Built site for AMR@2.1.1.9095: 40edc16

Built site for AMR@2.1.1.9095: 448b6ab
Built site for AMR@2.1.1.9095: 5c4d8fc
2024-12-26 08:06:12 +01:00 · 2024-10-15 15:37:30 +00:00 · 2024-10-15 15:32:56 +00:00 · 2024-10-15 15:24:09 +00:00
79 changed files with 652 additions and 399 deletions
--- a/404.html
+++ b/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="">2.1.1.9094</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
--- a/LICENSE-text.html
+++ b/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="">2.1.1.9094</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
--- a/articles/AMR.html
+++ b/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="">2.1.1.9094</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
@ -87,7 +87,7 @@
 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 10 October 2024.</p>
+generated on 15 October 2024.</p>
 <div class="section level2">
 <h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
 </h2>
@ -143,21 +143,21 @@ make the structure of your data generally look like this:</p>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2024-10-10</td>
+<td align="center">2024-10-15</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">2024-10-10</td>
+<td align="center">2024-10-15</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">2024-10-10</td>
+<td align="center">2024-10-15</td>
 <td align="center">efgh</td>
 <td align="center">Escherichia coli</td>
 <td align="center">R</td>
--- a/articles/AMR_for_Python.html
+++ b/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="">2.1.1.9094</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
@ -86,203 +86,562 @@
 <div class="section level2">
 <h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
 </h2>
-<p>The <code>AMR</code> package for R is an incredible tool for
-antimicrobial resistance (AMR) data analysis, providing extensive
-functionality for working with microbial and antimicrobial properties.
-But what if you’re working in Python and still want to benefit from the
-robust features of <code>AMR</code>?</p>
-<p>The best way is to access R directly from Python with the help of
-<code>rpy2</code>, a simple yet powerful Python package. You can easily
-call functions from the <code>AMR</code> package to process your own
-data in your own Python environment. This post will guide you through
-setting up <code>rpy2</code> and show you how to use R functions from
-<code>AMR</code> in Python to supercharge your antimicrobial resistance
-analysis.</p>
-</div>
-<div class="section level2">
-<h2 id="what-is-rpy2">What is <code>rpy2</code>?<a class="anchor" aria-label="anchor" href="#what-is-rpy2"></a>
-</h2>
-<p><code>rpy2</code> is a Python library that allows Python users to run
-R code within their Python scripts. Essentially, it acts as a bridge
-between the two languages, allowing you to tap into the rich ecosystem
-of R libraries (like <code>AMR</code>) while maintaining the flexibility
-of Python.</p>
+<p>The <code>AMR</code> package for R is a powerful tool for
+antimicrobial resistance (AMR) analysis. It provides extensive features
+for handling microbial and antimicrobial data. However, for those who
+work primarily in Python, we now have a more intuitive option available:
+the <code>AMR</code> Python package, which uses <code>rpy2</code>
+internally. This package allows Python users to access all the functions
+from the R <code>AMR</code> package without the need to set up
+<code>rpy2</code> themselves. Since this Python package is not a true
+‘port’ (which would require all R functions to be rewritten into
+Python), R and the AMR R package are still required to be installed.
+Yet, Python users can now easily work with AMR data directly through
+Python code.</p>
+<p>In this document, we explain how this works and provide simple
+examples of using the <code>AMR</code> Python package.</p>
 <div class="section level3">
-<h3 id="key-features-of-rpy2">Key Features of <code>rpy2</code>:<a class="anchor" aria-label="anchor" href="#key-features-of-rpy2"></a>
+<h3 id="how-it-works">How It Works<a class="anchor" aria-label="anchor" href="#how-it-works"></a>
 </h3>
+<p>The <code>AMR</code> Python package acts as a wrapper around the
+functions in the <code>AMR</code> R package. The package simplifies the
+process of calling R functions in Python, eliminating the need to
+manually manage the <code>rpy2</code> setup, which Python uses
+internally to be able to work with the R package. By just using
+<code>import AMR</code>, Python users can directly use the functions
+from the <code>AMR</code> R package as if they were native Python
+functions.</p>
+<p>Internally, <code>rpy2</code> is still being used, but all complexity
+is hidden from the user. This approach keeps the Python code clean and
+Pythonic, while still leveraging the full power of the R
+<code>AMR</code> package.</p>
+</div>
+<div class="section level3">
+<h3 id="example-of-usage">Example of Usage<a class="anchor" aria-label="anchor" href="#example-of-usage"></a>
+</h3>
+<p>Here’s an example that demonstrates how to clean microorganism and
+drug names using the <code>AMR</code> Python package:</p>
+<div class="sourceCode" id="cb1"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="im">import</span> pandas <span class="im">as</span> pd</span>
+<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a><span class="im">import</span> AMR</span>
+<span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a></span>
+<span id="cb1-4"><a href="#cb1-4" tabindex="-1"></a><span class="co"># Sample data</span></span>
+<span id="cb1-5"><a href="#cb1-5" tabindex="-1"></a>data <span class="op">=</span> {</span>
+<span id="cb1-6"><a href="#cb1-6" tabindex="-1"></a>    <span class="st">"MOs"</span>: [<span class="st">'E. coli'</span>, <span class="st">'ESCCOL'</span>, <span class="st">'esco'</span>, <span class="st">'Esche coli'</span>],</span>
+<span id="cb1-7"><a href="#cb1-7" tabindex="-1"></a>    <span class="st">"Drug"</span>: [<span class="st">'Cipro'</span>, <span class="st">'CIP'</span>, <span class="st">'J01MA02'</span>, <span class="st">'Ciproxin'</span>]</span>
+<span id="cb1-8"><a href="#cb1-8" tabindex="-1"></a>}</span>
+<span id="cb1-9"><a href="#cb1-9" tabindex="-1"></a>df <span class="op">=</span> pd.DataFrame(data)</span>
+<span id="cb1-10"><a href="#cb1-10" tabindex="-1"></a></span>
+<span id="cb1-11"><a href="#cb1-11" tabindex="-1"></a><span class="co"># Use AMR functions to clean microorganism and drug names</span></span>
