Built site for AMR@2.1.1.9268: 2461631

2026-10-01 04:13:33 +02:00 · 2025-05-01 12:53:35 +00:00
1 parent dd091f606e
commit ac714f6778
@@ -31,7 +31,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -7,7 +7,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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">
@@ -5,7 +5,7 @@
 <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>How to conduct AMR data analysis • AMR (for R)</title>
+<title>Conduct AMR data analysis • AMR (for R)</title>
 <!-- favicons --><link rel="icon" type="image/png" sizes="96x96" href="../favicon-96x96.png">
 <link rel="icon" type="”image/svg+xml”" href="../favicon.svg">
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@@ -18,7 +18,7 @@
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 <link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet">
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-<script src="../extra.js"></script><meta property="og:title" content="How to conduct AMR data analysis">
+<script src="../extra.js"></script><meta property="og:title" content="Conduct AMR data analysis">
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 </head>
@@ -30,7 +30,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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">
@@ -78,7 +78,7 @@

 <div class="row">
  <main id="main" class="col-md-9"><div class="page-header">
-      <img src="../logo.svg" class="logo" alt=""><h1>How to conduct AMR data analysis</h1>
+      <img src="../logo.svg" class="logo" alt=""><h1>Conduct AMR data analysis</h1>
            
      
      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/AMR.Rmd" class="external-link"><code>vignettes/AMR.Rmd</code></a></small>
@@ -1147,8 +1147,8 @@ incidence and antimicrobial susceptibility patterns.</p>
 </tr></thead>
 <tbody><tr class="odd">
 <td align="left">69.4% (64.3-74.3%)</td>
-<td align="left">92.6% (91.2-93.8%)</td>
-<td align="left">88.7% (85.9-91.2%)</td>
+<td align="left">92.6% (91.1-93.9%)</td>
+<td align="left">88.7% (85.8-91.2%)</td>
 </tr></tbody>
 </table>
 <p>WISCA uses a <strong>Bayesian decision model</strong> to integrate
@@ -1190,57 +1190,57 @@ function on a grouped <code>tibble</code>, i.e., using
 <td align="left">0-24</td>
 <td align="left">F</td>
 <td align="left">56.6% (25.2-83.9%)</td>
-<td align="left">74% (50.5-91.9%)</td>
-<td align="left">68% (39.7-88.9%)</td>
+<td align="left">73.6% (48-91.6%)</td>
+<td align="left">68.6% (42.9-89.5%)</td>
 </tr>
 <tr class="even">
 <td align="left">0-24</td>
 <td align="left">M</td>
 <td align="left">60.3% (28.4-87.1%)</td>
-<td align="left">79.3% (59.5-94.2%)</td>
-<td align="left">60.1% (29.3-87.5%)</td>
+<td align="left">79.7% (57.6-94.2%)</td>
+<td align="left">60.1% (29.5-87.7%)</td>
 </tr>
 <tr class="odd">
 <td align="left">25-49</td>
 <td align="left">F</td>
 <td align="left">66.6% (45.6-85.5%)</td>
-<td align="left">91.8% (85.1-96.5%)</td>
-<td align="left">82.6% (66.7-93.9%)</td>
+<td align="left">91.7% (84.6-96.7%)</td>
+<td align="left">83% (67.9-94%)</td>
 </tr>
 <tr class="even">
 <td align="left">25-49</td>
 <td align="left">M</td>
 <td align="left">56.4% (29.1-81.7%)</td>
-<td align="left">89.5% (80-95.6%)</td>
-<td align="left">72.2% (47.1-90%)</td>
+<td align="left">89.2% (80.3-95.7%)</td>
+<td align="left">72.4% (49.7-90%)</td>
 </tr>
 <tr class="odd">
 <td align="left">50-74</td>
 <td align="left">F</td>
 <td align="left">67.8% (55.8-80.1%)</td>
-<td align="left">95.6% (93.2-97.7%)</td>
-<td align="left">88% (80.2-94.2%)</td>
+<td align="left">95.6% (93.2-97.5%)</td>
+<td align="left">88.1% (80.4-94.6%)</td>
 </tr>
 <tr class="even">
 <td align="left">50-74</td>
 <td align="left">M</td>
 <td align="left">66.2% (54.8-75.8%)</td>
-<td align="left">95.3% (92.5-97.4%)</td>
-<td align="left">84.2% (75.2-92.4%)</td>
+<td align="left">95.2% (92.4-97.4%)</td>
+<td align="left">84.4% (74.4-92.5%)</td>
 </tr>
 <tr class="odd">
 <td align="left">75+</td>
 <td align="left">F</td>
 <td align="left">71.7% (61-81.7%)</td>
-<td align="left">96.5% (94.4-98.2%)</td>
-<td align="left">90.7% (84.4-95.7%)</td>
+<td align="left">96.6% (94.4-98.2%)</td>
+<td align="left">90.6% (84.6-95.3%)</td>
 </tr>
 <tr class="even">
 <td align="left">75+</td>
 <td align="left">M</td>
 <td align="left">72.9% (63.8-82%)</td>
-<td align="left">96.6% (94.5-98.1%)</td>
-<td align="left">92.8% (87.6-96.3%)</td>
+<td align="left">96.6% (94.6-98.1%)</td>
+<td align="left">92.8% (87.8-96.5%)</td>
 </tr>
 </tbody>
 </table>
@@ -30,7 +30,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -30,7 +30,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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">
@@ -89,8 +89,8 @@
    
 <blockquote>
 <p>This page was entirely written by our <a href="https://chat.amr-for-r.org" class="external-link">AMR for R Assistant</a>, a ChatGPT
-manually-trained model able to answer any question about the AMR
-package.</p>
+manually-trained model able to answer any question about the
+<code>AMR</code> package.</p>
 </blockquote>
 <p>Antimicrobial resistance (AMR) is a global health crisis, and
 understanding resistance patterns is crucial for managing effective
@@ -5,7 +5,7 @@
 <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>How to apply EUCAST rules • AMR (for R)</title>
+<title>Apply EUCAST rules • AMR (for R)</title>
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 <link rel="icon" type="”image/svg+xml”" href="../favicon.svg">
 <link rel="apple-touch-icon" sizes="180x180" href="../apple-touch-icon.png">
@@ -18,7 +18,7 @@
 <link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet">
 <link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet">
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-<script src="../extra.js"></script><meta property="og:title" content="How to apply EUCAST rules">
+<script src="../extra.js"></script><meta property="og:title" content="Apply EUCAST rules">
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 </head>
@@ -30,7 +30,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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">
@@ -78,7 +78,7 @@

 <div class="row">
  <main id="main" class="col-md-9"><div class="page-header">
-      <img src="../logo.svg" class="logo" alt=""><h1>How to apply EUCAST rules</h1>
+      <img src="../logo.svg" class="logo" alt=""><h1>Apply EUCAST rules</h1>
            
      
      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/EUCAST.Rmd" class="external-link"><code>vignettes/EUCAST.Rmd</code></a></small>
@@ -5,7 +5,7 @@
 <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>How to determine multi-drug resistance (MDR) • AMR (for R)</title>
+<title>Determine multi-drug resistance (MDR) • AMR (for R)</title>
 <!-- favicons --><link rel="icon" type="image/png" sizes="96x96" href="../favicon-96x96.png">
 <link rel="icon" type="”image/svg+xml”" href="../favicon.svg">
 <link rel="apple-touch-icon" sizes="180x180" href="../apple-touch-icon.png">
@@ -18,7 +18,7 @@
 <link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet">
 <link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet">
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-<script src="../extra.js"></script><meta property="og:title" content="How to determine multi-drug resistance (MDR)">
+<script src="../extra.js"></script><meta property="og:title" content="Determine multi-drug resistance (MDR)">
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 </head>
@@ -30,7 +30,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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">
@@ -78,7 +78,7 @@

 <div class="row">
  <main id="main" class="col-md-9"><div class="page-header">
-      <img src="../logo.svg" class="logo" alt=""><h1>How to determine multi-drug resistance (MDR)</h1>
+      <img src="../logo.svg" class="logo" alt=""><h1>Determine multi-drug resistance (MDR)</h1>
            
      
      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/MDR.Rmd" class="external-link"><code>vignettes/MDR.Rmd</code></a></small>
@@ -5,7 +5,7 @@
 <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>How to conduct principal component analysis (PCA) for AMR • AMR (for R)</title>
+<title>Conduct principal component analysis (PCA) for AMR • AMR (for R)</title>
 <!-- favicons --><link rel="icon" type="image/png" sizes="96x96" href="../favicon-96x96.png">
 <link rel="icon" type="”image/svg+xml”" href="../favicon.svg">
 <link rel="apple-touch-icon" sizes="180x180" href="../apple-touch-icon.png">
@@ -18,7 +18,7 @@
 <link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet">
 <link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet">
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-<script src="../extra.js"></script><meta property="og:title" content="How to conduct principal component analysis (PCA) for AMR">
+<script src="../extra.js"></script><meta property="og:title" content="Conduct principal component analysis (PCA) for AMR">
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 </head>
@@ -30,7 +30,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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">
@@ -78,7 +78,7 @@

 <div class="row">
  <main id="main" class="col-md-9"><div class="page-header">
-      <img src="../logo.svg" class="logo" alt=""><h1>How to conduct principal component analysis (PCA) for AMR</h1>
+      <img src="../logo.svg" class="logo" alt=""><h1>Conduct principal component analysis (PCA) for AMR</h1>
            
      
      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/PCA.Rmd" class="external-link"><code>vignettes/PCA.Rmd</code></a></small>
@@ -5,7 +5,7 @@
 <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>How to work with WHONET data • AMR (for R)</title>
+<title>Work with WHONET data • AMR (for R)</title>
 <!-- favicons --><link rel="icon" type="image/png" sizes="96x96" href="../favicon-96x96.png">
 <link rel="icon" type="”image/svg+xml”" href="../favicon.svg">
 <link rel="apple-touch-icon" sizes="180x180" href="../apple-touch-icon.png">
@@ -18,7 +18,7 @@
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-<script src="../extra.js"></script><meta property="og:title" content="How to work with WHONET data">
+<script src="../extra.js"></script><meta property="og:title" content="Work with WHONET data">
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@@ -30,7 +30,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>


