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
The Research Compendium
Capturing the Environment
5
Pinning Packages with renv
6
Pinning the Environment with Docker
7
Backends and Runtimes: Nix, Podman, and Apptainer
Validation
8
Literate Programming and the Rendered Report
9
Testing and Code Quality
10
Continuous Integration and Verification
Collaboration and Stewardship
11
Collaboration, Archiving, and Stewardship
References
Appendices
Credits
Colophon
Reproducible Research for the Health Sciences
Code
Compendia, containers, and computational verification in R.
Copyright