R Analysis ... for El Gus

Purpose

A very tailored version of Matt Dray's great repo to begin a simple analytical project with R and RStudio that fits in my workflow.

You should read this blog post for a more in-depth explanation of the original repo.

How to use

Click here to open the page for copying the repo.

Feel free to fork or copy this and tweak it for your workflow.

File tree

See individual README.md files in the folders for specific information but in general:

• Docker images go on Docker/
• Data go on data/
• External data go on ext/
• Human readable reports go on docs/
• Output data and plots go on output/
• R scripts go on R/
• Python scripts go on python/
• Credentials go on secrets/ (never committed)
• Docker images go on Docker/

elgus-R-template/
├── .github/
│   └── copilot-instructions.md
├── data/
│   ├── README.md
├── Docker/
│   ├── README.md
├── docs/
│   ├── README.md
│   └── template-document-example.Rmd
├── ext/
│   └── README.md
├── output/
│   └── README.md
├── python/
│   └── README.md
├── R/
│   ├── functions.R
│   └── README.md
├── secrets/
│   └── README.md
├── AGENTS.md
├── CLAUDE.md
├── elgus-R-template.Rproj
├── GEMINI.md
└── README.md

AI coding agents

AGENTS.md gives AI coding assistants a starting point for working on your analysis: the repository layout, where generated files belong, code style and working practices. CLAUDE.md (Claude Code), GEMINI.md (Gemini CLI) and .github/copilot-instructions.md (GitHub Copilot) point at it, so edit AGENTS.md to modify their behaviour/approach.

When you start a project from this template, fill in the sections of AGENTS.md marked TODO — what the analysis is about, what the data are, and how to run the scripts. That project-specific context is what makes an agent actually useful; the rest already matches this structure and can be left alone.