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@@ -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="">3.0.1.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9009</small>
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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="">3.0.1.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9009</small>
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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="">3.0.1.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9009</small>
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@@ -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 22 December 2025.</p>
generated on 23 December 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">2025-12-22</td>
<td align="center">2025-12-23</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">2025-12-22</td>
<td align="center">2025-12-23</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">2025-12-22</td>
<td align="center">2025-12-23</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>

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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 22 December
methodology remains unchanged. This page was generated on 23 December
2025.
## Introduction
@@ -52,9 +52,9 @@ structure of your data generally look like this:
| date | patient_id | mo | AMX | CIP |
|:----------:|:----------:|:----------------:|:---:|:---:|
| 2025-12-22 | abcd | Escherichia coli | S | S |
| 2025-12-22 | abcd | Escherichia coli | S | R |
| 2025-12-22 | efgh | Escherichia coli | R | S |
| 2025-12-23 | abcd | Escherichia coli | S | S |
| 2025-12-23 | abcd | Escherichia coli | S | R |
| 2025-12-23 | efgh | Escherichia coli | R | S |
### Needed R packages

2
articles/AMR_for_Python.html
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<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="">3.0.1.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9009</small>
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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="">3.0.1.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9009</small>
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@@ -419,7 +419,7 @@ ROC curve looks like this:</p>
<h3 id="conclusion">
<strong>Conclusion</strong><a class="anchor" aria-label="anchor" href="#conclusion"></a>
</h3>
<p>In this post, we demonstrated how to build a machine learning
<p>In this example, we demonstrated how to build a machine learning
pipeline with the <code>tidymodels</code> framework and the
<code>AMR</code> package. By combining selector functions like
<code><a href="../reference/antimicrobial_selectors.html">aminoglycosides()</a></code> and <code><a href="../reference/antimicrobial_selectors.html">betalactams()</a></code> with
@@ -521,10 +521,9 @@ predictors can easily and agnostically selected using the new
<span><span class="co"># Define the recipe</span></span>
<span><span class="va">mic_recipe</span> <span class="op">&lt;-</span> <span class="fu">recipe</span><span class="op">(</span><span class="va">esbl</span> <span class="op">~</span> <span class="va">.</span>, data <span class="op">=</span> <span class="va">training_data</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu">remove_role</span><span class="op">(</span><span class="va">genus</span>, old_role <span class="op">=</span> <span class="st">"predictor"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="co"># Remove non-informative variable</span></span>
<span> <span class="fu"><a href="../reference/amr-tidymodels.html">step_mic_log2</a></span><span class="op">(</span><span class="fu"><a href="../reference/amr-tidymodels.html">all_mic_predictors</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="co">#%&gt;% # Log2 transform all MIC predictors</span></span>
<span> <span class="co"># prep()</span></span>
<span> <span class="fu"><a href="../reference/amr-tidymodels.html">step_mic_log2</a></span><span class="op">(</span><span class="fu"><a href="../reference/amr-tidymodels.html">all_mic_predictors</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="co"># Log2 transform all MIC predictors</span></span>
<span></span>
<span><span class="va">mic_recipe</span></span>
<span><span class="fu">prep</span><span class="op">(</span><span class="va">mic_recipe</span><span class="op">)</span></span>
<span><span class="co">#&gt; </span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">Recipe</span> <span style="color: #00BBBB;">──────────────────────────────────────────────────────────────────────</span></span></span>
<span><span class="co">#&gt; </span></span>
@@ -534,8 +533,11 @@ predictors can easily and agnostically selected using the new
<span><span class="co">#&gt; predictor: 17</span></span>
<span><span class="co">#&gt; undeclared role: 1</span></span>
<span><span class="co">#&gt; </span></span>
<span><span class="co">#&gt; ── Training information</span></span>
<span><span class="co">#&gt; Training data contained 375 data points and no incomplete rows.</span></span>
<span><span class="co">#&gt; </span></span>
<span><span class="co">#&gt; ── Operations</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">•</span> Log2 transformation of MIC columns: <span style="color: #0000BB;">all_mic_predictors()</span></span></span></code></pre></div>
<span><span class="co">#&gt; <span style="color: #00BBBB;">•</span> Log2 transformation of MIC columns: <span style="color: #0000BB;">AMC</span>, <span style="color: #0000BB;">AMP</span>, <span style="color: #0000BB;">TZP</span>, <span style="color: #0000BB;">CXM</span>, <span style="color: #0000BB;">FOX</span>, ... | <span style="font-style: italic;">Trained</span></span></span></code></pre></div>
<p><strong>Explanation:</strong></p>
<ul>
<li>
@@ -641,7 +643,7 @@ that we can use to check the predictions with.</li>
</ul>
<p>It appears we can predict ESBL gene presence with a positive
predictive value (PPV) of 92.1% and a negative predictive value (NPV) of
91.9 using a simplistic logistic regression model.</p>
91.9% using a simplistic logistic regression model.</p>
</div>
<div class="section level3">
<h3 id="visualising-predictions">
@@ -676,13 +678,17 @@ predictions?</p>
<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/scale_continuous.html" class="external-link">scale_y_continuous</a></span><span class="op">(</span>labels <span class="op">=</span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="va">x</span> <span class="op">*</span> <span class="fl">100</span>, <span class="st">"%"</span><span class="op">)</span>,</span>
<span> limits <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.5</span>, <span class="fl">1</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span>
<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggtheme.html" class="external-link">theme_minimal</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<p><img src="AMR_with_tidymodels_files/figure-html/unnamed-chunk-15-1.png" class="r-plt" alt="" width="720">
### <strong>Conclusion</strong></p>
<p><img src="AMR_with_tidymodels_files/figure-html/unnamed-chunk-15-1.png" class="r-plt" alt="" width="720"></p>
</div>
<div class="section level3">
<h3 id="conclusion-1">
<strong>Conclusion</strong><a class="anchor" aria-label="anchor" href="#conclusion-1"></a>
</h3>
<p>In this example, we showcased how the new <code>AMR</code>-specific
recipe steps simplify working with <code>&lt;mic&gt;</code> columns in
<code>tidymodels</code>. The <code><a href="../reference/amr-tidymodels.html">step_mic_log2()</a></code> transformation
converts ordered MICs to log2-transformed numerics, improving
compatibility with classification models.</p>
converts MICs (with or without operators) to log2-transformed numerics,
improving compatibility with classification models.</p>
<p>This pipeline enables realistic, reproducible, and interpretable
modelling of antimicrobial resistance data.</p>
<hr>
@@ -931,8 +937,8 @@ sets.</li>
<p><img src="AMR_with_tidymodels_files/figure-html/unnamed-chunk-22-1.png" class="r-plt" alt="" width="720"></p>
</div>
<div class="section level3">
<h3 id="conclusion-1">
<strong>Conclusion</strong><a class="anchor" aria-label="anchor" href="#conclusion-1"></a>
<h3 id="conclusion-2">
<strong>Conclusion</strong><a class="anchor" aria-label="anchor" href="#conclusion-2"></a>
</h3>
<p>In this example, we demonstrated how to analyze AMR trends over time
using <code>tidymodels</code>. By aggregating resistance rates by year