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@@ -78,7 +78,7 @@

 <div class="row">
  <main id="main" class="col-md-9"><div class="page-header">
-      <img src="../logo.svg" class="logo" alt=""><h1>How to work with WHONET data</h1>
+      <img src="../logo.svg" class="logo" alt=""><h1>Work with WHONET data</h1>
            
      
      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/WHONET.Rmd" class="external-link"><code>vignettes/WHONET.Rmd</code></a></small>
@@ -30,7 +30,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>


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@@ -87,6 +87,11 @@

    
    
+<blockquote>
+<p>This explainer was largely written by our <a href="https://chat.amr-for-r.org" class="external-link">AMR for R Assistant</a>, a ChatGPT
+manually-trained model able to answer any question about the
+<code>AMR</code> package.</p>
+</blockquote>
 <div class="section level2">
 <h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
 </h2>
@@ -94,33 +99,40 @@
 <em>probabilistic reasoning</em>: what is the chance that a regimen will
 cover the likely infecting organisms, before culture results are
 available?</p>
-<p>This is the purpose of <strong>WISCA</strong>, or:</p>
-<blockquote>
-<p><strong>Weighted-Incidence Syndromic Combination
-Antibiogram</strong></p>
-</blockquote>
-<p>WISCA is a Bayesian approach that integrates: - <strong>Pathogen
-prevalence</strong> (how often each species causes the syndrome), -
+<p>This is the purpose of <strong>WISCA</strong>, or
+<strong>Weighted-Incidence Syndromic Combination
+Antibiogram</strong>.</p>
+<p>WISCA is a Bayesian approach that integrates:</p>
+<ul>
+<li>
+<strong>Pathogen prevalence</strong> (how often each species causes
+the syndrome),</li>
+<li>
 <strong>Regimen susceptibility</strong> (how often a regimen works
-<em>if</em> the pathogen is known),</p>
+<em>if</em> the pathogen is known),</li>
+</ul>
 <p>to estimate the <strong>overall empirical coverage</strong> of
-antimicrobial regimens — with quantified uncertainty.</p>
+antimicrobial regimens, with quantified uncertainty.</p>
 <p>This vignette explains how WISCA works, why it is useful, and how to
-apply it in <strong>AMR</strong>.</p>
-<hr>
+apply it using the <code>AMR</code> package.</p>
 </div>
 <div class="section level2">
 <h2 id="why-traditional-antibiograms-fall-short">Why traditional antibiograms fall short<a class="anchor" aria-label="anchor" href="#why-traditional-antibiograms-fall-short"></a>
 </h2>
 <p>A standard antibiogram gives you:</p>
-<p>``` Species → Antibiotic → Susceptibility %</p>
+<pre><code>Species → Antibiotic → Susceptibility %</code></pre>
 <p>But clinicians don’t know the species <em>a priori</em>. They need to
-choose a regimen that covers the <strong>likely pathogens</strong> —
+choose a regimen that covers the <strong>likely pathogens</strong>,
 without knowing which one is present.</p>
-<p>Traditional antibiograms: - Fragment information by organism, - Do
-not weight by real-world prevalence, - Do not account for combination
-therapy or sample size, - Do not provide uncertainty.</p>
-<hr>
+<p>Traditional antibiograms calculate the susceptibility % as just the
+number of resistant isolates divided by the total number of tested
+isolates. Therefore, traditional antibiograms:</p>
+<ul>
+<li>Fragment information by organism,</li>
+<li>Do not weight by real-world prevalence,</li>
+<li>Do not account for combination therapy or sample size,</li>
+<li>Do not provide uncertainty.</li>
+</ul>
 </div>
 <div class="section level2">
 <h2 id="the-idea-of-wisca">The idea of WISCA<a class="anchor" aria-label="anchor" href="#the-idea-of-wisca"></a>
@@ -130,21 +142,31 @@ therapy or sample size, - Do not provide uncertainty.</p>
 <p>“What is the <strong>probability</strong> that this regimen
 <strong>will cover</strong> the pathogen, given the syndrome?”</p>
 </blockquote>
-<p>This means combining two things: - <strong>Incidence</strong> of each
-pathogen in the syndrome, - <strong>Susceptibility</strong> of each
-pathogen to the regimen.</p>
+<p>This means combining two things:</p>
+<ul>
+<li>
+<strong>Incidence</strong> of each pathogen in the syndrome,</li>
+<li>
+<strong>Susceptibility</strong> of each pathogen to the
+regimen.</li>
+</ul>
 <p>We can write this as:</p>
-<p>``` coverage = ∑ (pathogen incidence × susceptibility)</p>
-<p>For example, suppose: - E. coli causes 60% of cases, and 90% of
-<em>E. coli</em> are susceptible to a drug. - Klebsiella causes 40% of
-cases, and 70% of <em>Klebsiella</em> are susceptible.</p>
+<p><math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mtext mathvariant="normal">Coverage</mtext><mo>=</mo><munder><mo>∑</mo><mi>i</mi></munder><mrow><mo stretchy="true" form="prefix">(</mo><msub><mtext mathvariant="normal">Incidence</mtext><mi>i</mi></msub><mo>×</mo><msub><mtext mathvariant="normal">Susceptibility</mtext><mi>i</mi></msub><mo stretchy="true" form="postfix">)</mo></mrow></mrow><annotation encoding="application/x-tex">\text{Coverage} = \sum_i (\text{Incidence}_i \times \text{Susceptibility}_i)</annotation></semantics></math></p>
+<p>For example, suppose:</p>
+<ul>
+<li>
+<em>E. coli</em> causes 60% of cases, and 90% of <em>E. coli</em>
+are susceptible to a drug.</li>
+<li>
+<em>Klebsiella</em> causes 40% of cases, and 70% of
+<em>Klebsiella</em> are susceptible.</li>
+</ul>
 <p>Then:</p>
-<p>``` coverage = (0.6 × 0.9) + (0.4 × 0.7) = 0.82</p>
+<p><math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mtext mathvariant="normal">Coverage</mtext><mo>=</mo><mrow><mo stretchy="true" form="prefix">(</mo><mn>0.6</mn><mo>×</mo><mn>0.9</mn><mo stretchy="true" form="postfix">)</mo></mrow><mo>+</mo><mrow><mo stretchy="true" form="prefix">(</mo><mn>0.4</mn><mo>×</mo><mn>0.7</mn><mo stretchy="true" form="postfix">)</mo></mrow><mo>=</mo><mn>0.82</mn></mrow><annotation encoding="application/x-tex">\text{Coverage} = (0.6 \times 0.9) + (0.4 \times 0.7) = 0.82</annotation></semantics></math></p>
 <p>But in real data, incidence and susceptibility are <strong>estimated
-from samples</strong> — so they carry uncertainty. WISCA models this
+from samples</strong>, so they carry uncertainty. WISCA models this
 <strong>probabilistically</strong>, using conjugate Bayesian
 distributions.</p>
-<hr>
 </div>
 <div class="section level2">
 <h2 id="the-bayesian-engine-behind-wisca">The Bayesian engine behind WISCA<a class="anchor" aria-label="anchor" href="#the-bayesian-engine-behind-wisca"></a>
@@ -152,486 +174,270 @@ distributions.</p>
 <div class="section level3">
 <h3 id="pathogen-incidence">Pathogen incidence<a class="anchor" aria-label="anchor" href="#pathogen-incidence"></a>
 </h3>
-<p>Let: - K be the number of pathogens, -
-<code>α = (1, 1, ..., 1) be a **Dirichlet** prior (uniform), -</code> n
-= (n₁, …, nₖ) be the observed counts per species.</p>
-<p>Then the posterior incidence follows:</p>
-<p>``` incidence ∼ Dirichlet(α + n)</p>
-<p>In simulations, we draw from this posterior using:</p>
-<p>``` xᵢ ∼ Gamma(αᵢ + nᵢ, 1)</p>
-<p>``` incidenceᵢ = xᵢ / ∑ xⱼ</p>
-<hr>
+<p>Let:</p>
+<ul>
+<li>
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mi>K</mi><annotation encoding="application/x-tex">K</annotation></semantics></math>
+be the number of pathogens,</li>
+<li>
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi>α</mi><mo>=</mo><mrow><mo stretchy="true" form="prefix">(</mo><mn>1</mn><mo>,</mo><mn>1</mn><mo>,</mo><mi>…</mi><mo>,</mo><mn>1</mn><mo stretchy="true" form="postfix">)</mo></mrow></mrow><annotation encoding="application/x-tex">\alpha = (1, 1, \ldots, 1)</annotation></semantics></math>
+be a <strong>Dirichlet</strong> prior (uniform),</li>
+<li>
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi>n</mi><mo>=</mo><mrow><mo stretchy="true" form="prefix">(</mo><msub><mi>n</mi><mn>1</mn></msub><mo>,</mo><mi>…</mi><mo>,</mo><msub><mi>n</mi><mi>K</mi></msub><mo stretchy="true" form="postfix">)</mo></mrow></mrow><annotation encoding="application/x-tex">n = (n_1, \ldots, n_K)</annotation></semantics></math>
+be the observed counts per species.</li>
+</ul>
+<p>Then the posterior incidence is:</p>
+<p><math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi>p</mi><mo>∼</mo><mtext mathvariant="normal">Dirichlet</mtext><mrow><mo stretchy="true" form="prefix">(</mo><msub><mi>α</mi><mn>1</mn></msub><mo>+</mo><msub><mi>n</mi><mn>1</mn></msub><mo>,</mo><mi>…</mi><mo>,</mo><msub><mi>α</mi><mi>K</mi></msub><mo>+</mo><msub><mi>n</mi><mi>K</mi></msub><mo stretchy="true" form="postfix">)</mo></mrow></mrow><annotation encoding="application/x-tex">p \sim \text{Dirichlet}(\alpha_1 + n_1, \ldots, \alpha_K + n_K)</annotation></semantics></math></p>
+<p>To simulate from this, we use:</p>
+<p><math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><msub><mi>x</mi><mi>i</mi></msub><mo>∼</mo><mtext mathvariant="normal">Gamma</mtext><mrow><mo stretchy="true" form="prefix">(</mo><msub><mi>α</mi><mi>i</mi></msub><mo>+</mo><msub><mi>n</mi><mi>i</mi></msub><mo>,</mo><mspace width="0.222em"></mspace><mn>1</mn><mo stretchy="true" form="postfix">)</mo></mrow><mo>,</mo><mspace width="1.0em"></mspace><msub><mi>p</mi><mi>i</mi></msub><mo>=</mo><mfrac><msub><mi>x</mi><mi>i</mi></msub><mrow><munderover><mo>∑</mo><mrow><mi>j</mi><mo>=</mo><mn>1</mn></mrow><mi>K</mi></munderover><msub><mi>x</mi><mi>j</mi></msub></mrow></mfrac></mrow><annotation encoding="application/x-tex">x_i \sim \text{Gamma}(\alpha_i + n_i,\ 1), \quad p_i = \frac{x_i}{\sum_{j=1}^{K} x_j}</annotation></semantics></math></p>
 </div>
 <div class="section level3">
 <h3 id="susceptibility">Susceptibility<a class="anchor" aria-label="anchor" href="#susceptibility"></a>
 </h3>
-<p>Each pathogen–regimen pair has: - <code>prior: Beta(1, 1) -</code>
-data: S susceptible out of N tested</p>
-<p>Then:</p>
-<p>``` susceptibility ∼ Beta(1 + S, 1 + (N - S))</p>
-<p>In each simulation, we draw random susceptibility per species from
-this Beta distribution.</p>
-<hr>
+<p>Each pathogen–regimen pair has a prior and data:</p>
+<ul>
+<li>Prior:
