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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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<span class="navbar-toggler-icon"></span>
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</button>
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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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<li class="nav-item"><a class="nav-link" href="authors.html"><span class="fa fa-users"></span> Authors</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>
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<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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<div id="claudemd--amr-r-package" class="section level1">
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<p>This file provides context for Claude Code when working in this repository.</p>
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<div class="section level2">
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<h2 id="project-overview">Project Overview<a class="anchor" aria-label="anchor" href="#project-overview"></a></h2>
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<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>
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<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>
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</div>
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<div class="section level2">
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<h2 id="common-commands">Common Commands<a class="anchor" aria-label="anchor" href="#common-commands"></a></h2>
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<p>All commands run inside an R session:</p>
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<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
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<code class="sourceCode R"><span><span class="co"># Rebuild documentation (roxygen2 → .Rd files + NAMESPACE)</span></span>
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<span><span class="fu">devtools</span><span class="fu">::</span><span class="fu">document</span><span class="op">(</span><span class="op">)</span></span>
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<span></span>
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<span><span class="co"># Run all tests</span></span>
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<span><span class="fu">devtools</span><span class="fu">::</span><span class="fu">test</span><span class="op">(</span><span class="op">)</span></span>
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<span></span>
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<span><span class="co"># Full package check (CRAN-level: docs + tests + checks)</span></span>
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<span><span class="fu">devtools</span><span class="fu">::</span><span class="fu">check</span><span class="op">(</span><span class="op">)</span></span>
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<span></span>
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<span><span class="co"># Build pkgdown website locally</span></span>
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<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>
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<span></span>
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<span><span class="co"># Code coverage report</span></span>
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<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>
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<p>From the shell:</p>
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<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>
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<span id="cb2-2"><a href="#cb2-2" tabindex="-1"></a><span class="ex">R</span> CMD check AMR</span></code></pre></div>
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</div>
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<div class="section level2">
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<h2 id="repository-structure">Repository Structure<a class="anchor" aria-label="anchor" href="#repository-structure"></a></h2>
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<pre><code>R/ # All R source files (62 files, ~28,000 lines)
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man/ # Auto-generated .Rd documentation (do not edit manually)
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tests/testthat/ # testthat test files (test-*.R) and helper-functions.R
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data/ # Pre-compiled .rda datasets
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data-raw/ # Scripts used to generate data/ files
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vignettes/ # Rmd vignette articles
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inst/ # Installed files (translations, etc.)
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_pkgdown.yml # pkgdown website configuration</code></pre>
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</div>
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<div class="section level2">
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<h2 id="r-source-file-conventions">R Source File Conventions<a class="anchor" aria-label="anchor" href="#r-source-file-conventions"></a></h2>
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<p><strong>Naming conventions in <code>R/</code>:</strong></p>
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<table class="table"><thead><tr class="header"><th>Prefix/Name</th>
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<th>Purpose</th>
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</tr></thead><tbody><tr class="odd"><td><code>aa_*.R</code></td>
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<td>Loaded first (helpers, globals, options, package docs)</td>
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</tr><tr class="even"><td><code>zz_deprecated.R</code></td>
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<td>Deprecated function wrappers</td>
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</tr><tr class="odd"><td><code>zzz.R</code></td>
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<td>
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<code>.onLoad</code> / <code>.onAttach</code> initialization</td>
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</tr></tbody></table><p><strong>Key source files:</strong></p>
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<ul><li>
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<code>aa_helper_functions.R</code> / <code>aa_helper_pm_functions.R</code> — internal utility functions (large; ~63 KB and ~37 KB)</li>
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<li>
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<code>aa_globals.R</code> — global constants and breakpoint lookup structures</li>
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<li>
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<code>aa_options.R</code> — <code>amr_options()</code> / <code>get_AMR_option()</code> system</li>
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<li>
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<code>mo.R</code> / <code>mo_property.R</code> — microorganism lookup and properties</li>
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<li>
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<code>ab.R</code> / <code>ab_property.R</code> — antimicrobial drug functions</li>
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<li>
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<code>av.R</code> / <code>av_property.R</code> — antiviral drug functions</li>
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<li>
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<code>sir.R</code> / <code>sir_calc.R</code> / <code>sir_df.R</code> — SIR classification engine</li>
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<li>
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<code>mic.R</code> / <code>disk.R</code> — MIC and disk diffusion classes</li>
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<li>
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<code>antibiogram.R</code> — antibiogram generation (traditional, combined, syndromic, WISCA)</li>
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<li>
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<code>first_isolate.R</code> — first-isolate identification algorithms</li>
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<li>
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<code>mdro.R</code> — MDRO classification (EUCAST, CLSI, CDC, custom guidelines)</li>
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<li>
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<code>amr_selectors.R</code> — tidyselect helpers for selecting AMR columns</li>
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<li>
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<code>interpretive_rules.R</code> / <code>custom_eucast_rules.R</code> — clinical interpretation rules</li>
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<li>
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<code>translate.R</code> — 28-language translation system</li>
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<li>
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<code>ggplot_sir.R</code> / <code>ggplot_pca.R</code> / <code>plotting.R</code> — visualisation functions</li>
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</ul></div>
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<div class="section level2">
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<h2 id="custom-s3-classes">Custom S3 Classes<a class="anchor" aria-label="anchor" href="#custom-s3-classes"></a></h2>
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<p>The package defines five S3 classes with full print/format/plot/vctrs support:</p>
