P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-27 13:47:56 +02:00
Code Releases Activity

Built site for AMR@2.1.1.9266: a455acd

Browse Source
This commit is contained in:
github-actions
2025-04-30 15:43:27 +00:00
parent eb5d938435
commit 0f3f86c0e0
81 changed files with 854 additions and 353 deletions
Download Patch File Download Diff File Expand all files Collapse all files

10
articles/AMR.html
View File

@ -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="">2.1.1.9263</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -91,7 +91,7 @@
website update since they are based on randomly created values and the
page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
Markdown</a>. However, the methodology remains unchanged. This page was
generated on 29 April 2025.</p>
generated on 30 April 2025.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@ -147,21 +147,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2025-04-29</td>
<td align="center">2025-04-30</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="center">2025-04-29</td>
<td align="center">2025-04-30</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<tr class="odd">
<td align="center">2025-04-29</td>
<td align="center">2025-04-30</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>

2
articles/AMR_for_Python.html
View File

@ -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="">2.1.1.9263</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
articles/AMR_with_tidymodels.html
View File

@ -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="">2.1.1.9263</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
articles/EUCAST.html
View File

@ -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="">2.1.1.9263</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
articles/MDR.html
View File

@ -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="">2.1.1.9263</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
articles/PCA.html
View File

@ -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="">2.1.1.9263</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
articles/WHONET.html
View File

@ -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="">2.1.1.9263</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</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">

658
articles/WISCA.html Normal file
View File

@ -0,0 +1,658 @@
<!DOCTYPE html>
<!-- Generated by pkgdown: do not edit by hand --><html lang="en">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<title>Estimating Empirical Coverage with WISCA • 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">
<link rel="icon" sizes="any" href="../favicon.ico">
<link rel="manifest" href="../site.webmanifest">
<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.10/font.css" rel="stylesheet">
<link href="../deps/Fira_Code-0.4.10/font.css" rel="stylesheet">
<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">
<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script><meta property="og:title" content="Estimating Empirical Coverage with WISCA">
<link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous">
<script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script>
</head>
<body>
<a href="#main" class="visually-hidden-focusable">Skip to contents</a>
<nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
<span class="navbar-toggler-icon"></span>
</button>
<div id="navbar" class="collapse navbar-collapse ms-3">
<ul class="navbar-nav me-auto">
<li class="nav-item dropdown">
<button class="nav-link dropdown-toggle" type="button" id="dropdown-how-to" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true"><span class="fa fa-question-circle"></span> How to</button>
<ul class="dropdown-menu" aria-labelledby="dropdown-how-to">
<li><a class="dropdown-item" href="../articles/AMR.html"><span class="fa fa-directions"></span> Conduct AMR Analysis</a></li>
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>
<li><a class="dropdown-item" href="../articles/WHONET.html"><span class="fa fa-globe-americas"></span> Work with WHONET Data</a></li>
<li><a class="dropdown-item" href="../articles/EUCAST.html"><span class="fa fa-exchange-alt"></span> Apply EUCAST Rules</a></li>
<li><a class="dropdown-item" href="../reference/mo_property.html"><span class="fa fa-bug"></span> Get Taxonomy of a Microorganism</a></li>
<li><a class="dropdown-item" href="../reference/ab_property.html"><span class="fa fa-capsules"></span> Get Properties of an Antibiotic Drug</a></li>
<li><a class="dropdown-item" href="../reference/av_property.html"><span class="fa fa-capsules"></span> Get Properties of an Antiviral Drug</a></li>
</ul>
</li>
<li class="nav-item"><a class="nav-link" href="../articles/AMR_for_Python.html"><span class="fa fab fa-python"></span> AMR for Python</a></li>
<li class="nav-item"><a class="nav-link" href="../reference/index.html"><span class="fa fa-book-open"></span> Manual</a></li>
<li class="nav-item"><a class="nav-link" href="../authors.html"><span class="fa fa-users"></span> Authors</a></li>
</ul>
<ul class="navbar-nav">
<li class="nav-item"><form class="form-inline" role="search">
<input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
</form></li>
<li class="nav-item"><a class="nav-link" href="../news/index.html"><span class="fa fa-newspaper"></span> Changelog</a></li>
<li class="nav-item"><a class="external-link nav-link" href="https://github.com/msberends/AMR"><span class="fa fa-github"></span> Source Code</a></li>
</ul>
</div>
</div>
</nav><div class="container template-article">
<div class="row">
<main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Estimating Empirical Coverage with WISCA</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/WISCA.Rmd" class="external-link"><code>vignettes/WISCA.Rmd</code></a></small>
<div class="d-none name"><code>WISCA.Rmd</code></div>
</div>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
<p>Clinical guidelines for empirical antimicrobial therapy require
<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), -
<strong>Regimen susceptibility</strong> (how often a regimen works
<em>if</em> the pathogen is known),</p>
<p>to estimate the <strong>overall empirical coverage</strong> of
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>
</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>
<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> —
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>
</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>
</h2>
<p>WISCA asks:</p>
<blockquote>
<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>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>Then:</p>
<p>``` coverage = (0.6 × 0.9) + (0.4 × 0.7) = 0.82</p>
<p>But in real data, incidence and susceptibility are <strong>estimated
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>
</h2>
<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>
</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>
</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>
</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>
<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>
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://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>
</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>
<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>
</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">
<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%">
</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>
</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>
</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>
</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>
<table class="table">
<colgroup>
<col width="26%">
<col width="39%">
<col width="16%">
<col width="18%">
</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>
</tr></thead>
<tbody>
<tr class="odd">
<td>AMC</td>
<td>0.72</td>
<td>0.65</td>
<td>0.78</td>
</tr>
<tr class="even">
<td>AMC + GEN</td>
<td>0.88</td>
<td>0.83</td>
<td>0.93</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 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>
<ul>
<li>
<code>minimum = 30</code>: exclude regimens with &lt;30 isolates
tested.</li>
<li>
<code>simulations = 1000</code>: number of Monte Carlo samples.</li>
<li>
<code>conf_interval = 0.95</code>: coverage interval width.</li>
<li>
<code>combine_SI = TRUE</code>: count “I”/“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>
</ul>
<hr>
</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>
</div>
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
</nav></aside>
</div>
<footer><div class="pkgdown-footer-left">
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p>
</div>
<div class="pkgdown-footer-right">
<p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://amr-for-r.org/logo_rug.svg" style="max-width: 150px;"></a><a target="_blank" href="https://www.umcg.nl" class="external-link"><img src="https://amr-for-r.org/logo_umcg.svg" style="max-width: 150px;"></a></p>
</div>
</footer>
</div>
</body>
</html>