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mtext mathvariant="normal">Beta</mtext><mrow><mo stretchy="true" form="prefix">(</mo><msub><mi>α</mi><mn>0</mn></msub><mo>,</mo><msub><mi>β</mi><mn>0</mn></msub><mo stretchy="true" form="postfix">)</mo></mrow></mrow><annotation encoding="application/x-tex">\text{Beta}(\alpha_0, \beta_0)</annotation></semantics></math>,
+with default
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><msub><mi>α</mi><mn>0</mn></msub><mo>=</mo><msub><mi>β</mi><mn>0</mn></msub><mo>=</mo><mn>1</mn></mrow><annotation encoding="application/x-tex">\alpha_0 = \beta_0 = 1</annotation></semantics></math>
+</li>
+<li>Data:
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mi>S</mi><annotation encoding="application/x-tex">S</annotation></semantics></math>
+susceptible out of
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mi>N</mi><annotation encoding="application/x-tex">N</annotation></semantics></math>
+tested</li>
+</ul>
+<p>The
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mi>S</mi><annotation encoding="application/x-tex">S</annotation></semantics></math>
+category could also include values SDD (susceptible, dose-dependent) and
+I (intermediate [CLSI], or susceptible, increased exposure
+[EUCAST]).</p>
+<p>Then the posterior is:</p>
+<p><math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi>θ</mi><mo>∼</mo><mtext mathvariant="normal">Beta</mtext><mrow><mo stretchy="true" form="prefix">(</mo><msub><mi>α</mi><mn>0</mn></msub><mo>+</mo><mi>S</mi><mo>,</mo><mspace width="0.222em"></mspace><msub><mi>β</mi><mn>0</mn></msub><mo>+</mo><mi>N</mi><mo>−</mo><mi>S</mi><mo stretchy="true" form="postfix">)</mo></mrow></mrow><annotation encoding="application/x-tex">\theta \sim \text{Beta}(\alpha_0 + S,\ \beta_0 + N - S)</annotation></semantics></math></p>
 </div>
 <div class="section level3">
 <h3 id="final-coverage-estimate">Final coverage estimate<a class="anchor" aria-label="anchor" href="#final-coverage-estimate"></a>
 </h3>
 <p>Putting it together:</p>
-<p>``` For each simulation: - Draw incidence ∼ Dirichlet - Draw
-susceptibility ∼ Beta - Multiply → coverage estimate</p>
-<p>We repeat this (e.g. 1000×) and summarise: - <strong>Mean</strong>:
-expected coverage - <strong>Quantiles</strong>: credible interval
-(default 95%)</p>
-<hr>
+<ol style="list-style-type: decimal">
+<li>Simulate pathogen incidence:
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi>𝐩</mi><mo>∼</mo><mtext mathvariant="normal">Dirichlet</mtext></mrow><annotation encoding="application/x-tex">\boldsymbol{p} \sim \text{Dirichlet}</annotation></semantics></math>
+</li>
+<li>Simulate susceptibility:
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><msub><mi>θ</mi><mi>i</mi></msub><mo>∼</mo><mtext mathvariant="normal">Beta</mtext><mrow><mo stretchy="true" form="prefix">(</mo><mn>1</mn><mo>+</mo><msub><mi>S</mi><mi>i</mi></msub><mo>,</mo><mspace width="0.222em"></mspace><mn>1</mn><mo>+</mo><msub><mi>R</mi><mi>i</mi></msub><mo stretchy="true" form="postfix">)</mo></mrow></mrow><annotation encoding="application/x-tex">\theta_i \sim \text{Beta}(1 + S_i,\ 1 + R_i)</annotation></semantics></math>
+</li>
+<li>Combine:</li>
+</ol>
+<p><math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mtext mathvariant="normal">Coverage</mtext><mo>=</mo><munderover><mo>∑</mo><mrow><mi>i</mi><mo>=</mo><mn>1</mn></mrow><mi>K</mi></munderover><msub><mi>p</mi><mi>i</mi></msub><mo>⋅</mo><msub><mi>θ</mi><mi>i</mi></msub></mrow><annotation encoding="application/x-tex">\text{Coverage} = \sum_{i=1}^{K} p_i \cdot \theta_i</annotation></semantics></math></p>
+<p>Repeat this simulation (e.g. 1000×) and summarise:</p>
+<ul>
+<li>
+<strong>Mean</strong> = expected coverage</li>
+<li>
+<strong>Quantiles</strong> = credible interval</li>
+</ul>
 </div>
 </div>
 <div class="section level2">
-<h2 id="practical-use-in-amr">Practical use in AMR<a class="anchor" aria-label="anchor" href="#practical-use-in-amr"></a>
+<h2 id="practical-use-in-the-amr-package">Practical use in the <code>AMR</code> package<a class="anchor" aria-label="anchor" href="#practical-use-in-the-amr-package"></a>
 </h2>
 <div class="section level3">
-<h3 id="simulate-a-synthetic-syndrome">Simulate a synthetic syndrome<a class="anchor" aria-label="anchor" href="#simulate-a-synthetic-syndrome"></a>
+<h3 id="prepare-data-and-simulate-synthetic-syndrome">Prepare data and simulate synthetic syndrome<a class="anchor" aria-label="anchor" href="#prepare-data-and-simulate-synthetic-syndrome"></a>
 </h3>
-<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://amr-for-r.org">AMR</a></span><span class="op">)</span></span>
 <span><span class="va">data</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span></span>
 <span></span>
-<span><span class="co"># Add a fake syndrome column for stratification</span></span>
-<span><span class="va">data</span><span class="op">$</span><span class="va">syndrome</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="va">data</span><span class="op">$</span><span class="va">mo</span> <span class="op"><a href="../reference/like.html">%like%</a></span> <span class="st">"coli"</span>, <span class="st">"UTI"</span>, <span class="st">"Other"</span><span class="op">)</span></span></code></pre></div>
+<span><span class="co"># Structure of our data</span></span>
+<span><span class="va">data</span></span>
+<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,000 × 46</span></span></span>
+<span><span class="co">#&gt;    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX  </span></span>
+<span><span class="co">#&gt;    <span style="color: #949494; font-style: italic;">&lt;date&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span 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;mo&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334     65 F      Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FFAFAF;">  R  </span> <span style="color: #B2B2B2;">  NA</span>  <span style="color: #B2B2B2;">  NA</span>  <span style="color: #B2B2B2;">  NA</span> </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> 2002-01-03 A77334     65 F      Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FFAFAF;">  R  </span> <span style="color: #B2B2B2;">  NA</span>  <span style="color: #B2B2B2;">  NA</span>  <span style="color: #B2B2B2;">  NA</span> </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> 2002-01-07 067927     45 F      ICU      <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;">  R  </span> <span style="color: #B2B2B2;">  NA</span>  <span style="color: #080808; background-color: #FFAFAF;">  R  </span> <span style="color: #B2B2B2;">  NA</span> </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> 2002-01-07 067927     45 F      ICU      <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;">  R  </span> <span style="color: #B2B2B2;">  NA</span>  <span style="color: #080808; background-color: #FFAFAF;">  R  </span> <span style="color: #B2B2B2;">  NA</span> </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> 2002-01-13 067927     45 F      ICU      <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;">  R  </span> <span style="color: #B2B2B2;">  NA</span>  <span style="color: #080808; background-color: #FFAFAF;">  R  </span> <span style="color: #B2B2B2;">  NA</span> </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> 2002-01-13 067927     45 F      ICU      <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;">  R  </span> <span style="color: #B2B2B2;">  NA</span>  <span style="color: #080808; background-color: #FFAFAF;">  R  </span> <span style="color: #B2B2B2;">  NA</span> </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> 2002-01-14 462729     78 M      Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FFAFAF;">  R  </span> <span style="color: #B2B2B2;">  NA</span>  <span style="color: #080808; background-color: #5FD7AF;">  S  </span> <span style="color: #080808; background-color: #FFAFAF;">  R  </span></span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> 2002-01-14 462729     78 M      Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FFAFAF;">  R  </span> <span style="color: #B2B2B2;">  NA</span>  <span style="color: #080808; background-color: #5FD7AF;">  S  </span> <span style="color: #080808; background-color: #FFAFAF;">  R  </span></span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> 2002-01-16 067927     45 F      ICU      <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;">  R  </span> <span style="color: #B2B2B2;">  NA</span>  <span style="color: #080808; background-color: #FFAFAF;">  R  </span> <span style="color: #B2B2B2;">  NA</span> </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> 2002-01-17 858515     79 F      ICU      <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;">  R  </span> <span style="color: #B2B2B2;">  NA</span>  <span style="color: #080808; background-color: #5FD7AF;">  S  </span> <span style="color: #B2B2B2;">  NA</span> </span></span>
+<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 1,990 more rows</span></span></span>
+<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;,</span></span></span>
+<span><span class="co">#&gt; <span style="color: #949494;">#   CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;,</span></span></span>
+<span><span class="co">#&gt; <span style="color: #949494;">#   TOB &lt;sir&gt;, AMK &lt;sir&gt;, KAN &lt;sir&gt;, TMP &lt;sir&gt;, SXT &lt;sir&gt;, NIT &lt;sir&gt;,</span></span></span>
+<span><span class="co">#&gt; <span style="color: #949494;">#   FOS &lt;sir&gt;, LNZ &lt;sir&gt;, CIP &lt;sir&gt;, MFX &lt;sir&gt;, VAN &lt;sir&gt;, TEC &lt;sir&gt;,</span></span></span>
+<span><span class="co">#&gt; <span style="color: #949494;">#   TCY &lt;sir&gt;, TGC &lt;sir&gt;, DOX &lt;sir&gt;, ERY &lt;sir&gt;, CLI &lt;sir&gt;, AZM &lt;sir&gt;,</span></span></span>
+<span><span class="co">#&gt; <span style="color: #949494;">#   IPM &lt;sir&gt;, MEM &lt;sir&gt;, MTR &lt;sir&gt;, CHL &lt;sir&gt;, COL &lt;sir&gt;, MUP &lt;sir&gt;, …</span></span></span>
