Built site for AMR@2.1.1.9121: 15fc72f

404.html

@@ -30,7 +30,7 @@
 
     <a class="navbar-brand me-2" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -46,6 +46,7 @@
     <li><a class="dropdown-item" href="https://msberends.github.io/AMR/reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="https://msberends.github.io/AMR/articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="https://msberends.github.io/AMR/articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="https://msberends.github.io/AMR/articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="https://msberends.github.io/AMR/reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="https://msberends.github.io/AMR/articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="https://msberends.github.io/AMR/articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

LICENSE-text.html

@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -21,6 +21,7 @@
     <li><a class="dropdown-item" href="reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

articles/AMR.html

@@ -29,7 +29,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -45,6 +45,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>
@@ -87,7 +88,7 @@
 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 15 December 2024.</p>
+generated on 19 December 2024.</p>
 <div class="section level2">
 <h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
 </h2>
@@ -143,21 +144,21 @@ make the structure of your data generally look like this:</p>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2024-12-15</td>
+<td align="center">2024-12-19</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">2024-12-15</td>
+<td align="center">2024-12-19</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">2024-12-15</td>
+<td align="center">2024-12-19</td>
 <td align="center">efgh</td>
 <td align="center">Escherichia coli</td>
 <td align="center">R</td>
@@ -176,8 +177,11 @@ creating beautiful plots in R.</p>
 <p>We will also use the <code>cleaner</code> package, that can be used
 for cleaning data and creating frequency tables.</p>
 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span>
+<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span></code></pre></div>
-<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://ggplot2.tidyverse.org" class="external-link">ggplot2</a></span><span class="op">)</span></span>
+<p>Error in get(paste0(generic, “.”, class), envir = get_method_env()) :
+object ‘type_sum.accel’ not found</p>
+<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://ggplot2.tidyverse.org" class="external-link">ggplot2</a></span><span class="op">)</span></span>
 <span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span></span>
 <span></span>
 <span><span class="co"># (if not yet installed, install with:)</span></span>
@@ -185,7 +189,7 @@ for cleaning data and creating frequency tables.</p>
 <p>The <code>AMR</code> package contains a data set
 <code>example_isolates_unclean</code>, which might look data that users
 have extracted from their laboratory systems:</p>
-<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">example_isolates_unclean</span></span>
 <span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 3,000 × 8</span></span></span>
 <span><span class="co">#&gt;    patient_id hospital date       bacteria      AMX   AMC   CIP   GEN  </span></span>
@@ -218,7 +222,7 @@ included data were retrieved on 24 Jun 2024.</p>
 <p>The codes of the AMR packages that come from <code><a href="../reference/as.mo.html">as.mo()</a></code> are
 short, but still human readable. More importantly, <code><a href="../reference/as.mo.html">as.mo()</a></code>
 supports all kinds of input:</p>
-<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span>
 <span><span class="co">#&gt; Class 'mo'</span></span>
 <span><span class="co">#&gt; [1] B_KLBSL_PNMN</span></span>
@@ -238,7 +242,7 @@ retrieve taxonomic properties, such as the name, genus, species, family,
 order, and even Gram-stain. They all start with <code>mo_</code> and
 they use <code><a href="../reference/as.mo.html">as.mo()</a></code> internally, so that still any arbitrary
 user input can be used:</p>
-<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/mo_property.html">mo_family</a></span><span class="op">(</span><span class="st">"K. pneumoniae"</span><span class="op">)</span></span>
 <span><span class="co">#&gt; [1] "Enterobacteriaceae"</span></span>
 <span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="st">"K. pneumoniae"</span><span class="op">)</span></span>
@@ -257,14 +261,14 @@ user input can be used:</p>
 <span><span class="co">#&gt; [1] "1098101000112102" "446870005"        "1098201000112108" "409801009"       </span></span>
 <span><span class="co">#&gt; [5] "56415008"         "714315002"        "713926009"</span></span></code></pre></div>
 <p>Now we can thus clean our data:</p>
-<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">our_data</span><span class="op">$</span><span class="va">bacteria</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="va">our_data</span><span class="op">$</span><span class="va">bacteria</span>, info <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
 <span><span class="co">#&gt; ℹ Microorganism translation was uncertain for four microorganisms. Run</span></span>
 <span><span class="co">#&gt;   mo_uncertainties() to review these uncertainties, or use</span></span>
 <span><span class="co">#&gt;   add_custom_microorganisms() to add custom entries.</span></span></code></pre></div>
 <p>Apparently, there was some uncertainty about the translation to
 taxonomic codes. Let’s check this:</p>
-<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/as.mo.html">mo_uncertainties</a></span><span class="op">(</span><span class="op">)</span></span>
 <span><span class="co">#&gt; Matching scores are based on the resemblance between the input and the full</span></span>
 <span><span class="co">#&gt; taxonomic name, and the pathogenicity in humans. See ?mo_matching_score.</span></span>
@@ -321,10 +325,10 @@ diffusion values, read more about that on the <code><a href="../reference/as.sir
 page.</p>
 <p>For now, we will just clean the SIR columns in our data using
 dplyr:</p>
-<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="co"># method 1, be explicit about the columns:</span></span>
 <span><span class="va">our_data</span> <span class="op">&lt;-</span> <span class="va">our_data</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/mutate_all.html" class="external-link">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">:</span><span class="va">GEN</span><span class="op">)</span>, <span class="va">as.sir</span><span class="op">)</span></span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">:</span><span class="va">GEN</span><span class="op">)</span>, <span class="va">as.sir</span><span class="op">)</span></span>
 <span></span>
 <span><span class="co"># method 2, let the AMR package determine the eligible columns</span></span>
 <span><span class="va">our_data</span> <span class="op">&lt;-</span> <span class="va">our_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
@@ -389,7 +393,7 @@ analysis, but the default phenotype-based method is in any case the
 method to properly correct for most duplicate isolates. Read more about
 the methods on the <code><a href="../reference/first_isolate.html">first_isolate()</a></code> page.</p>
 <p>The outcome of the function can easily be added to our data:</p>
-<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">our_data</span> <span class="op">&lt;-</span> <span class="va">our_data</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/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>first <span class="op">=</span> <span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span><span class="op">(</span>info <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span>
 <span><span class="co">#&gt; ℹ Determining first isolates using an episode length of 365 days</span></span>
@@ -403,16 +407,16 @@ the methods on the <code><a href="../reference/first_isolate.html">first_isolate
 <p>So only 91% is suitable for resistance analysis! We can now filter on
 it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the
 <code>dplyr</code> package:</p>
-<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">our_data_1st</span> <span class="op">&lt;-</span> <span class="va">our_data</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/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">first</span> <span class="op">==</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
 <p>For future use, the above two syntaxes can be shortened:</p>
-<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">our_data_1st</span> <span class="op">&lt;-</span> <span class="va">our_data</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="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
 <p>So we end up with 2 724 isolates for analysis. Now our data looks
 like:</p>
-<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb12"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">our_data_1st</span></span>
 <span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,724 × 9</span></span></span>
 <span><span class="co">#&gt;    patient_id hospital date       bacteria     AMX   AMC   CIP   GEN   first</span></span>
@@ -437,7 +441,7 @@ like:</p>
 <p>The base R <code><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary()</a></code> function gives a good first
 impression, as it comes with support for the new <code>mo</code> and
 <code>sir</code> classes that we now have in our data set:</p>
-<div class="sourceCode" id="cb12"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb13"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">our_data_1st</span><span class="op">)</span></span>
 <span><span class="co">#&gt;   patient_id          hospital              date           </span></span>
 <span><span class="co">#&gt;  Length:2724        Length:2724        Min.   :2011-01-01  </span></span>
@@ -486,7 +490,7 @@ impression, as it comes with support for the new <code>mo</code> and
 <p>To just get an idea how the species are distributed, create a
 frequency table with <code><a href="../reference/count.html">count()</a></code> based on the name of the
 microorganisms:</p>
-<div class="sourceCode" id="cb13"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb14"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">our_data</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="../reference/count.html">count</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">bacteria</span><span class="op">)</span>, sort <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
 <span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 4 × 2</span></span></span>
@@ -513,7 +517,7 @@ microorganisms:</p>
 <p>Using so-called antibiotic class selectors, you can select or filter
 columns based on the antibiotic class that your antibiotic results are
 in:</p>
-<div class="sourceCode" id="cb14"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">our_data_1st</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/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">date</span>, <span class="fu"><a href="../reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span>
 <span><span class="co">#&gt; ℹ For aminoglycosides() using column 'GEN' (gentamicin)</span></span>
@@ -658,7 +662,7 @@ failure</li>
 function to create any of the above antibiogram types. For starters,
 this is what the included <code>example_isolates</code> data set looks
 like:</p>
-<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">example_isolates</span></span>
 <span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,000 × 46</span></span></span>
 <span><span class="co">#&gt;    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX  </span></span>
@@ -687,7 +691,7 @@ like:</p>
 should be used. The <code>antibiotics</code> argument in the
 <code><a href="../reference/antibiogram.html">antibiogram()</a></code> function supports any (combination) of the
 previously mentioned antibiotic class selectors:</p>
-<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
 <span>            antibiotics <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="fu"><a href="../reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="../reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span>
 <span><span class="co">#&gt; ℹ The function aminoglycosides() should be used inside a dplyr verb or</span></span>
@@ -831,7 +835,7 @@ Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian,
 Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish,
 Swedish, Turkish, or Ukrainian. In this next example, we force the
 language to be Spanish using the <code>language</code> argument:</p>
-<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb18"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
 <span>            mo_transform <span class="op">=</span> <span class="st">"gramstain"</span>,</span>
 <span>            antibiotics <span class="op">=</span> <span class="fu"><a href="../reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>,</span>
@@ -885,7 +889,7 @@ language to be Spanish using the <code>language</code> argument:</p>
 </h4>
 <p>To create a combined antibiogram, use antibiotic codes or names with
 a plus <code>+</code> character like this:</p>
-<div class="sourceCode" id="cb18"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb19"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
 <span>            antibiotics <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="st">"TZP"</span>, <span class="st">"TZP+TOB"</span>, <span class="st">"TZP+GEN"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
 <table class="table">
@@ -965,7 +969,7 @@ a plus <code>+</code> character like this:</p>
 <p>To create a syndromic antibiogram, the <code>syndromic_group</code>
 argument must be used. This can be any column in the data, or e.g. an
 <code><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse()</a></code> with calculations based on certain columns:</p>
-<div class="sourceCode" id="cb19"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
 <span>            antibiotics <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="fu"><a href="../reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="../reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>,</span>
 <span>            syndromic_group <span class="op">=</span> <span class="st">"ward"</span><span class="op">)</span></span>
@@ -1165,7 +1169,7 @@ Antibiogram) in which cases are predefined based on clinical or
 demographic characteristics (e.g., endocarditis in 75+ females). This
 next example is a simplification without clinical characteristics, but
 just gives an idea of how a WISCA can be created:</p>
-<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb21"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">wisca</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
 <span>                     antibiotics <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="st">"AMC"</span>, <span class="st">"AMC+CIP"</span>, <span class="st">"TZP"</span>, <span class="st">"TZP+TOB"</span><span class="op">)</span>,</span>
 <span>                     mo_transform <span class="op">=</span> <span class="st">"gramstain"</span>,</span>
@@ -1233,7 +1237,7 @@ just gives an idea of how a WISCA can be created:</p>
 <p>Antibiograms can be plotted using <code><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot()</a></code> from the
 <code>ggplot2</code> packages, since this <code>AMR</code> package
 provides an extension to that function:</p>
-<div class="sourceCode" id="cb21"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb22"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">wisca</span><span class="op">)</span></span></code></pre></div>
 <p><img src="AMR_files/figure-html/unnamed-chunk-10-1.png" width="720"></p>
 <p>To calculate antimicrobial resistance in a more sensible way, also by
@@ -1262,12 +1266,12 @@ proportion of R (<code><a href="../reference/proportion.html">proportion_R()</a>
 I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equal to
 <code><a href="../reference/proportion.html">susceptibility()</a></code>). These functions can be used on their
 own:</p>
-<div class="sourceCode" id="cb22"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span></span>
 <span><span class="co">#&gt; [1] 0.4203377</span></span></code></pre></div>
 <p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and
 <code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
-<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb24"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">our_data_1st</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/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">hospital</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/summarise.html" class="external-link">summarise</a></span><span class="op">(</span>amoxicillin <span class="op">=</span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span><span class="op">)</span></span>

