \< NI  
+Levels: 8: S \< SDD \< I \< R \< NI \< WT \< NWT \< NS  
 Available: 481 (96.2%, NA: 19 = 3.8%)  
 Unique: 3
@@ -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="">3.0.1.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9019</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">
@@ -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="">3.0.1.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9019</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">16 January 2026</h4>
+            <h4 data-toc-skip class="date">08 February 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>
@@ -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="">3.0.1.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9019</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">
@@ -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="">3.0.1.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9019</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">
@@ -2,4 +2,4 @@
   * Bootstrap  v5.3.1 (https://getbootstrap.com/)
   * Copyright 2011-2023 The Bootstrap Authors
   * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)
-   */:root,[data-bs-theme="light"]{--bs-blue: #2c3e50;--bs-indigo: #6610f2;--bs-purple: #6f42c1;--bs-pink: #e83e8c;--bs-red: #e74c3c;--bs-orange: #fd7e14;--bs-yellow: #f39c12;--bs-green: #18bc9c;--bs-teal: #20c997;--bs-cyan: #3498db;--bs-black: #000;--bs-white: #fff;--bs-gray: #95a5a6;--bs-gray-dark: #343a40;--bs-gray-100: #f8f9fa;--bs-gray-200: #ecf0f1;--bs-gray-300: #dee2e6;--bs-gray-400: #ced4da;--bs-gray-500: #b4bcc2;--bs-gray-600: #95a5a6;--bs-gray-700: #7b8a8b;--bs-gray-800: #343a40;--bs-gray-900: #212529;--bs-default: #95a5a6;--bs-primary: #2c3e50;--bs-secondary: #95a5a6;--bs-success: #18bc9c;--bs-info: #3498db;--bs-warning: #f39c12;--bs-danger: #e74c3c;--bs-light: #ecf0f1;--bs-dark: #7b8a8b;--bs-default-rgb: 149,165,166;--bs-primary-rgb: 44,62,80;--bs-secondary-rgb: 149,165,166;--bs-success-rgb: 24,188,156;--bs-info-rgb: 52,152,219;--bs-warning-rgb: 243,156,18;--bs-danger-rgb: 231,76,60;--bs-light-rgb: 236,240,241;--bs-dark-rgb: 123,138,139;--bs-primary-text-emphasis: 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#8b2e24;--bs-light-border-subtle:Line truncated
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