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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> <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>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</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>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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@@ -30,7 +30,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <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 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 page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
Markdown</a>. However, the methodology remains unchanged. This page was 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"> <div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a> <h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2> </h2>
@@ -147,21 +147,21 @@ make the structure of your data generally look like this:</p>
</tr></thead> </tr></thead>
<tbody> <tbody>
<tr class="odd"> <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">abcd</td>
<td align="center">Escherichia coli</td> <td align="center">Escherichia coli</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
</tr> </tr>
<tr class="even"> <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">abcd</td>
<td align="center">Escherichia coli</td> <td align="center">Escherichia coli</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">R</td> <td align="center">R</td>
</tr> </tr>
<tr class="odd"> <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">efgh</td>
<td align="center">Escherichia coli</td> <td align="center">Escherichia coli</td>
<td align="center">R</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 **Note:** values on this page will change with every website update
since they are based on randomly created values and the page was written since they are based on randomly created values and the page was written
in [R Markdown](https://rmarkdown.rstudio.com/). However, the 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. 2025.
## Introduction ## Introduction
@@ -52,9 +52,9 @@ structure of your data generally look like this:
| date | patient_id | mo | AMX | CIP | | date | patient_id | mo | AMX | CIP |
|:----------:|:----------:|:----------------:|:---:|:---:| |:----------:|:----------:|:----------------:|:---:|:---:|
| 2025-12-22 | abcd | Escherichia coli | S | S | | 2025-12-23 | abcd | Escherichia coli | S | S |
| 2025-12-22 | abcd | Escherichia coli | S | R | | 2025-12-23 | abcd | Escherichia coli | S | R |
| 2025-12-22 | efgh | Escherichia coli | R | S | | 2025-12-23 | efgh | Escherichia coli | R | S |
### Needed R packages ### Needed R packages

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@@ -30,7 +30,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