+<span></span>
+<span><span class="co"># Add a fake syndrome column</span></span>
+<span><span class="va">data</span><span class="op">$</span><span class="va">syndrome</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="va">data</span><span class="op">$</span><span class="va">mo</span> <span class="op"><a href="../reference/like.html">%like%</a></span> <span class="st">"coli"</span>, <span class="st">"UTI"</span>, <span class="st">"No UTI"</span><span class="op">)</span></span></code></pre></div>
 </div>
 <div class="section level3">
 <h3 id="basic-wisca-antibiogram">Basic WISCA antibiogram<a class="anchor" aria-label="anchor" href="#basic-wisca-antibiogram"></a>
 </h3>
-<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">data</span>,</span>
-<span>            wisca <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
+<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">wisca</a></span><span class="op">(</span><span class="va">data</span>,</span>
+<span>      antimicrobials <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"AMC"</span>, <span class="st">"CIP"</span>, <span class="st">"GEN"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
 <table class="table">
-<colgroup>
-<col width="2%">
-<col width="2%">
-<col width="3%">
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="1%">
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="3%">
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="3%">
-<col width="2%">
-</colgroup>
 <thead><tr class="header">
-<th align="left">Amikacin</th>
-<th align="left">Amoxicillin</th>
 <th align="left">Amoxicillin/clavulanic acid</th>
-<th align="left">Ampicillin</th>
-<th align="left">Azithromycin</th>
-<th align="left">Benzylpenicillin</th>
-<th align="left">Cefazolin</th>
-<th align="left">Cefepime</th>
-<th align="left">Cefotaxime</th>
-<th align="left">Cefoxitin</th>
-<th align="left">Ceftazidime</th>
-<th align="left">Ceftriaxone</th>
-<th align="left">Cefuroxime</th>
-<th align="left">Chloramphenicol</th>
 <th align="left">Ciprofloxacin</th>
-<th align="left">Clindamycin</th>
-<th align="left">Colistin</th>
-<th align="left">Doxycycline</th>
-<th align="left">Erythromycin</th>
-<th align="left">Flucloxacillin</th>
-<th align="left">Fosfomycin</th>
 <th align="left">Gentamicin</th>
-<th align="left">Imipenem</th>
-<th align="left">Kanamycin</th>
-<th align="left">Linezolid</th>
-<th align="left">Meropenem</th>
-<th align="left">Metronidazole</th>
-<th align="left">Moxifloxacin</th>
-<th align="left">Mupirocin</th>
-<th align="left">Nitrofurantoin</th>
-<th align="left">Oxacillin</th>
-<th align="left">Piperacillin/tazobactam</th>
-<th align="left">Rifampicin</th>
-<th align="left">Teicoplanin</th>
-<th align="left">Tetracycline</th>
-<th align="left">Tigecycline</th>
-<th align="left">Tobramycin</th>
-<th align="left">Trimethoprim</th>
-<th align="left">Trimethoprim/sulfamethoxazole</th>
-<th align="left">Vancomycin</th>
 </tr></thead>
 <tbody><tr class="odd">
-<td align="left">41.7% (37.2-47.5%)</td>
-<td align="left">35.7% (33.3-38.2%)</td>
 <td align="left">73.7% (71.7-75.8%)</td>
-<td align="left">35.8% (33.6-38.1%)</td>
-<td align="left">43.8% (41.5-46%)</td>
-<td align="left">28.2% (25.8-30.8%)</td>
-<td align="left">69.3% (64.9-73.8%)</td>
-<td align="left">74.8% (70.5-78.8%)</td>
-<td align="left">73.3% (69.2-77.3%)</td>
-<td align="left">69.6% (65.5-73.7%)</td>
-<td align="left">35.9% (33.6-38.2%)</td>
-<td align="left">73.3% (68.9-77.2%)</td>
-<td align="left">71.9% (69.8-74%)</td>
-<td align="left">64.9% (51.7-78.5%)</td>
-<td align="left">77% (74.5-79.6%)</td>
-<td align="left">47.3% (44.7-49.6%)</td>
-<td align="left">33% (30.8-35.1%)</td>
-<td align="left">63.6% (52.1-74.9%)</td>
-<td align="left">43.7% (41.6-46%)</td>
-<td align="left">59.3% (47-71%)</td>
-<td align="left">60.5% (55.5-65.8%)</td>
-<td align="left">72.7% (70.7-74.8%)</td>
-<td align="left">78.2% (74-82.2%)</td>
-<td align="left">25.6% (13.5-37.7%)</td>
-<td align="left">54.9% (50.4-59%)</td>
-<td align="left">77.1% (72.8-81.2%)</td>
-<td align="left">56.1% (39.5-70.7%)</td>
-<td align="left">49.6% (43.6-55.6%)</td>
-<td align="left">65.2% (52.7-78.1%)</td>
-<td align="left">76.5% (69.4-82.3%)</td>
-<td align="left">57.8% (45.4-69.6%)</td>
-<td align="left">69.4% (64.2-74.2%)</td>
-<td align="left">52.4% (47.6-56.8%)</td>
-<td align="left">48.1% (43.4-52.9%)</td>
-<td align="left">61.4% (53.6-70.5%)</td>
-<td align="left">81.9% (78.1-85.5%)</td>
-<td align="left">60.7% (57.8-63.5%)</td>
-<td align="left">61% (58.8-63.5%)</td>
-<td align="left">76.5% (74.5-78.5%)</td>
-<td align="left">61.9% (59.8-64.2%)</td>
+<td align="left">77% (74.3-79.4%)</td>
+<td align="left">72.8% (70.7-74.8%)</td>
+</tr></tbody>
+</table>
+</div>
+<div class="section level3">
+<h3 id="use-combination-regimens">Use combination regimens<a class="anchor" aria-label="anchor" href="#use-combination-regimens"></a>
+</h3>
+<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">wisca</a></span><span class="op">(</span><span class="va">data</span>,</span>
+<span>      antimicrobials <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"AMC"</span>, <span class="st">"AMC + CIP"</span>, <span class="st">"AMC + GEN"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
+<table class="table">
+<colgroup>
+<col width="24%">
+<col width="38%">
+<col width="36%">
+</colgroup>
+<thead><tr class="header">
+<th align="left">Amoxicillin/clavulanic acid</th>
+<th align="left">Amoxicillin/clavulanic acid + Ciprofloxacin</th>
+<th align="left">Amoxicillin/clavulanic acid + Gentamicin</th>
+</tr></thead>
+<tbody><tr class="odd">
+<td align="left">73.8% (71.8-75.7%)</td>
+<td align="left">87.5% (85.9-89%)</td>
+<td align="left">89.7% (88.2-91.1%)</td>
 </tr></tbody>
 </table>
 </div>
 <div class="section level3">
 <h3 id="stratify-by-syndrome">Stratify by syndrome<a class="anchor" aria-label="anchor" href="#stratify-by-syndrome"></a>
 </h3>
-<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">data</span>,</span>
-<span>            syndromic_group <span class="op">=</span> <span class="st">"syndrome"</span>,</span>
-<span>            wisca <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
-<table style="width:100%;" class="table">
+<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">wisca</a></span><span class="op">(</span><span class="va">data</span>,</span>
+<span>      antimicrobials <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"AMC"</span>, <span class="st">"AMC + CIP"</span>, <span class="st">"AMC + GEN"</span><span class="op">)</span>,</span>
+<span>      syndromic_group <span class="op">=</span> <span class="st">"syndrome"</span><span class="op">)</span></span></code></pre></div>
+<table class="table">
 <colgroup>
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="3%">
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="3%">
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="2%">
-<col width="3%">
-<col width="2%">
+<col width="12%">
+<col width="21%">
+<col width="34%">
+<col width="31%">
 </colgroup>
 <thead><tr class="header">
 <th align="left">Syndromic Group</th>
-<th align="left">Amikacin</th>
-<th align="left">Amoxicillin</th>
 <th align="left">Amoxicillin/clavulanic acid</th>
-<th align="left">Ampicillin</th>
-<th align="left">Azithromycin</th>
-<th align="left">Benzylpenicillin</th>
-<th align="left">Cefazolin</th>
-<th align="left">Cefepime</th>
-<th align="left">Cefotaxime</th>
-<th align="left">Cefoxitin</th>
-<th align="left">Ceftazidime</th>
-<th align="left">Ceftriaxone</th>
-<th align="left">Cefuroxime</th>
-<th align="left">Chloramphenicol</th>
-<th align="left">Ciprofloxacin</th>
-<th align="left">Clindamycin</th>
-<th align="left">Colistin</th>
-<th align="left">Doxycycline</th>
-<th align="left">Erythromycin</th>
-<th align="left">Flucloxacillin</th>
-<th align="left">Fosfomycin</th>
-<th align="left">Gentamicin</th>
-<th align="left">Imipenem</th>
-<th align="left">Kanamycin</th>
-<th align="left">Linezolid</th>
-<th align="left">Meropenem</th>
-<th align="left">Metronidazole</th>
-<th align="left">Moxifloxacin</th>
-<th align="left">Mupirocin</th>
-<th align="left">Nitrofurantoin</th>
-<th align="left">Oxacillin</th>
-<th align="left">Piperacillin/tazobactam</th>
-<th align="left">Rifampicin</th>
-<th align="left">Teicoplanin</th>
-<th align="left">Tetracycline</th>
-<th align="left">Tigecycline</th>
-<th align="left">Tobramycin</th>
-<th align="left">Trimethoprim</th>
-<th align="left">Trimethoprim/sulfamethoxazole</th>
-<th align="left">Vancomycin</th>
+<th align="left">Amoxicillin/clavulanic acid + Ciprofloxacin</th>
+<th align="left">Amoxicillin/clavulanic acid + Gentamicin</th>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="left">Other</td>
-<td align="left">25% (20.2-31.7%)</td>
-<td align="left">31.6% (28.7-34%)</td>
-<td align="left">70.1% (67.7-72.4%)</td>
-<td align="left">31.6% (29.1-34.1%)</td>
-<td align="left">56.4% (53.8-58.8%)</td>
-<td align="left">36.3% (33.1-39.4%)</td>
-<td align="left">61.5% (55.7-66.5%)</td>
-<td align="left">68.5% (63.4-73.8%)</td>
-<td align="left">66.7% (61.4-71.9%)</td>
-<td align="left">63% (57.7-68.6%)</td>
-<td align="left">18.3% (15.9-20.8%)</td>
-<td align="left">66.6% (61.4-71.5%)</td>
-<td align="left">65.5% (62.7-68%)</td>
-<td align="left">69.6% (60-77.2%)</td>
-<td align="left">74% (70.8-77.2%)</td>
-<td align="left">60.9% (58.1-63.6%)</td>
-<td align="left">13.9% (11.8-15.8%)</td>
-<td align="left">67.4% (63.7-70.9%)</td>
-<td align="left">56.4% (54-58.9%)</td>
-<td align="left">61.4% (56-67.6%)</td>
-<td align="left">49.6% (43.2-56.3%)</td>
-<td align="left">65.6% (62.8-68.1%)</td>
-<td align="left">71.8% (66.7-77%)</td>
-<td align="left">18.6% (13.1-25.9%)</td>
-<td align="left">70.8% (65.1-75.8%)</td>
-<td align="left">70.6% (65.1-75.7%)</td>
-<td align="left">49.8% (34.2-66.6%)</td>
-<td align="left">63.3% (56.2-70.3%)</td>
-<td align="left">69.8% (62.6-76.4%)</td>
-<td align="left">70.5% (61.2-77.5%)</td>
-<td align="left">60% (54.4-65.4%)</td>
