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<!DOCTYPE html>
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<!-- 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>CLAUDE.md — AMR R 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="CLAUDE.md — AMR R Package"><meta property="og:image" content="https://amr-for-r.org/logo.svg"><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>
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<a href="#main" class="visually-hidden-focusable">Skip to contents</a>
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<nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
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<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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<div id="navbar" class="collapse navbar-collapse ms-3">
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<ul class="navbar-nav me-auto"><li class="nav-item dropdown">
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<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>
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<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>
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||||
<li><a class="dropdown-item" href="reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
|
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<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>
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<li><a class="dropdown-item" href="articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
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<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>
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<li><a class="dropdown-item" href="articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
|
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<li><a class="dropdown-item" href="reference/mdro.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>
|
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<li><a class="dropdown-item" href="articles/WHONET.html"><span class="fa fa-globe-americas"></span> Work with WHONET Data</a></li>
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<li><a class="dropdown-item" href="articles/EUCAST.html"><span class="fa fa-exchange-alt"></span> Apply EUCAST Rules</a></li>
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<li><a class="dropdown-item" href="reference/mo_property.html"><span class="fa fa-bug"></span> Get Taxonomy of a Microorganism</a></li>
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<li><a class="dropdown-item" href="reference/ab_property.html"><span class="fa fa-capsules"></span> Get Properties of an Antibiotic Drug</a></li>
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<li><a class="dropdown-item" href="reference/av_property.html"><span class="fa fa-capsules"></span> Get Properties of an Antiviral Drug</a></li>
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</ul></li>
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<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>
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<li class="nav-item"><a class="nav-link" href="reference/index.html"><span class="fa fa-book-open"></span> Manual</a></li>
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</ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
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<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>
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<li class="nav-item"><a class="nav-link" href="news/index.html"><span class="fa fa-newspaper"></span> Changelog</a></li>
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<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>
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</ul></div>
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</div>
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</nav><div class="container template-title-body">
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<div class="row">
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<main id="main" class="col-md-9"><div class="page-header">
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||||
<img src="logo.svg" class="logo" alt=""><h1>CLAUDE.md — AMR R Package</h1>
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/CLAUDE.md" class="external-link"><code>CLAUDE.md</code></a></small>
|
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</div>
|
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|
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<div id="claudemd--amr-r-package" class="section level1">