articles/AMR_for_Python.html

@@ -29,7 +29,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -45,6 +45,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

articles/AMR_with_tidymodels.html

@@ -0,0 +1,403 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en">
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+<title>`AMR` with `tidymodels` • AMR (for R)</title>
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+<script src="../extra.js"></script><meta property="og:title" content="`AMR` with `tidymodels`">
+</head>
+<body>
+    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
+    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
+
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
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+    </button>
+
+    <div id="navbar" class="collapse navbar-collapse ms-3">
+      <ul class="navbar-nav me-auto">
+<li class="active nav-item dropdown">
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-how-to" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true"><span class="fa fa-question-circle"></span> How to</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-how-to">
+<li><a class="dropdown-item" href="../articles/AMR.html"><span class="fa fa-directions"></span> Conduct AMR Analysis</a></li>
+    <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
+    <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
+    <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
+    <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
+    <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
+    <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>
+    <li><a class="dropdown-item" href="../articles/WHONET.html"><span class="fa fa-globe-americas"></span> Work with WHONET Data</a></li>
+    <li><a class="dropdown-item" href="../articles/EUCAST.html"><span class="fa fa-exchange-alt"></span> Apply Eucast Rules</a></li>
+    <li><a class="dropdown-item" href="../reference/mo_property.html"><span class="fa fa-bug"></span> Get Taxonomy of a Microorganism</a></li>
+    <li><a class="dropdown-item" href="../reference/ab_property.html"><span class="fa fa-capsules"></span> Get Properties of an Antibiotic Drug</a></li>
+    <li><a class="dropdown-item" href="../reference/av_property.html"><span class="fa fa-capsules"></span> Get Properties of an Antiviral Drug</a></li>
+  </ul>
+</li>
+<li class="nav-item"><a class="nav-link" href="../articles/AMR_for_Python.html"><span class="fa fab fa-python"></span> AMR for Python</a></li>
+<li class="nav-item"><a class="nav-link" href="../reference/index.html"><span class="fa fa-book-open"></span> Manual</a></li>
+<li class="nav-item"><a class="nav-link" href="../authors.html"><span class="fa fa-users"></span> Authors</a></li>
+      </ul>
+<ul class="navbar-nav">
+<li class="nav-item"><a class="nav-link" href="../news/index.html"><span class="fa far fa-newspaper"></span> Changelog</a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/msberends/AMR"><span class="fa fab fa-github"></span> Source Code</a></li>
+      </ul>
+</div>
+
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+</nav><div class="container template-article">
+
+
+
+
+<div class="row">
+  <main id="main" class="col-md-9"><div class="page-header">
+      <img src="../logo.svg" class="logo" alt=""><h1>`AMR` with `tidymodels`</h1>
+            
+      
+      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/AMR_with_tidymodels.Rmd" class="external-link"><code>vignettes/AMR_with_tidymodels.Rmd</code></a></small>
+      <div class="d-none name"><code>AMR_with_tidymodels.Rmd</code></div>
+    </div>
+
+    
+    
+<p>Antimicrobial resistance (AMR) is a global health crisis, and
+understanding resistance patterns is crucial for managing effective
+treatments. The <code>AMR</code> R package provides robust tools for
+analysing AMR data, including convenient antibiotic selector functions
+like <code><a href="../reference/antibiotic_class_selectors.html">aminoglycosides()</a></code> and <code><a href="../reference/antibiotic_class_selectors.html">betalactams()</a></code>. In
+this post, we will explore how to use the <code>tidymodels</code>
+framework to predict resistance patterns in the
+<code>example_isolates</code> dataset.</p>
+<p>By leveraging the power of <code>tidymodels</code> and the
+<code>AMR</code> package, we’ll build a reproducible machine learning
+workflow to predict resistance to two important antibiotic classes:
+aminoglycosides and beta-lactams.</p>
+<hr>
+<div class="section level3">
+<h3 id="objective">
+<strong>Objective</strong><a class="anchor" aria-label="anchor" href="#objective"></a>
+</h3>
+<p>Our goal is to build a predictive model using the
+<code>tidymodels</code> framework to determine resistance patterns based
+on microbial data. We will:</p>
+<ol style="list-style-type: decimal">
+<li>Preprocess data using the selector functions
+<code><a href="../reference/antibiotic_class_selectors.html">aminoglycosides()</a></code> and <code><a href="../reference/antibiotic_class_selectors.html">betalactams()</a></code>.</li>
+<li>Define a logistic regression model for prediction.</li>
+<li>Use a structured <code>tidymodels</code> workflow to preprocess,
+train, and evaluate the model.</li>
+</ol>
+<hr>
+</div>
+<div class="section level3">
+<h3 id="data-preparation">
+<strong>Data Preparation</strong><a class="anchor" aria-label="anchor" href="#data-preparation"></a>
+</h3>
+<p>We begin by loading the required libraries and preparing the
+<code>example_isolates</code> dataset from the <code>AMR</code>
+package.</p>
+<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="co"># Load required libraries</span></span>
+<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://tidymodels.tidymodels.org" class="external-link">tidymodels</a></span><span class="op">)</span>   <span class="co"># For machine learning workflows, and data manipulation (dplyr, tidyr, ...)</span></span>
+<span><span class="co">#&gt; Error in get(paste0(generic, ".", class), envir = get_method_env()) : </span></span>
+<span><span class="co">#&gt;   object 'type_sum.accel' not found</span></span>
+<span><span class="co">#&gt; ── <span style="font-weight: bold;">Attaching packages</span> ────────────────────────────────────── tidymodels 1.2.0 ──</span></span>
+<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">broom       </span> 1.0.7     <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">recipes     </span> 1.1.0</span></span>
+<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">dials       </span> 1.3.0     <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">rsample     </span> 1.2.1</span></span>
+<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">dplyr       </span> 1.1.4     <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">tibble      </span> 3.2.1</span></span>
+<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">ggplot2     </span> 3.5.1     <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">tidyr       </span> 1.3.1</span></span>
+<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">infer       </span> 1.0.7     <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">tune        </span> 1.2.1</span></span>
+<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">modeldata   </span> 1.4.0     <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">workflows   </span> 1.1.4</span></span>
+<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">parsnip     </span> 1.2.1     <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">workflowsets</span> 1.1.0</span></span>
+<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">purrr       </span> 1.0.2     <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">yardstick   </span> 1.3.1</span></span>
+<span><span class="co">#&gt; ── <span style="font-weight: bold;">Conflicts</span> ───────────────────────────────────────── tidymodels_conflicts() ──</span></span>
+<span><span class="co">#&gt; <span style="color: #BB0000;">✖</span> <span style="color: #0000BB;">purrr</span>::<span style="color: #00BB00;">discard()</span> masks <span style="color: #0000BB;">scales</span>::discard()</span></span>
+<span><span class="co">#&gt; <span style="color: #BB0000;">✖</span> <span style="color: #0000BB;">dplyr</span>::<span style="color: #00BB00;">filter()</span>  masks <span style="color: #0000BB;">stats</span>::filter()</span></span>
+<span><span class="co">#&gt; <span style="color: #BB0000;">✖</span> <span style="color: #0000BB;">dplyr</span>::<span style="color: #00BB00;">lag()</span>     masks <span style="color: #0000BB;">stats</span>::lag()</span></span>
+<span><span class="co">#&gt; <span style="color: #BB0000;">✖</span> <span style="color: #0000BB;">recipes</span>::<span style="color: #00BB00;">step()</span>  masks <span style="color: #0000BB;">stats</span>::step()</span></span>
+<span><span class="co">#&gt; <span style="color: #0000BB;">•</span> Use <span style="color: #00BB00;">tidymodels_prefer()</span> to resolve common conflicts.</span></span>
+<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span>          <span class="co"># For AMR data analysis</span></span>
+<span></span>
+<span><span class="co"># Load the example_isolates dataset</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="st">"example_isolates"</span><span class="op">)</span>  <span class="co"># Preloaded dataset with AMR results</span></span>
+<span></span>
+<span><span class="co"># Select relevant columns for prediction</span></span>
+<span><span class="va">data</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
+<span>  <span class="co"># select AB results dynamically</span></span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">mo</span>, <span class="fu"><a href="../reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="../reference/antibiotic_class_selectors.html">betalactams</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
+<span>  <span class="co"># replace NAs with NI (not-interpretable)</span></span>
+<span>   <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.sir</span><span class="op">)</span>,</span>
+<span>                 <span class="op">~</span><span class="fu">replace_na</span><span class="op">(</span><span class="va">.x</span>, <span class="st">"NI"</span><span class="op">)</span><span class="op">)</span>,</span>
+<span>          <span class="co"># make factors of SIR columns</span></span>
+<span>          <span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.sir</span><span class="op">)</span>,</span>