36
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> <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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -419,7 +419,7 @@ ROC curve looks like this:</p>
<h3 id="conclusion"> <h3 id="conclusion">
<strong>Conclusion</strong><a class="anchor" aria-label="anchor" href="#conclusion"></a> <strong>Conclusion</strong><a class="anchor" aria-label="anchor" href="#conclusion"></a>
</h3> </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 pipeline with the <code>tidymodels</code> framework and the
<code>AMR</code> package. By combining selector functions like <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 <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="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="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">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="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 class="co"># prep()</span></span>
<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></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 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> <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; predictor: 17</span></span>
<span><span class="co">#&gt; undeclared role: 1</span></span> <span><span class="co">#&gt; undeclared role: 1</span></span>
<span><span class="co">#&gt; </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; ── 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> <p><strong>Explanation:</strong></p>
<ul> <ul>
<li> <li>
@@ -641,7 +643,7 @@ that we can use to check the predictions with.</li>
</ul> </ul>
<p>It appears we can predict ESBL gene presence with a positive <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 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>
<div class="section level3"> <div class="section level3">
<h3 id="visualising-predictions"> <h3 id="visualising-predictions">
@@ -672,17 +674,21 @@ predictions?</p>
<span> colour <span class="op">=</span> <span class="va">correct</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span> <span> colour <span class="op">=</span> <span class="va">correct</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/scale_manual.html" class="external-link">scale_colour_manual</a></span><span class="op">(</span>values <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>Right <span class="op">=</span> <span class="st">"green3"</span>, Wrong <span class="op">=</span> <span class="st">"red2"</span><span class="op">)</span>,</span> <span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/scale_manual.html" class="external-link">scale_colour_manual</a></span><span class="op">(</span>values <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>Right <span class="op">=</span> <span class="st">"green3"</span>, Wrong <span class="op">=</span> <span class="st">"red2"</span><span class="op">)</span>,</span>
<span> name <span class="op">=</span> <span class="st">"Correct?"</span><span class="op">)</span> <span class="op">+</span></span> <span> name <span class="op">=</span> <span class="st">"Correct?"</span><span class="op">)</span> <span class="op">+</span></span>
<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_point.html" class="external-link">geom_point</a></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/geom_point.html" class="external-link">geom_point</a></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/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> <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> 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> <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"> <p><img src="AMR_with_tidymodels_files/figure-html/unnamed-chunk-15-1.png" class="r-plt" alt="" width="720"></p>
### <strong>Conclusion</strong></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 <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 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 <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 converts MICs (with or without operators) to log2-transformed numerics,
compatibility with classification models.</p> improving compatibility with classification models.</p>
<p>This pipeline enables realistic, reproducible, and interpretable <p>This pipeline enables realistic, reproducible, and interpretable
modelling of antimicrobial resistance data.</p> modelling of antimicrobial resistance data.</p>
<hr> <hr>
@@ -872,7 +878,7 @@ evaluate performance.</p>
<span><span class="co"># Make predictions</span></span> <span><span class="co"># Make predictions</span></span>
<span><span class="va">predictions_time</span> <span class="op">&lt;-</span> <span class="va">fitted_workflow_time</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span> <span><span class="va">predictions_time</span> <span class="op">&lt;-</span> <span class="va">fitted_workflow_time</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="https://rdrr.io/r/stats/predict.html" class="external-link">predict</a></span><span class="op">(</span><span class="va">test_time</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"><a href="https://rdrr.io/r/stats/predict.html" class="external-link">predict</a></span><span class="op">(</span><span class="va">test_time</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"><a href="https://dplyr.tidyverse.org/reference/bind_cols.html" class="external-link">bind_cols</a></span><span class="op">(</span><span class="va">test_time</span><span class="op">)</span> </span> <span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/bind_cols.html" class="external-link">bind_cols</a></span><span class="op">(</span><span class="va">test_time</span><span class="op">)</span></span>
<span></span> <span></span>
<span><span class="co"># Evaluate model</span></span> <span><span class="co"># Evaluate model</span></span>
<span><span class="va">metrics_time</span> <span class="op">&lt;-</span> <span class="va">predictions_time</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span> <span><span class="va">metrics_time</span> <span class="op">&lt;-</span> <span class="va">predictions_time</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
@@ -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> <p><img src="AMR_with_tidymodels_files/figure-html/unnamed-chunk-22-1.png" class="r-plt" alt="" width="720"></p>
</div> </div>
<div class="section level3"> <div class="section level3">
<h3 id="conclusion-1"> <h3 id="conclusion-2">
<strong>Conclusion</strong><a class="anchor" aria-label="anchor" href="#conclusion-1"></a> <strong>Conclusion</strong><a class="anchor" aria-label="anchor" href="#conclusion-2"></a>
</h3> </h3>
<p>In this example, we demonstrated how to analyze AMR trends over time <p>In this example, we demonstrated how to analyze AMR trends over time
using <code>tidymodels</code>. By aggregating resistance rates by year using <code>tidymodels</code>. By aggregating resistance rates by year

