AMR/CLAUDE.md

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:

# 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:

# 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()	Microorganism code
<ab>	as.ab()	Antimicrobial drug code
<av>	as.av()	Antiviral drug code
<sir>	as.sir()	SIR value (S/I/R/SDD)
<mic>	as.mic()	Minimum inhibitory concentration
<disk>	as.disk()	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:

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.