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articles/AMR_with_tidymodels.md
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@@ -332,9 +332,9 @@ predictions %>%
### **Conclusion**
In this post, we demonstrated how to build a machine learning pipeline
with the `tidymodels` framework and the `AMR` package. By combining
selector functions like
In this example, we demonstrated how to build a machine learning
pipeline with the `tidymodels` framework and the `AMR` package. By
combining selector functions like
[`aminoglycosides()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
and
[`betalactams()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
@@ -431,10 +431,9 @@ testing_data <- testing(split)
# Define the recipe
mic_recipe <- recipe(esbl ~ ., data = training_data) %>%
remove_role(genus, old_role = "predictor") %>% # Remove non-informative variable
step_mic_log2(all_mic_predictors()) #%>% # Log2 transform all MIC predictors
# prep()
step_mic_log2(all_mic_predictors()) # Log2 transform all MIC predictors
mic_recipe
prep(mic_recipe)
#>
#> ── Recipe ──────────────────────────────────────────────────────────────────────
#>
@@ -444,8 +443,11 @@ mic_recipe
#> predictor: 17
#> undeclared role: 1
#>
#> ── Training information
#> Training data contained 375 data points and no incomplete rows.
#>
#> ── Operations
#> • Log2 transformation of MIC columns: all_mic_predictors()
#> • Log2 transformation of MIC columns: AMC, AMP, TZP, CXM, FOX, ... | Trained
```
**Explanation:**
@@ -540,8 +542,8 @@ metrics
check the predictions with.
It appears we can predict ESBL gene presence with a positive predictive
value (PPV) of 92.1% and a negative predictive value (NPV) of 91.9 using
a simplistic logistic regression model.
value (PPV) of 92.1% and a negative predictive value (NPV) of 91.9%
using a simplistic logistic regression model.
### **Visualising Predictions**
@@ -580,14 +582,16 @@ predictions %>%
theme_minimal()
```
![](AMR_with_tidymodels_files/figure-html/unnamed-chunk-15-1.png) \###
**Conclusion**
![](AMR_with_tidymodels_files/figure-html/unnamed-chunk-15-1.png)
### **Conclusion**
In this example, we showcased how the new `AMR`-specific recipe steps
simplify working with `<mic>` columns in `tidymodels`. The
[`step_mic_log2()`](https://amr-for-r.org/reference/amr-tidymodels.md)
transformation converts ordered MICs to log2-transformed numerics,
improving compatibility with classification models.
transformation converts MICs (with or without operators) to
log2-transformed numerics, improving compatibility with classification
models.
This pipeline enables realistic, reproducible, and interpretable
modelling of antimicrobial resistance data.