-<td align="left">62.4% (56.4-68.6%)</td>
-<td align="left">67.6% (61.9-73.2%)</td>
-<td align="left">61.9% (55.4-67.6%)</td>
-<td align="left">67.8% (64.8-70.6%)</td>
-<td align="left">77% (72.3-81.8%)</td>
-<td align="left">50.1% (46.7-53.6%)</td>
-<td align="left">61.1% (58.4-64%)</td>
-<td align="left">78.8% (76.4-80.9%)</td>
-<td align="left">79.6% (77.4-81.8%)</td>
+<td align="left">No UTI</td>
+<td align="left">70.1% (67.8-72.3%)</td>
+<td align="left">85.2% (83.1-87.2%)</td>
+<td align="left">87.1% (85.3-88.7%)</td>
 </tr>
 <tr class="even">
 <td align="left">UTI</td>
-<td align="left">91.5% (88.8-93.5%)</td>
-<td align="left">50% (45.5-54.6%)</td>
-<td align="left">80.9% (77.8-84%)</td>
-<td align="left">49.9% (45.6-54.3%)</td>
-<td align="left">8.2% (6.4-10.5%)</td>
-<td align="left">8.2% (6.3-10.3%)</td>
-<td align="left">88.9% (84.2-92.3%)</td>
-<td align="left">89.4% (86.5-91.8%)</td>
-<td align="left">89.9% (87.4-92.1%)</td>
-<td align="left">86.1% (82.9-88.9%)</td>
-<td align="left">89.8% (87.2-91.9%)</td>
-<td align="left">89.8% (87.1-92.1%)</td>
-<td align="left">87.4% (84.5-89.8%)</td>
-<td align="left">NA</td>
-<td align="left">81.4% (78.3-84.3%)</td>
-<td align="left">8.2% (6.3-10.4%)</td>
-<td align="left">91.7% (89.6-93.8%)</td>
-<td align="left">NA</td>
-<td align="left">8.1% (6.3-10.4%)</td>
-<td align="left">NA</td>
-<td align="left">90.6% (86.5-93.3%)</td>
-<td align="left">90.2% (87.9-92.2%)</td>
-<td align="left">91.8% (89.7-93.8%)</td>
-<td align="left">NA</td>
-<td align="left">8.1% (6.1-10.2%)</td>
-<td align="left">91.8% (89.6-93.8%)</td>
-<td align="left">71.4% (31.8-91.6%)</td>
-<td align="left">9.3% (6.7-13.3%)</td>
-<td align="left">NA</td>
-<td align="left">89.4% (86.9-91.7%)</td>
-<td align="left">NA</td>
-<td align="left">87.2% (84.4-89.6%)</td>
-<td align="left">8.2% (6.3-10.4%)</td>
-<td align="left">8.2% (6.3-10.3%)</td>
-<td align="left">41.2% (14.3-74.4%)</td>
-<td align="left">90.9% (87.7-93.3%)</td>
-<td align="left">89.6% (87.1-91.8%)</td>
-<td align="left">59.1% (54.7-63.4%)</td>
-<td align="left">65.3% (61.3-69.2%)</td>
-<td align="left">8.2% (6.2-10.3%)</td>
+<td align="left">80.9% (77.7-83.8%)</td>
+<td align="left">88.2% (85.7-90.5%)</td>
+<td align="left">90.9% (88.7-93%)</td>
 </tr>
 </tbody>
 </table>
-</div>
-<div class="section level3">
-<h3 id="use-combination-regimens">Use combination regimens<a class="anchor" aria-label="anchor" href="#use-combination-regimens"></a>
-</h3>
-<p>The <code><a href="../reference/antibiogram.html">antibiogram()</a></code> function supports combination
-regimens:</p>
-<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">data</span>,</span>
-<span>            antimicrobials <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"AMC"</span>, <span class="st">"GEN"</span>, <span class="st">"AMC + GEN"</span>, <span class="st">"CIP"</span><span class="op">)</span>,</span>
-<span>            wisca <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
+<p>The <code>AMR</code> package is available in 20 languages, which can
+all be used for the <code><a href="../reference/antibiogram.html">wisca()</a></code> function too:</p>
+<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">wisca</a></span><span class="op">(</span><span class="va">data</span>,</span>
+<span>      antimicrobials <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"AMC"</span>, <span class="st">"AMC + CIP"</span>, <span class="st">"AMC + GEN"</span><span class="op">)</span>,</span>
+<span>      syndromic_group <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/grep.html" class="external-link">gsub</a></span><span class="op">(</span><span class="st">"UTI"</span>, <span class="st">"UCI"</span>, <span class="va">data</span><span class="op">$</span><span class="va">syndrome</span><span class="op">)</span>,</span>
+<span>      language <span class="op">=</span> <span class="st">"Spanish"</span><span class="op">)</span></span></code></pre></div>
 <table class="table">
 <colgroup>
-<col width="26%">
-<col width="39%">
-<col width="16%">
-<col width="18%">
+<col width="12%">
+<col width="21%">
+<col width="34%">
+<col width="31%">
 </colgroup>
 <thead><tr class="header">
-<th align="left">Amoxicillin/clavulanic acid</th>
-<th align="left">Amoxicillin/clavulanic acid + Gentamicin</th>
-<th align="left">Ciprofloxacin</th>
-<th align="left">Gentamicin</th>
-</tr></thead>
-<tbody><tr class="odd">
-<td align="left">73.8% (71.7-75.8%)</td>
-<td align="left">89.7% (88.2-91.2%)</td>
-<td align="left">77% (74.3-79.6%)</td>
-<td align="left">72.8% (70.6-74.9%)</td>
-</tr></tbody>
-</table>
-<hr>
-</div>
-</div>
-<div class="section level2">
-<h2 id="interpretation">Interpretation<a class="anchor" aria-label="anchor" href="#interpretation"></a>
-</h2>
-<p>Suppose you get this output:</p>
-<table class="table">
-<thead><tr class="header">
-<th>Regimen</th>
-<th>Coverage</th>
-<th>Lower_CI</th>
-<th>Upper_CI</th>
+<th align="left">Grupo sindrómico</th>
+<th align="left">Amoxicilina/ácido clavulánico</th>
+<th align="left">Amoxicilina/ácido clavulánico + Ciprofloxacina</th>
+<th align="left">Amoxicilina/ácido clavulánico + Gentamicina</th>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td>AMC</td>
-<td>0.72</td>
-<td>0.65</td>
-<td>0.78</td>
+<td align="left">No UCI</td>
+<td align="left">70% (67.8-72.4%)</td>
+<td align="left">85.3% (83.3-87.2%)</td>
+<td align="left">87% (85.3-88.8%)</td>
 </tr>
 <tr class="even">
-<td>AMC + GEN</td>
-<td>0.88</td>
-<td>0.83</td>
-<td>0.93</td>
+<td align="left">UCI</td>
+<td align="left">80.9% (77.7-83.9%)</td>
+<td align="left">88.2% (85.5-90.6%)</td>
+<td align="left">90.9% (88.7-93%)</td>
 </tr>
 </tbody>
 </table>
-<p>Interpretation:</p>
-<blockquote>
-<p><em>“AMC + GEN covers 88% of expected pathogens for this syndrome,
-with 95% certainty that the true coverage lies between 83% and
-93%.”</em></p>
-</blockquote>
-<p>Regimens with few tested isolates will show <strong>wider
-intervals</strong>.</p>
-<hr>
+</div>
 </div>
 <div class="section level2">
-<h2 id="sensible-defaults-but-you-can-customise">Sensible defaults, but you can customise<a class="anchor" aria-label="anchor" href="#sensible-defaults-but-you-can-customise"></a>
+<h2 id="sensible-defaults-which-can-be-customised">Sensible defaults, which can be customised<a class="anchor" aria-label="anchor" href="#sensible-defaults-which-can-be-customised"></a>
 </h2>
 <ul>
 <li>
-<code>minimum = 30</code>: exclude regimens with &lt;30 isolates
-tested.</li>
+<code>simulations = 1000</code>: number of Monte Carlo draws</li>
 <li>
-<code>simulations = 1000</code>: number of Monte Carlo samples.</li>
+<code>conf_interval = 0.95</code>: coverage interval width</li>
 <li>
-<code>conf_interval = 0.95</code>: coverage interval width.</li>
-<li>
-<code>combine_SI = TRUE</code>: count “I”/“SDD” as susceptible.</li>
+<code>combine_SI = TRUE</code>: count “I” and “SDD” as
+susceptible</li>
 </ul>
-<hr>
 </div>
 <div class="section level2">
 <h2 id="limitations">Limitations<a class="anchor" aria-label="anchor" href="#limitations"></a>
 </h2>
 <ul>
-<li>WISCA does not model time trends or temporal resistance shifts.</li>
-<li>It assumes data are representative of current clinical
-practice.</li>
-<li>It does not account for patient-level covariates (yet).</li>
-<li>Species-specific data are abstracted into syndrome-level
-estimates.</li>
+<li>It assumes your data are representative</li>
+<li>No adjustment for patient-level covariates, although these could be
+passed onto the <code>syndromic_group</code> argument</li>
+<li>WISCA does not model resistance over time, you might want to use
+<code>tidymodels</code> for that, for which we <a href="https://amr-for-r.org/articles/AMR_with_tidymodels.html">wrote a
+basic introduction</a>
+</li>
 </ul>
-<hr>
+</div>
+<div class="section level2">
+<h2 id="summary">Summary<a class="anchor" aria-label="anchor" href="#summary"></a>
+</h2>
+<p>WISCA enables:</p>
+<ul>
+<li>Empirical regimen comparison,</li>
+<li>Syndrome-specific coverage estimation,</li>
+<li>Fully probabilistic interpretation.</li>
+</ul>
+<p>It is available in the <code>AMR</code> package via either:</p>
+<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">wisca</a></span><span class="op">(</span><span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">...</span>, wisca <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
 </div>
 <div class="section level2">
 <h2 id="reference">Reference<a class="anchor" aria-label="anchor" href="#reference"></a>
 </h2>
-<p>Bielicki JA et al. (2016).<br><em>Weighted-incidence syndromic combination antibiograms to guide
-empiric treatment in pediatric bloodstream infections.</em><br><strong>J Antimicrob Chemother</strong>, 71(2):529–536. <a href="doi:10.1093/jac/dkv397" class="uri">doi:10.1093/jac/dkv397</a></p>
-<hr>
-</div>
-<div class="section level2">
-<h2 id="conclusion">Conclusion<a class="anchor" aria-label="anchor" href="#conclusion"></a>
-</h2>
-<p>WISCA shifts empirical therapy from simple percent susceptible toward
-<strong>probabilistic, syndrome-based decision support</strong>. It is a
-statistically principled, clinically intuitive method to guide regimen
-selection — and easy to use via the <code><a href="../reference/antibiogram.html">antibiogram()</a></code> function
-in the <strong>AMR</strong> package.</p>
-<p>For antimicrobial stewardship teams, it enables
-<strong>disease-specific, reproducible, and data-driven
-guidance</strong> — even in the face of sparse data.</p>
+<p>Bielicki, JA, et al. (2016). <em>Selecting appropriate empirical
+antibiotic regimens for paediatric bloodstream infections: application
+of a Bayesian decision model to local and pooled antimicrobial
+resistance surveillance data.</em> <strong>J Antimicrob
+Chemother</strong>. 71(3):794-802. <a href="https://doi.org/10.1093/jac/dkv397" class="external-link uri">https://doi.org/10.1093/jac/dkv397</a></p>
 </div>
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@@ -30,7 +30,7 @@

