Built site for AMR@3.0.1.9021: 2c21eba

2026-06-01 07:01:44 +02:00 · 2026-02-27 16:25:41 +00:00
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+# 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.