|
||||
|
||||
<p>This file provides context for Claude Code when working in this repository.</p>
|
||||
<div class="section level2">
|
||||
<h2 id="project-overview">Project Overview<a class="anchor" aria-label="anchor" href="#project-overview"></a></h2>
|
||||
<p><strong>AMR</strong> is a zero-dependency R package for antimicrobial resistance (AMR) data analysis using a One Health approach. It is peer-reviewed, used in 175+ countries, and supports 28 languages.</p>
|
||||
<p>Key capabilities: - SIR (Susceptible/Intermediate/Resistant) classification using EUCAST 2011–2025 and CLSI 2011–2025 breakpoints - Antibiogram generation: traditional, combined, syndromic, and WISCA - Microorganism taxonomy database (~79,000 species) - Antimicrobial drug database (~620 drugs) - Multi-drug resistant organism (MDRO) classification - First-isolate identification - Minimum Inhibitory Concentration (MIC) and disk diffusion handling - Multilingual output (28 languages)</p>
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="common-commands">Common Commands<a class="anchor" aria-label="anchor" href="#common-commands"></a></h2>
|
||||
<p>All commands run inside an R session:</p>
|
||||
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="co"># Rebuild documentation (roxygen2 → .Rd files + NAMESPACE)</span></span>
|
||||
<span><span class="fu">devtools</span><span class="fu">::</span><span class="fu">document</span><span class="op">(</span><span class="op">)</span></span>
|
||||
<span></span>
|
||||
<span><span class="co"># Run all tests</span></span>
|
||||
<span><span class="fu">devtools</span><span class="fu">::</span><span class="fu">test</span><span class="op">(</span><span class="op">)</span></span>
|
||||
<span></span>
|
||||
<span><span class="co"># Full package check (CRAN-level: docs + tests + checks)</span></span>
|
||||
<span><span class="fu">devtools</span><span class="fu">::</span><span class="fu">check</span><span class="op">(</span><span class="op">)</span></span>
|
||||
<span></span>
|
||||
<span><span class="co"># Build pkgdown website locally</span></span>
|
||||
<span><span class="fu">pkgdown</span><span class="fu">::</span><span class="fu"><a href="https://pkgdown.r-lib.org/reference/build_site.html" class="external-link">build_site</a></span><span class="op">(</span><span class="op">)</span></span>
|
||||
<span></span>
|
||||
<span><span class="co"># Code coverage report</span></span>
|
||||
<span><span class="fu">covr</span><span class="fu">::</span><span class="fu"><a href="http://covr.r-lib.org/reference/package_coverage.html" class="external-link">package_coverage</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
|
||||
<p>From the shell:</p>
|
||||
<div class="sourceCode" id="cb2"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" tabindex="-1"></a><span class="co"># CRAN check from parent directory</span></span>
|
||||
<span id="cb2-2"><a href="#cb2-2" tabindex="-1"></a><span class="ex">R</span> CMD check AMR</span></code></pre></div>
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="repository-structure">Repository Structure<a class="anchor" aria-label="anchor" href="#repository-structure"></a></h2>
|
||||
<pre><code>R/ # All R source files (62 files, ~28,000 lines)
|
||||
man/ # Auto-generated .Rd documentation (do not edit manually)
|
||||
tests/testthat/ # testthat test files (test-*.R) and helper-functions.R
|
||||
data/ # Pre-compiled .rda datasets
|
||||
data-raw/ # Scripts used to generate data/ files
|
||||
vignettes/ # Rmd vignette articles
|
||||
inst/ # Installed files (translations, etc.)
|
||||
_pkgdown.yml # pkgdown website configuration</code></pre>
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="r-source-file-conventions">R Source File Conventions<a class="anchor" aria-label="anchor" href="#r-source-file-conventions"></a></h2>
|
||||
<p><strong>Naming conventions in <code>R/</code>:</strong></p>
|
||||
<table class="table"><thead><tr class="header"><th>Prefix/Name</th>
|
||||
<th>Purpose</th>
|
||||
</tr></thead><tbody><tr class="odd"><td><code>aa_*.R</code></td>
|
||||
<td>Loaded first (helpers, globals, options, package docs)</td>
|
||||
</tr><tr class="even"><td><code>zz_deprecated.R</code></td>
|
||||
<td>Deprecated function wrappers</td>
|
||||
</tr><tr class="odd"><td><code>zzz.R</code></td>
|
||||
<td>
|
||||
<code>.onLoad</code> / <code>.onAttach</code> initialization</td>
|
||||
</tr></tbody></table><p><strong>Key source files:</strong></p>
|
||||
<ul><li>
|
||||
<code>aa_helper_functions.R</code> / <code>aa_helper_pm_functions.R</code> — internal utility functions (large; ~63 KB and ~37 KB)</li>