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+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>


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@@ -78,7 +78,7 @@

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  <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>
+      <img src="../logo.svg" class="logo" alt=""><h1>Download data sets for download / own use</h1>
            
            <h4 data-toc-skip class="date">01 May 2025</h4>
      
@@ -7,7 +7,7 @@

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@@ -55,17 +55,17 @@
        <dd>
        </dd><dt><a href="AMR_with_tidymodels.html">AMR with tidymodels</a></dt>
        <dd>
-        </dd><dt><a href="AMR.html">How to conduct AMR data analysis</a></dt>
+        </dd><dt><a href="AMR.html">Conduct AMR data analysis</a></dt>
        <dd>
-        </dd><dt><a href="datasets.html">Data sets for download / own use</a></dt>
+        </dd><dt><a href="datasets.html">Download data sets for download / own use</a></dt>
        <dd>
-        </dd><dt><a href="EUCAST.html">How to apply EUCAST rules</a></dt>
+        </dd><dt><a href="EUCAST.html">Apply EUCAST rules</a></dt>
        <dd>
-        </dd><dt><a href="MDR.html">How to determine multi-drug resistance (MDR)</a></dt>
+        </dd><dt><a href="MDR.html">Determine multi-drug resistance (MDR)</a></dt>
        <dd>
-        </dd><dt><a href="PCA.html">How to conduct principal component analysis (PCA) for AMR</a></dt>
+        </dd><dt><a href="PCA.html">Conduct principal component analysis (PCA) for AMR</a></dt>
        <dd>
-        </dd><dt><a href="WHONET.html">How to work with WHONET data</a></dt>
+        </dd><dt><a href="WHONET.html">Work with WHONET data</a></dt>
        <dd>
        </dd><dt><a href="WISCA.html">Estimating Empirical Coverage with WISCA</a></dt>
        <dd>
@@ -7,7 +7,7 @@

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@@ -33,7 +33,7 @@

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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
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@@ -7,7 +7,7 @@

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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>


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@@ -49,11 +49,11 @@
    </div>

    <div class="section level2">
-<h2 class="pkg-version" data-toc-text="2.1.1.9267" id="amr-2119267">AMR 2.1.1.9267<a class="anchor" aria-label="anchor" href="#amr-2119267"></a></h2>
+<h2 class="pkg-version" data-toc-text="2.1.1.9268" id="amr-2119268">AMR 2.1.1.9268<a class="anchor" aria-label="anchor" href="#amr-2119268"></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://amr-for-r.org/#get-this-package">the instructions here</a>.)</em></p>
 <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 class="section level3">
-<h3 id="tldr-2-1-1-9267">tl;dr<a class="anchor" aria-label="anchor" href="#tldr-2-1-1-9267"></a></h3>
+<h3 id="tldr-2-1-1-9268">tl;dr<a class="anchor" aria-label="anchor" href="#tldr-2-1-1-9268"></a></h3>
 <ul><li>
 <strong>Scope Expansion</strong>: One Health support (Human + Veterinary + Environmental microbiology).</li>
 <li>
@@ -113,15 +113,15 @@
 </ul></li>
 </ul></div>
 <div class="section level3">
-<h3 id="full-changelog-2-1-1-9267">Full Changelog<a class="anchor" aria-label="anchor" href="#full-changelog-2-1-1-9267"></a></h3>
+<h3 id="full-changelog-2-1-1-9268">Full Changelog<a class="anchor" aria-label="anchor" href="#full-changelog-2-1-1-9268"></a></h3>
 <div class="section level4">
-<h4 id="breaking-2-1-1-9267">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9267"></a></h4>
+<h4 id="breaking-2-1-1-9268">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9268"></a></h4>
 <ul><li>Dataset <code>antibiotics</code> has been renamed to <code>antimicrobials</code> as the data set contains more than just antibiotics. Using <code>antibiotics</code> will still work, but now returns a warning.</li>
 <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 two years ago.</li>
 <li>Functions <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code> and <code><a href="../reference/resistance_predict.html">sir_predict()</a></code> are now deprecated and will be removed in a future version. Use the <code>tidymodels</code> framework instead, for which we <a href="https://amr-for-r.org/articles/AMR_with_tidymodels.html">wrote a basic introduction</a>.</li>
 </ul></div>
 <div class="section level4">
-<h4 id="new-2-1-1-9267">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9267"></a></h4>
+<h4 id="new-2-1-1-9268">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9268"></a></h4>
 <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>
@@ -176,7 +176,7 @@
 </ul></li>
 </ul></div>
 <div class="section level4">
-<h4 id="changed-2-1-1-9267">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9267"></a></h4>
+<h4 id="changed-2-1-1-9268">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9268"></a></h4>
 <ul><li>SIR interpretation
 <ul><li>Support for parallel computing to greatly improve speed using the <code>parallel</code> package (part of base R). Use <code>as.sir(your_data, parallel = TRUE)</code> to run SIR interpretation using multiple cores.</li>
 <li>It is now possible to use column names for arguments <code>guideline</code>, <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>
@@ -258,7 +258,7 @@
 <li>Added console colours support of <code>sir</code> class for Positron</li>
 </ul></div>
 <div class="section level4">
-<h4 id="other-2-1-1-9267">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9267"></a></h4>
+<h4 id="other-2-1-1-9268">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9268"></a></h4>
 <ul><li>New website domain: <a href="https://amr-for-r.org" class="uri">https://amr-for-r.org</a>! The old domain (<a href="http://amr-for-r.org/" class="external-link uri">http://amr-for-r.org/</a>) will remain to work.</li>
 <li>Added Dr. Larisse Bolton and Aislinn Cook as contributors for their fantastic implementation of WISCA in a mathematically solid way</li>
 <li>Added Matthew Saab, Dr. Jordan Stull, and Prof. Javier Sanchez as contributors for their tremendous input on veterinary breakpoints and interpretations</li>
@@ -269,7 +269,7 @@
 </ul></div>
 </div>
 <div class="section level3">
-<h3 id="older-versions-2-1-1-9267">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9267"></a></h3>
+<h3 id="older-versions-2-1-1-9268">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9268"></a></h3>
 <p>This changelog only contains changes from AMR v3.0 (March 2025) 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>
@@ -11,7 +11,7 @@ articles:
  PCA: PCA.html
  WHONET: WHONET.html
  WISCA: WISCA.html
-last_built: 2025-05-01T09:52Z
+last_built: 2025-05-01T12:49Z
 urls:
  reference: https://amr-for-r.org/reference
  article: https://amr-for-r.org/articles
@@ -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="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -7,7 +7,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -21,7 +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="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -7,7 +7,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -7,7 +7,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -7,7 +7,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -7,7 +7,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -7,7 +7,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -7,7 +7,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -7,7 +7,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -7,7 +7,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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">
@@ -9,7 +9,7 @@ Adhering to previously described approaches (see Source) and especially the Baye