+<span>                 <span class="va">as.integer</span><span class="op">)</span>,</span>
+<span>          <span class="co"># get Gramstain of microorganisms</span></span>
+<span>          mo <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">as.factor</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
+<span>  <span class="co"># drop NAs - the ones without a Gramstain (fungi, etc.)</span></span>
+<span>  <span class="fu">drop_na</span><span class="op">(</span><span class="op">)</span> <span class="co"># %&gt;%</span></span>
+<span><span class="co">#&gt; ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span></span>
+<span><span class="co">#&gt;   (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span></span>
+<span><span class="co">#&gt; ℹ For betalactams() using columns 'PEN' (benzylpenicillin), 'OXA'</span></span>
+<span><span class="co">#&gt;   (oxacillin), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC'</span></span>
+<span><span class="co">#&gt;   (amoxicillin/clavulanic acid), 'AMP' (ampicillin), 'TZP'</span></span>
+<span><span class="co">#&gt;   (piperacillin/tazobactam), 'CZO' (cefazolin), 'FEP' (cefepime), 'CXM'</span></span>
+<span><span class="co">#&gt;   (cefuroxime), 'FOX' (cefoxitin), 'CTX' (cefotaxime), 'CAZ' (ceftazidime),</span></span>
+<span><span class="co">#&gt;   'CRO' (ceftriaxone), 'IPM' (imipenem), and 'MEM' (meropenem)</span></span>
+<span>  <span class="co"># Cefepime is not reliable</span></span>
+<span>  <span class="co">#select(-FEP)</span></span></code></pre></div>
+<p><strong>Explanation:</strong> - <code><a href="../reference/antibiotic_class_selectors.html">aminoglycosides()</a></code> and
+<code><a href="../reference/antibiotic_class_selectors.html">betalactams()</a></code> dynamically select columns for antibiotics in
+these classes. - <code>drop_na()</code> ensures the model receives
+complete cases for training.</p>
+<hr>
+</div>
+<div class="section level3">
+<h3 id="defining-the-workflow">
+<strong>Defining the Workflow</strong><a class="anchor" aria-label="anchor" href="#defining-the-workflow"></a>
+</h3>
+<p>We now define the <code>tidymodels</code> workflow, which consists of
+three steps: preprocessing, model specification, and fitting.</p>
+<div class="section level4">
+<h4 id="preprocessing-with-a-recipe">1. Preprocessing with a Recipe<a class="anchor" aria-label="anchor" href="#preprocessing-with-a-recipe"></a>
+</h4>
+<p>We create a recipe to preprocess the data for modelling. This
+includes: - Encoding resistance results (<code>S</code>, <code>I</code>,
+<code>R</code>) as binary (resistant or not resistant). - Converting
+microbial organism names (<code>mo</code>) into numerical features using
+one-hot encoding.</p>
+<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="co"># Define the recipe for data preprocessing</span></span>
+<span><span class="va">resistance_recipe</span> <span class="op">&lt;-</span> <span class="fu">recipe</span><span class="op">(</span><span class="va">mo</span> <span class="op">~</span> <span class="va">.</span>, data <span class="op">=</span> <span class="va">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">step_corr</span><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="fu"><a href="../reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="../reference/antibiotic_class_selectors.html">betalactams</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>, threshold <span class="op">=</span> <span class="fl">0.9</span><span class="op">)</span></span>
+<span><span class="va">resistance_recipe</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>
+<span><span class="co">#&gt; ── Inputs</span></span>
+<span><span class="co">#&gt; Number of variables by role</span></span>
+<span><span class="co">#&gt; outcome:    1</span></span>
+<span><span class="co">#&gt; predictor: 20</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> Correlation filter on: <span style="color: #0000BB;">c(aminoglycosides(), betalactams())</span></span></span></code></pre></div>
+<p><strong>Explanation:</strong> - <code>step_mutate()</code> transforms
+resistance results (<code>R</code>) into binary variables (TRUE/FALSE).
+- <code>step_dummy()</code> converts categorical organism
+(<code>mo</code>) names into one-hot encoded numerical features, making
+them compatible with the model.</p>
+</div>
+<div class="section level4">
+<h4 id="specifying-the-model">2. Specifying the Model<a class="anchor" aria-label="anchor" href="#specifying-the-model"></a>
+</h4>
+<p>We define a logistic regression model since resistance prediction is
+a binary classification task.</p>
+<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="co"># Specify a logistic regression model</span></span>
+<span><span class="va">logistic_model</span> <span class="op">&lt;-</span> <span class="fu">logistic_reg</span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
+<span>  <span class="fu">set_engine</span><span class="op">(</span><span class="st">"glm"</span><span class="op">)</span> <span class="co"># Use the Generalized Linear Model engine</span></span>
+<span><span class="va">logistic_model</span></span>
+<span><span class="co">#&gt; Logistic Regression Model Specification (classification)</span></span>
+<span><span class="co">#&gt; </span></span>
+<span><span class="co">#&gt; Computational engine: glm</span></span></code></pre></div>
+<p><strong>Explanation:</strong> - <code>logistic_reg()</code> sets up a
+logistic regression model. - <code>set_engine("glm")</code> specifies
+the use of R’s built-in GLM engine.</p>
+</div>
+<div class="section level4">
+<h4 id="building-the-workflow">3. Building the Workflow<a class="anchor" aria-label="anchor" href="#building-the-workflow"></a>
+</h4>
+<p>We bundle the recipe and model together into a <code>workflow</code>,
+which organizes the entire modeling process.</p>
+<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="co"># Combine the recipe and model into a workflow</span></span>
+<span><span class="va">resistance_workflow</span> <span class="op">&lt;-</span> <span class="fu">workflow</span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
+<span>  <span class="fu">add_recipe</span><span class="op">(</span><span class="va">resistance_recipe</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"># Add the preprocessing recipe</span></span>
+<span>  <span class="fu">add_model</span><span class="op">(</span><span class="va">logistic_model</span><span class="op">)</span> <span class="co"># Add the logistic regression model</span></span>
+<span><span class="va">resistance_workflow</span></span>
+<span><span class="co">#&gt; ══ Workflow ════════════════════════════════════════════════════════════════════</span></span>
+<span><span class="co">#&gt; <span style="font-style: italic;">Preprocessor:</span> Recipe</span></span>
+<span><span class="co">#&gt; <span style="font-style: italic;">Model:</span> logistic_reg()</span></span>
+<span><span class="co">#&gt; </span></span>
+<span><span class="co">#&gt; ── Preprocessor ────────────────────────────────────────────────────────────────</span></span>
+<span><span class="co">#&gt; 1 Recipe Step</span></span>
+<span><span class="co">#&gt; </span></span>
+<span><span class="co">#&gt; • step_corr()</span></span>
+<span><span class="co">#&gt; </span></span>
+<span><span class="co">#&gt; ── Model ───────────────────────────────────────────────────────────────────────</span></span>
+<span><span class="co">#&gt; Logistic Regression Model Specification (classification)</span></span>
+<span><span class="co">#&gt; </span></span>
+<span><span class="co">#&gt; Computational engine: glm</span></span></code></pre></div>
+<hr>
+</div>
+</div>
+<div class="section level3">
+<h3 id="training-and-evaluating-the-model">
+<strong>Training and Evaluating the Model</strong><a class="anchor" aria-label="anchor" href="#training-and-evaluating-the-model"></a>
+</h3>
+<p>To train the model, we split the data into training and testing sets.
+Then, we fit the workflow on the training set and evaluate its
+performance.</p>
+<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="co"># Split data into training and testing sets</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/base/Random.html" class="external-link">set.seed</a></span><span class="op">(</span><span class="fl">123</span><span class="op">)</span> <span class="co"># For reproducibility</span></span>
+<span><span class="va">data_split</span> <span class="op">&lt;-</span> <span class="fu">initial_split</span><span class="op">(</span><span class="va">data</span>, prop <span class="op">=</span> <span class="fl">0.8</span><span class="op">)</span> <span class="co"># 80% training, 20% testing</span></span>
+<span><span class="va">training_data</span> <span class="op">&lt;-</span> <span class="fu">training</span><span class="op">(</span><span class="va">data_split</span><span class="op">)</span> <span class="co"># Training set</span></span>
+<span><span class="va">testing_data</span> <span class="op">&lt;-</span> <span class="fu">testing</span><span class="op">(</span><span class="va">data_split</span><span class="op">)</span>   <span class="co"># Testing set</span></span>
+<span></span>
+<span><span class="co"># Fit the workflow to the training data</span></span>
+<span><span class="va">fitted_workflow</span> <span class="op">&lt;-</span> <span class="va">resistance_workflow</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
+<span>  <span class="fu">fit</span><span class="op">(</span><span class="va">training_data</span><span class="op">)</span> <span class="co"># Train the model</span></span>
+<span><span class="co">#&gt; ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span></span>
+<span><span class="co">#&gt;   (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span></span>
+<span><span class="co">#&gt; ℹ For betalactams() using columns 'PEN' (benzylpenicillin), 'OXA'</span></span>
+<span><span class="co">#&gt;   (oxacillin), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC'</span></span>
+<span><span class="co">#&gt;   (amoxicillin/clavulanic acid), 'AMP' (ampicillin), 'TZP'</span></span>
+<span><span class="co">#&gt;   (piperacillin/tazobactam), 'CZO' (cefazolin), 'FEP' (cefepime), 'CXM'</span></span>
+<span><span class="co">#&gt;   (cefuroxime), 'FOX' (cefoxitin), 'CTX' (cefotaxime), 'CAZ' (ceftazidime),</span></span>
+<span><span class="co">#&gt;   'CRO' (ceftriaxone), 'IPM' (imipenem), and 'MEM' (meropenem)</span></span>
+<span></span>
+<span><span class="va">fitted_workflow</span></span>