30
articles/AMR_with_tidymodels.md
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@@ -332,9 +332,9 @@ predictions %>%
### **Conclusion** ### **Conclusion**
In this post, we demonstrated how to build a machine learning pipeline In this example, we demonstrated how to build a machine learning
with the `tidymodels` framework and the `AMR` package. By combining pipeline with the `tidymodels` framework and the `AMR` package. By
selector functions like combining selector functions like
[`aminoglycosides()`](https://amr-for-r.org/reference/antimicrobial_selectors.md) [`aminoglycosides()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
and and
[`betalactams()`](https://amr-for-r.org/reference/antimicrobial_selectors.md) [`betalactams()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
@@ -431,10 +431,9 @@ testing_data <- testing(split)
# Define the recipe # Define the recipe
mic_recipe <- recipe(esbl ~ ., data = training_data) %>% mic_recipe <- recipe(esbl ~ ., data = training_data) %>%
remove_role(genus, old_role = "predictor") %>% # Remove non-informative variable remove_role(genus, old_role = "predictor") %>% # Remove non-informative variable
step_mic_log2(all_mic_predictors()) #%>% # Log2 transform all MIC predictors step_mic_log2(all_mic_predictors()) # Log2 transform all MIC predictors
# prep()
mic_recipe prep(mic_recipe)
#> #>
#> ── Recipe ────────────────────────────────────────────────────────────────────── #> ── Recipe ──────────────────────────────────────────────────────────────────────
#> #>
@@ -444,8 +443,11 @@ mic_recipe
#> predictor: 17 #> predictor: 17
#> undeclared role: 1 #> undeclared role: 1
#> #>
#> ── Training information
#> Training data contained 375 data points and no incomplete rows.
#>
#> ── Operations #> ── Operations
#> • Log2 transformation of MIC columns: all_mic_predictors() #> • Log2 transformation of MIC columns: AMC, AMP, TZP, CXM, FOX, ... | Trained
``` ```
**Explanation:** **Explanation:**
@@ -540,8 +542,8 @@ metrics
check the predictions with. check the predictions with.
It appears we can predict ESBL gene presence with a positive predictive 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 value (PPV) of 92.1% and a negative predictive value (NPV) of 91.9%
a simplistic logistic regression model. using a simplistic logistic regression model.
### **Visualising Predictions** ### **Visualising Predictions**
@@ -580,14 +582,16 @@ predictions %>%
theme_minimal() theme_minimal()
``` ```
![](AMR_with_tidymodels_files/figure-html/unnamed-chunk-15-1.png) \### ![](AMR_with_tidymodels_files/figure-html/unnamed-chunk-15-1.png)
**Conclusion**
### **Conclusion**
In this example, we showcased how the new `AMR`-specific recipe steps In this example, we showcased how the new `AMR`-specific recipe steps
simplify working with `<mic>` columns in `tidymodels`. The simplify working with `<mic>` columns in `tidymodels`. The
[`step_mic_log2()`](https://amr-for-r.org/reference/amr-tidymodels.md) [`step_mic_log2()`](https://amr-for-r.org/reference/amr-tidymodels.md)
transformation converts ordered MICs to log2-transformed numerics, transformation converts MICs (with or without operators) to
improving compatibility with classification models. log2-transformed numerics, improving compatibility with classification
models.
This pipeline enables realistic, reproducible, and interpretable This pipeline enables realistic, reproducible, and interpretable
modelling of antimicrobial resistance data. modelling of antimicrobial resistance data.

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@@ -30,7 +30,7 @@
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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> <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"> <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> <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> <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> <div class="d-none name"><code>datasets.Rmd</code></div>

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@@ -7,7 +7,7 @@
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@@ -33,7 +33,7 @@
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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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@@ -49,9 +49,9 @@
</div> </div>
<div class="section level2"> <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"> <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>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> <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> <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> <li>Data set <code>esbl_isolates</code> to practise with AMR modelling</li>
</ul></div> </ul></div>
<div class="section level4"> <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> <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>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> <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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# Changelog # Changelog
## AMR 3.0.1.9007 ## AMR 3.0.1.9009
#### New #### New

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PCA: PCA.html PCA: PCA.html
WHONET: WHONET.html WHONET: WHONET.html
WISCA: WISCA.html WISCA: WISCA.html
last_built: 2025-12-22T08:44Z last_built: 2025-12-23T10:08Z
urls: urls:
reference: https://amr-for-r.org/reference reference: https://amr-for-r.org/reference
article: https://amr-for-r.org/articles article: https://amr-for-r.org/articles