+<span id="cb1-12"><a href="#cb1-12" tabindex="-1"></a>df[<span class="st">'MO_clean'</span>] <span class="op">=</span> AMR.mo_name(df[<span class="st">'MOs'</span>])</span>
+<span id="cb1-13"><a href="#cb1-13" tabindex="-1"></a>df[<span class="st">'Drug_clean'</span>] <span class="op">=</span> AMR.ab_name(df[<span class="st">'Drug'</span>])</span>
+<span id="cb1-14"><a href="#cb1-14" tabindex="-1"></a></span>
+<span id="cb1-15"><a href="#cb1-15" tabindex="-1"></a><span class="co"># Display the results</span></span>
+<span id="cb1-16"><a href="#cb1-16" tabindex="-1"></a><span class="bu">print</span>(df)</span></code></pre></div>
+<table class="table">
+<thead><tr class="header">
+<th>MOs</th>
+<th>Drug</th>
+<th>MO_clean</th>
+<th>Drug_clean</th>
+</tr></thead>
+<tbody>
+<tr class="odd">
+<td>E. coli</td>
+<td>Cipro</td>
+<td>Escherichia coli</td>
+<td>Ciprofloxacin</td>
+</tr>
+<tr class="even">
+<td>ESCCOL</td>
+<td>CIP</td>
+<td>Escherichia coli</td>
+<td>Ciprofloxacin</td>
+</tr>
+<tr class="odd">
+<td>esco</td>
+<td>J01MA02</td>
+<td>Escherichia coli</td>
+<td>Ciprofloxacin</td>
+</tr>
+<tr class="even">
+<td>Esche coli</td>
+<td>Ciproxin</td>
+<td>Escherichia coli</td>
+<td>Ciprofloxacin</td>
+</tr>
+</tbody>
+</table>
+<div class="section level4">
+<h4 id="explanation">Explanation<a class="anchor" aria-label="anchor" href="#explanation"></a>
+</h4>
 <ul>
-<li>Seamlessly call R functions from Python.</li>
-<li>Convert R data structures into Python data structures like pandas
-DataFrames.</li>
-<li>Leverage the full power of R libraries without leaving your Python
-environment.</li>
+<li><p><strong>mo_name:</strong> This function standardises
+microorganism names. Here, different variations of <em>Escherichia
+coli</em> (such as “E. coli”, “ESCCOL”, “esco”, and “Esche coli”) are
+all converted into the correct, standardised form, “Escherichia
+coli”.</p></li>
+<li><p><strong>ab_name</strong>: Similarly, this function standardises
+antimicrobial names. The different representations of ciprofloxacin
+(e.g., “Cipro”, “CIP”, “J01MA02”, and “Ciproxin”) are all converted to
+the standard name, “Ciprofloxacin”.</p></li>
 </ul>
 </div>
+<div class="section level4">
+<h4 id="taxonomic-data-sets-now-in-python">Taxonomic Data Sets Now in Python!<a class="anchor" aria-label="anchor" href="#taxonomic-data-sets-now-in-python"></a>
+</h4>
+<p>As a Python user, you might like that the most important data sets of
+the <code>AMR</code> R package, <code>microorganisms</code>,
+<code>antibiotics</code>, <code>clinical_breakpoints</code>, and
+<code>example_isolates</code>, are now available as regular Python data
+frames:</p>
+<div class="sourceCode" id="cb2"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb2-1"><a href="#cb2-1" tabindex="-1"></a>AMR.microorganisms</span></code></pre></div>
+<table class="table">
+<colgroup>
+<col width="11%">
+<col width="29%">
+<col width="8%">
+<col width="8%">
+<col width="8%">
+<col width="10%">
+<col width="13%">
+<col width="9%">
+</colgroup>
+<thead><tr class="header">
+<th>mo</th>
+<th>fullname</th>
+<th>status</th>
+<th>kingdom</th>
+<th>gbif</th>
+<th>gbif_parent</th>
+<th>gbif_renamed_to</th>
+<th>prevalence</th>
+</tr></thead>
+<tbody>
+<tr class="odd">
+<td>B_GRAMN</td>
+<td>(unknown Gram-negatives)</td>
+<td>unknown</td>
+<td>Bacteria</td>
+<td>None</td>
+<td>None</td>
+<td>None</td>
+<td>2.0</td>
+</tr>
+<tr class="even">
+<td>B_GRAMP</td>
+<td>(unknown Gram-positives)</td>
+<td>unknown</td>
+<td>Bacteria</td>
+<td>None</td>
+<td>None</td>
+<td>None</td>
+<td>2.0</td>
+</tr>
+<tr class="odd">
+<td>B_ANAER-NEG</td>
+<td>(unknown anaerobic Gram-negatives)</td>
+<td>unknown</td>
+<td>Bacteria</td>
+<td>None</td>
+<td>None</td>
+<td>None</td>
+<td>2.0</td>
+</tr>
+<tr class="even">
+<td>B_ANAER-POS</td>
+<td>(unknown anaerobic Gram-positives)</td>
+<td>unknown</td>
+<td>Bacteria</td>
+<td>None</td>
+<td>None</td>
+<td>None</td>
+<td>2.0</td>
+</tr>
+<tr class="odd">
+<td>B_ANAER</td>
+<td>(unknown anaerobic bacteria)</td>
+<td>unknown</td>
+<td>Bacteria</td>
+<td>None</td>
+<td>None</td>
+<td>None</td>
+<td>2.0</td>
+</tr>
+<tr class="even">
+<td>…</td>
+<td>…</td>
+<td>…</td>
+<td>…</td>
+<td>…</td>
+<td>…</td>
+<td>…</td>
+<td>…</td>
+</tr>
+<tr class="odd">
+<td>B_ZYMMN_POMC</td>
+<td>Zymomonas pomaceae</td>
+<td>accepted</td>
+<td>Bacteria</td>
+<td>10744418</td>
+<td>3221412</td>
+<td>None</td>
+<td>2.0</td>
+</tr>
+<tr class="even">
+<td>B_ZYMPH</td>
+<td>Zymophilus</td>
+<td>synonym</td>
+<td>Bacteria</td>
+<td>None</td>
+<td>9475166</td>
+<td>None</td>
+<td>2.0</td>
+</tr>
+<tr class="odd">
+<td>B_ZYMPH_PCVR</td>
+<td>Zymophilus paucivorans</td>
+<td>synonym</td>
+<td>Bacteria</td>
+<td>None</td>
+<td>None</td>
+<td>None</td>
+<td>2.0</td>
+</tr>
+<tr class="even">
+<td>B_ZYMPH_RFFN</td>
+<td>Zymophilus raffinosivorans</td>
+<td>synonym</td>
+<td>Bacteria</td>
+<td>None</td>
+<td>None</td>
+<td>None</td>
+<td>2.0</td>
+</tr>
+<tr class="odd">
+<td>F_ZYZYG</td>
+<td>Zyzygomyces</td>
+<td>unknown</td>
+<td>Fungi</td>
+<td>None</td>
+<td>7581</td>
+<td>None</td>
+<td>2.0</td>
+</tr>
+</tbody>
+</table>
+<div class="sourceCode" id="cb3"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb3-1"><a href="#cb3-1" tabindex="-1"></a>AMR.antibiotics</span></code></pre></div>
+<table style="width:100%;" class="table">
+<colgroup>
+<col width="4%">
+<col width="12%">
+<col width="20%">
+<col width="25%">
+<col width="9%">
+<col width="11%">
+<col width="7%">
+<col width="9%">
+</colgroup>
+<thead><tr class="header">
+<th>ab</th>
+<th>cid</th>
+<th>name</th>
+<th>group</th>
+<th>oral_ddd</th>
+<th>oral_units</th>
+<th>iv_ddd</th>
+<th>iv_units</th>
+</tr></thead>
+<tbody>
+<tr class="odd">
+<td>AMA</td>
+<td>4649.0</td>
+<td>4-aminosalicylic acid</td>
+<td>Antimycobacterials</td>
+<td>12.00</td>
+<td>g</td>
+<td>NaN</td>
+<td>None</td>
+</tr>
+<tr class="even">
+<td>ACM</td>
+<td>6450012.0</td>
+<td>Acetylmidecamycin</td>
+<td>Macrolides/lincosamides</td>
+<td>NaN</td>
+<td>None</td>
+<td>NaN</td>
+<td>None</td>
+</tr>
+<tr class="odd">
+<td>ASP</td>
+<td>49787020.0</td>
+<td>Acetylspiramycin</td>
+<td>Macrolides/lincosamides</td>
+<td>NaN</td>
+<td>None</td>
+<td>NaN</td>
+<td>None</td>
+</tr>
+<tr class="even">
+<td>ALS</td>
+<td>8954.0</td>
+<td>Aldesulfone sodium</td>
+<td>Other antibacterials</td>
+<td>0.33</td>
+<td>g</td>
+<td>NaN</td>
+<td>None</td>
+</tr>
+<tr class="odd">
+<td>AMK</td>
+<td>37768.0</td>