|
||||
<li>
|
||||
<code>aa_globals.R</code> — global constants and breakpoint lookup structures</li>
|
||||
<li>
|
||||
<code>aa_options.R</code> — <code>amr_options()</code> / <code>get_AMR_option()</code> system</li>
|
||||
<li>
|
||||
<code>mo.R</code> / <code>mo_property.R</code> — microorganism lookup and properties</li>
|
||||
<li>
|
||||
<code>ab.R</code> / <code>ab_property.R</code> — antimicrobial drug functions</li>
|
||||
<li>
|
||||
<code>av.R</code> / <code>av_property.R</code> — antiviral drug functions</li>
|
||||
<li>
|
||||
<code>sir.R</code> / <code>sir_calc.R</code> / <code>sir_df.R</code> — SIR classification engine</li>
|
||||
<li>
|
||||
<code>mic.R</code> / <code>disk.R</code> — MIC and disk diffusion classes</li>
|
||||
<li>
|
||||
<code>antibiogram.R</code> — antibiogram generation (traditional, combined, syndromic, WISCA)</li>
|
||||
<li>
|
||||
<code>first_isolate.R</code> — first-isolate identification algorithms</li>
|
||||
<li>
|
||||
<code>mdro.R</code> — MDRO classification (EUCAST, CLSI, CDC, custom guidelines)</li>
|
||||
<li>
|
||||
<code>amr_selectors.R</code> — tidyselect helpers for selecting AMR columns</li>
|
||||
<li>
|
||||
<code>interpretive_rules.R</code> / <code>custom_eucast_rules.R</code> — clinical interpretation rules</li>
|
||||
<li>
|
||||
<code>translate.R</code> — 28-language translation system</li>
|
||||
<li>
|
||||
<code>ggplot_sir.R</code> / <code>ggplot_pca.R</code> / <code>plotting.R</code> — visualisation functions</li>
|
||||
</ul></div>
|
||||
<div class="section level2">
|
||||
<h2 id="custom-s3-classes">Custom S3 Classes<a class="anchor" aria-label="anchor" href="#custom-s3-classes"></a></h2>
|
||||
<p>The package defines five S3 classes with full print/format/plot/vctrs support:</p>
|
||||
<table class="table"><thead><tr class="header"><th>Class</th>
|
||||
<th>Created by</th>
|
||||
<th>Represents</th>
|
||||
</tr></thead><tbody><tr class="odd"><td><code><mo></code></td>
|
||||
<td><code><a href="reference/as.mo.html">as.mo()</a></code></td>
|
||||
<td>Microorganism code</td>
|
||||
</tr><tr class="even"><td><code><ab></code></td>
|
||||
<td><code><a href="reference/as.ab.html">as.ab()</a></code></td>
|
||||
<td>Antimicrobial drug code</td>
|
||||
</tr><tr class="odd"><td><code><av></code></td>
|
||||
<td><code><a href="reference/as.av.html">as.av()</a></code></td>
|
||||
<td>Antiviral drug code</td>
|
||||
</tr><tr class="even"><td><code><sir></code></td>
|
||||
<td><code><a href="reference/as.sir.html">as.sir()</a></code></td>
|
||||
<td>SIR value (S/I/R/SDD)</td>
|
||||
</tr><tr class="odd"><td><code><mic></code></td>
|
||||
<td><code><a href="reference/as.mic.html">as.mic()</a></code></td>
|
||||
<td>Minimum inhibitory concentration</td>
|
||||
</tr><tr class="even"><td><code><disk></code></td>
|
||||
<td><code><a href="reference/as.disk.html">as.disk()</a></code></td>
|
||||
<td>Disk diffusion diameter</td>
|
||||
</tr></tbody></table></div>
|
||||
<div class="section level2">
|
||||
<h2 id="data-files">Data Files<a class="anchor" aria-label="anchor" href="#data-files"></a></h2>
|
||||
<p>Pre-compiled in <code>data/</code> (do not edit directly; regenerate via <code>data-raw/</code> scripts):</p>
|
||||
<table class="table"><colgroup><col width="50%"><col width="50%"></colgroup><thead><tr class="header"><th>File</th>
|
||||
<th>Contents</th>
|
||||
</tr></thead><tbody><tr class="odd"><td><code>microorganisms.rda</code></td>
|
||||
<td>~79,000 microbial species with full taxonomy</td>
|
||||
</tr><tr class="even"><td><code>antimicrobials.rda</code></td>
|
||||
<td>~620 antimicrobial drugs with ATC codes</td>
|
||||
</tr><tr class="odd"><td><code>antivirals.rda</code></td>
|
||||
<td>Antiviral drugs</td>
|
||||
</tr><tr class="even"><td><code>clinical_breakpoints.rda</code></td>
|
||||
<td>EUCAST + CLSI breakpoints (2011–2025)</td>
|
||||
</tr><tr class="odd"><td><code>intrinsic_resistant.rda</code></td>
|
||||
<td>Intrinsic resistance patterns</td>
|
||||
</tr><tr class="even"><td><code>example_isolates.rda</code></td>
|
||||
<td>Example AMR dataset for documentation/testing</td>
|
||||
</tr><tr class="odd"><td><code>WHONET.rda</code></td>
|
||||
<td>Example WHONET-format dataset</td>
|
||||
</tr></tbody></table></div>
|
||||
<div class="section level2">
|
||||
<h2 id="zero-dependency-design">Zero-Dependency Design<a class="anchor" aria-label="anchor" href="#zero-dependency-design"></a></h2>
|
||||
<p>The package has <strong>no <code>Imports</code></strong> in <code>DESCRIPTION</code>. All optional integrations (ggplot2, dplyr, data.table, tidymodels, cli, crayon, etc.) are listed in <code>Suggests</code> and guarded with:</p>