+<span><span class="co">#&gt; ══ Workflow [trained] ══════════════════════════════════════════════════════════</span></span>
+<span><span class="co">#&gt; <span style="font-style: italic;">Preprocessor:</span> Recipe</span></span>
+<span><span class="co">#&gt; <span style="font-style: italic;">Model:</span> logistic_reg()</span></span>
+<span><span class="co">#&gt; </span></span>
+<span><span class="co">#&gt; ── Preprocessor ────────────────────────────────────────────────────────────────</span></span>
+<span><span class="co">#&gt; 1 Recipe Step</span></span>
+<span><span class="co">#&gt; </span></span>
+<span><span class="co">#&gt; • step_corr()</span></span>
+<span><span class="co">#&gt; </span></span>
+<span><span class="co">#&gt; ── Model ───────────────────────────────────────────────────────────────────────</span></span>
+<span><span class="co">#&gt; </span></span>
+<span><span class="co">#&gt; Call:  stats::glm(formula = ..y ~ ., family = stats::binomial, data = data)</span></span>
+<span><span class="co">#&gt; </span></span>
+<span><span class="co">#&gt; Coefficients:</span></span>
+<span><span class="co">#&gt; (Intercept)          GEN          TOB          AMK          KAN          PEN  </span></span>
+<span><span class="co">#&gt;   101.11641     -3.69738      4.55879      1.86703    -23.37497     -0.57182  </span></span>
+<span><span class="co">#&gt;         OXA          FLC          AMC          AMP          TZP          CZO  </span></span>
+<span><span class="co">#&gt;    -4.68575    -11.69742      0.79748     -1.56197      0.87667     -2.28424  </span></span>
+<span><span class="co">#&gt;         FEP          CXM          FOX          CAZ          CRO          IPM  </span></span>
+<span><span class="co">#&gt;    -0.19847      0.02659     10.32455     10.27248      0.97321     -0.93096  </span></span>
+<span><span class="co">#&gt;         MEM  </span></span>
+<span><span class="co">#&gt;    -0.88753  </span></span>
+<span><span class="co">#&gt; </span></span>
+<span><span class="co">#&gt; Degrees of Freedom: 1573 Total (i.e. Null);  1555 Residual</span></span>
+<span><span class="co">#&gt; Null Deviance:       2071 </span></span>
+<span><span class="co">#&gt; Residual Deviance: 74.91     AIC: 112.9</span></span></code></pre></div>
+<p><strong>Explanation:</strong> - <code>initial_split()</code> splits
+the data into training and testing sets. - <code>fit()</code> trains the
+workflow on the training set.</p>
+<p>Next, we evaluate the model on the testing data.</p>
+<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="co"># Make predictions on the testing set</span></span>
+<span><span class="va">predictions</span> <span class="op">&lt;-</span> <span class="va">fitted_workflow</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">testing_data</span><span class="op">)</span>                <span class="co"># Generate predictions</span></span>
+<span><span class="va">probabilities</span> <span class="op">&lt;-</span> <span class="va">fitted_workflow</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">testing_data</span>, type <span class="op">=</span> <span class="st">"prob"</span><span class="op">)</span> <span class="co"># Generate probabilities</span></span>
+<span></span>
+<span><span class="va">predictions</span> <span class="op">&lt;-</span> <span class="va">predictions</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">probabilities</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">testing_data</span><span class="op">)</span> <span class="co"># Combine with true labels</span></span>
+<span></span>
+<span><span class="va">predictions</span></span>
+<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 394 × 24</span></span></span>
+<span><span class="co">#&gt;    .pred_class   `.pred_Gram-negative` `.pred_Gram-positive` mo        GEN   TOB</span></span>
+<span><span class="co">#&gt;    <span style="color: #949494; font-style: italic;">&lt;fct&gt;</span>                         <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span>                 <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;fct&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> Gram-positive              1.07<span style="color: #949494;">e</span><span style="color: #BB0000;">- 1</span>              8.93<span style="color: #949494;">e</span><span style="color: #BB0000;">- 1</span> Gram-p…     5     5</span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> Gram-positive              3.17<span style="color: #949494;">e</span><span style="color: #BB0000;">- 8</span>              1.00<span style="color: #949494;">e</span>+ 0 Gram-p…     5     1</span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> Gram-negative              9.99<span style="color: #949494;">e</span><span style="color: #BB0000;">- 1</span>              1.42<span style="color: #949494;">e</span><span style="color: #BB0000;">- 3</span> Gram-n…     5     5</span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> Gram-positive              2.22<span style="color: #949494;">e</span><span style="color: #BB0000;">-16</span>              1   <span style="color: #949494;">e</span>+ 0 Gram-p…     5     5</span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> Gram-negative              9.46<span style="color: #949494;">e</span><span style="color: #BB0000;">- 1</span>              5.42<span style="color: #949494;">e</span><span style="color: #BB0000;">- 2</span> Gram-n…     5     5</span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> Gram-positive              1.07<span style="color: #949494;">e</span><span style="color: #BB0000;">- 1</span>              8.93<span style="color: #949494;">e</span><span style="color: #BB0000;">- 1</span> Gram-p…     5     5</span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> Gram-positive              2.22<span style="color: #949494;">e</span><span style="color: #BB0000;">-16</span>              1   <span style="color: #949494;">e</span>+ 0 Gram-p…     1     5</span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> Gram-positive              2.22<span style="color: #949494;">e</span><span style="color: #BB0000;">-16</span>              1   <span style="color: #949494;">e</span>+ 0 Gram-p…     4     4</span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> Gram-negative              1   <span style="color: #949494;">e</span>+ 0              2.22<span style="color: #949494;">e</span><span style="color: #BB0000;">-16</span> Gram-n…     1     1</span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> Gram-positive              6.05<span style="color: #949494;">e</span><span style="color: #BB0000;">-11</span>              1.00<span style="color: #949494;">e</span>+ 0 Gram-p…     4     4</span></span>
+<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 384 more rows</span></span></span>
+<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 18 more variables: AMK &lt;int&gt;, KAN &lt;int&gt;, PEN &lt;int&gt;, OXA &lt;int&gt;, FLC &lt;int&gt;,</span></span></span>
+<span><span class="co">#&gt; <span style="color: #949494;">#   AMX &lt;int&gt;, AMC &lt;int&gt;, AMP &lt;int&gt;, TZP &lt;int&gt;, CZO &lt;int&gt;, FEP &lt;int&gt;,</span></span></span>
+<span><span class="co">#&gt; <span style="color: #949494;">#   CXM &lt;int&gt;, FOX &lt;int&gt;, CTX &lt;int&gt;, CAZ &lt;int&gt;, CRO &lt;int&gt;, IPM &lt;int&gt;, MEM &lt;int&gt;</span></span></span>
+<span></span>
+<span><span class="co"># Evaluate model performance</span></span>
+<span><span class="va">metrics</span> <span class="op">&lt;-</span> <span class="va">predictions</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
+<span>  <span class="fu">metrics</span><span class="op">(</span>truth <span class="op">=</span> <span class="va">mo</span>, estimate <span class="op">=</span> <span class="va">.pred_class</span><span class="op">)</span> <span class="co"># Calculate performance metrics</span></span>
+<span></span>
+<span><span class="va">metrics</span></span>
+<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2 × 3</span></span></span>
+<span><span class="co">#&gt;   .metric  .estimator .estimate</span></span>
+<span><span class="co">#&gt;   <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>          <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;">1</span> accuracy binary         0.995</span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;">2</span> kap      binary         0.989</span></span></code></pre></div>
+<p><strong>Explanation:</strong> - <code><a href="https://rdrr.io/r/stats/predict.html" class="external-link">predict()</a></code> generates
+predictions on the testing set. - <code>metrics()</code> computes
+evaluation metrics like accuracy and AUC.</p>
+<p>It appears we can predict the Gram based on AMR results with a 0.995
+accuracy. The ROC curve looks like:</p>
+<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="va">predictions</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
+<span>  <span class="fu">roc_curve</span><span class="op">(</span><span class="va">mo</span>, <span class="va">`.pred_Gram-negative`</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://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</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-7-1.png" width="720"></p>
+<hr>
+</div>
+<div class="section level3">
+<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
+pipeline with the <code>tidymodels</code> framework and the
+<code>AMR</code> package. By combining selector functions like
+<code><a href="../reference/antibiotic_class_selectors.html">aminoglycosides()</a></code> and <code><a href="../reference/antibiotic_class_selectors.html">betalactams()</a></code> with
+<code>tidymodels</code>, we efficiently prepared data, trained a model,
+and evaluated its performance.</p>
+<p>This workflow is extensible to other antibiotic classes and
+resistance patterns, empowering users to analyse AMR data systematically
+and reproducibly.</p>
+<hr>
+</div>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+    </nav></aside>
+</div>
+
+
+
+    <footer><div class="pkgdown-footer-left">
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p>
+</div>
+
+<div class="pkgdown-footer-right">
+  <p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/assets/logo_rug.svg" style="max-width: 150px;"></a><a target="_blank" href="https://www.umcg.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/assets/logo_umcg.svg" style="max-width: 150px;"></a></p>
+</div>
+
+    </footer>
+</div>
+
+
+
+
+
+  </body>
+</html>