+<td>Amikacin</td>
+<td>Aminoglycosides</td>
+<td>NaN</td>
+<td>None</td>
+<td>1.0</td>
+<td>g</td>
+</tr>
+<tr class="even">
+<td>…</td>
+<td>…</td>
+<td>…</td>
+<td>…</td>
+<td>…</td>
+<td>…</td>
+<td>…</td>
+<td>…</td>
+</tr>
+<tr class="odd">
+<td>VIR</td>
+<td>11979535.0</td>
+<td>Virginiamycine</td>
+<td>Other antibacterials</td>
+<td>NaN</td>
+<td>None</td>
+<td>NaN</td>
+<td>None</td>
+</tr>
+<tr class="even">
+<td>VOR</td>
+<td>71616.0</td>
+<td>Voriconazole</td>
+<td>Antifungals/antimycotics</td>
+<td>0.40</td>
+<td>g</td>
+<td>0.4</td>
+<td>g</td>
+</tr>
+<tr class="odd">
+<td>XBR</td>
+<td>72144.0</td>
+<td>Xibornol</td>
+<td>Other antibacterials</td>
+<td>NaN</td>
+<td>None</td>
+<td>NaN</td>
+<td>None</td>
+</tr>
+<tr class="even">
+<td>ZID</td>
+<td>77846445.0</td>
+<td>Zidebactam</td>
+<td>Other antibacterials</td>
+<td>NaN</td>
+<td>None</td>
+<td>NaN</td>
+<td>None</td>
+</tr>
+<tr class="odd">
+<td>ZFD</td>
+<td>NaN</td>
+<td>Zoliflodacin</td>
+<td>None</td>
+<td>NaN</td>
+<td>None</td>
+<td>NaN</td>
+<td>None</td>
+</tr>
+</tbody>
+</table>
+</div>
+</div>
 </div>
 <div class="section level2">
-<h2 id="setting-up-rpy2">Setting Up <code>rpy2</code><a class="anchor" aria-label="anchor" href="#setting-up-rpy2"></a>
+<h2 id="installation">Installation<a class="anchor" aria-label="anchor" href="#installation"></a>
 </h2>
-<p>Before diving into the examples, you’ll need to install both R and
-<code>rpy2</code>. Here’s a step-by-step guide on setting things up.</p>
-<div class="section level3">
-<h3 id="step-1-install-r">Step 1: Install R<a class="anchor" aria-label="anchor" href="#step-1-install-r"></a>
-</h3>
-<p>Ensure that R is installed on your system. R has minimal dependencies
-and is very simple to install:</p>
-<ul>
-<li>
-<strong>Linux</strong>
-<ul>
-<li>Ubuntu / Debian:<br><code>sudo apt install r-base</code>
-</li>
-<li>Fedora:<br><code>sudo dnf install R</code>
-</li>
-<li>CentOS/RHEL:<br><code>sudo yum install R</code>
-</li>
-<li>Arch Linux:<br><code>sudo pacman -S r</code>
-</li>
-</ul>
-</li>
-<li>
-<strong>macOS</strong> (with Homebrew):<br><code>brew install r</code>
-</li>
-<li>
-<strong>Other Systems:</strong><br>
-Visit the <a href="https://cran.r-project.org" class="external-link">CRAN download
-page</a>.</li>
-</ul>
+<p>To be able to use the <code>AMR</code> Python package, it is required
+to install both R and the <code>AMR</code> R package.</p>
+<div class="section level4">
+<h4 id="preparation-install-r-and-amr-r-package">Preparation: Install R and <code>AMR</code> R package<a class="anchor" aria-label="anchor" href="#preparation-install-r-and-amr-r-package"></a>
+</h4>
+<p>For Linux and macOS, this is just:</p>
+<div class="sourceCode" id="cb4"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb4-1"><a href="#cb4-1" tabindex="-1"></a><span class="co"># Ubuntu / Debian</span></span>
+<span id="cb4-2"><a href="#cb4-2" tabindex="-1"></a><span class="fu">sudo</span> apt install r-base <span class="kw">&amp;&amp;</span> <span class="ex">Rscript</span> <span class="at">-e</span> <span class="st">'install.packages("AMR")'</span></span>
+<span id="cb4-3"><a href="#cb4-3" tabindex="-1"></a><span class="co"># Fedora:</span></span>
+<span id="cb4-4"><a href="#cb4-4" tabindex="-1"></a><span class="fu">sudo</span> dnf install R <span class="kw">&amp;&amp;</span> <span class="ex">Rscript</span> <span class="at">-e</span> <span class="st">'install.packages("AMR")'</span></span>
+<span id="cb4-5"><a href="#cb4-5" tabindex="-1"></a><span class="co"># CentOS/RHEL</span></span>
+<span id="cb4-6"><a href="#cb4-6" tabindex="-1"></a><span class="fu">sudo</span> yum install R <span class="kw">&amp;&amp;</span> <span class="ex">Rscript</span> <span class="at">-e</span> <span class="st">'install.packages("AMR")'</span></span>
+<span id="cb4-7"><a href="#cb4-7" tabindex="-1"></a><span class="co"># Arch Linux</span></span>
+<span id="cb4-8"><a href="#cb4-8" tabindex="-1"></a><span class="fu">sudo</span> pacman <span class="at">-S</span> r <span class="kw">&amp;&amp;</span> <span class="ex">Rscript</span> <span class="at">-e</span> <span class="st">'install.packages("AMR")'</span></span>
+<span id="cb4-9"><a href="#cb4-9" tabindex="-1"></a><span class="co"># macOS</span></span>
+<span id="cb4-10"><a href="#cb4-10" tabindex="-1"></a><span class="ex">brew</span> install r <span class="kw">&amp;&amp;</span> <span class="ex">Rscript</span> <span class="at">-e</span> <span class="st">'install.packages("AMR")'</span></span></code></pre></div>
+<p>For Windows, visit the <a href="https://cran.r-project.org" class="external-link">CRAN
+download page</a> in install R, then afterwards install the ‘AMR’
+package manually.</p>
 </div>
-<div class="section level3">
-<h3 id="step-2-install-the-amr-package-in-r">Step 2: Install the <code>AMR</code> package in R<a class="anchor" aria-label="anchor" href="#step-2-install-the-amr-package-in-r"></a>
-</h3>
-<p>On Linux and macOS, open Terminal and run:</p>
-<div class="sourceCode" id="cb1"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="ex">Rscript</span> <span class="at">-e</span> <span class="st">'install.packages("AMR")'</span></span></code></pre></div>
-<p>For other systems, open your R console and install the
-<code>AMR</code> package by running:</p>
-<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"AMR"</span><span class="op">)</span></span></code></pre></div>
-<p>On any system, you can also install the latest development version of
-the <code>AMR</code> package by setting <code>repos</code> to our beta
-channel:</p>
-<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"AMR"</span>, repos <span class="op">=</span> <span class="st">"https://msberends.r-universe.dev"</span><span class="op">)</span></span></code></pre></div>
-</div>
-<div class="section level3">
-<h3 id="step-3-install-rpy2-in-python">Step 3: Install <code>rpy2</code> in Python<a class="anchor" aria-label="anchor" href="#step-3-install-rpy2-in-python"></a>
-</h3>
-<p>To install <code>rpy2</code>, simply run the following command in
-your terminal:</p>
-<div class="sourceCode" id="cb4"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb4-1"><a href="#cb4-1" tabindex="-1"></a><span class="ex">pip</span> install rpy2</span></code></pre></div>
-</div>
-<div class="section level3">
-<h3 id="step-4-test-rpy2-installation">Step 4: Test <code>rpy2</code> Installation<a class="anchor" aria-label="anchor" href="#step-4-test-rpy2-installation"></a>