|
||||
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/ns-load.html" class="external-link">requireNamespace</a></span><span class="op">(</span><span class="st">"pkg"</span>, quietly <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span> <span class="va">...</span> <span class="op">}</span></span></code></pre></div>
|
||||
<p>Never add packages to <code>Imports</code>. If new functionality requires an external package, add it to <code>Suggests</code> and guard usage appropriately.</p>
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="testing">Testing<a class="anchor" aria-label="anchor" href="#testing"></a></h2>
|
||||
<ul><li>
|
||||
<strong>Framework:</strong> <code>testthat</code> (R ≥ 3.1); legacy <code>tinytest</code> used for R 3.0–3.6 CI</li>
|
||||
<li>
|
||||
<strong>Test files:</strong> <code>tests/testthat/test-*.R</code>
|
||||
</li>
|
||||
<li>
|
||||
<strong>Helpers:</strong> <code>tests/testthat/helper-functions.R</code>
|
||||
</li>
|
||||
<li>
|
||||
<strong>CI matrix:</strong> GitHub Actions across Windows / macOS / Linux × R devel / release / oldrel-1 through oldrel-4</li>
|
||||
<li>
|
||||
<strong>Coverage:</strong> <code>covr</code> (some files excluded: <code>atc_online.R</code>, <code>mo_source.R</code>, <code>translate.R</code>, <code>resistance_predict.R</code>, <code>zz_deprecated.R</code>, helper files, <code>zzz.R</code>)</li>
|
||||
</ul></div>
|
||||
<div class="section level2">
|
||||
<h2 id="documentation">Documentation<a class="anchor" aria-label="anchor" href="#documentation"></a></h2>
|
||||
<ul><li>All exported functions use <strong>roxygen2</strong> blocks (<code>RoxygenNote: 7.3.3</code>, markdown enabled)</li>
|
||||
<li>Run <code>devtools::document()</code> after any change to roxygen comments</li>
|
||||
<li>Never edit files in <code>man/</code> directly — they are auto-generated</li>
|
||||
<li>Vignettes live in <code>vignettes/</code> as <code>.Rmd</code> files</li>
|
||||
<li>The pkgdown website is configured in <code>_pkgdown.yml</code>
|
||||
</li>
|
||||
</ul></div>
|
||||
<div class="section level2">
|
||||
<h2 id="versioning">Versioning<a class="anchor" aria-label="anchor" href="#versioning"></a></h2>
|
||||
<p>Version format: <code>major.minor.patch.dev</code> (e.g., <code>3.0.1.9021</code>)</p>
|
||||
<ul><li>Development versions use a <code>.9xxx</code> suffix</li>
|
||||
<li>Stable CRAN releases drop the dev suffix (e.g., <code>3.0.1</code>)</li>
|
||||
<li>
|
||||
<code>NEWS.md</code> uses sections <strong>New</strong>, <strong>Fixes</strong>, <strong>Updates</strong> with GitHub issue references (<code>#NNN</code>)</li>
|
||||
</ul><div class="section level3">
|
||||
<h3 id="version-bump-required-for-every-pr">Version bump required for every PR<a class="anchor" aria-label="anchor" href="#version-bump-required-for-every-pr"></a></h3>
|
||||
<p>Before opening a pull request, always increment the four-digit dev counter by 1 in <strong>both</strong> of these files:</p>
|
||||
<ol style="list-style-type: decimal"><li>
|
||||
<p><strong><code>DESCRIPTION</code></strong> — the <code>Version:</code> field:</p>
|
||||
<pre><code>Version: 3.0.1.9021 → Version: 3.0.1.9022</code></pre>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong><code>NEWS.md</code></strong> — the top-level heading:</p>
|
||||
<pre><code><span><span class="co"># AMR 3.0.1.9021 → # AMR 3.0.1.9022</span></span></code></pre>
|
||||
</li>
|
||||
</ol><p>Read the current version from <code>DESCRIPTION</code>, add 1 to the last numeric component, and write the new version to both files in the same commit as the rest of the PR changes.</p>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="internal-state">Internal State<a class="anchor" aria-label="anchor" href="#internal-state"></a></h2>
|
||||
<p>The package uses a private <code>AMR_env</code> environment (created in <code>aa_globals.R</code>) for caching expensive lookups (e.g., microorganism matching scores, breakpoint tables). This avoids re-computation within a session.</p>
|
||||
</div>
|
||||
</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>
|
||||
|
||||
186
CLAUDE.md
Normal file
186
CLAUDE.md
Normal file
@@ -0,0 +1,186 @@
|
||||
# CLAUDE.md — AMR R Package
|
||||
|
||||
This file provides context for Claude Code when working in this
|
||||
repository.
|
||||
|
||||
## Project Overview
|
||||
|
||||
**AMR** is a zero-dependency R package for antimicrobial resistance
|
||||
(AMR) data analysis using a One Health approach. It is peer-reviewed,
|
||||
used in 175+ countries, and supports 28 languages.