4
articles/datasets.html
View File

@ -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="">2.1.1.9263</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</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">
@ -80,7 +80,7 @@
<main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
<h4 data-toc-skip class="date">29 April 2025</h4>
<h4 data-toc-skip class="date">30 April 2025</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<div class="d-none name"><code>datasets.Rmd</code></div>

6
articles/index.html
View File

@ -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="">2.1.1.9263</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</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">
@ -65,10 +65,10 @@
<dd>
</dd><dt><a href="PCA.html">How to conduct principal component analysis (PCA) for AMR</a></dt>
<dd>
</dd><dt><a href="welcome_to_AMR.html">Welcome to the `AMR` package</a></dt>
<dd>
</dd><dt><a href="WHONET.html">How to work with WHONET data</a></dt>
<dd>
</dd><dt><a href="WISCA.html">Estimating Empirical Coverage with WISCA</a></dt>
<dd>
</dd></dl></div>
</main></div>

200
articles/welcome_to_AMR.html
View File

@ -1,200 +0,0 @@
<!DOCTYPE html>
<!-- Generated by pkgdown: do not edit by hand --><html lang="en">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<title>Welcome to the `AMR` package • 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">
<link rel="icon" sizes="any" href="../favicon.ico">
<link rel="manifest" href="../site.webmanifest">
<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.10/font.css" rel="stylesheet">
<link href="../deps/Fira_Code-0.4.10/font.css" rel="stylesheet">
<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">
<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script><meta property="og:title" content="Welcome to the `AMR` package">
<link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous">
<script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script>
</head>
<body>
<a href="#main" class="visually-hidden-focusable">Skip to contents</a>
<nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9263</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
<span class="navbar-toggler-icon"></span>
</button>
<div id="navbar" class="collapse navbar-collapse ms-3">
<ul class="navbar-nav me-auto">
<li class="nav-item dropdown">
<button class="nav-link dropdown-toggle" type="button" id="dropdown-how-to" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true"><span class="fa fa-question-circle"></span> How to</button>
<ul class="dropdown-menu" aria-labelledby="dropdown-how-to">
<li><a class="dropdown-item" href="../articles/AMR.html"><span class="fa fa-directions"></span> Conduct AMR Analysis</a></li>
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>
<li><a class="dropdown-item" href="../articles/WHONET.html"><span class="fa fa-globe-americas"></span> Work with WHONET Data</a></li>
<li><a class="dropdown-item" href="../articles/EUCAST.html"><span class="fa fa-exchange-alt"></span> Apply EUCAST Rules</a></li>
<li><a class="dropdown-item" href="../reference/mo_property.html"><span class="fa fa-bug"></span> Get Taxonomy of a Microorganism</a></li>
<li><a class="dropdown-item" href="../reference/ab_property.html"><span class="fa fa-capsules"></span> Get Properties of an Antibiotic Drug</a></li>
<li><a class="dropdown-item" href="../reference/av_property.html"><span class="fa fa-capsules"></span> Get Properties of an Antiviral Drug</a></li>
</ul>
</li>
<li class="nav-item"><a class="nav-link" href="../articles/AMR_for_Python.html"><span class="fa fab fa-python"></span> AMR for Python</a></li>
<li class="nav-item"><a class="nav-link" href="../reference/index.html"><span class="fa fa-book-open"></span> Manual</a></li>
<li class="nav-item"><a class="nav-link" href="../authors.html"><span class="fa fa-users"></span> Authors</a></li>
</ul>
<ul class="navbar-nav">
<li class="nav-item"><form class="form-inline" role="search">