-</h3>
-<p>To ensure everything is set up correctly, you can test your
-installation by running the following Python script, which essentially
-runs R in the background:</p>
-<div class="sourceCode" id="cb5"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb5-1"><a href="#cb5-1" tabindex="-1"></a><span class="im">import</span> rpy2.robjects <span class="im">as</span> ro</span>
-<span id="cb5-2"><a href="#cb5-2" tabindex="-1"></a></span>
-<span id="cb5-3"><a href="#cb5-3" tabindex="-1"></a><span class="co"># Test a simple R function from Python</span></span>
-<span id="cb5-4"><a href="#cb5-4" tabindex="-1"></a>ro.r(<span class="st">'1 + 1'</span>)</span></code></pre></div>
-<p>If this returns <code>2</code>, you’re good to go!</p>
+<div class="section level4">
+<h4 id="install-amr-python-package">Install <code>AMR</code> Python Package<a class="anchor" aria-label="anchor" href="#install-amr-python-package"></a>
+</h4>
+<p>Since the Python package is available on the official <a href="https://pypi.org/project/AMR/" class="external-link">Python Package Index</a>, you can
+just run:</p>
+<div class="sourceCode" id="cb5"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb5-1"><a href="#cb5-1" tabindex="-1"></a><span class="ex">pip</span> install AMR</span></code></pre></div>
 </div>
 </div>
 <div class="section level2">
 <h2 id="working-with-amr-in-python">Working with <code>AMR</code> in Python<a class="anchor" aria-label="anchor" href="#working-with-amr-in-python"></a>
 </h2>
-<p>Now that we have <code>rpy2</code> set up, let’s walk through some
-practical examples of using the <code>AMR</code> package within
-Python.</p>
+<p>Now that we have everything set up, let’s walk through some practical
+examples of using the <code>AMR</code> package within Python.</p>
 <div class="section level3">
-<h3 id="example-1-converting-taxonomic-data">Example 1: Converting Taxonomic Data<a class="anchor" aria-label="anchor" href="#example-1-converting-taxonomic-data"></a>
+<h3 id="example-1-calculating-amr">Example 1: Calculating AMR<a class="anchor" aria-label="anchor" href="#example-1-calculating-amr"></a>
 </h3>
-<p>Let’s start by converting taxonomic user input to valid taxonomy
-using the <code>AMR</code> package, from within Python:</p>
-<div class="sourceCode" id="cb6"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb6-1"><a href="#cb6-1" tabindex="-1"></a><span class="im">import</span> pandas <span class="im">as</span> pd</span>
-<span id="cb6-2"><a href="#cb6-2" tabindex="-1"></a><span class="im">import</span> rpy2.robjects <span class="im">as</span> ro</span>
-<span id="cb6-3"><a href="#cb6-3" tabindex="-1"></a><span class="im">from</span> rpy2.robjects.packages <span class="im">import</span> importr</span>
-<span id="cb6-4"><a href="#cb6-4" tabindex="-1"></a><span class="im">from</span> rpy2.robjects <span class="im">import</span> pandas2ri</span>
-<span id="cb6-5"><a href="#cb6-5" tabindex="-1"></a></span>
-<span id="cb6-6"><a href="#cb6-6" tabindex="-1"></a><span class="co"># Load the AMR package from R</span></span>
-<span id="cb6-7"><a href="#cb6-7" tabindex="-1"></a>amr <span class="op">=</span> importr(<span class="st">'AMR'</span>)</span>
-<span id="cb6-8"><a href="#cb6-8" tabindex="-1"></a></span>
-<span id="cb6-9"><a href="#cb6-9" tabindex="-1"></a><span class="co"># Example user dataset in Python</span></span>
-<span id="cb6-10"><a href="#cb6-10" tabindex="-1"></a>data <span class="op">=</span> pd.DataFrame({</span>
-<span id="cb6-11"><a href="#cb6-11" tabindex="-1"></a>    <span class="st">'microorganism'</span>: [<span class="st">'E. coli'</span>, <span class="st">'S. aureus'</span>, <span class="st">'P. aeruginosa'</span>, <span class="st">'K. pneumoniae'</span>]</span>
-<span id="cb6-12"><a href="#cb6-12" tabindex="-1"></a>})</span>
-<span id="cb6-13"><a href="#cb6-13" tabindex="-1"></a></span>
-<span id="cb6-14"><a href="#cb6-14" tabindex="-1"></a><span class="co"># Apply mo_name() from the AMR package to the 'microorganism' column</span></span>
-<span id="cb6-15"><a href="#cb6-15" tabindex="-1"></a>ro.globalenv[<span class="st">'r_data'</span>] <span class="op">=</span> data</span>
-<span id="cb6-16"><a href="#cb6-16" tabindex="-1"></a>ro.r(<span class="st">'r_data$mo_name &lt;- mo_name(r_data$microorganism)'</span>)</span>
-<span id="cb6-17"><a href="#cb6-17" tabindex="-1"></a></span>
-<span id="cb6-18"><a href="#cb6-18" tabindex="-1"></a><span class="co"># Retrieve and print the modified R DataFrame in Python</span></span>
-<span id="cb6-19"><a href="#cb6-19" tabindex="-1"></a>result <span class="op">=</span> ro.r(<span class="st">'r_data'</span>)</span>
-<span id="cb6-20"><a href="#cb6-20" tabindex="-1"></a>result <span class="op">=</span> pandas2ri.rpy2py(result)</span>
-<span id="cb6-21"><a href="#cb6-21" tabindex="-1"></a><span class="bu">print</span>(result)</span></code></pre></div>
-<p>In this example, a Python dataset with microorganism names like
-<em>E. coli</em> and <em>S. aureus</em> is passed to the R function
-<code><a href="../reference/mo_property.html">mo_name()</a></code>. The result is an updated <code>DataFrame</code>
-that includes the standardised microorganism names based on the
-<code><a href="../reference/mo_property.html">mo_name()</a></code> function from the <code>AMR</code> package.</p>
+<div class="sourceCode" id="cb6"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb6-1"><a href="#cb6-1" tabindex="-1"></a><span class="im">import</span> AMR</span>
+<span id="cb6-2"><a href="#cb6-2" tabindex="-1"></a><span class="im">import</span> pandas <span class="im">as</span> pd</span>
+<span id="cb6-3"><a href="#cb6-3" tabindex="-1"></a></span>
+<span id="cb6-4"><a href="#cb6-4" tabindex="-1"></a>df <span class="op">=</span> AMR.example_isolates</span>
+<span id="cb6-5"><a href="#cb6-5" tabindex="-1"></a>result <span class="op">=</span> AMR.resistance(df[<span class="st">"AMX"</span>])</span>
+<span id="cb6-6"><a href="#cb6-6" tabindex="-1"></a><span class="bu">print</span>(result)</span></code></pre></div>
+<pre><code>[0.59555556]</code></pre>
 </div>
 <div class="section level3">
-<h3 id="example-2-generating-an-antibiogram">Example 2: Generating an Antibiogram<a class="anchor" aria-label="anchor" href="#example-2-generating-an-antibiogram"></a>
+<h3 id="example-2-generating-antibiograms">Example 2: Generating Antibiograms<a class="anchor" aria-label="anchor" href="#example-2-generating-antibiograms"></a>
 </h3>