articles/EUCAST.html

@@ -29,7 +29,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -45,6 +45,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

articles/MDR.html

@@ -29,7 +29,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -45,6 +45,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

articles/PCA.html

@@ -29,7 +29,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -45,6 +45,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>
@@ -96,6 +97,8 @@ is currently being developed.</strong></p>
 <code>example_isolates</code> data set in this package looks like:</p>
 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span></span>
+<span><span class="co">#&gt; Error in get(paste0(generic, ".", class), envir = get_method_env()) : </span></span>
+<span><span class="co">#&gt;   object 'type_sum.accel' not found</span></span>
 <span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span>
 <span><span class="fu"><a href="https://pillar.r-lib.org/reference/glimpse.html" class="external-link">glimpse</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span></span>
 <span><span class="co">#&gt; Rows: 2,000</span></span>
@@ -107,45 +110,45 @@ is currently being developed.</strong></p>
 <span><span class="co">#&gt; $ ward    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> "Clinical", "Clinical", "ICU", "ICU", "ICU", "ICU", "Clinical"…</span></span>
 <span><span class="co">#&gt; $ mo      <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> "B_ESCHR_COLI", "B_ESCHR_COLI", "B_STPHY_EPDR", "B_STPHY_EPDR",…</span></span>
 <span><span class="co">#&gt; $ PEN     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, S,…</span></span>
-<span><span class="co">#&gt; $ OXA     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
+<span><span class="co">#&gt; $ OXA     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>…</span></span>
-<span><span class="co">#&gt; $ FLC     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, R, R, R, R, S, S, R, S, S, S, NA, NA, NA, NA, NA, R, R…</span></span>
+<span><span class="co">#&gt; $ FLC     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R, R, R, R, S, S, R, S, S, S, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R, R…</span></span>
-<span><span class="co">#&gt; $ AMX     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, R, R, NA, NA, NA, NA, NA, NA, R, NA, N…</span></span>
+<span><span class="co">#&gt; $ AMX     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R, R, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">N</span>…</span></span>
-<span><span class="co">#&gt; $ AMC     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> I, I, NA, NA, NA, NA, S, S, NA, NA, S, S, I, I, R, I, I, NA, N…</span></span>
+<span><span class="co">#&gt; $ AMC     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> I, I, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, S, S, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, S, S, I, I, R, I, I, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">N</span>…</span></span>
-<span><span class="co">#&gt; $ AMP     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, R, R, NA, NA, NA, NA, NA, NA, R, NA, N…</span></span>
+<span><span class="co">#&gt; $ AMP     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R, R, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">N</span>…</span></span>
-<span><span class="co">#&gt; $ TZP     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
+<span><span class="co">#&gt; $ TZP     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>…</span></span>
-<span><span class="co">#&gt; $ CZO     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, NA,…</span></span>
+<span><span class="co">#&gt; $ CZO     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R, <span style="color: #BB0000;">NA</span>,…</span></span>
-<span><span class="co">#&gt; $ FEP     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
+<span><span class="co">#&gt; $ FEP     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>…</span></span>
-<span><span class="co">#&gt; $ CXM     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> I, I, R, R, R, R, S, S, R, S, S, S, S, S, NA, S, S, R, R, S, S…</span></span>
+<span><span class="co">#&gt; $ CXM     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> I, I, R, R, R, R, S, S, R, S, S, S, S, S, <span style="color: #BB0000;">NA</span>, S, S, R, R, S, S…</span></span>
-<span><span class="co">#&gt; $ FOX     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, NA,…</span></span>
+<span><span class="co">#&gt; $ FOX     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R, <span style="color: #BB0000;">NA</span>,…</span></span>
-<span><span class="co">#&gt; $ CTX     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, S, S…</span></span>
+<span><span class="co">#&gt; $ CTX     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, S, S, <span style="color: #BB0000;">NA</span>, S, S…</span></span>
-<span><span class="co">#&gt; $ CAZ     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, S, S, R, R, …</span></span>
+<span><span class="co">#&gt; $ CAZ     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R, R, R, R, R, R, R, R, R, R, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, S, S, R, R, …</span></span>
-<span><span class="co">#&gt; $ CRO     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, S, S…</span></span>
+<span><span class="co">#&gt; $ CRO     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, S, S, <span style="color: #BB0000;">NA</span>, S, S…</span></span>
-<span><span class="co">#&gt; $ GEN     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
+<span><span class="co">#&gt; $ GEN     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>…</span></span>
-<span><span class="co">#&gt; $ TOB     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA, S, S, NA, NA, NA…</span></span>
+<span><span class="co">#&gt; $ TOB     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, S, S, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, S, S, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>…</span></span>
-<span><span class="co">#&gt; $ AMK     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
+<span><span class="co">#&gt; $ AMK     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>…</span></span>
-<span><span class="co">#&gt; $ KAN     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
+<span><span class="co">#&gt; $ KAN     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>…</span></span>
-<span><span class="co">#&gt; $ TMP     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> R, R, S, S, R, R, R, R, S, S, NA, NA, S, S, S, S, S, R, R, R, …</span></span>
+<span><span class="co">#&gt; $ TMP     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> R, R, S, S, R, R, R, R, S, S, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, S, S, S, S, S, R, R, R, …</span></span>
-<span><span class="co">#&gt; $ SXT     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> R, R, S, S, NA, NA, NA, NA, S, S, NA, NA, S, S, S, S, S, NA, N…</span></span>
+<span><span class="co">#&gt; $ SXT     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> R, R, S, S, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, S, S, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, S, S, S, S, S, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">N</span>…</span></span>
-<span><span class="co">#&gt; $ NIT     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R,…</span></span>
+<span><span class="co">#&gt; $ NIT     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R,…</span></span>
-<span><span class="co">#&gt; $ FOS     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
+<span><span class="co">#&gt; $ FOS     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>…</span></span>
-<span><span class="co">#&gt; $ LNZ     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R, R, R, N…</span></span>
+<span><span class="co">#&gt; $ LNZ     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> R, R, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R, R, R, R, R, <span style="color: #BB0000;">N</span>…</span></span>
-<span><span class="co">#&gt; $ CIP     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA, NA, S, S…</span></span>
+<span><span class="co">#&gt; $ CIP     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, S, S, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, S, S…</span></span>
-<span><span class="co">#&gt; $ MFX     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
+<span><span class="co">#&gt; $ MFX     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>…</span></span>
-<span><span class="co">#&gt; $ VAN     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> R, R, S, S, S, S, S, S, S, S, NA, NA, R, R, R, R, R, S, S, S, …</span></span>
+<span><span class="co">#&gt; $ VAN     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> R, R, S, S, S, S, S, S, S, S, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R, R, R, R, R, S, S, S, …</span></span>
-<span><span class="co">#&gt; $ TEC     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R, R, R, N…</span></span>
+<span><span class="co">#&gt; $ TEC     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> R, R, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R, R, R, R, R, <span style="color: #BB0000;">N</span>…</span></span>
-<span><span class="co">#&gt; $ TCY     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> R, R, S, S, S, S, S, S, S, I, S, S, NA, NA, I, R, R, S, I, R, …</span></span>
+<span><span class="co">#&gt; $ TCY     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> R, R, S, S, S, S, S, S, S, I, S, S, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, I, R, R, S, I, R, …</span></span>
-<span><span class="co">#&gt; $ TGC     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, S, S, S, S, S, S, S, NA, S, S, NA, NA, NA, R, R, S, NA…</span></span>
+<span><span class="co">#&gt; $ TGC     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, S, S, S, S, S, S, S, <span style="color: #BB0000;">NA</span>, S, S, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R, R, S, <span style="color: #BB0000;">NA</span>…</span></span>
-<span><span class="co">#&gt; $ DOX     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, S, S, S, S, S, S, S, NA, S, S, NA, NA, NA, R, R, S, NA…</span></span>
+<span><span class="co">#&gt; $ DOX     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, S, S, S, S, S, S, S, <span style="color: #BB0000;">NA</span>, S, S, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R, R, S, <span style="color: #BB0000;">NA</span>…</span></span>
 <span><span class="co">#&gt; $ ERY     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R, R, R, S,…</span></span>
-<span><span class="co">#&gt; $ CLI     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> R, R, NA, NA, NA, R, NA, NA, NA, NA, NA, NA, R, R, R, R, R, NA…</span></span>
+<span><span class="co">#&gt; $ CLI     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> R, R, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R, R, R, R, R, <span style="color: #BB0000;">NA</span>…</span></span>
 <span><span class="co">#&gt; $ AZM     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R, R, R, S,…</span></span>
-<span><span class="co">#&gt; $ IPM     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, S, S…</span></span>
+<span><span class="co">#&gt; $ IPM     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, S, S, <span style="color: #BB0000;">NA</span>, S, S…</span></span>
-<span><span class="co">#&gt; $ MEM     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
+<span><span class="co">#&gt; $ MEM     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>…</span></span>
-<span><span class="co">#&gt; $ MTR     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
+<span><span class="co">#&gt; $ MTR     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>…</span></span>
-<span><span class="co">#&gt; $ CHL     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
+<span><span class="co">#&gt; $ CHL     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>…</span></span>
-<span><span class="co">#&gt; $ COL     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, R, R, R, R, …</span></span>
+<span><span class="co">#&gt; $ COL     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R, R, R, R, R, R, R, R, R, R, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R, R, R, R, …</span></span>
-<span><span class="co">#&gt; $ MUP     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
+<span><span class="co">#&gt; $ MUP     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>…</span></span>
-<span><span class="co">#&gt; $ RIF     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R, R, R, N…</span></span></code></pre></div>
+<span><span class="co">#&gt; $ RIF     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> R, R, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R, R, R, R, R, <span style="color: #BB0000;">N</span>…</span></span></code></pre></div>
 <p>Now to transform this to a data set with only resistance percentages
 per taxonomic order and genus:</p>
 <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">

