r-reproducibility-guide
Create reproducible research workflows with R and RMarkdown/Quarto
Profile →npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill r-reproducibility-guide --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Reproducible Research with R A skill for creating fully reproducible research workflows in R using RMarkdown, Quarto, package management with renv, and project organization best practices. Covers literate programming, environment management, automated reporting, and sharing reproducible analyses. ## Project Organization ### Recommended Directory Structure ``` my-research-project/ README.md my-project.Rproj # RStudio project file renv.lock # Package versions (managed by renv) renv/ # renv library directory data/ raw/ # Untouched original data processed/ # Cleaned, analysis-ready data R/ 01-clean.R # Data cleaning functions 02-analyze.R # Analysis functions 03-visualize.R # Plotting functions utils.R # Helper functions analysis/ main-analysis.Rmd # Primary analysis notebook supplementary.Rmd # Supplementary analyses output/ figures/ # Generated plots tables/ # Generated tables manuscript.pdf # Compiled document Makefile # Reproducible build commands ``` ### Key Principles ``` 1. Raw data is read-only (never modify original data files) 2. All processing steps are scripted (no manual spreadsheet edits) 3. Generated outputs can be deleted and recreated from source 4. Package versions
- Project Organization
- Recommended Directory Structure
- Key Principles
- RMarkdown and Quarto
- RMarkdown Document
- Quarto (Next Generation)
- Package Management with renv
- Setting Up renv
- How renv Works
- Automated Reporting
- Make-Based Pipeline
- targets Package (R-native Pipeline)
- Sharing Reproducible Analyses
- Options for Sharing
What does the r-reproducibility-guide skill do?
Create reproducible research workflows with R and RMarkdown/Quarto
How do I install it?
Run `npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill r-reproducibility-guide --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From brycewang-stanford/Auto-Empirical-Research-Skills, a repository with 3,244 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.