 <p>One of the core functions of the <code>AMR</code> package is
 generating an antibiogram, a table that summarises the antimicrobial
 susceptibility of bacterial isolates. Here’s how you can generate an
 antibiogram from Python:</p>
-<div class="sourceCode" id="cb7"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb7-1"><a href="#cb7-1" tabindex="-1"></a><span class="co"># Run an antibiogram in R from Python</span></span>
-<span id="cb7-2"><a href="#cb7-2" tabindex="-1"></a>ro.r(<span class="st">'result &lt;- antibiogram(example_isolates, antibiotics = c(aminoglycosides(), carbapenems()))'</span>)</span>
-<span id="cb7-3"><a href="#cb7-3" tabindex="-1"></a></span>
-<span id="cb7-4"><a href="#cb7-4" tabindex="-1"></a><span class="co"># Retrieve the result in Python</span></span>
-<span id="cb7-5"><a href="#cb7-5" tabindex="-1"></a>result <span class="op">=</span> ro.r(<span class="st">'as.data.frame(result)'</span>)</span>
-<span id="cb7-6"><a href="#cb7-6" tabindex="-1"></a><span class="bu">print</span>(result)</span></code></pre></div>
-<p>In this example, we generate an antibiogram by selecting
-aminoglycosides and carbapenems, two classes of antibiotics, and then
-convert the resulting R data frame into a Python-readable format.</p>
-</div>
-<div class="section level3">
-<h3 id="example-3-filtering-data-based-on-gram-negative-bacteria">Example 3: Filtering Data Based on Gram-Negative Bacteria<a class="anchor" aria-label="anchor" href="#example-3-filtering-data-based-on-gram-negative-bacteria"></a>
-</h3>
-<p>Let’s say you want to filter the dataset for Gram-negative bacteria
-and display their resistance to certain antibiotics:</p>
-<div class="sourceCode" id="cb8"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb8-1"><a href="#cb8-1" tabindex="-1"></a><span class="co"># Filter for Gram-negative bacteria with intrinsic resistance to cefotaxime</span></span>
-<span id="cb8-2"><a href="#cb8-2" tabindex="-1"></a>ro.r(<span class="st">'result &lt;- example_isolates[which(mo_is_gram_negative() &amp; mo_is_intrinsic_resistant(ab = "cefotax")), c("bacteria", aminoglycosides(), carbapenems())]'</span>)</span>
-<span id="cb8-3"><a href="#cb8-3" tabindex="-1"></a></span>
-<span id="cb8-4"><a href="#cb8-4" tabindex="-1"></a><span class="co"># Retrieve the filtered result in Python</span></span>
-<span id="cb8-5"><a href="#cb8-5" tabindex="-1"></a>result <span class="op">=</span> ro.r(<span class="st">'as.data.frame(result)'</span>)</span>
-<span id="cb8-6"><a href="#cb8-6" tabindex="-1"></a><span class="bu">print</span>(result)</span></code></pre></div>
-<p>This example uses the AMR functions
-<code><a href="../reference/mo_property.html">mo_is_gram_negative()</a></code> and
-<code><a href="../reference/mo_property.html">mo_is_intrinsic_resistant()</a></code> to filter the dataset and
-returns a subset of bacteria with resistance data.</p>
-</div>
-<div class="section level3">
-<h3 id="example-4-customising-the-antibiogram">Example 4: Customising the Antibiogram<a class="anchor" aria-label="anchor" href="#example-4-customising-the-antibiogram"></a>
-</h3>
-<p>You can easily customise the antibiogram by passing different
-antibiotics or microorganism transformations, as shown below:</p>
-<div class="sourceCode" id="cb9"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb9-1"><a href="#cb9-1" tabindex="-1"></a><span class="co"># Customise the antibiogram with different settings</span></span>
-<span id="cb9-2"><a href="#cb9-2" tabindex="-1"></a>ro.r(<span class="st">'result &lt;- antibiogram(example_isolates, antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"), mo_transform = "gramstain")'</span>)</span>
-<span id="cb9-3"><a href="#cb9-3" tabindex="-1"></a></span>
-<span id="cb9-4"><a href="#cb9-4" tabindex="-1"></a><span class="co"># Retrieve and print the result</span></span>
-<span id="cb9-5"><a href="#cb9-5" tabindex="-1"></a>result <span class="op">=</span> ro.r(<span class="st">'as.data.frame(result)'</span>)</span>
-<span id="cb9-6"><a href="#cb9-6" tabindex="-1"></a><span class="bu">print</span>(result)</span></code></pre></div>
-<p>Here, we use piperacillin/tazobactam (TZP) in combination with
-tobramycin (TOB) and gentamicin (GEN) to see how they perform against
-various Gram-negative bacteria.</p>
+<div class="sourceCode" id="cb8"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb8-1"><a href="#cb8-1" tabindex="-1"></a>result2a <span class="op">=</span> AMR.antibiogram(df[[<span class="st">"mo"</span>, <span class="st">"AMX"</span>, <span class="st">"CIP"</span>, <span class="st">"TZP"</span>]])</span>
+<span id="cb8-2"><a href="#cb8-2" tabindex="-1"></a><span class="bu">print</span>(result2a)</span></code></pre></div>
+<table class="table">
+<colgroup>
+<col width="22%">
+<col width="22%">
+<col width="22%">
+<col width="33%">
+</colgroup>
+<thead><tr class="header">
+<th>Pathogen</th>
+<th>Amoxicillin</th>
+<th>Ciprofloxacin</th>
+<th>Piperacillin/tazobactam</th>
+</tr></thead>
+<tbody>
+<tr class="odd">
+<td>CoNS</td>
+<td>7% (10/142)</td>
+<td>73% (183/252)</td>
+<td>30% (10/33)</td>
+</tr>
+<tr class="even">
+<td>E. coli</td>
+<td>50% (196/392)</td>
+<td>88% (399/456)</td>
+<td>94% (393/416)</td>
+</tr>
+<tr class="odd">
+<td>K. pneumoniae</td>
+<td>0% (0/58)</td>
+<td>96% (53/55)</td>
+<td>89% (47/53)</td>
+</tr>
+<tr class="even">
+<td>P. aeruginosa</td>
+<td>0% (0/30)</td>
+<td>100% (30/30)</td>
+<td>None</td>
+</tr>
+<tr class="odd">
+<td>P. mirabilis</td>
+<td>None</td>
+<td>94% (34/36)</td>
+<td>None</td>
+</tr>
+<tr class="even">
+<td>S. aureus</td>
+<td>6% (8/131)</td>
+<td>90% (171/191)</td>
+<td>None</td>
+</tr>
+<tr class="odd">
+<td>S. epidermidis</td>
+<td>1% (1/91)</td>
+<td>64% (87/136)</td>
+<td>None</td>
+</tr>
+<tr class="even">
+<td>S. hominis</td>
+<td>None</td>
+<td>80% (56/70)</td>
+<td>None</td>
+</tr>
+<tr class="odd">
+<td>S. pneumoniae</td>
+<td>100% (112/112)</td>
+<td>None</td>
+<td>100% (112/112)</td>
+</tr>
+</tbody>
+</table>
+<div class="sourceCode" id="cb9"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb9-1"><a href="#cb9-1" tabindex="-1"></a>result2b <span class="op">=</span> AMR.antibiogram(df[[<span class="st">"mo"</span>, <span class="st">"AMX"</span>, <span class="st">"CIP"</span>, <span class="st">"TZP"</span>]], mo_transform <span class="op">=</span> <span class="st">"gramstain"</span>)</span>
+<span id="cb9-2"><a href="#cb9-2" tabindex="-1"></a><span class="bu">print</span>(result2b)</span></code></pre></div>
