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Repository Guidelines

Project Structure & Module Organization

This repository is a package-first R project. Core package code lives in R/, generated help pages in man/, long-form documentation in vignettes/, and CI in .github/workflows/. The main workflow surface is the exported API: import_suts(), extract_domestic_block(), build_matrices(), compute_sube(), estimate_elasticities(), prepare_sube_comparison(), and the plotting/export helpers. A narrow compatibility bridge for script-era users remains at inst/scripts/run_legacy_pipeline.R, but it is not the primary interface.

Build, Test, and Development Commands

Run the maintained local check path from the repository root with:

R -q -e 'testthat::test_dir("tests/testthat")'
R CMD build .
R CMD check sube_0.1.2.tar.gz --no-manual

This mirrors the GitHub Actions R-CMD-check workflow. For focused iteration, run the main workflow regression file with:

R -q -e 'testthat::test_file("tests/testthat/test-workflow.R")'

If you need the compatibility bridge, invoke:

Rscript inst/scripts/run_legacy_pipeline.R <sut_path> <cpa_map.csv> <ind_map.csv> <inputs.csv> [output_dir]

Coding Style & Naming Conventions

Use 2-space indentation and keep functions side-effect-light unless file writing is explicit. Follow the existing package naming patterns: snake_case for objects, descriptive helper names, and roxygen-backed function documentation for public APIs. Prefer relative paths inside the repo. Treat historical absolute paths like W:/... and D://... as technical debt and do not introduce new ones.

Testing Guidelines

testthat is the automated baseline. Before committing, rerun tests/testthat/test-workflow.R for touched workflow surfaces and the full tests/testthat/ suite for release-facing changes. If you touch CI, wrapper, or vignette-evaluated examples, also confirm R CMD build . still succeeds. Treat the shipped example data as the canonical reproducibility baseline for tests and docs.

Commit & Pull Request Guidelines

Use short imperative commit subjects under 72 characters, for example Harden R-CMD-check workflow or Clarify legacy wrapper usage. Pull requests should state which workflow surfaces changed, whether CI or release behavior changed, and whether migration guidance or wrapper behavior was affected. Include the commands you ran when the change is release- or CI-facing.

Data & Configuration Notes

Do not commit large generated datasets unless explicitly required. Keep the package bundle lightweight and sample-data-driven. When changing CI, release instructions, or migration guidance, make sure README, AGENTS.md, and .github/workflows/R-CMD-check.yaml stay aligned.