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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="">3.0.1.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9009</small>
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@@ -30,7 +30,7 @@
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9007</small>
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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="">3.0.1.9007</small>
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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="">3.0.1.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9009</small>
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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="">3.0.1.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9009</small>
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@@ -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">22 December 2025</h4>
<h4 data-toc-skip class="date">23 December 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>

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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="">3.0.1.9007</small>
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authors.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="">3.0.1.9007</small>
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index.html
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@@ -33,7 +33,7 @@
<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="">3.0.1.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9009</small>
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news/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="">3.0.1.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9009</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">
@@ -49,9 +49,9 @@
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="3.0.1.9007" id="amr-3019007">AMR 3.0.1.9007<a class="anchor" aria-label="anchor" href="#amr-3019007"></a></h2>
<h2 class="pkg-version" data-toc-text="3.0.1.9009" id="amr-3019009">AMR 3.0.1.9009<a class="anchor" aria-label="anchor" href="#amr-3019009"></a></h2>
<div class="section level4">
<h4 id="new-3-0-1-9007">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9007"></a></h4>
<h4 id="new-3-0-1-9009">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9009"></a></h4>
<ul><li>Integration with the <strong>tidymodels</strong> framework to allow seamless use of SIR, MIC and disk data in modelling pipelines via <code>recipes</code>
<ul><li>
<code><a href="../reference/amr-tidymodels.html">step_mic_log2()</a></code> to transform <code>&lt;mic&gt;</code> columns with log2, and <code><a href="../reference/amr-tidymodels.html">step_sir_numeric()</a></code> to convert <code>&lt;sir&gt;</code> columns to numeric</li>
@@ -61,7 +61,7 @@
<li>Data set <code>esbl_isolates</code> to practise with AMR modelling</li>
</ul></div>
<div class="section level4">
<h4 id="changed-3-0-1-9007">Changed<a class="anchor" aria-label="anchor" href="#changed-3-0-1-9007"></a></h4>
<h4 id="changed-3-0-1-9009">Changed<a class="anchor" aria-label="anchor" href="#changed-3-0-1-9009"></a></h4>
<ul><li>Fixed a bug in <code><a href="../reference/antibiogram.html">antibiogram()</a></code> for when no antimicrobials are set</li>
<li>Added taniborbactam (<code>TAN</code>) and cefepime/taniborbactam (<code>FTA</code>) to the <code>antimicrobials</code> data set</li>
<li>Fixed a bug in <code><a href="../reference/as.sir.html">as.sir()</a></code> where for numeric input the arguments <code>S</code>, <code>i</code>, and <code>R</code> would not be considered (<a href="https://github.com/msberends/AMR/issues/244" class="external-link">#244</a>)</li>

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news/index.md
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# Changelog
## AMR 3.0.1.9007
## AMR 3.0.1.9009
#### New

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pkgdown.yml
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@@ -10,7 +10,7 @@ articles:
PCA: PCA.html
WHONET: WHONET.html
WISCA: WISCA.html
last_built: 2025-12-22T08:44Z
last_built: 2025-12-23T10:08Z
urls:
reference: https://amr-for-r.org/reference
article: https://amr-for-r.org/articles