+<table class="table">
+<colgroup>
+<col width="20%">
+<col width="22%">
+<col width="23%">
+<col width="33%">
+</colgroup>
+<thead><tr class="header">
+<th>Pathogen</th>
+<th>Amoxicillin</th>
+<th>Ciprofloxacin</th>
+<th>Piperacillin/tazobactam</th>
+</tr></thead>
+<tbody>
+<tr class="odd">
+<td>Gram-negative</td>
+<td>36% (226/631)</td>
+<td>91% (621/684)</td>
+<td>88% (565/641)</td>
+</tr>
+<tr class="even">
+<td>Gram-positive</td>
+<td>43% (305/703)</td>
+<td>77% (560/724)</td>
+<td>86% (296/345)</td>
+</tr>
+</tbody>
+</table>
+<p>In this example, we generate an antibiogram by selecting various
+antibiotics.</p>
 </div>
 </div>
 <div class="section level2">
 <h2 id="conclusion">Conclusion<a class="anchor" aria-label="anchor" href="#conclusion"></a>
 </h2>
-<p>Using <code>rpy2</code>, you can easily integrate the power of R’s
-<code>AMR</code> package into your Python workflows. Whether you are
-generating antibiograms, analyzing resistance data, or performing
-complex filtering, <code>rpy2</code> gives you the flexibility to run R
-code without leaving the Python environment. This makes it a perfect
-solution for teams working across both R and Python.</p>
+<p>With the <code>AMR</code> Python package, Python users can now
+effortlessly call R functions from the <code>AMR</code> R package. This
+eliminates the need for complex <code>rpy2</code> configurations and
+provides a clean, easy-to-use interface for antimicrobial resistance
+analysis. The examples provided above demonstrate how this can be
+applied to typical workflows, such as standardising microorganism and
+antimicrobial names or calculating resistance.</p>
+<p>By using <code>import AMR</code>, you can seamlessly integrate the
+robust features of the R <code>AMR</code> package into your Python
+workflows. Whether you’re cleaning data or analysing resistance
+patterns, the <code>AMR</code> Python package makes it easy to work with
+AMR data in Python.</p>
 </div>
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+++ b/articles/EUCAST.html
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+++ b/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="">2.1.1.9094</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
--- a/articles/datasets.html
+++ b/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="">2.1.1.9094</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
@ -76,7 +76,7 @@
  <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">10 October 2024</h4>
+            <h4 data-toc-skip class="date">15 October 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>
--- a/articles/index.html
+++ b/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="">2.1.1.9094</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
@ -59,8 +59,6 @@
        <dd>
        </dd><dt><a href="MDR.html">How to determine multi-drug resistance (MDR)</a></dt>
        <dd>
-        </dd><dt><a href="other_pkg.html">Using AMR with other packages: AMR &amp; dplyr/tidyverse</a></dt>
-        <dd>
        </dd><dt><a href="PCA.html">How to conduct principal component analysis (PCA) for AMR</a></dt>
        <dd>
        </dd><dt><a href="resistance_predict.html">How to predict antimicrobial resistance</a></dt>
--- a/articles/other_pkg.html
+++ b/articles/other_pkg.html
@ -1,110 +0,0 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en">
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-<title>Using AMR with other packages: AMR &amp; dplyr/tidyverse • AMR (for R)</title>
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-<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
-<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet">
-<link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet">
-<link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
-<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
-<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet">
-<script src="../extra.js"></script><meta property="og:title" content="Using AMR with other packages: AMR &amp; dplyr/tidyverse">
-</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="">2.1.1.9094</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">
-      <span class="navbar-toggler-icon"></span>
-    </button>
-
-    <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto">
-<li class="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="../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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-  </div>
-</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>Using AMR with other packages: AMR &amp; dplyr/tidyverse</h1>
-            
-      
-      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/other_pkg.Rmd" class="external-link"><code>vignettes/other_pkg.Rmd</code></a></small>
-      <div class="d-none name"><code>other_pkg.Rmd</code></div>
-    </div>
-
-    
-    
-<p>This page will be updated shortly, to give explicit examples of how
-to work ideally with the <code>AMR</code> package, for those who are
-used to working in <code>dplyr</code> or other tidyverse packages.</p>
-  </main>
-</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>
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-</html>
--- a/articles/resistance_predict.html
+++ b/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="">2.1.1.9094</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
--- a/articles/welcome_to_AMR.html
+++ b/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="">2.1.1.9094</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
--- a/authors.html
+++ b/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="">2.1.1.9094</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
--- a/index.html
+++ b/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="">2.1.1.9094</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -91,6 +91,9 @@
 <li>100% free of costs and dependencies, highly suitable for places with <strong>limited resources</strong>
 </li>
 </ul>
+<blockquote>
+<p>Now available for Python too! <a href="./articles/AMR_for_Python.html">Click here</a> to read more.</p>
+</blockquote>
 <div style="display: flex; font-size: 0.8em;">
 <p style="text-align:left; width: 50%;">
 <small><a href="https://msberends.github.io/AMR/">https://msberends.github.io/AMR</a></small>
--- a/news/index.html
+++ b/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="">2.1.1.9094</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
@ -47,18 +47,18 @@
    </div>