    <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="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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">
@@ -63,16 +63,17 @@ Adhering to previously described approaches (see Source) and especially the Baye
 <span>  only_all_tested <span class="op">=</span> <span class="cn">FALSE</span>, digits <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="va">wisca</span>, <span class="fl">1</span>, <span class="fl">0</span><span class="op">)</span>,</span>
 <span>  formatting_type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_antibiogram_formatting_type"</span>,</span>
 <span>  <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="va">wisca</span>, <span class="fl">14</span>, <span class="fl">18</span><span class="op">)</span><span class="op">)</span>, col_mo <span class="op">=</span> <span class="cn">NULL</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
-<span>  minimum <span class="op">=</span> <span class="fl">30</span>, combine_SI <span class="op">=</span> <span class="cn">TRUE</span>, sep <span class="op">=</span> <span class="st">" + "</span>, wisca <span class="op">=</span> <span class="cn">FALSE</span>,</span>
-<span>  simulations <span class="op">=</span> <span class="fl">1000</span>, conf_interval <span class="op">=</span> <span class="fl">0.95</span>, interval_side <span class="op">=</span> <span class="st">"two-tailed"</span>,</span>
-<span>  info <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
+<span>  minimum <span class="op">=</span> <span class="fl">30</span>, combine_SI <span class="op">=</span> <span class="cn">TRUE</span>, sep <span class="op">=</span> <span class="st">" + "</span>, sort_columns <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  wisca <span class="op">=</span> <span class="cn">FALSE</span>, simulations <span class="op">=</span> <span class="fl">1000</span>, conf_interval <span class="op">=</span> <span class="fl">0.95</span>,</span>
+<span>  interval_side <span class="op">=</span> <span class="st">"two-tailed"</span>, info <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
 <span><span class="fu">wisca</span><span class="op">(</span><span class="va">x</span>, antimicrobials <span class="op">=</span> <span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.sir</span><span class="op">)</span>, ab_transform <span class="op">=</span> <span class="st">"name"</span>,</span>
 <span>  syndromic_group <span class="op">=</span> <span class="cn">NULL</span>, only_all_tested <span class="op">=</span> <span class="cn">FALSE</span>, digits <span class="op">=</span> <span class="fl">1</span>,</span>
 <span>  formatting_type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_antibiogram_formatting_type"</span>, <span class="fl">14</span><span class="op">)</span>,</span>
 <span>  col_mo <span class="op">=</span> <span class="cn">NULL</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, combine_SI <span class="op">=</span> <span class="cn">TRUE</span>,</span>
-<span>  sep <span class="op">=</span> <span class="st">" + "</span>, simulations <span class="op">=</span> <span class="fl">1000</span>, conf_interval <span class="op">=</span> <span class="fl">0.95</span>,</span>
-<span>  interval_side <span class="op">=</span> <span class="st">"two-tailed"</span>, info <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
+<span>  sep <span class="op">=</span> <span class="st">" + "</span>, sort_columns <span class="op">=</span> <span class="cn">TRUE</span>, simulations <span class="op">=</span> <span class="fl">1000</span>,</span>
+<span>  conf_interval <span class="op">=</span> <span class="fl">0.95</span>, interval_side <span class="op">=</span> <span class="st">"two-tailed"</span>,</span>
+<span>  info <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
 <span><span class="fu">retrieve_wisca_parameters</span><span class="op">(</span><span class="va">wisca_model</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
@@ -168,6 +169,10 @@ Adhering to previously described approaches (see Source) and especially the Baye
 <dd><p>A separating character for antimicrobial columns in combination antibiograms.</p></dd>


+<dt id="arg-sort-columns">sort_columns<a class="anchor" aria-label="anchor" href="#arg-sort-columns"></a></dt>
+<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether the antimicrobial columns must be sorted on name.</p></dd>
+
+
 <dt id="arg-wisca">wisca<a class="anchor" aria-label="anchor" href="#arg-wisca"></a></dt>
 <dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether a Weighted-Incidence Syndromic Combination Antibiogram (WISCA) must be generated (default is <code>FALSE</code>). This will use a Bayesian decision model to estimate regimen coverage probabilities using <a href="https://en.wikipedia.org/wiki/Monte_Carlo_method" class="external-link">Monte Carlo simulations</a>. Set <code>simulations</code>, <code>conf_interval</code>, and <code>interval_side</code> to adjust.</p></dd>

@@ -572,9 +577,9 @@ Adhering to previously described approaches (see Source) and especially the Baye
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram (WISCA / 95% CI): 3 × 4</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   `Syndromic Group` `Piperacillin/tazobactam` Piperacillin/tazobactam + Gentam…¹</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>             <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>                     <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>                             </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical          73.4% (68.3-78.6%)        92.4% (90.7-93.8%)                </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU               57.4% (49.7-65.4%)        85% (82.1-87.9%)                  </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient        57% (47.4-66.7%)          74.4% (68.6-79.5%)                </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical          73.4% (68.3-78.6%)        92.3% (90.7-93.7%)                </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU               57.4% (49.7-65.4%)        84.9% (82.1-87.6%)                </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient        57% (47.4-66.7%)          74.6% (68.8-79.8%)                </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ abbreviated name: ¹`Piperacillin/tazobactam + Gentamicin`</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 1 more variable: `Piperacillin/tazobactam + Tobramycin` &lt;chr&gt;</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Use `ggplot2::autoplot()` or base R `plot()` to create a plot of this antibiogram,</span></span>
@@ -17,7 +17,7 @@ my_data_with_all_these_columns %&amp;gt;%

    <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="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -7,7 +7,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -7,7 +7,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -7,7 +7,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -7,7 +7,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -7,7 +7,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -7,7 +7,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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">
@@ -9,7 +9,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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">
@@ -409,10 +409,10 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4 × 18</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   datetime            index method ab_given    mo_given   host_given input_given</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span>              <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>  <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>       <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>      <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>      <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2025-05-01 <span style="color: #949494;">09:53:45</span>     1 MIC    amoxicillin Escherich… human      8          </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2025-05-01 <span style="color: #949494;">09:53:45</span>     1 MIC    cipro       Escherich… human      0.256      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2025-05-01 <span style="color: #949494;">09:53:45</span>     1 DISK   tobra       Escherich… human      16         </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2025-05-01 <span style="color: #949494;">09:53:45</span>     1 DISK   genta       Escherich… human      18         </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2025-05-01 <span style="color: #949494;">12:50:15</span>     1 MIC    amoxicillin Escherich… human      8          </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2025-05-01 <span style="color: #949494;">12:50:15</span>     1 MIC    cipro       Escherich… human      0.256      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2025-05-01 <span style="color: #949494;">12:50:15</span>     1 DISK   tobra       Escherich… human      16         </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2025-05-01 <span style="color: #949494;">12:50:15</span>     1 DISK   genta       Escherich… human      18         </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 11 more variables: ab &lt;ab&gt;, mo &lt;mo&gt;, host &lt;chr&gt;, input &lt;chr&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   outcome &lt;sir&gt;, notes &lt;chr&gt;, guideline &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   breakpoint_S_R &lt;chr&gt;, site &lt;chr&gt;</span></span>
@@ -7,7 +7,7 @@

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@@ -7,7 +7,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
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@@ -7,7 +7,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>


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@@ -7,7 +7,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -7,7 +7,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -21,7 +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="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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">
@@ -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="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>


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@@ -7,7 +7,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -7,7 +7,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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">
@@ -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="">2.1.1.9267</small>
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@@ -7,7 +7,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>


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@@ -7,7 +7,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>


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@@ -7,7 +7,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>


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@@ -9,7 +9,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>


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@@ -7,7 +7,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>


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@@ -7,7 +7,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>


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@@ -7,7 +7,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>


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@@ -7,7 +7,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>


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@@ -7,7 +7,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>


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@@ -7,7 +7,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>


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@@ -7,7 +7,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>


