Reproducible Research for the Health Sciences
Reproducible Research for the Health Sciences
Reproducible Research for the Health Sciences
Copyright
Welcome
Preface
Conventions
1
Introduction: reproducibility as a computational problem
Foundations
2
The Reproducibility Crisis
3
Levels of Reproducibility
4
Version Control with Git and GitHub
5
The Research Compendium
Capturing the Environment
6
Pinning Packages with renv
7
Pinning the Environment with Docker
8
Backends and Runtimes: Nix, Podman, and Apptainer
Validation
9
Literate Programming and the Rendered Report
10
Automating the Analysis: Make and targets
11
Testing and Code Quality
12
Continuous Integration and Verification
Collaboration and Stewardship
13
Collaboration, Archiving, and Stewardship
References
Appendices
Glossary
Credits
Colophon
Reproducible Research for the Health Sciences
Code
Compendia, containers, and computational verification in R.
Copyright