    <div class="section level2">
-<h2 class="pkg-version" data-toc-text="2.1.1.9094" id="amr-2119094">AMR 2.1.1.9094<a class="anchor" aria-label="anchor" href="#amr-2119094"></a></h2>
+<h2 class="pkg-version" data-toc-text="2.1.1.9095" id="amr-2119095">AMR 2.1.1.9095<a class="anchor" aria-label="anchor" href="#amr-2119095"></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-2-1-1-9094">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-2-1-1-9094"></a></h5>
+<h5 id="a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9095">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-2-1-1-9095"></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-2-1-1-9094">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9094"></a></h3>
+<h3 id="breaking-2-1-1-9095">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9095"></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-2-1-1-9094">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9094"></a></h3>
+<h3 id="new-2-1-1-9095">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9095"></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>
@ -90,12 +90,16 @@
 <li>New function <code><a href="../reference/as.mic.html">rescale_mic()</a></code>, which allows users to rescale MIC values to a manually set range. This is the powerhouse behind the <code>scale_*_mic()</code> functions, but it can be used independently to, for instance, compare equality in MIC distributions by rescaling them to the same range first.</li>
 </ul></li>
 <li>
+<strong>Support for Python</strong>
+<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>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-2-1-1-9094">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9094"></a></h3>
+<h3 id="changed-2-1-1-9095">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9095"></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>
@ -125,6 +129,7 @@
 <li>Sorting of MIC values (using <code><a href="https://rdrr.io/r/base/sort.html" class="external-link">sort()</a></code>) was fixed in the same manner; <code>&lt;0.001</code> now gets sorted before <code>0.001</code>, and <code>&gt;0.001</code> gets sorted after <code>0.001</code>.</li>
 <li>Intermediate log2 levels used for MIC plotting are now more common values instead of following a strict dilution range</li>
 </ul></li>
+<li>Disks of 0 to 5 mm are now allowed, the newly allowed range for disk diffusion (<code><a href="../reference/as.disk.html">as.disk()</a></code>) is now between 0 and 50 mm</li>
 <li>Updated <code><a href="../reference/italicise_taxonomy.html">italicise_taxonomy()</a></code> to support HTML output</li>
 <li>
 <code><a href="../reference/custom_eucast_rules.html">custom_eucast_rules()</a></code> now supports multiple antibiotics and antibiotic groups to be affected by a single rule</li>
@ -147,14 +152,14 @@
 <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>
 </ul></div>
 <div class="section level3">
-<h3 id="other-2-1-1-9094">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9094"></a></h3>
+<h3 id="other-2-1-1-9095">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9095"></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-2-1-1-9094">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9094"></a></h3>
+<h3 id="older-versions-2-1-1-9095">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9095"></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>
--- a/pkgdown.yml
+++ b/pkgdown.yml
@ -7,12 +7,11 @@ articles:
  datasets: datasets.html
  EUCAST: EUCAST.html
  MDR: MDR.html
-  other_pkg: other_pkg.html
  PCA: PCA.html
  resistance_predict: resistance_predict.html
  welcome_to_AMR: welcome_to_AMR.html
  WHONET: WHONET.html
-last_built: 2024-10-10T14:41Z
+last_built: 2024-10-15T15:34Z
 urls:
  reference: https://msberends.github.io/AMR/reference
  article: https://msberends.github.io/AMR/articles
--- a/reference/AMR-options.html
+++ b/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="">2.1.1.9094</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
--- a/reference/AMR.html
+++ b/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="">2.1.1.9094</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
--- a/reference/WHOCC.html
+++ b/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="">2.1.1.9094</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
--- a/reference/WHONET.html
+++ b/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="">2.1.1.9094</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
--- a/reference/ab_from_text.html
+++ b/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="">2.1.1.9094</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
--- a/reference/ab_property.html
+++ b/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="">2.1.1.9094</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
--- a/reference/add_custom_antimicrobials.html
+++ b/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="">2.1.1.9094</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
--- a/reference/add_custom_microorganisms.html
+++ b/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="">2.1.1.9094</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
--- a/reference/age.html
+++ b/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="">2.1.1.9094</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
@ -110,16 +110,16 @@
 <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  58  58.84699         34</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2  1980-03-01  44  44.60929         19</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3  1949-11-01  74  74.93989         50</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4  1947-02-14  77  77.65301         52</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5  1940-02-19  84  84.63934         59</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6  1988-01-10  36  36.74863         11</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7  1997-08-27  27  27.12022          2</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8  1978-01-26  46  46.70492         21</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9  1972-06-17  52  52.31421         27</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1986-08-10  38  38.16667         13</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1  1965-12-05  58  58.86066         34</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2  1980-03-01  44  44.62295         19</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3  1949-11-01  74  74.95355         50</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4  1947-02-14  77  77.66667         52</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5  1940-02-19  84  84.65301         59</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6  1988-01-10  36  36.76230         11</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7  1997-08-27  27  27.13388          2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8  1978-01-26  46  46.71858         21</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9  1972-06-17  52  52.32787         27</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1986-08-10  38  38.18033         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>
--- a/reference/age_groups.html
+++ b/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="">2.1.1.9094</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
--- a/reference/antibiogram.html
+++ b/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="">2.1.1.9094</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
--- a/reference/antibiotic_class_selectors.html
+++ b/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="">2.1.1.9094</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
--- a/reference/antibiotics.html
+++ b/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="">2.1.1.9094</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
--- a/reference/as.ab.html
+++ b/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="">2.1.1.9094</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
--- a/reference/as.av.html
+++ b/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="">2.1.1.9094</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
--- a/reference/as.disk.html
+++ b/reference/as.disk.html
@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Transform Input to Disk Diffusion Diameters — as.disk • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Transform Input to Disk Diffusion Diameters — as.disk"><meta name="description" content="This transforms a vector to a new class disk, which is a disk diffusion growth zone size (around an antibiotic disk) in millimetres between 6 and 50."><meta property="og:description" content="This transforms a vector to a new class disk, which is a disk diffusion growth zone size (around an antibiotic disk) in millimetres between 6 and 50."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Transform Input to Disk Diffusion Diameters — as.disk • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Transform Input to Disk Diffusion Diameters — as.disk"><meta name="description" content="This transforms a vector to a new class disk, which is a disk diffusion growth zone size (around an antibiotic disk) in millimetres between 0 and 50."><meta property="og:description" content="This transforms a vector to a new class disk, which is a disk diffusion growth zone size (around an antibiotic disk) in millimetres between 0 and 50."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"></head><body>
    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>