2
reference/AMR-deprecated.html
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@@ -7,7 +7,7 @@
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reference/AMR-options.html
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@@ -7,7 +7,7 @@
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reference/AMR.html
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@@ -21,7 +21,7 @@ The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish
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reference/WHOCC.html
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@@ -7,7 +7,7 @@
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reference/WHONET.html
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@@ -7,7 +7,7 @@
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reference/ab_from_text.html
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@@ -7,7 +7,7 @@
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2
reference/ab_property.html
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@@ -7,7 +7,7 @@
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2
reference/add_custom_antimicrobials.html
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@@ -7,7 +7,7 @@
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2
reference/add_custom_microorganisms.html
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@@ -7,7 +7,7 @@
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22
reference/age.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="">3.0.1.9007</small>
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@@ -112,16 +112,16 @@
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">df</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> birth_date age age_exact age_at_y2k</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1980-02-27 45 45.81644 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1953-07-26 72 72.40822 46</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1949-09-02 76 76.30411 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1986-08-03 39 39.38630 13</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1932-11-19 93 93.09041 67</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1949-03-30 76 76.73151 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1996-06-23 29 29.49863 3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1963-09-16 62 62.26575 36</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1952-05-16 73 73.60274 47</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1952-11-14 73 73.10411 47</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1980-02-27 45 45.81918 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1953-07-26 72 72.41096 46</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1949-09-02 76 76.30685 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1986-08-03 39 39.38904 13</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1932-11-19 93 93.09315 67</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1949-03-30 76 76.73425 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1996-06-23 29 29.50137 3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1963-09-16 62 62.26849 36</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1952-05-16 73 73.60548 47</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1952-11-14 73 73.10685 47</span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>

