Open Code

October 24, 2019. 3:30 - 5pm

This workshop is part of a series on Reproducibility for Biomedical Researchers hosted by the UCSF library.

Slides

This repositories contains slides and links to various resources mentioned during the workshop. For any questions or clarifications please file an issue.

Resources

The National Academy of Sciences report on Reproducibility and Replicability in Science Free PDF available for download.

My talk on research compendia in R from Rstudio Conference in January 2019 (includes video, slides, and a bunch of resources)

Docker - An introduction to Docker for reproducible research, with examples from the R environment.

https://github.com/pypa/pipenv

Git and GitHub

Ten Simple Rules for Taking Advantage of Git and GitHub

Coordinate releases between GitHub and Zenodo

Research compendia

Packaging Data Analytical Work Reproducibly Using R (and Friends) (OA preprint). A practical introduction to setting up a research compendium in R.

Examples of research compendia on GitHub (Python)

Examples of research compendia on GitHub (R)

Browse the Research Compendium topic on GitHub

Examples of Research Compendia on GitHub Below are a few links to real world examples of research compendia in R. To have a minimal compendium, all you really need is a valid DESCRIPTION file containing a handful of fields such as type, name, version and dependencies. See Marwick et al 2017 for a detailed description of the different types of compendia.

Small

Code and data associated with Duffy, James, and Longworth Applied and Environmental Microbiology paper describing the ecology, virulence, and phylogeny of a brood parasite of Daphnia, Blastulidium paedophthorum;

Medium

Resolving the measurement uncertainty paradox in ecological management

Large

Non-parametric Bayesian Inference for Conservation Decisions
Find various other compendia on Github and Zenodo using the research-compendium tag.

Software packages related to research compendia

📦 rrtools by Ben Marwick (also the author of the packaging data analysis paper mentioned above) extends functions in devtools and provides instructions, templates, and functions to make a basic compendium suitable for doing reproducible research with R.
- Also see 📦 workflowr by John Blischak and the task view on R-based data analysis projects maintained by John Blischak, Anna Krystalli, Ben Marwick, Daniel Nüst.
📦 usethis Many of the major function in rrtools are imported from usethis. A savvy user can get by setting up and maintaining a compendium purely with usethis functions.
📦 goodpractice - Designed to help you build more robust packages, the package does a deep dive on your package contents and provide advice on syntax pitfalls to avoid, code formatting suggestions, and helps you improve overall package structure.
The 📦 rticles package by JJ has numerous journal templates and together with Rstudio addins like word countaddin and citr + knitcitations.

Computational environments: Binder and friends

My Binder is a free binderhub deployment that turns any Git repo into a collection of interactive notebooks. Now with better R support!
For instructions on how to set this up for your R project, see my notes here
Introducing Binder 2.0 — share your interactive research environment Paper describing the architecture of Binder in case you were interested in what was happening under the hood
🎥 A talk about Binder at Scipy 2018. Also see conference proceedings PDF.
repo2docker A Python module that will turn any repo (or local folder) into a Docker Image.
The holepunch package helps you easily add binder to your R project

Other hosted Binder hubs

Pangeo binder Pangeo encourages everyone to use it.
gesis
Syzgy Binder + JupyterHub for Compute Canada