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<table class="table"><thead><tr class="header"><th>Class</th>
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<th>Created by</th>
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<th>Represents</th>
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</tr></thead><tbody><tr class="odd"><td><code><mo></code></td>
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<td><code><a href="reference/as.mo.html">as.mo()</a></code></td>
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<td>Microorganism code</td>
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</tr><tr class="even"><td><code><ab></code></td>
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<td><code><a href="reference/as.ab.html">as.ab()</a></code></td>
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<td>Antimicrobial drug code</td>
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</tr><tr class="odd"><td><code><av></code></td>
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<td><code><a href="reference/as.av.html">as.av()</a></code></td>
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<td>Antiviral drug code</td>
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</tr><tr class="even"><td><code><sir></code></td>
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<td><code><a href="reference/as.sir.html">as.sir()</a></code></td>
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<td>SIR value (S/I/R/SDD)</td>
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</tr><tr class="odd"><td><code><mic></code></td>
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<td><code><a href="reference/as.mic.html">as.mic()</a></code></td>
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<td>Minimum inhibitory concentration</td>
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</tr><tr class="even"><td><code><disk></code></td>
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<td><code><a href="reference/as.disk.html">as.disk()</a></code></td>
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<td>Disk diffusion diameter</td>
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</tr></tbody></table></div>
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<div class="section level2">
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<h2 id="data-files">Data Files<a class="anchor" aria-label="anchor" href="#data-files"></a></h2>
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<p>Pre-compiled in <code>data/</code> (do not edit directly; regenerate via <code>data-raw/</code> scripts):</p>
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<table class="table"><colgroup><col width="50%"><col width="50%"></colgroup><thead><tr class="header"><th>File</th>
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<th>Contents</th>
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</tr></thead><tbody><tr class="odd"><td><code>microorganisms.rda</code></td>
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<td>~79,000 microbial species with full taxonomy</td>
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</tr><tr class="even"><td><code>antimicrobials.rda</code></td>
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<td>~620 antimicrobial drugs with ATC codes</td>
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</tr><tr class="odd"><td><code>antivirals.rda</code></td>
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<td>Antiviral drugs</td>
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</tr><tr class="even"><td><code>clinical_breakpoints.rda</code></td>
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<td>EUCAST + CLSI breakpoints (2011–2025)</td>
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</tr><tr class="odd"><td><code>intrinsic_resistant.rda</code></td>
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<td>Intrinsic resistance patterns</td>
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</tr><tr class="even"><td><code>example_isolates.rda</code></td>
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<td>Example AMR dataset for documentation/testing</td>
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</tr><tr class="odd"><td><code>WHONET.rda</code></td>
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<td>Example WHONET-format dataset</td>
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</tr></tbody></table></div>
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<div class="section level2">
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<h2 id="zero-dependency-design">Zero-Dependency Design<a class="anchor" aria-label="anchor" href="#zero-dependency-design"></a></h2>
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<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>
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<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
|
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<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>
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<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>
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</div>
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<div class="section level2">
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<h2 id="testing">Testing<a class="anchor" aria-label="anchor" href="#testing"></a></h2>
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<ul><li>
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<strong>Framework:</strong> <code>testthat</code> (R ≥ 3.1); legacy <code>tinytest</code> used for R 3.0–3.6 CI</li>
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<li>
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<strong>Test files:</strong> <code>tests/testthat/test-*.R</code>
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</li>
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<li>
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<strong>Helpers:</strong> <code>tests/testthat/helper-functions.R</code>
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</li>
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<li>
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<strong>CI matrix:</strong> GitHub Actions across Windows / macOS / Linux × R devel / release / oldrel-1 through oldrel-4</li>
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<li>
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<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>
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||
</ul></div>
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<div class="section level2">
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<h2 id="documentation">Documentation<a class="anchor" aria-label="anchor" href="#documentation"></a></h2>
|
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<ul><li>All exported functions use <strong>roxygen2</strong> blocks (<code>RoxygenNote: 7.3.3</code>, markdown enabled)</li>
|
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<li>Run <code>devtools::document()</code> after any change to roxygen comments</li>
|
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<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>
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<div class="section level2">
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<h2 id="versioning">Versioning<a class="anchor" aria-label="anchor" href="#versioning"></a></h2>
|
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<p>Version format: <code>major.minor.patch.dev</code> (e.g., <code>3.0.1.9021</code>)</p>
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<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>
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||
<li>
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<code>NEWS.md</code> uses sections <strong>New</strong>, <strong>Fixes</strong>, <strong>Updates</strong> with GitHub issue references (<code>#NNN</code>)</li>
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||
</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>
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<ol style="list-style-type: decimal"><li>
|
||
<p><strong><code>DESCRIPTION</code></strong> — the <code>Version:</code> field:</p>
|
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<pre><code>Version: 3.0.1.9021 → Version: 3.0.1.9022</code></pre>
|
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</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>
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</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>
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</div>
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</div>
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<div class="section level2">
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<h2 id="internal-state">Internal State<a class="anchor" aria-label="anchor" href="#internal-state"></a></h2>
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<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>
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</div>
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</div>
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</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
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</nav></aside></div>
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<footer><div class="pkgdown-footer-left">
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<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>
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</div>
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<div class="pkgdown-footer-right">
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<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>
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</div>
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||
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</footer></div>
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</body></html>
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