R Example Research Project

An example R project managed with Calkit that demonstrates reproducible data analysis and figure generation.

Project Structure

.
├── data/
│   ├── raw/              # Original, untouched data (input)
│   ├── processed/        # Cleaned/transformed data (output from analyze stage)
│   └── README.md         # Data dictionary
├── R/
│   ├── analyze.R         # Data processing and statistical analysis
│   └── plot.R            # Create publication figures
├── figures/              # Generated plots and visualizations
├── output/               # Analysis results and summaries
├── calkit.yaml           # Calkit pipeline configuration
├── DESCRIPTION           # Project metadata and R dependencies
├── renv/                 # R environment configuration and packages
├── references.bib        # Citation database
└── README.md             # This file

Workflow

The entire project is reproduced with a single command:

calkit run

This executes the pipeline defined in calkit.yaml:

1. Analyze stage (R/analyze.R):

   • Reads raw data from data/raw/data.csv
   • Performs statistical analysis
   • Outputs processed data to data/processed/data.csv
   • Saves analysis results to output/analysis_results.rds

2. Plot stage (R/plot.R):

   • Uses processed data from data/processed/data.csv
   • Generates publication-ready figures
   • Outputs plots to figures/

Key Features

• Calkit pipeline: Declarative workflow defined in calkit.yaml ensures reproducible execution
• DESCRIPTION file: Declares R package dependencies
• renv: Locks package versions for complete reproducibility
• Modular R scripts: Each analysis step is a separate, focused R script
• Dependency tracking: Pipeline automatically runs stages in correct order with proper inputs/outputs

Getting Started

1. Run the entire pipeline: calkit run
2. Modify R scripts in R/ as needed for your analysis
3. Run again: calkit run (only affected stages will re-execute)

Requirements

• R (>= 4.0)
• Calkit CLI
• Dependencies listed in DESCRIPTION (managed by renv)