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@@ -7,7 +7,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>


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@@ -7,7 +7,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>


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@@ -7,7 +7,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>


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@@ -7,7 +7,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>


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@@ -7,7 +7,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -7,7 +7,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -7,7 +7,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -7,7 +7,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -7,7 +7,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>


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@@ -9,7 +9,7 @@ This data set is carefully crafted, yet made 100% reproducible from public and a

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -7,7 +7,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -7,7 +7,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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">
@@ -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="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -7,7 +7,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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">
@@ -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="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>


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@@ -9,7 +9,7 @@ resistance() should be used to calculate resistance, susceptibility() should be

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -7,7 +7,7 @@

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

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@@ -9,7 +9,7 @@ NOTE: These functions are deprecated and will be removed in a future version. Us

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

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@@ -9,7 +9,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu

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

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-[{"path":"https://amr-for-r.org/articles/AMR.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"How to conduct AMR data analysis","text":"Conducting AMR data analysis unfortunately requires -depth knowledge different scientific fields, makes hard right. least, requires: Good questions (always start !) reliable data thorough understanding (clinical) epidemiology, understand clinical epidemiological relevance possible bias results thorough understanding (clinical) microbiology/infectious diseases, understand microorganisms causal infections implications pharmaceutical treatment, well understanding intrinsic acquired microbial resistance Experience data analysis microbiological tests results, understand determination limitations MIC values interpretations SIR values Availability biological taxonomy microorganisms probably normalisation factors pharmaceuticals, defined daily doses (DDD) Available (inter-)national guidelines, profound methods apply course, instantly provide knowledge experience. AMR package, aimed providing (1) tools simplify antimicrobial resistance data cleaning, transformation analysis, (2) methods easily incorporate international guidelines (3) scientifically reliable reference data, including requirements mentioned . AMR package enables standardised reproducible AMR data analysis, application evidence-based rules, determination first isolates, translation various codes microorganisms antimicrobial agents, determination (multi-drug) resistant microorganisms, calculation antimicrobial resistance, prevalence future trends.","code":""},{"path":"https://amr-for-r.org/articles/AMR.html","id":"preparation","dir":"Articles","previous_headings":"","what":"Preparation","title":"How to conduct AMR data analysis","text":"tutorial, create fake demonstration data work . can skip Cleaning data already data ready. start analysis, try make structure data generally look like :","code":""},{"path":"https://amr-for-r.org/articles/AMR.html","id":"needed-r-packages","dir":"Articles","previous_headings":"Preparation","what":"Needed R packages","title":"How to conduct AMR data analysis","text":"many uses R, need additional packages AMR data analysis. package works closely together tidyverse packages dplyr ggplot2 RStudio. tidyverse tremendously improves way conduct data science - allows natural way writing syntaxes creating beautiful plots R. also use cleaner package, can used cleaning data creating frequency tables. AMR package contains data set example_isolates_unclean, might look data users extracted laboratory systems: AMR data analysis, like microorganism column contain valid, --date taxonomy, antibiotic columns cleaned SIR values well.","code":"library(dplyr) library(ggplot2) library(AMR)  # (if not yet installed, install with:) # install.packages(c(\"dplyr\", \"ggplot2\", \"AMR\")) example_isolates_unclean #> # A tibble: 3,000 × 8 #>    patient_id hospital date       bacteria      AMX   AMC   CIP   GEN   #>    <chr>      <chr>    <date>     <chr>         <chr> <chr> <chr> <chr> #>  1 J3         A        2012-11-21 E. coli       R     I     S     S     #>  2 R7         A        2018-04-03 K. pneumoniae R     I     S     S     #>  3 P3         A        2014-09-19 E. coli       R     S     S     S     #>  4 P10        A        2015-12-10 E. coli       S     I     S     S     #>  5 B7         A        2015-03-02 E. coli       S     S     S     S     #>  6 W3         A        2018-03-31 S. aureus     R     S     R     S     #>  7 J8         A        2016-06-14 E. coli       R     S     S     S     #>  8 M3         A        2015-10-25 E. coli       R     S     S     S     #>  9 J3         A        2019-06-19 E. coli       S     S     S     S     #> 10 G6         A        2015-04-27 S. aureus     S     S     S     S     #> # ℹ 2,990 more rows  # we will use 'our_data' as the data set name for this tutorial our_data <- example_isolates_unclean"},{"path":"https://amr-for-r.org/articles/AMR.html","id":"taxonomy-of-microorganisms","dir":"Articles","previous_headings":"Preparation","what":"Taxonomy of microorganisms","title":"How to conduct AMR data analysis","text":".mo(), users can transform arbitrary microorganism names codes current taxonomy. AMR package contains --date taxonomic data. specific, currently included data retrieved 24 Jun 2024. codes AMR packages come .mo() short, still human readable. importantly, .mo() supports kinds input: first character codes denote taxonomic kingdom, Bacteria (B), Fungi (F), Protozoa (P). AMR package also contain functions directly retrieve taxonomic properties, name, genus, species, family, order, even Gram-stain. start mo_ use .mo() internally, still arbitrary user input can used: Now can thus clean data: Apparently, uncertainty translation taxonomic codes. Let’s check : ’s good.","code":"as.mo(\"Klebsiella pneumoniae\") #> Class 'mo' #> [1] B_KLBSL_PNMN as.mo(\"K. pneumoniae\") #> Class 'mo' #> [1] B_KLBSL_PNMN as.mo(\"KLELine truncated
+[{"path":"https://amr-for-r.org/articles/AMR.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Conduct AMR data analysis","text":"Conducting AMR data analysis unfortunately requires -depth knowledge different scientific fields, makes hard right. least, requires: Good questions (always start !) reliable data thorough understanding (clinical) epidemiology, understand clinical epidemiological relevance possible bias results thorough understanding (clinical) microbiology/infectious diseases, understand microorganisms causal infections implications pharmaceutical treatment, well understanding intrinsic acquired microbial resistance Experience data analysis microbiological tests results, understand determination limitations MIC values interpretations SIR values Availability biological taxonomy microorganisms probably normalisation factors pharmaceuticals, defined daily doses (DDD) Available (inter-)national guidelines, profound methods apply course, instantly provide knowledge experience. AMR package, aimed providing (1) tools simplify antimicrobial resistance data cleaning, transformation analysis, (2) methods easily incorporate international guidelines (3) scientifically reliable reference data, including requirements mentioned . AMR package enables standardised reproducible AMR data analysis, application evidence-based rules, determination first isolates, translation various codes microorganisms antimicrobial agents, determination (multi-drug) resistant microorganisms, calculation antimicrobial resistance, prevalence future trends.","code":""},{"path":"https://amr-for-r.org/articles/AMR.html","id":"preparation","dir":"Articles","previous_headings":"","what":"Preparation","title":"Conduct AMR data analysis","text":"tutorial, create fake demonstration data work . can skip Cleaning data already data ready. start analysis, try make structure data generally look like :","code":""},{"path":"https://amr-for-r.org/articles/AMR.html","id":"needed-r-packages","dir":"Articles","previous_headings":"Preparation","what":"Needed R packages","title":"Conduct AMR data analysis","text":"many uses R, need additional packages AMR data analysis. package works closely together tidyverse packages dplyr ggplot2 RStudio. tidyverse tremendously improves way conduct data science - allows natural way writing syntaxes creating beautiful plots R. also use cleaner package, can used cleaning data creating frequency tables. AMR package contains data set example_isolates_unclean, might look data users extracted laboratory systems: AMR data analysis, like microorganism column contain valid, --date taxonomy, antibiotic columns cleaned SIR values well.","code":"library(dplyr) library(ggplot2) library(AMR)  # (if not yet installed, install with:) # install.packages(c(\"dplyr\", \"ggplot2\", \"AMR\")) example_isolates_unclean #> # A tibble: 3,000 × 8 #>    patient_id hospital date       bacteria      AMX   AMC   CIP   GEN   #>    <chr>      <chr>    <date>     <chr>         <chr> <chr> <chr> <chr> #>  1 J3         A        2012-11-21 E. coli       R     I     S     S     #>  2 R7         A        2018-04-03 K. pneumoniae R     I     S     S     #>  3 P3         A        2014-09-19 E. coli       R     S     S     S     #>  4 P10        A        2015-12-10 E. coli       S     I     S     S     #>  5 B7         A        2015-03-02 E. coli       S     S     S     S     #>  6 W3         A        2018-03-31 S. aureus     R     S     R     S     #>  7 J8         A        2016-06-14 E. coli       R     S     S     S     #>  8 M3         A        2015-10-25 E. coli       R     S     S     S     #>  9 J3         A        2019-06-19 E. coli       S     S     S     S     #> 10 G6         A        2015-04-27 S. aureus     S     S     S     S     #> # ℹ 2,990 more rows  # we will use 'our_data' as the data set name for this tutorial our_data <- example_isolates_unclean"},{"path":"https://amr-for-r.org/articles/AMR.html","id":"taxonomy-of-microorganisms","dir":"Articles","previous_headings":"Preparation","what":"Taxonomy of microorganisms","title":"Conduct AMR data analysis","text":".mo(), users can transform arbitrary microorganism names codes current taxonomy. AMR package contains --date taxonomic data. specific, currently included data retrieved 24 Jun 2024. codes AMR packages come .mo() short, still human readable. importantly, .mo() supports kinds input: first character codes denote taxonomic kingdom, Bacteria (B), Fungi (F), Protozoa (P). AMR package also contain functions directly retrieve taxonomic properties, name, genus, species, family, order, even Gram-stain. start mo_ use .mo() internally, still arbitrary user input can used: Now can thus clean data: Apparently, uncertainty translation taxonomic codes. Let’s check : ’s good.","code":"as.mo(\"Klebsiella pneumoniae\") #> Class 'mo' #> [1] B_KLBSL_PNMN as.mo(\"K. pneumoniae\") #> Class 'mo' #> [1] B_KLBSL_PNMN as.mo(\"KLEPNE\") #> Class 'mo' #> [1] Line truncated