<input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
</form></li>
<li class="nav-item"><a class="nav-link" href="../news/index.html"><span class="fa fa-newspaper"></span> Changelog</a></li>
<li class="nav-item"><a class="external-link nav-link" href="https://github.com/msberends/AMR"><span class="fa fa-github"></span> Source Code</a></li>
</ul>
</div>
</div>
</nav><div class="container template-article">
<div class="row">
<main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Welcome to the `AMR` package</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/welcome_to_AMR.Rmd" class="external-link"><code>vignettes/welcome_to_AMR.Rmd</code></a></small>
<div class="d-none name"><code>welcome_to_AMR.Rmd</code></div>
</div>
<p>Note: to keep the package size as small as possible, we only include
this vignette on CRAN. You can read more vignettes on our website about
how to conduct AMR data analysis, determine MDROs, find explanation of
EUCAST and CLSI breakpoints, and much more: <a href="https://amr-for-r.org" class="uri">https://amr-for-r.org</a>.</p>
<hr>
<p>The <code>AMR</code> package is a peer-reviewed, <a href="https://amr-for-r.org/#copyright">free and open-source</a> R
package with <a href="https://en.wikipedia.org/wiki/Dependency_hell" class="external-link">zero
dependencies</a> to simplify the analysis and prediction of
Antimicrobial Resistance (AMR) and to work with microbial and
antimicrobial data and properties, by using evidence-based methods.
<strong>Our aim is to provide a standard</strong> for clean and
reproducible AMR data analysis, that can therefore empower
epidemiological analyses to continuously enable surveillance and
treatment evaluation in any setting. We are a team of <a href="https://amr-for-r.org/authors.html">many different researchers</a>
from around the globe to make this a successful and durable project!</p>
<p>This work was published in the Journal of Statistical Software
(Volume 104(3); ) and formed the basis of two PhD theses ( and ).</p>
<p>After installing this package, R knows <a href="https://amr-for-r.org/reference/microorganisms.html"><strong>~79
000 distinct microbial species</strong></a> (updated June 2024) and all
<a href="https://amr-for-r.org/reference/antimicrobials.html"><strong>~620
antimicrobial and antiviral drugs</strong></a> by name and code
(including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and
knows all about valid SIR and MIC values. The integral clinical
breakpoint guidelines from CLSI 2011-2025 and EUCAST 2011-2025 are
included, even with epidemiological cut-off (ECOFF) values. It supports
and can read any data format, including WHONET data. This package works
on Windows, macOS and Linux with all versions of R since R-3.0 (April
2013). <strong>It was designed to work in any setting, including those
with very limited resources</strong>. It was created for both routine
data analysis and academic research at the Faculty of Medical Sciences
of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a> and the
<a href="https://www.umcg.nl" class="external-link">University Medical Center
Groningen</a>.</p>
<p>The <code>AMR</code> package is available in English, Chinese, Czech,
Danish, Dutch, Finnish, French, German, Greek, Italian, Japanese,
Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swedish,
Turkish, and Ukrainian. Antimicrobial drug (group) names and colloquial
microorganism names are provided in these languages.</p>
<p>This package was intended as a comprehensive toolbox for integrated
AMR data analysis. This package can be used for:</p>
<ul>
<li>Reference for the taxonomy of microorganisms, since the package
contains all microbial (sub)species from the List of Prokaryotic names
with Standing in Nomenclature (<a href="(https://lpsn.dsmz.de)" class="external-link">LPSN</a>) and the Global Biodiversity
Information Facility (<a href="https://www.gbif.org" class="external-link">GBIF</a>) (<a href="https://amr-for-r.org/reference/mo_property.html">manual</a>)</li>