articles/WHONET.html

@@ -29,7 +29,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -45,6 +45,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>
@@ -107,6 +108,8 @@ the tidyverse for all of my analyses. All of them. If you don’t know it
 yet, I suggest you read about it on their website: <a href="https://www.tidyverse.org/" class="external-link uri">https://www.tidyverse.org/</a>.</p>
 <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span> <span class="co"># part of tidyverse</span></span>
+<span><span class="co">#&gt; Error in get(paste0(generic, ".", class), envir = get_method_env()) : </span></span>
+<span><span class="co">#&gt;   object 'type_sum.accel' not found</span></span>
 <span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://ggplot2.tidyverse.org" class="external-link">ggplot2</a></span><span class="op">)</span> <span class="co"># part of tidyverse</span></span>
 <span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span> <span class="co"># this package</span></span>
 <span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/cleaner/" class="external-link">cleaner</a></span><span class="op">)</span> <span class="co"># to create frequency tables</span></span></code></pre></div>

articles/datasets.html

@@ -29,7 +29,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -45,6 +45,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>
@@ -76,7 +77,7 @@
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
             
-            <h4 data-toc-skip class="date">15 December 2024</h4>
+            <h4 data-toc-skip class="date">19 December 2024</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>

articles/index.html

@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -21,6 +21,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>
@@ -50,6 +51,8 @@
       <div class="section-desc"></div>
 
       <dl><dt><a href="AMR_for_Python.html">AMR for Python</a></dt>
+        <dd>
+        </dd><dt><a href="AMR_with_tidymodels.html">`AMR` with `tidymodels`</a></dt>
         <dd>
         </dd><dt><a href="AMR.html">How to conduct AMR data analysis</a></dt>
         <dd>

articles/resistance_predict.html

@@ -29,7 +29,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -45,6 +45,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>
@@ -95,6 +96,8 @@ plots in R.</p>
 extends their use and functions.</p>
 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span>
+<span><span class="co">#&gt; Error in get(paste0(generic, ".", class), envir = get_method_env()) : </span></span>
+<span><span class="co">#&gt;   object 'type_sum.accel' not found</span></span>
 <span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://ggplot2.tidyverse.org" class="external-link">ggplot2</a></span><span class="op">)</span></span>
 <span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span></span>
 <span></span>

articles/welcome_to_AMR.html

@@ -29,7 +29,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -45,6 +45,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

authors.html

@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -21,6 +21,7 @@
     <li><a class="dropdown-item" href="reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

index.html

@@ -32,7 +32,7 @@
 
     <a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -48,6 +48,7 @@
     <li><a class="dropdown-item" href="reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

news/index.html

@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -21,6 +21,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>
@@ -47,18 +48,18 @@
     </div>
 
