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REPRODUCIBILITY.md

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Reproducibility

Levels

  • Level 1, public inspection: read scripts, docs, samples, paper, figures, and CSV summaries without raw data.
  • Level 2, processed-cache rerun: rerun validation, figure, dashboard, paper, sample, and final-check scripts from processed outputs.
  • Level 3, full rebuild: provide local source paths in config/paths.local.yml and run R/99_run_all.R.

Local Paths

Personal absolute source paths must appear only in config/paths.local.yml. This file is ignored by Git. Public files should use placeholders or relative paths.

Randomness

The Phase 2 figure scripts use seed 20260711 for network layout reproducibility.

Expected Ignored Files

  • data/raw/
  • data/interim/*.rds and data/interim/*.parquet
  • data/processed/*.rds and data/processed/*.parquet
  • outputs/models/*.rds
  • paper/*.pdf
  • config/paths.local.yml

Main Commands

Rscript scripts/validate_project.R
Rscript scripts/phase2_stage2_validation.R
Rscript scripts/phase2_stage3_models_figures.R
Rscript scripts/phase2_stage4_dashboard_paper_docs.R
Rscript scripts/phase2_stage5_samples_tests_cleanup.R