resources.md

Additional Resources / Readings

Style Guides

• "The tidyverse style guide"

  • Hadley Wickham's online resource with details on naming and styling R code

• "Style Guide for Python Code"

  • the Python Enhancement Proposal from Guido van Rossum, Barry Warsaw, and Nick Coghlan

Code Smells and Recommendations

• "Code Smells and Feels"

  • GitHub repo from Jenny Bryan on "code smells" - also check out the related slides

• "Writing clear code"

  • notes from Karl Broman

• "Writing Clean Scientific Software"

  • slides from Nick Murphy on clean coding (examples in Python, a bit physics-oriented)

• "Column Names as Contracts"

  • Blogpost from Emily Riederer on selecting good column names to facilitate a data analysis workflow

• "How patterns in variable names can make code easier to read."

  • Short video from Felienne Hermans on variable and object naming

• "Twelve quick tips for software design"

  • paper from Greg Wilson about designing larger pieces of code

Writing Functions

• "Functions"
  • book chapter from Hadley Wickham & Garrett Grolemund's "R for Data Science"

Advanced Topics

• "RMarkdown Driven Development (RmdDD)"

  • Blogpost from Emily Riederer on structuring RMarkdown documents for data analysis; see also the "RMarkdown Driven Development: the Technical Appendix"

• "The Wrong Abstraction"

  • blogpost from Sandi Metz on refactoring and complexity

• "The targets R package"

  • targets is a workflow package to help manage large and complex analyses

• "My Workflow for Open and Reproducible Science as an Academic Researcher in Biomedicine"

  • a broad overview of combining snakemake, RStudio projects, and github for reproducible workflows, from Ruben Van Paemel

https://twitter.com/zevross/status/1519318012846817282?s=20&t=MH7bo9SJVImUbt0N6h7AzA

Books and Longer-form Guides

• "The Good Research Code Handbook"

  • guide to good research code (python-centric)

• "The Art of Readable Code"

  • via https://twitter.com/mv_evans/status/1354435566981545988

• "Clean Code: A Handbook of Craftsmanship"

  • via https://twitter.com/mxwlj/status/1354170627695861761

• "Research Software Engineering with Python: Building software that makes research possible"
  (online bookdown version)

  • book from Damien Irving, Kate Hertweck, Luke Johnston, Joel Ostblom, Charlotte Wickham, and Greg Wilson on introductory Research Software Engineering