     <div class="section level2">
-<h2 class="pkg-version" data-toc-text="2.1.1.9120" id="amr-2119120">AMR 2.1.1.9120<a class="anchor" aria-label="anchor" href="#amr-2119120"></a></h2>
+<h2 class="pkg-version" data-toc-text="2.1.1.9121" id="amr-2119121">AMR 2.1.1.9121<a class="anchor" aria-label="anchor" href="#amr-2119121"></a></h2>
 <p><em>(this beta version will eventually become v3.0. We’re happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using <a href="https://msberends.github.io/AMR/#latest-development-version">the instructions here</a>.)</em></p>
 <div class="section level5">
-<h5 id="a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9120">A New Milestone: AMR v3.0 with One Health Support (= Human + Veterinary + Environmental)<a class="anchor" aria-label="anchor" href="#a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9120"></a></h5>
+<h5 id="a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9121">A New Milestone: AMR v3.0 with One Health Support (= Human + Veterinary + Environmental)<a class="anchor" aria-label="anchor" href="#a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9121"></a></h5>
 <p>This package now supports not only tools for AMR data analysis in clinical settings, but also for veterinary and environmental microbiology. This was made possible through a collaboration with the <a href="https://www.upei.ca/avc" class="external-link">University of Prince Edward Island’s Atlantic Veterinary College</a>, Canada. To celebrate this great improvement of the package, we also updated the package logo to reflect this change.</p>
 </div>
 <div class="section level3">
-<h3 id="breaking-2-1-1-9120">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9120"></a></h3>
+<h3 id="breaking-2-1-1-9121">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9121"></a></h3>
 <ul><li>Removed all functions and references that used the deprecated <code>rsi</code> class, which were all replaced with their <code>sir</code> equivalents over a year ago</li>
 </ul></div>
 <div class="section level3">
-<h3 id="new-2-1-1-9120">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9120"></a></h3>
+<h3 id="new-2-1-1-9121">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9121"></a></h3>
 <ul><li>
 <strong>One Health implementation</strong>
 <ul><li>Function <code><a href="../reference/as.sir.html">as.sir()</a></code> now has extensive support for veterinary breakpoints from CLSI. Use <code>breakpoint_type = "animal"</code> and set the <code>host</code> argument to a variable that contains animal species names.</li>
@@ -94,12 +95,16 @@
 <ul><li>While using R for the heavy lifting, <a href="https://pypi.org/project/AMR/" class="external-link">our ‘AMR’ Python Package</a> was developed to run the AMR R package natively in Python. The Python package will always have the same version number as the R package, as it is built automatically with every code change.</li>
 </ul></li>
 <li>
+<strong>Support for <code>tidymodels</code></strong>
+<ul><li>All antimicrobial selectors (such as <code><a href="../reference/antibiotic_class_selectors.html">aminoglycosides()</a></code> and <code><a href="../reference/antibiotic_class_selectors.html">betalactams()</a></code>) are now supported in <code>tidymodels</code> packages such as <code>recipe</code> and <code>parsnip</code>. See for more info <a href="https://msberends.github.io/AMR/articles/AMR_with_tidymodels.html">our tutorial</a> on using AMR function for predictive modelling.</li>
+</ul></li>
+<li>
 <strong>Other</strong>
 <ul><li>New function <code><a href="../reference/mo_property.html">mo_group_members()</a></code> to retrieve the member microorganisms of a microorganism group. For example, <code>mo_group_members("Strep group C")</code> returns a vector of all microorganisms that belong to that group.</li>
 </ul></li>
 </ul></div>
 <div class="section level3">
-<h3 id="changed-2-1-1-9120">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9120"></a></h3>
+<h3 id="changed-2-1-1-9121">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9121"></a></h3>
 <ul><li>SIR interpretation
 <ul><li>It is now possible to use column names for argument <code>ab</code>, <code>mo</code>, and <code>uti</code>: <code>as.sir(..., ab = "column1", mo = "column2", uti = "column3")</code>. This greatly improves the flexibility for users.</li>
 <li>Users can now set their own criteria (using regular expressions) as to what should be considered S, I, R, SDD, and NI.</li>
@@ -153,17 +158,20 @@
 <li>Improved algorithm of <code><a href="../reference/first_isolate.html">first_isolate()</a></code> when using the phenotype-based method, to prioritise records with the highest availability of SIR values</li>
 <li>
 <code><a href="../reference/plot.html">scale_y_percent()</a></code> can now cope with ranges outside the 0-100% range</li>
-<li>Support for new Dutch national MDRO guideline (SRI-richtlijn BRMO, Nov 2024)</li>
+<li>MDRO determination (using <code><a href="../reference/mdro.html">mdro()</a></code>)
+<ul><li>Implemented the new Dutch national MDRO guideline (SRI-richtlijn BRMO, Nov 2024)</li>
+<li>Added arguments <code>esbl</code>, <code>carbapenemase</code>, <code>mecA</code>, <code>mecC</code>, <code>vanA</code>, <code>vanB</code> to denote column names or logical values indicating presence of these genes (or production of their proteins)</li>
+</ul></li>
 </ul></div>
 <div class="section level3">
-<h3 id="other-2-1-1-9120">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9120"></a></h3>
+<h3 id="other-2-1-1-9121">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9121"></a></h3>
 <ul><li>Greatly improved <code>vctrs</code> integration, a Tidyverse package working in the background for many Tidyverse functions. For users, this means that functions such as <code>dplyr</code>’s <code><a href="https://dplyr.tidyverse.org/reference/bind_rows.html" class="external-link">bind_rows()</a></code>, <code><a href="https://dplyr.tidyverse.org/reference/rowwise.html" class="external-link">rowwise()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/c_across.html" class="external-link">c_across()</a></code> are now supported for e.g. columns of class <code>mic</code>. Despite this, this <code>AMR</code> package is still zero-dependent on any other package, including <code>dplyr</code> and <code>vctrs</code>.</li>
 <li>Greatly updated and expanded documentation</li>
 <li>Added Larisse Bolton, Jordan Stull, Matthew Saab, and Javier Sanchez as contributors, to thank them for their valuable input</li>
 <li>Stopped support for SAS (<code>.xpt</code>) files, since their file structure and extremely inefficient and requires more disk space than GitHub allows in a single commit.</li>
 </ul></div>
 <div class="section level3">
-<h3 id="older-versions-2-1-1-9120">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9120"></a></h3>
+<h3 id="older-versions-2-1-1-9121">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9121"></a></h3>
 <p>This changelog only contains changes from AMR v3.0 (October 2024) and later.</p>
 <ul><li>For prior v2 versions, please see <a href="https://github.com/msberends/AMR/blob/v2.1.1/NEWS.md" class="external-link">our v2 archive</a>.</li>
 <li>For prior v1 versions, please see <a href="https://github.com/msberends/AMR/blob/v1.8.2/NEWS.md" class="external-link">our v1 archive</a>.</li>

pkgdown.yml

@@ -3,6 +3,7 @@ pkgdown: 2.1.1
 pkgdown_sha: ~
 articles:
   AMR_for_Python: AMR_for_Python.html
+  AMR_with_tidymodels: AMR_with_tidymodels.html
   AMR: AMR.html
   datasets: datasets.html
   EUCAST: EUCAST.html
@@ -11,7 +12,7 @@ articles:
   resistance_predict: resistance_predict.html
   welcome_to_AMR: welcome_to_AMR.html
   WHONET: WHONET.html
-last_built: 2024-12-15T19:36Z
+last_built: 2024-12-19T19:21Z
 urls:
   reference: https://msberends.github.io/AMR/reference
   article: https://msberends.github.io/AMR/articles

reference/AMR-options.html

@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -21,6 +21,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

reference/AMR.html

@@ -21,7 +21,7 @@ The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish,
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -35,6 +35,7 @@ The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish,
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

reference/WHOCC.html

@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -21,6 +21,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

reference/WHONET.html

@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -21,6 +21,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

reference/ab_from_text.html

@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -21,6 +21,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

reference/ab_property.html

@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -21,6 +21,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

reference/add_custom_antimicrobials.html

@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -21,6 +21,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

reference/add_custom_microorganisms.html

@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -21,6 +21,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

reference/age.html

@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -21,6 +21,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>
@@ -110,16 +111,16 @@
 <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  1965-12-05  59  59.02732         34</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1  1965-12-05  59  59.03825         34</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2  1980-03-01  44  44.78962         19</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2  1980-03-01  44  44.80055         19</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3  1949-11-01  75  75.12022         50</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3  1949-11-01  75  75.13115         50</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4  1947-02-14  77  77.83333         52</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4  1947-02-14  77  77.84426         52</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5  1940-02-19  84  84.81967         59</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5  1940-02-19  84  84.83060         59</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6  1988-01-10  36  36.92896         11</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6  1988-01-10  36  36.93989         11</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7  1997-08-27  27  27.30055          2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7  1997-08-27  27  27.31148          2</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8  1978-01-26  46  46.88525         21</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8  1978-01-26  46  46.89617         21</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9  1972-06-17  52  52.49454         27</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9  1972-06-17  52  52.50546         27</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1986-08-10  38  38.34699         13</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1986-08-10  38  38.35792         13</span>
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>

reference/age_groups.html

@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -21,6 +21,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

reference/antibiogram.html

@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -21,6 +21,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

reference/antibiotic_class_selectors.html

@@ -9,7 +9,7 @@ In short, if you have a column name that resembles an antimicrobial drug, it wil
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -23,6 +23,7 @@ In short, if you have a column name that resembles an antimicrobial drug, it wil
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

reference/antibiotics.html

@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -21,6 +21,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

reference/as.ab.html

@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -21,6 +21,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

reference/as.av.html

@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -21,6 +21,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

reference/as.disk.html

@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -21,6 +21,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

reference/as.mic.html

@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -21,6 +21,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

reference/as.mo.html

@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -21,6 +21,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

reference/as.sir.html

@@ -21,7 +21,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -35,6 +35,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>
@@ -785,16 +786,16 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 57 × 16</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    datetime            index ab_given mo_given host_given ab   mo              </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  <span style="color: #BCBCBC;">*</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;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span>            </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2024-12-15 <span style="color: #949494;">19:37:06</span>     4 AMX      B_STRPT… human      AMX  B_STRPT_PNMN    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2024-12-19 <span style="color: #949494;">19:22:22</span>     4 AMX      B_STRPT… human      AMX  B_STRPT_PNMN    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2024-12-15 <span style="color: #949494;">19:37:13</span>     4 genta    Escheri… human      GEN  B_[ORD]_ENTRBCTR</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2024-12-19 <span style="color: #949494;">19:22:29</span>     4 genta    Escheri… human      GEN  B_[ORD]_ENTRBCTR</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2024-12-15 <span style="color: #949494;">19:37:13</span>     4 genta    Escheri… human      GEN  B_[ORD]_ENTRBCTR</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2024-12-19 <span style="color: #949494;">19:22:29</span>     4 genta    Escheri… human      GEN  B_[ORD]_ENTRBCTR</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2024-12-15 <span style="color: #949494;">19:37:14</span>     4 genta    Escheri… cattle     GEN  B_ESCHR_COLI    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2024-12-19 <span style="color: #949494;">19:22:30</span>     4 genta    Escheri… cattle     GEN  B_ESCHR_COLI    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2024-12-15 <span style="color: #949494;">19:37:14</span>     4 genta    Escheri… cattle     GEN  B_ESCHR_COLI    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2024-12-19 <span style="color: #949494;">19:22:30</span>     4 genta    Escheri… cattle     GEN  B_ESCHR_COLI    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2024-12-15 <span style="color: #949494;">19:37:06</span>     3 AMX      B_STRPT… human      AMX  B_STRPT_PNMN    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2024-12-19 <span style="color: #949494;">19:22:22</span>     3 AMX      B_STRPT… human      AMX  B_STRPT_PNMN    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2024-12-15 <span style="color: #949494;">19:37:13</span>     3 tobra    Escheri… human      TOB  B_[ORD]_ENTRBCTR</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2024-12-19 <span style="color: #949494;">19:22:29</span>     3 tobra    Escheri… human      TOB  B_[ORD]_ENTRBCTR</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2024-12-15 <span style="color: #949494;">19:37:13</span>     3 tobra    Escheri… human      TOB  B_[ORD]_ENTRBCTR</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2024-12-19 <span style="color: #949494;">19:22:29</span>     3 tobra    Escheri… human      TOB  B_[ORD]_ENTRBCTR</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2024-12-15 <span style="color: #949494;">19:37:14</span>     3 tobra    Escheri… horses     TOB  B_ESCHR_COLI    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2024-12-19 <span style="color: #949494;">19:22:30</span>     3 tobra    Escheri… horses     TOB  B_ESCHR_COLI    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2024-12-15 <span style="color: #949494;">19:37:14</span>     3 tobra    Escheri… horses     TOB  B_ESCHR_COLI    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2024-12-19 <span style="color: #949494;">19:22:30</span>     3 tobra    Escheri… horses     TOB  B_ESCHR_COLI    </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 47 more rows</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 9 more variables: host &lt;chr&gt;, method &lt;chr&gt;, input &lt;dbl&gt;, outcome &lt;sir&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   notes &lt;chr&gt;, guideline &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;,</span></span>

