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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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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9034</small>
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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>
<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>
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<main id="main" class="col-md-9"><div class="page-header">
<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>
</div>
<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 20112025 and CLSI 20112025 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>&lt;mo&gt;</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>&lt;ab&gt;</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>&lt;av&gt;</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>&lt;sir&gt;</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>&lt;mic&gt;</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>&lt;disk&gt;</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 (20112025)</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 3.03.6 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-and-date-bump-required-for-every-pr">Version and date bump required for every PR<a class="anchor" aria-label="anchor" href="#version-and-date-bump-required-for-every-pr"></a></h3>
<p>All PRs are <strong>squash-merged</strong>, so each PR lands as exactly <strong>one commit</strong> on the default branch. Version numbers are kept in sync with the cumulative commit count since the last released tag. Therefore <strong>exactly one version bump is allowed per PR</strong>, regardless of how many intermediate commits are made on the branch.</p>
<div class="section level4">
<h4 id="computing-the-correct-version-number">Computing the correct version number<a class="anchor" aria-label="anchor" href="#computing-the-correct-version-number"></a></h4>
<p>Run the following from the repo root to determine the version string to use:</p>
<div class="sourceCode" id="cb5"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb5-1"><a href="#cb5-1" tabindex="-1"></a><span class="va">currenttag</span><span class="op">=</span><span class="va">$(</span><span class="fu">git</span> describe <span class="at">--tags</span> <span class="at">--abbrev</span><span class="op">=</span>0 <span class="kw">|</span> <span class="fu">sed</span> <span class="st">'s/v//'</span><span class="va">)</span></span>
<span id="cb5-2"><a href="#cb5-2" tabindex="-1"></a><span class="va">currenttagfull</span><span class="op">=</span><span class="va">$(</span><span class="fu">git</span> describe <span class="at">--tags</span> <span class="at">--abbrev</span><span class="op">=</span>0<span class="va">)</span></span>
<span id="cb5-3"><a href="#cb5-3" tabindex="-1"></a><span class="va">defaultbranch</span><span class="op">=</span><span class="va">$(</span><span class="fu">git</span> branch <span class="kw">|</span> <span class="fu">cut</span> <span class="at">-c</span> 3- <span class="kw">|</span> <span class="fu">grep</span> <span class="at">-E</span> <span class="st">'^master$|^main$'</span><span class="va">)</span></span>
<span id="cb5-4"><a href="#cb5-4" tabindex="-1"></a><span class="va">currentcommit</span><span class="op">=</span><span class="va">$(</span><span class="fu">git</span> rev-list <span class="at">--count</span> <span class="va">${currenttagfull}</span>..<span class="va">${defaultbranch})</span></span>
<span id="cb5-5"><a href="#cb5-5" tabindex="-1"></a><span class="va">currentversion</span><span class="op">=</span><span class="st">"</span><span class="va">${currenttag}</span><span class="st">.</span><span class="va">$((currentcommit</span> <span class="op">+</span> <span class="dv">9001</span> <span class="op">+</span> <span class="dv">1</span><span class="va">))</span><span class="st">"</span></span>
<span id="cb5-6"><a href="#cb5-6" tabindex="-1"></a><span class="bu">echo</span> <span class="st">"</span><span class="va">$currentversion</span><span class="st">"</span></span></code></pre></div>
<p>The <code>+ 1</code> accounts for the fact that this PRs squash commit is not yet on the default branch. Set <strong>both</strong> of these files to the resulting version string (and only once per PR, even across multiple commits):</p>
<ol style="list-style-type: decimal"><li>
<strong><code>DESCRIPTION</code></strong> — the <code>Version:</code> field</li>
<li>
<strong><code>NEWS.md</code></strong> — the top-level heading <code># AMR &lt;version&gt;</code>
</li>
</ol><p>If <code>git describe</code> fails (e.g. no tags exist in the environment), fall back to reading the current version from <code>DESCRIPTION</code> and adding 1 to the last numeric component — but only if no bump has already been made in this PR.</p>
</div>
<div class="section level4">
<h4 id="date-field">Date field<a class="anchor" aria-label="anchor" href="#date-field"></a></h4>
<p>The <code>Date:</code> field in <code>DESCRIPTION</code> must reflect the date of the <strong>last commit to the PR</strong> (not the first), in ISO format. Update it with every commit so it is always current:</p>
<pre><code><span><span class="va">Date</span><span class="op">:</span> <span class="fl">2026</span><span class="op">-</span><span class="fl">03</span><span class="op">-</span><span class="fl">07</span></span></code></pre>
</div>
</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>
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