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@@ -7,7 +7,7 @@
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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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@@ -112,16 +112,16 @@
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">df</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> 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> 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 72.40822 46</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 76.30411 50</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 39.38630 13</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 93.09041 67</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 76.73151 50</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 29.49863 3</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 62.26575 36</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 73.60274 47</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 73.10411 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> </code></pre></div>
</div> </div>
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> </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 df
#> birth_date age age_exact age_at_y2k #> birth_date age age_exact age_at_y2k
#> 1 1980-02-27 45 45.81644 19 #> 1 1980-02-27 45 45.81918 19
#> 2 1953-07-26 72 72.40822 46 #> 2 1953-07-26 72 72.41096 46
#> 3 1949-09-02 76 76.30411 50 #> 3 1949-09-02 76 76.30685 50
#> 4 1986-08-03 39 39.38630 13 #> 4 1986-08-03 39 39.38904 13
#> 5 1932-11-19 93 93.09041 67 #> 5 1932-11-19 93 93.09315 67
#> 6 1949-03-30 76 76.73151 50 #> 6 1949-03-30 76 76.73425 50
#> 7 1996-06-23 29 29.49863 3 #> 7 1996-06-23 29 29.50137 3
#> 8 1963-09-16 62 62.26575 36 #> 8 1963-09-16 62 62.26849 36
#> 9 1952-05-16 73 73.60274 47 #> 9 1952-05-16 73 73.60548 47
#> 10 1952-11-14 73 73.10411 47 #> 10 1952-11-14 73 73.10685 47
``` ```

2
reference/age_groups.html
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@@ -7,7 +7,7 @@
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reference/amr-tidymodels.html
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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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@@ -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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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,
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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> <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> 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: #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;">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> 2025-12-22 <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;">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> 2025-12-22 <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;">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> 2025-12-22 <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;">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;"># 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;"># 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> <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 #> # A tibble: 4 × 18
#> datetime index method ab_given mo_given host_given input_given #> datetime index method ab_given mo_given host_given input_given
#> <dttm> <int> <chr> <chr> <chr> <chr> <chr> #> <dttm> <int> <chr> <chr> <chr> <chr> <chr>
#> 1 2025-12-22 08:45:24 1 MIC amoxicillin Escherich… human 8 #> 1 2025-12-23 10:09:01 1 MIC amoxicillin Escherich… human 8
#> 2 2025-12-22 08:45:24 1 MIC cipro Escherich… human 0.256 #> 2 2025-12-23 10:09:02 1 MIC cipro Escherich… human 0.256
#> 3 2025-12-22 08:45:24 1 DISK tobra Escherich… human 16 #> 3 2025-12-23 10:09:02 1 DISK tobra Escherich… human 16
#> 4 2025-12-22 08:45:24 1 DISK genta Escherich… human 18 #> 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>, #> # ℹ 11 more variables: ab <ab>, mo <mo>, host <chr>, input <chr>,
#> # outcome <sir>, notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>, #> # outcome <sir>, notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,
#> # breakpoint_S_R <chr>, site <chr> #> # breakpoint_S_R <chr>, site <chr>

2
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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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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
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@@ -9,7 +9,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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2
reference/custom_eucast_rules.html
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@@ -7,7 +7,7 @@
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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> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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reference/dosage.html
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@@ -7,7 +7,7 @@
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reference/esbl_isolates.html
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@@ -7,7 +7,7 @@
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reference/eucast_rules.html
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@@ -9,7 +9,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
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reference/example_isolates.html
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@@ -7,7 +7,7 @@
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2
reference/example_isolates_unclean.html
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@@ -7,7 +7,7 @@
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reference/export_ncbi_biosample.html
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@@ -7,7 +7,7 @@
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reference/first_isolate.html
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@@ -9,7 +9,7 @@
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reference/g.test.html
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@@ -7,7 +7,7 @@
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reference/get_episode.html
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@@ -7,7 +7,7 @@
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reference/ggplot_pca.html
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@@ -7,7 +7,7 @@
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reference/ggplot_sir.html
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@@ -7,7 +7,7 @@
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reference/guess_ab_col.html
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@@ -7,7 +7,7 @@
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reference/index.html
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@@ -7,7 +7,7 @@
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reference/intrinsic_resistant.html
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@@ -7,7 +7,7 @@
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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> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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2
reference/join.html
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@@ -7,7 +7,7 @@
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2
reference/key_antimicrobials.html
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@@ -7,7 +7,7 @@
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2
reference/kurtosis.html
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@@ -7,7 +7,7 @@
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2
reference/like.html
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@@ -7,7 +7,7 @@
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2
reference/mdro.html
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@@ -7,7 +7,7 @@
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2
reference/mean_amr_distance.html
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@@ -7,7 +7,7 @@
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2
reference/microorganisms.codes.html
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@@ -7,7 +7,7 @@
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2
reference/microorganisms.groups.html
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@@ -7,7 +7,7 @@
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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
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2
reference/mo_matching_score.html
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@@ -7,7 +7,7 @@
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2
reference/mo_property.html
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@@ -7,7 +7,7 @@
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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
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reference/pca.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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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> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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reference/proportion.html
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@@ -9,7 +9,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
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reference/random.html
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@@ -7,7 +7,7 @@
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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
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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
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reference/top_n_microorganisms.html
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@@ -7,7 +7,7 @@
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reference/translate.html
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@@ -7,7 +7,7 @@
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search.json
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