<li>Interpreting raw MIC and disk diffusion values, based on any CLSI or
EUCAST guideline (<a href="https://amr-for-r.org/reference/as.sir.html">manual</a>)</li>
<li>Retrieving antimicrobial drug names, doses and forms of
administration from clinical health care records (<a href="https://amr-for-r.org/reference/ab_from_text.html">manual</a>)</li>
<li>Determining first isolates to be used for AMR data analysis (<a href="https://amr-for-r.org/reference/first_isolate.html">manual</a>)</li>
<li>Calculating antimicrobial resistance (<a href="https://amr-for-r.org/articles/AMR.html">tutorial</a>)</li>
<li>Determining multi-drug resistance (MDR) / multi-drug resistant
organisms (MDRO) (<a href="https://amr-for-r.org/articles/MDR.html">tutorial</a>)</li>
<li>Calculating (empirical) susceptibility of both mono therapy and
combination therapies (<a href="https://amr-for-r.org/articles/AMR.html">tutorial</a>)</li>
<li>Apply AMR function in predictive modelling (<a href="https://amr-for-r.org/articles/AMR_with_tidymodels.html">tutorial</a>)</li>
<li>Getting properties for any microorganism (like Gram stain, species,
genus or family) (<a href="https://amr-for-r.org/reference/mo_property.html">manual</a>)</li>
<li>Getting properties for any antimicrobial (like name, code of
EARS-Net/ATC/LOINC/PubChem, defined daily dose or trade name) (<a href="https://amr-for-r.org/reference/ab_property.html">manual</a>)</li>
<li>Plotting antimicrobial resistance (<a href="https://amr-for-r.org/articles/AMR.html">tutorial</a>)</li>
<li>Applying EUCAST expert rules (<a href="https://amr-for-r.org/reference/eucast_rules.html">manual</a>)</li>
<li>Getting SNOMED codes of a microorganism, or getting properties of a
microorganism based on a SNOMED code (<a href="https://amr-for-r.org/reference/mo_property.html">manual</a>)</li>
<li>Getting LOINC codes of an antibiotic, or getting properties of an
antibiotic based on a LOINC code (<a href="https://amr-for-r.org/reference/ab_property.html">manual</a>)</li>
<li>Machine reading the EUCAST and CLSI guidelines from 2011-2021 to
translate MIC values and disk diffusion diameters to SIR (<a href="https://amr-for-r.org/articles/datasets.html">link</a>)</li>
<li>Principal component analysis for AMR (<a href="https://amr-for-r.org/articles/PCA.html">tutorial</a>)</li>
</ul>
<p>All reference data sets in the AMR package - including information on
microorganisms, antimicrobials, and clinical breakpoints - are freely
available for download in multiple formats: R, MS Excel, Apache Feather,
Apache Parquet, SPSS, and Stata.</p>
<p>For maximum compatibility, we also provide machine-readable,
tab-separated plain text files suitable for use in any software,
including laboratory information systems.</p>
<p>Visit <a href="https://amr-for-r.org/articles/datasets.html">our
website for direct download links</a>, or explore the actual files in <a href="https://github.com/msberends/AMR/tree/main/data-raw/datasets" class="external-link">our
GitHub repository</a>.</p>
<hr>
<p><small> This AMR package for R is free, open-source software and
licensed under the <a href="https://amr-for-r.org/LICENSE-text.html">GNU
General Public License v2.0 (GPL-2)</a>. These requirements are
consequently legally binding: modifications must be released under the
same license when distributing the package, changes made to the code
must be documented, source code must be made available when the package
is distributed, and a copy of the license and copyright notice must be
included with the package. </small></p>
</main>
</div>
<footer><div class="pkgdown-footer-left">
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p>
</div>
<div class="pkgdown-footer-right">
<p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://amr-for-r.org/logo_rug.svg" style="max-width: 150px;"></a><a target="_blank" href="https://www.umcg.nl" class="external-link"><img src="https://amr-for-r.org/logo_umcg.svg" style="max-width: 150px;"></a></p>
</div>
</footer>
</div>
</body>
</html>