|
||||
|
||||
Key capabilities: - SIR (Susceptible/Intermediate/Resistant)
|
||||
classification using EUCAST 2011–2025 and CLSI 2011–2025 breakpoints -
|
||||
Antibiogram generation: traditional, combined, syndromic, and WISCA -
|
||||
Microorganism taxonomy database (~79,000 species) - Antimicrobial drug
|
||||
database (~620 drugs) - Multi-drug resistant organism (MDRO)
|
||||
classification - First-isolate identification - Minimum Inhibitory
|
||||
Concentration (MIC) and disk diffusion handling - Multilingual output
|
||||
(28 languages)
|
||||
|
||||
## Common Commands
|
||||
|
||||
All commands run inside an R session:
|
||||
|
||||
``` r
|
||||
# Rebuild documentation (roxygen2 → .Rd files + NAMESPACE)
|
||||
devtools::document()
|
||||
|
||||
# Run all tests
|
||||
devtools::test()
|
||||
|
||||
# Full package check (CRAN-level: docs + tests + checks)
|
||||
devtools::check()
|
||||
|
||||
# Build pkgdown website locally
|
||||
pkgdown::build_site()
|
||||
|
||||
# Code coverage report
|
||||
covr::package_coverage()
|
||||
```
|
||||
|
||||
From the shell:
|
||||
|
||||
``` bash
|
||||
# CRAN check from parent directory
|
||||
R CMD check AMR
|
||||
```
|
||||
|
||||
## Repository Structure
|
||||
|
||||
R/ # All R source files (62 files, ~28,000 lines)
|
||||
man/ # Auto-generated .Rd documentation (do not edit manually)
|
||||
tests/testthat/ # testthat test files (test-*.R) and helper-functions.R
|
||||
data/ # Pre-compiled .rda datasets
|
||||
data-raw/ # Scripts used to generate data/ files
|
||||
vignettes/ # Rmd vignette articles
|
||||
inst/ # Installed files (translations, etc.)
|
||||
_pkgdown.yml # pkgdown website configuration
|
||||
|
||||
## R Source File Conventions
|
||||
|
||||
**Naming conventions in `R/`:**
|
||||
|
||||
| Prefix/Name | Purpose |
|
||||
|-------------------|--------------------------------------------------------|
|
||||
| `aa_*.R` | Loaded first (helpers, globals, options, package docs) |
|
||||
| `zz_deprecated.R` | Deprecated function wrappers |
|
||||
| `zzz.R` | `.onLoad` / `.onAttach` initialization |
|
||||
|
||||
**Key source files:**
|
||||
|
||||
- `aa_helper_functions.R` / `aa_helper_pm_functions.R` — internal
|
||||
utility functions (large; ~63 KB and ~37 KB)
|
||||
- `aa_globals.R` — global constants and breakpoint lookup structures
|
||||
- `aa_options.R` — `amr_options()` / `get_AMR_option()` system
|
||||
- `mo.R` / `mo_property.R` — microorganism lookup and properties
|
||||
- `ab.R` / `ab_property.R` — antimicrobial drug functions
|
||||
- `av.R` / `av_property.R` — antiviral drug functions
|
||||
- `sir.R` / `sir_calc.R` / `sir_df.R` — SIR classification engine
|
||||
- `mic.R` / `disk.R` — MIC and disk diffusion classes
|
||||
- `antibiogram.R` — antibiogram generation (traditional, combined,
|
||||
syndromic, WISCA)
|
||||
- `first_isolate.R` — first-isolate identification algorithms
|
||||
- `mdro.R` — MDRO classification (EUCAST, CLSI, CDC, custom guidelines)
|
||||
- `amr_selectors.R` — tidyselect helpers for selecting AMR columns
|
||||
- `interpretive_rules.R` / `custom_eucast_rules.R` — clinical
|
||||
interpretation rules
|
||||
- `translate.R` — 28-language translation system
|
||||
- `ggplot_sir.R` / `ggplot_pca.R` / `plotting.R` — visualisation
|
||||
functions
|
||||
|
||||
## Custom S3 Classes
|
||||
|
||||
The package defines five S3 classes with full print/format/plot/vctrs
|
||||
support:
|
||||
|
||||
| Class | Created by | Represents |
|
||||
|----------|-----------------------------------------------------------|----------------------------------|
|
||||
| `<mo>` | [`as.mo()`](https://amr-for-r.org/reference/as.mo.md) | Microorganism code |