reference/atc_online.html

@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -21,6 +21,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

reference/av_from_text.html

@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -21,6 +21,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

reference/av_property.html

@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -21,6 +21,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

reference/availability.html

@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -21,6 +21,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

reference/bug_drug_combinations.html

@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -21,6 +21,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

reference/clinical_breakpoints.html

@@ -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="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -35,6 +35,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

reference/count.html

@@ -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="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -23,6 +23,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

reference/custom_eucast_rules.html

@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -21,6 +21,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

reference/dosage.html

@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -21,6 +21,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

reference/eucast_rules.html

@@ -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="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -23,6 +23,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

reference/example_isolates.html

@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -21,6 +21,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

reference/example_isolates_unclean.html

@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -21,6 +21,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

reference/export_ncbi_biosample.html

@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -21,6 +21,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

reference/first_isolate.html

@@ -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="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -23,6 +23,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

reference/g.test.html

@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -21,6 +21,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

reference/get_episode.html

@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -21,6 +21,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

reference/ggplot_pca.html

@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -21,6 +21,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

reference/ggplot_sir.html

@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -21,6 +21,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

reference/guess_ab_col.html

@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -21,6 +21,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

reference/index.html

@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -21,6 +21,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

reference/intrinsic_resistant.html

@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -21,6 +21,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

reference/italicise_taxonomy.html

@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -21,6 +21,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

reference/join.html

@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -21,6 +21,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

reference/key_antimicrobials.html

@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -21,6 +21,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

reference/kurtosis.html

@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -21,6 +21,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

reference/like.html

@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -21,6 +21,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

reference/mdro.html

@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -21,6 +21,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>
@@ -57,6 +58,12 @@
 <span>  x <span class="op">=</span> <span class="cn">NULL</span>,</span>
 <span>  guideline <span class="op">=</span> <span class="st">"CMI2012"</span>,</span>
 <span>  col_mo <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span>  esbl <span class="op">=</span> <span class="cn">NA</span>,</span>
+<span>  carbapenemase <span class="op">=</span> <span class="cn">NA</span>,</span>
+<span>  mecA <span class="op">=</span> <span class="cn">NA</span>,</span>
+<span>  mecC <span class="op">=</span> <span class="cn">NA</span>,</span>
+<span>  vanA <span class="op">=</span> <span class="cn">NA</span>,</span>
+<span>  vanB <span class="op">=</span> <span class="cn">NA</span>,</span>
 <span>  info <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span>,</span>
 <span>  pct_required_classes <span class="op">=</span> <span class="fl">0.5</span>,</span>
 <span>  combine_SI <span class="op">=</span> <span class="cn">TRUE</span>,</span>
@@ -69,13 +76,18 @@
 <span></span>
 <span><span class="fu">brmo</span><span class="op">(</span>x <span class="op">=</span> <span class="cn">NULL</span>, only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
-<span><span class="fu">mrgn</span><span class="op">(</span>x <span class="op">=</span> <span class="cn">NULL</span>, only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
+<span><span class="fu">mrgn</span><span class="op">(</span>x <span class="op">=</span> <span class="cn">NULL</span>, only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
-<span><span class="fu">mdr_tb</span><span class="op">(</span>x <span class="op">=</span> <span class="cn">NULL</span>, only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
+<span><span class="fu">mdr_tb</span><span class="op">(</span>x <span class="op">=</span> <span class="cn">NULL</span>, only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
-<span><span class="fu">mdr_cmi2012</span><span class="op">(</span>x <span class="op">=</span> <span class="cn">NULL</span>, only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
+<span><span class="fu">mdr_cmi2012</span><span class="op">(</span>x <span class="op">=</span> <span class="cn">NULL</span>, only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
-<span><span class="fu">eucast_exceptional_phenotypes</span><span class="op">(</span>x <span class="op">=</span> <span class="cn">NULL</span>, only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
+<span><span class="fu">eucast_exceptional_phenotypes</span><span class="op">(</span></span>
+<span>  x <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span>  only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  verbose <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  <span class="va">...</span></span>
+<span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
@@ -98,6 +110,30 @@
 <dd><p>column name of the names or codes of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>) - the default is the first column of class <code><a href="as.mo.html">mo</a></code>. Values will be coerced using <code><a href="as.mo.html">as.mo()</a></code>.</p></dd>
 
 
+<dt id="arg-esbl">esbl<a class="anchor" aria-label="anchor" href="#arg-esbl"></a></dt>
+<dd><p><a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> values, or a column name containing logical values, indicating the presence of an ESBL gene (or production of its proteins)</p></dd>
+
+
+<dt id="arg-carbapenemase">carbapenemase<a class="anchor" aria-label="anchor" href="#arg-carbapenemase"></a></dt>
+<dd><p><a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> values, or a column name containing logical values, indicating the presence of a carbapenemase gene (or production of its proteins)</p></dd>
+
+
+<dt id="arg-meca">mecA<a class="anchor" aria-label="anchor" href="#arg-meca"></a></dt>
+<dd><p><a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> values, or a column name containing logical values, indicating the presence of a <em>mecA</em> gene (or production of its proteins)</p></dd>
+
+
+<dt id="arg-mecc">mecC<a class="anchor" aria-label="anchor" href="#arg-mecc"></a></dt>
+<dd><p><a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> values, or a column name containing logical values, indicating the presence of a <em>mecC</em> gene (or production of its proteins)</p></dd>
+
+
+<dt id="arg-vana">vanA<a class="anchor" aria-label="anchor" href="#arg-vana"></a></dt>
+<dd><p><a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> values, or a column name containing logical values, indicating the presence of a <em>vanA</em> gene (or production of its proteins)</p></dd>
+
+
+<dt id="arg-vanb">vanB<a class="anchor" aria-label="anchor" href="#arg-vanb"></a></dt>
+<dd><p><a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> values, or a column name containing logical values, indicating the presence of a <em>vanB</em> gene (or production of its proteins)</p></dd>
+
+
 <dt id="arg-info">info<a class="anchor" aria-label="anchor" href="#arg-info"></a></dt>
 <dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether progress should be printed to the console - the default is only print while in interactive sessions</p></dd>
 

reference/mean_amr_distance.html

@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -21,6 +21,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

reference/microorganisms.codes.html

@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -21,6 +21,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

reference/microorganisms.groups.html

@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -21,6 +21,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

reference/microorganisms.html

@@ -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="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -23,6 +23,7 @@ This data set is carefully crafted, yet made 100% reproducible from public and a
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

reference/mo_matching_score.html

@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -21,6 +21,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

reference/mo_property.html

@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -21,6 +21,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

reference/mo_source.html

@@ -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="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -23,6 +23,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

reference/pca.html

@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -21,6 +21,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

reference/plot.html

@@ -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="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -23,6 +23,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

reference/proportion.html

@@ -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="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -23,6 +23,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

reference/random.html

@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -21,6 +21,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

reference/resistance_predict.html

@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -21,6 +21,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

reference/skewness.html

@@ -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="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -23,6 +23,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

reference/translate.html

@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@@ -21,6 +21,7 @@
     <li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
     <li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
     <li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
+    <li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
     <li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
     <li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
     <li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

sitemap.xml

@@ -3,6 +3,7 @@
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 <url><loc>https://msberends.github.io/AMR/articles/AMR.html</loc></url>
 <url><loc>https://msberends.github.io/AMR/articles/AMR_for_Python.html</loc></url>
+<url><loc>https://msberends.github.io/AMR/articles/AMR_with_tidymodels.html</loc></url>
 <url><loc>https://msberends.github.io/AMR/articles/EUCAST.html</loc></url>
 <url><loc>https://msberends.github.io/AMR/articles/MDR.html</loc></url>
 <url><loc>https://msberends.github.io/AMR/articles/PCA.html</loc></url>