@ -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="">2.1.1.9094</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
@ -48,7 +48,7 @@
    </div>

    <div class="ref-description section level2">
-    <p>This transforms a vector to a new class <code>disk</code>, which is a disk diffusion growth zone size (around an antibiotic disk) in millimetres between 6 and 50.</p>
+    <p>This transforms a vector to a new class <code>disk</code>, which is a disk diffusion growth zone size (around an antibiotic disk) in millimetres between 0 and 50.</p>
    </div>

    <div class="section level2">
@ -83,7 +83,7 @@
    <div class="section level2">
    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
    <p>Interpret disk values as SIR values with <code><a href="as.sir.html">as.sir()</a></code>. It supports guidelines from EUCAST and CLSI.</p>
-<p>Disk diffusion growth zone sizes must be between 6 and 50 millimetres. Values higher than 50 but lower than 100 will be maximised to 50. All others input values outside the 6-50 range will return <code>NA</code>.</p>
+<p>Disk diffusion growth zone sizes must be between 0 and 50 millimetres. Values higher than 50 but lower than 100 will be maximised to 50. All others input values outside the 0-50 range will return <code>NA</code>.</p>
 <p><code>NA_disk_</code> is a missing value of the new <code>disk</code> class.</p>
    </div>
    <div class="section level2">
--- a/reference/as.mic.html
+++ b/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="">2.1.1.9094</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
--- a/reference/as.mo.html
+++ b/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="">2.1.1.9094</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
--- a/reference/as.sir.html
+++ b/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="">2.1.1.9094</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
@ -727,8 +727,8 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   all the details of the breakpoint interpretations.</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: column 'nitrofuratoin' (NIT, nitrofurantoin),</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2024...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: column 'nitrofuratoin' (NIT,</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> nitrofurantoin), EUCAST 2024...</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>  OK </span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Assuming value "urine" in column 'specimen' reflects a urinary tract</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   infection.</span>
@ -736,8 +736,8 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   all the details of the breakpoint interpretations.</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: column 'nitrofuratoin' (NIT, nitrofurantoin),</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2024...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: column 'nitrofuratoin' (NIT,</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> nitrofurantoin), EUCAST 2024...</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>  OK </span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
@ -785,16 +785,16 @@ 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> 2024-10-10 <span style="color: #949494;">14:42:40</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> 2024-10-10 <span style="color: #949494;">14:42:47</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> 2024-10-10 <span style="color: #949494;">14:42:47</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> 2024-10-10 <span style="color: #949494;">14:42:48</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> 2024-10-10 <span style="color: #949494;">14:42:48</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> 2024-10-10 <span style="color: #949494;">14:42:40</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> 2024-10-10 <span style="color: #949494;">14:42:47</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> 2024-10-10 <span style="color: #949494;">14:42:47</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> 2024-10-10 <span style="color: #949494;">14:42:48</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> 2024-10-10 <span style="color: #949494;">14:42:48</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;"> 1</span> 2024-10-15 <span style="color: #949494;">15:35:01</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> 2024-10-15 <span style="color: #949494;">15:35:08</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> 2024-10-15 <span style="color: #949494;">15:35:09</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> 2024-10-15 <span style="color: #949494;">15:35:09</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> 2024-10-15 <span style="color: #949494;">15:35:10</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> 2024-10-15 <span style="color: #949494;">15:35:01</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> 2024-10-15 <span style="color: #949494;">15:35:08</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> 2024-10-15 <span style="color: #949494;">15:35:08</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> 2024-10-15 <span style="color: #949494;">15:35:09</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> 2024-10-15 <span style="color: #949494;">15:35:10</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>
--- a/reference/atc_online.html
+++ b/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="">2.1.1.9094</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
--- a/reference/av_from_text.html
+++ b/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="">2.1.1.9094</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
--- a/reference/av_property.html
+++ b/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="">2.1.1.9094</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
--- a/reference/availability.html
+++ b/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="">2.1.1.9094</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
--- a/reference/bug_drug_combinations.html
+++ b/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="">2.1.1.9094</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
--- a/reference/clinical_breakpoints.html
+++ b/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="">2.1.1.9094</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
--- a/reference/count.html
+++ b/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="">2.1.1.9094</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
--- a/reference/custom_eucast_rules.html
+++ b/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="">2.1.1.9094</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
--- a/reference/dosage.html
+++ b/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="">2.1.1.9094</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
--- a/reference/eucast_rules.html
+++ b/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="">2.1.1.9094</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
--- a/reference/example_isolates.html
+++ b/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="">2.1.1.9094</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
--- a/reference/example_isolates_unclean.html
+++ b/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="">2.1.1.9094</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
--- a/reference/export_ncbi_biosample.html
+++ b/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="">2.1.1.9094</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
--- a/reference/first_isolate.html
+++ b/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="">2.1.1.9094</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
--- a/reference/g.test.html
+++ b/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="">2.1.1.9094</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
--- a/reference/get_episode.html
+++ b/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="">2.1.1.9094</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
--- a/reference/ggplot_pca.html
+++ b/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="">2.1.1.9094</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
--- a/reference/ggplot_sir.html
+++ b/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="">2.1.1.9094</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
--- a/reference/guess_ab_col.html
+++ b/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="">2.1.1.9094</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
--- a/reference/index.html
+++ b/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="">2.1.1.9094</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
--- a/reference/intrinsic_resistant.html
+++ b/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="">2.1.1.9094</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
--- a/reference/italicise_taxonomy.html
+++ b/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="">2.1.1.9094</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
--- a/reference/join.html
+++ b/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="">2.1.1.9094</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
--- a/reference/key_antimicrobials.html
+++ b/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="">2.1.1.9094</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
--- a/reference/kurtosis.html
+++ b/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="">2.1.1.9094</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
--- a/reference/like.html
+++ b/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="">2.1.1.9094</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
--- a/reference/mdro.html
+++ b/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="">2.1.1.9094</small>
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--- a/reference/mean_amr_distance.html
+++ b/reference/mean_amr_distance.html
@ -7,7 +7,7 @@

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+++ b/reference/microorganisms.codes.html
@ -7,7 +7,7 @@

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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9094</small>
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+++ b/reference/microorganisms.groups.html
@ -7,7 +7,7 @@

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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9094</small>
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--- a/reference/microorganisms.html
+++ b/reference/microorganisms.html
@ -9,7 +9,7 @@ This data set is carefully crafted, yet made 100% reproducible from public and a

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--- a/reference/mo_matching_score.html
+++ b/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="">2.1.1.9094</small>
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+++ b/reference/mo_property.html
@ -7,7 +7,7 @@

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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9094</small>
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--- a/reference/mo_source.html
+++ b/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="">2.1.1.9094</small>
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--- a/reference/pca.html
+++ b/reference/pca.html
@ -7,7 +7,7 @@

    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>

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--- a/reference/plot.html
+++ b/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="">2.1.1.9094</small>
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--- a/reference/proportion.html
+++ b/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>

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+++ b/reference/random.html
@ -7,7 +7,7 @@

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+++ b/reference/resistance_predict.html
@ -7,7 +7,7 @@

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--- a/reference/skewness.html
+++ b/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="">2.1.1.9094</small>
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+++ b/reference/translate.html
@ -7,7 +7,7 @@

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+++ b/search.json
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Author	SHA1	Message	Date
github-actions	943ca7c7de	Built site for AMR@2.1.1.9095: `40edc16`	2024-10-15 15:37:30 +00:00
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github-actions	4ddb872f23	Built site for AMR@2.1.1.9095: `5c4d8fc`	2024-10-15 15:24:09 +00:00