|
||||
| `<ab>` | [`as.ab()`](https://amr-for-r.org/reference/as.ab.md) | Antimicrobial drug code |
|
||||
| `<av>` | [`as.av()`](https://amr-for-r.org/reference/as.av.md) | Antiviral drug code |
|
||||
| `<sir>` | [`as.sir()`](https://amr-for-r.org/reference/as.sir.md) | SIR value (S/I/R/SDD) |
|
||||
| `<mic>` | [`as.mic()`](https://amr-for-r.org/reference/as.mic.md) | Minimum inhibitory concentration |
|
||||
| `<disk>` | [`as.disk()`](https://amr-for-r.org/reference/as.disk.md) | Disk diffusion diameter |
|
||||
|
||||
## Data Files
|
||||
|
||||
Pre-compiled in `data/` (do not edit directly; regenerate via
|
||||
`data-raw/` scripts):
|
||||
|
||||
| File | Contents |
|
||||
|----------------------------|-----------------------------------------------|
|
||||
| `microorganisms.rda` | ~79,000 microbial species with full taxonomy |
|
||||
| `antimicrobials.rda` | ~620 antimicrobial drugs with ATC codes |
|
||||
| `antivirals.rda` | Antiviral drugs |
|
||||
| `clinical_breakpoints.rda` | EUCAST + CLSI breakpoints (2011–2025) |
|
||||
| `intrinsic_resistant.rda` | Intrinsic resistance patterns |
|
||||
| `example_isolates.rda` | Example AMR dataset for documentation/testing |
|
||||
| `WHONET.rda` | Example WHONET-format dataset |
|
||||
|
||||
## Zero-Dependency Design
|
||||
|
||||
The package has **no `Imports`** in `DESCRIPTION`. All optional
|
||||
integrations (ggplot2, dplyr, data.table, tidymodels, cli, crayon, etc.)
|
||||
are listed in `Suggests` and guarded with:
|
||||
|
||||
``` r
|
||||
if (requireNamespace("pkg", quietly = TRUE)) { ... }
|
||||
```
|
||||
|
||||
Never add packages to `Imports`. If new functionality requires an
|
||||
external package, add it to `Suggests` and guard usage appropriately.
|
||||
|
||||
## Testing
|
||||
|
||||
- **Framework:** `testthat` (R ≥ 3.1); legacy `tinytest` used for R
|
||||
3.0–3.6 CI
|
||||
- **Test files:** `tests/testthat/test-*.R`
|
||||
- **Helpers:** `tests/testthat/helper-functions.R`
|
||||
- **CI matrix:** GitHub Actions across Windows / macOS / Linux × R devel
|
||||
/ release / oldrel-1 through oldrel-4
|
||||
- **Coverage:** `covr` (some files excluded: `atc_online.R`,
|
||||
`mo_source.R`, `translate.R`, `resistance_predict.R`,
|
||||
`zz_deprecated.R`, helper files, `zzz.R`)
|
||||
|
||||
## Documentation
|
||||
|
||||
- All exported functions use **roxygen2** blocks (`RoxygenNote: 7.3.3`,
|
||||
markdown enabled)
|
||||
- Run `devtools::document()` after any change to roxygen comments
|
||||
- Never edit files in `man/` directly — they are auto-generated
|
||||
- Vignettes live in `vignettes/` as `.Rmd` files
|
||||
- The pkgdown website is configured in `_pkgdown.yml`
|
||||
|
||||
## Versioning
|
||||
|
||||
Version format: `major.minor.patch.dev` (e.g., `3.0.1.9021`)
|
||||
|
||||
- Development versions use a `.9xxx` suffix
|
||||
- Stable CRAN releases drop the dev suffix (e.g., `3.0.1`)
|
||||
- `NEWS.md` uses sections **New**, **Fixes**, **Updates** with GitHub
|
||||
issue references (`#NNN`)
|
||||
|
||||
### Version bump required for every PR
|
||||
|
||||
Before opening a pull request, always increment the four-digit dev
|
||||
counter by 1 in **both** of these files:
|
||||
|
||||
1. **`DESCRIPTION`** — the `Version:` field:
|
||||
|
||||
Version: 3.0.1.9021 → Version: 3.0.1.9022
|
||||
|
||||
2. **`NEWS.md`** — the top-level heading:
|
||||
|
||||
# AMR 3.0.1.9021 → # AMR 3.0.1.9022
|
||||
|
||||
Read the current version from `DESCRIPTION`, add 1 to the last numeric
|
||||
component, and write the new version to both files in the same commit as
|
||||
the rest of the PR changes.
