Cheat-Sheet Index

Each content chapter ends with a two-column reference table of the commands, rules, and terms introduced in that chapter. This appendix collects those tables in one place. Every entry links to the full table in its chapter, where the surrounding context explains any term that is not self-explanatory.

Part I: Foundations

Chapter 2:The Reproducibility Crisis Terms and distinctions: reproducibility vs. replicability vs. robustness; computational vs. statistical failure; RNGkind(); the stringsAsFactors default change; the determinant stack. These are the vocabulary the rest of the book assumes.

Chapter 3:Levels of Reproducibility The L0-L3 ladder; the capture-vs.-validation distinction; zzc verify --full; how each level is claimed and confirmed. The single most referenced table in the book.

Chapter 4:Version Control Core git commands: init, add, commit, status, log, show, switch -c, remote add, push, tag. The .gitignore pattern syntax. The rule of thumb for commit messages.

Chapter 5:The Research Compendium The minimal R-package skin (DESCRIPTION, NAMESPACE, R/); the Five Pillars; the raw-vs.-derived boundary test; the five archetypes; progressive disclosure.

Part II: Capturing the Environment

Chapter 6:Managing Dependencies renv::init(), snapshot(), restore(), dependencies(); zzrenvcheck CI and development forms; CRAN snapshot URLs; options(renv.config.autoloader.enabled = FALSE).

Chapter 7:Containers FROM image@sha256:; ARG PPM_SNAPSHOT; ENV variables for locale, timezone, and thread count; the two-stage COPY for renv; docker build, run, exec, inspect; the --platform flag.

Chapter 8:Backends and Runtimes Podman and Apptainer equivalents to Docker; rix::rix() and nix-shell; Binder and Dev Containers; the L2 guarantee each tool provides.

Part III: Validation

Chapter 9:Literate Programming Inline R expressions; knitr::opts_chunk$set(); SOURCE_DATE_EPOCH; make docker-render; the five render landmines; the sealed-render rule of thumb.

Chapter 10:Automating the Analysis Make syntax (target: prerequisites, tab-indented recipes, touch); targets (tar_target(), tar_make(), tar_outdated(), tar_visnetwork()); snakemake --cores.

Chapter 11:Testing and Code Quality tinytest expectations (expect_equal, expect_true, etc.); test_package(); exit_file(); make lint / make style; the test-baseline*.R naming convention; the stated-tolerance rule.

Chapter 12:Continuous Integration error-on: '"warning"'; zzrenvcheck with error_on_fail = TRUE; renv::dependencies(); the render gate; docker build on a clean machine; zzc verify --full; the L3 rebuild requirement.

Part IV: Collaboration and Stewardship

Chapter 13:Archiving and Sharing docker inspect for digest retrieval; apptainer build from a digest-pinned image; the two-layer (environment/packages) model; the union lockfile; rang and groundhog; Zenodo and OSF deposition; FAIR principles and DataCite metadata.