20
reference/age.md
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@@ -81,14 +81,14 @@ df$age_at_y2k <- age(df$birth_date, "2000-01-01")
df
#> birth_date age age_exact age_at_y2k
#> 1 1980-02-27 45 45.81644 19
#> 2 1953-07-26 72 72.40822 46
#> 3 1949-09-02 76 76.30411 50
#> 4 1986-08-03 39 39.38630 13
#> 5 1932-11-19 93 93.09041 67
#> 6 1949-03-30 76 76.73151 50
#> 7 1996-06-23 29 29.49863 3
#> 8 1963-09-16 62 62.26575 36
#> 9 1952-05-16 73 73.60274 47
#> 10 1952-11-14 73 73.10411 47
#> 1 1980-02-27 45 45.81918 19
#> 2 1953-07-26 72 72.41096 46
#> 3 1949-09-02 76 76.30685 50
#> 4 1986-08-03 39 39.38904 13
#> 5 1932-11-19 93 93.09315 67
#> 6 1949-03-30 76 76.73425 50
#> 7 1996-06-23 29 29.50137 3
#> 8 1963-09-16 62 62.26849 36
#> 9 1952-05-16 73 73.60548 47
#> 10 1952-11-14 73 73.10685 47
```

2
reference/age_groups.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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reference/amr-tidymodels.html
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@@ -7,7 +7,7 @@
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reference/antibiogram.html
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@@ -9,7 +9,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
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reference/antimicrobial_selectors.html
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@@ -17,7 +17,7 @@ my_data_with_all_these_columns %&amp;gt;%
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reference/antimicrobials.html
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@@ -9,7 +9,7 @@ The antibiotics data set has been renamed to antimicrobials. The old name will b
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reference/as.ab.html
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@@ -7,7 +7,7 @@
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reference/as.av.html
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@@ -7,7 +7,7 @@
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reference/as.disk.html
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@@ -7,7 +7,7 @@
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reference/as.mic.html
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@@ -7,7 +7,7 @@
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2
reference/as.mo.html
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@@ -7,7 +7,7 @@
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10
reference/as.sir.html
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@@ -9,7 +9,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@@ -416,10 +416,10 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4 × 18</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index method ab_given mo_given host_given input_given</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2025-12-22 <span style="color: #949494;">08:45:24</span> 1 MIC amoxicillin Escherich… human 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2025-12-22 <span style="color: #949494;">08:45:24</span> 1 MIC cipro Escherich… human 0.256 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2025-12-22 <span style="color: #949494;">08:45:24</span> 1 DISK tobra Escherich… human 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2025-12-22 <span style="color: #949494;">08:45:24</span> 1 DISK genta Escherich… human 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2025-12-23 <span style="color: #949494;">10:09:01</span> 1 MIC amoxicillin Escherich… human 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2025-12-23 <span style="color: #949494;">10:09:02</span> 1 MIC cipro Escherich… human 0.256 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2025-12-23 <span style="color: #949494;">10:09:02</span> 1 DISK tobra Escherich… human 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2025-12-23 <span style="color: #949494;">10:09:02</span> 1 DISK genta Escherich… human 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 11 more variables: ab &lt;ab&gt;, mo &lt;mo&gt;, host &lt;chr&gt;, input &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># outcome &lt;sir&gt;, notes &lt;chr&gt;, guideline &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># breakpoint_S_R &lt;chr&gt;, site &lt;chr&gt;</span></span>

8
reference/as.sir.md
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@@ -648,10 +648,10 @@ sir_interpretation_history()
#> # A tibble: 4 × 18
#> datetime index method ab_given mo_given host_given input_given
#> <dttm> <int> <chr> <chr> <chr> <chr> <chr>
#> 1 2025-12-22 08:45:24 1 MIC amoxicillin Escherich… human 8
#> 2 2025-12-22 08:45:24 1 MIC cipro Escherich… human 0.256
#> 3 2025-12-22 08:45:24 1 DISK tobra Escherich… human 16
#> 4 2025-12-22 08:45:24 1 DISK genta Escherich… human 18
#> 1 2025-12-23 10:09:01 1 MIC amoxicillin Escherich… human 8
#> 2 2025-12-23 10:09:02 1 MIC cipro Escherich… human 0.256
#> 3 2025-12-23 10:09:02 1 DISK tobra Escherich… human 16
#> 4 2025-12-23 10:09:02 1 DISK genta Escherich… human 18
#> # ℹ 11 more variables: ab <ab>, mo <mo>, host <chr>, input <chr>,
#> # outcome <sir>, notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,
#> # breakpoint_S_R <chr>, site <chr>

2
reference/atc_online.html
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@@ -7,7 +7,7 @@
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reference/av_from_text.html
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@@ -7,7 +7,7 @@
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reference/av_property.html
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@@ -7,7 +7,7 @@
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reference/availability.html
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@@ -7,7 +7,7 @@
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reference/bug_drug_combinations.html
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@@ -7,7 +7,7 @@
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9009</small>
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2
reference/clinical_breakpoints.html
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@@ -21,7 +21,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
<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="">3.0.1.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9009</small>
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2
reference/count.html
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@@ -9,7 +9,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<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="">3.0.1.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9009</small>
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2
reference/custom_eucast_rules.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="">3.0.1.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9009</small>
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2
reference/custom_mdro_guideline.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9009</small>
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2
reference/dosage.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9009</small>
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2
reference/esbl_isolates.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9009</small>
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2
reference/eucast_rules.html
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@@ -9,7 +9,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
<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="">3.0.1.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9009</small>
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2
reference/example_isolates.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9009</small>
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2
reference/example_isolates_unclean.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9009</small>
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2
reference/export_ncbi_biosample.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9009</small>
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2
reference/first_isolate.html
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@@ -9,7 +9,7 @@
<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="">3.0.1.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9009</small>
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2
reference/g.test.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9009</small>
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2
reference/get_episode.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9009</small>
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2
reference/ggplot_pca.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9009</small>
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2
reference/ggplot_sir.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9009</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
reference/guess_ab_col.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="">3.0.1.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9009</small>
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2
reference/index.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9009</small>
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2
reference/intrinsic_resistant.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9009</small>
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2
reference/italicise_taxonomy.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9009</small>
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2
reference/join.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="">3.0.1.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9009</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
reference/key_antimicrobials.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9009</small>
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2
reference/kurtosis.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="">3.0.1.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9009</small>
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2
reference/like.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="">3.0.1.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9009</small>
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2
reference/mdro.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="">3.0.1.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9009</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
reference/mean_amr_distance.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="">3.0.1.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9009</small>
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2
reference/microorganisms.codes.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="">3.0.1.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9009</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
reference/microorganisms.groups.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="">3.0.1.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9009</small>
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2
reference/microorganisms.html
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@@ -9,7 +9,7 @@ This data set is carefully crafted, yet made 100% reproducible from public and a
<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="">3.0.1.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9009</small>
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2
reference/mo_matching_score.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9009</small>
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2
reference/mo_property.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="">3.0.1.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9009</small>
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2
reference/mo_source.html
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@@ -9,7 +9,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<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="">3.0.1.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9009</small>
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2
reference/pca.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="">3.0.1.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9009</small>
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2
reference/plot.html
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@@ -9,7 +9,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<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="">3.0.1.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9009</small>
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2
reference/proportion.html
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@@ -9,7 +9,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<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="">3.0.1.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9009</small>
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2
reference/random.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="">3.0.1.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9009</small>
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2
reference/resistance_predict.html
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@@ -9,7 +9,7 @@ NOTE: These functions are deprecated and will be removed in a future version. Us
<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="">3.0.1.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9009</small>
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2
reference/skewness.html
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@@ -9,7 +9,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
<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="">3.0.1.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9009</small>
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2
reference/top_n_microorganisms.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="">3.0.1.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9009</small>
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2
reference/translate.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="">3.0.1.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9009</small>
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2
search.json
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