|
||||
|
||||
## Internal State
|
||||
|
||||
The package uses a private `AMR_env` environment (created in
|
||||
`aa_globals.R`) for caching expensive lookups (e.g., microorganism
|
||||
matching scores, breakpoint tables). This avoids re-computation within a
|
||||
session.
|
||||
@@ -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 12 February 2026.</p>
|
||||
generated on 27 February 2026.</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">2026-02-12</td>
|
||||
<td align="center">2026-02-27</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">2026-02-12</td>
|
||||
<td align="center">2026-02-27</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">2026-02-12</td>
|
||||
<td align="center">2026-02-27</td>
|
||||
<td align="center">efgh</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">R</td>
|
||||
|
||||
@@ -3,7 +3,7 @@
|
||||
**Note:** values on this page will change with every website update
|
||||
since they are based on randomly created values and the page was written
|
||||
in [R Markdown](https://rmarkdown.rstudio.com/). However, the
|
||||
methodology remains unchanged. This page was generated on 12 February
|
||||
methodology remains unchanged. This page was generated on 27 February
|
||||
2026.
|
||||
|
||||
## Introduction
|
||||
@@ -52,9 +52,9 @@ structure of your data generally look like this:
|
||||
|
||||
| date | patient_id | mo | AMX | CIP |
|
||||
|:----------:|:----------:|:----------------:|:---:|:---:|
|
||||
| 2026-02-12 | abcd | Escherichia coli | S | S |
|
||||
| 2026-02-12 | abcd | Escherichia coli | S | R |
|
||||
| 2026-02-12 | efgh | Escherichia coli | R | S |
|
||||
| 2026-02-27 | abcd | Escherichia coli | S | S |
|
||||
| 2026-02-27 | abcd | Escherichia coli | S | R |
|
||||
| 2026-02-27 | efgh | Escherichia coli | R | S |
|
||||
|
||||
### Needed R packages
|
||||
|
||||
|
||||
@@ -80,7 +80,7 @@
|
||||
<main id="main" class="col-md-9"><div class="page-header">
|
||||
<img src="../logo.svg" class="logo" alt=""><h1>Download data sets for download / own use</h1>
|
||||
|
||||
<h4 data-toc-skip class="date">12 February 2026</h4>
|
||||
<h4 data-toc-skip class="date">27 February 2026</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>
|
||||
|
||||
@@ -10,7 +10,7 @@ articles:
|
||||
PCA: PCA.html
|
||||
WHONET: WHONET.html
|
||||
WISCA: WISCA.html
|
||||
last_built: 2026-02-12T19:40Z
|
||||
last_built: 2026-02-27T16:21Z
|
||||
urls:
|
||||
reference: https://amr-for-r.org/reference
|
||||
article: https://amr-for-r.org/articles
|
||||
|
||||
@@ -112,16 +112,16 @@
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="va">df</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> birth_date age age_exact age_at_y2k</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 1980-02-27 45 45.95890 19</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 1953-07-26 72 72.55068 46</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 1949-09-02 76 76.44658 50</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 1986-08-03 39 39.52877 13</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 1932-11-19 93 93.23288 67</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 1949-03-30 76 76.87397 50</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 1996-06-23 29 29.64110 3</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 1963-09-16 62 62.40822 36</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 1952-05-16 73 73.74521 47</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 1952-11-14 73 73.24658 47</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 1980-02-27 46 46.00000 19</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 1953-07-26 72 72.59178 46</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 1949-09-02 76 76.48767 50</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 1986-08-03 39 39.56986 13</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 1932-11-19 93 93.27397 67</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 1949-03-30 76 76.91507 50</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 1996-06-23 29 29.68219 3</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 1963-09-16 62 62.44932 36</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 1952-05-16 73 73.78630 47</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 1952-11-14 73 73.28767 47</span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
|
||||
|
||||
@@ -81,14 +81,14 @@ df$age_at_y2k <- age(df$birth_date, "2000-01-01")
|
||||
|
||||
df
|
||||
#> birth_date age age_exact age_at_y2k
|
||||
#> 1 1980-02-27 45 45.95890 19
|
||||
#> 2 1953-07-26 72 72.55068 46
|
||||
#> 3 1949-09-02 76 76.44658 50
|
||||
#> 4 1986-08-03 39 39.52877 13
|
||||
#> 5 1932-11-19 93 93.23288 67
|
||||
#> 6 1949-03-30 76 76.87397 50
|
||||
#> 7 1996-06-23 29 29.64110 3
|
||||
#> 8 1963-09-16 62 62.40822 36
|
||||
#> 9 1952-05-16 73 73.74521 47
|
||||
#> 10 1952-11-14 73 73.24658 47
|
||||
#> 1 1980-02-27 46 46.00000 19
|
||||
#> 2 1953-07-26 72 72.59178 46
|
||||
#> 3 1949-09-02 76 76.48767 50
|
||||
#> 4 1986-08-03 39 39.56986 13
|
||||
#> 5 1932-11-19 93 93.27397 67
|
||||
#> 6 1949-03-30 76 76.91507 50
|
||||
#> 7 1996-06-23 29 29.68219 3
|
||||
#> 8 1963-09-16 62 62.44932 36
|
||||
#> 9 1952-05-16 73 73.78630 47
|
||||
#> 10 1952-11-14 73 73.28767 47
|
||||
```
|
||||
|
||||
@@ -424,10 +424,10 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 4 × 18</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> datetime index method ab_given mo_given host_given input_given</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><dttm></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> 2026-02-12 <span style="color: #949494;">19:41:27</span> 1 MIC amoxicillin Escherich… human 8 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> 2026-02-12 <span style="color: #949494;">19:41:27</span> 1 MIC cipro Escherich… human 0.256 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> 2026-02-12 <span style="color: #949494;">19:41:28</span> 1 DISK tobra Escherich… human 16 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">4</span> 2026-02-12 <span style="color: #949494;">19:41:28</span> 1 DISK genta Escherich… human 18 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> 2026-02-27 <span style="color: #949494;">16:22:03</span> 1 MIC amoxicillin Escherich… human 8 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> 2026-02-27 <span style="color: #949494;">16:22:03</span> 1 MIC cipro Escherich… human 0.256 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> 2026-02-27 <span style="color: #949494;">16:22:03</span> 1 DISK tobra Escherich… human 16 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">4</span> 2026-02-27 <span style="color: #949494;">16:22:03</span> 1 DISK genta Escherich… human 18 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 11 more variables: ab <ab>, mo <mo>, host <chr>, input <chr>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># outcome <sir>, notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># breakpoint_S_R <chr>, site <chr></span></span>
|
||||
|
||||
@@ -660,10 +660,10 @@ sir_interpretation_history()
|
||||
#> # A tibble: 4 × 18
|
||||
#> datetime index method ab_given mo_given host_given input_given
|
||||
#> <dttm> <int> <chr> <chr> <chr> <chr> <chr>
|
||||
#> 1 2026-02-12 19:41:27 1 MIC amoxicillin Escherich… human 8
|
||||
#> 2 2026-02-12 19:41:27 1 MIC cipro Escherich… human 0.256
|
||||
#> 3 2026-02-12 19:41:28 1 DISK tobra Escherich… human 16
|
||||
#> 4 2026-02-12 19:41:28 1 DISK genta Escherich… human 18
|
||||
#> 1 2026-02-27 16:22:03 1 MIC amoxicillin Escherich… human 8
|
||||
#> 2 2026-02-27 16:22:03 1 MIC cipro Escherich… human 0.256
|
||||
#> 3 2026-02-27 16:22:03 1 DISK tobra Escherich… human 16
|
||||
#> 4 2026-02-27 16:22:03 1 DISK genta Escherich… human 18
|
||||
#> # ℹ 11 more variables: ab <ab>, mo <mo>, host <chr>, input <chr>,
|
||||
#> # outcome <sir>, notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,
|
||||
#> # breakpoint_S_R <chr>, site <chr>
|
||||
|
||||
File diff suppressed because one or more lines are too long
@@ -1,5 +1,6 @@
|
||||
<urlset xmlns = 'http://www.sitemaps.org/schemas/sitemap/0.9'>
|
||||
<url><loc>https://amr-for-r.org/404.html</loc></url>
|
||||
<url><loc>https://amr-for-r.org/CLAUDE.html</loc></url>
|
||||
<url><loc>https://amr-for-r.org/LICENSE-text.html</loc></url>
|
||||
<url><loc>https://amr-for-r.org/articles/AMR.html</loc></url>
|
||||
<url><loc>https://amr-for-r.org/articles/AMR_for_Python.html</loc></url>
|
||||
|
||||
Reference in New Issue
Block a user