Init Research Project

Set up a new research project from data files. Inspect data, generate codebook, conduct interactive research planning, scaffold project structure with reproducible pipeline.

When to Use

• •Starting fresh with a new dataset (CSV, .dta, .rds)
• •User says "new project", "init project", "set up research", "start analysis"
• •User provides raw data files and wants to begin planning
• •Setting up a new research directory from scratch

When NOT to Use

• •Returning to an existing project (use /catch-up)
• •One-off data inspection (use /datacheck)
• •Already have clean scripts and want to finalize (use /finalize-analysis)

Workflow

Phase 1: Data Inspection

Run /datacheck on each data file provided. Additionally for .dta files, extract variable and value labels with haven. For CSV files, profile with data.table::fread.

Generate codebook to docs/codebook.md. See references/codebook-generation.md for format and R code.

Done when: Codebook written to docs/codebook.md and user confirms variable descriptions look correct.

Phase 2: Questionnaire Cross-Reference (if provided)

Parse the questionnaire document. Match questionnaire items to data variables using labels and name patterns. Flag any unmatched variables or questionnaire items.

Done when: All variables matched or unmatched ones documented in the codebook.

Phase 3: Research Planning Interview

Use AskUserQuestion (following /brainstorming patterns) for multiple rounds:

1. •Round 1: Research question, contribution, what's new
2. •Round 2: Key DV/IV, planned analyses, survey design elements (weights, clusters, strata)
3. •Round 3: Target audience/journal, envisioned figures and tables
4. •Round 4+: Clarifications until user says "that's enough" or questions become redundant

Done when: User indicates sufficient information gathered.

Phase 4: Analysis Plan

Enter Plan mode. Write a living document to docs/analysis-plan.md with evolving specs for each expected output. Script numbering matches analysis step numbering. See references/analysis-plan-template.md.

Done when: Plan written and user approves the overall structure.

Phase 5: External Review

Invoke /codex and /gemini to review the analysis plan. If either skill is unavailable, ask user to review manually or skip. Incorporate feedback.

Done when: Feedback incorporated and user confirms final plan.

Phase 6: Scaffold Project

Create directory structure:

project/
├── data/raw/          # immutable original data
├── data/processed/
├── scripts/           # 01_cleaning.R, 02_measures.R, ...
├── output/figures/
├── output/tables/
├── docs/              # codebook.md, analysis-plan.md
├── manuscript/
├── config.yaml        # random seeds, parameters
├── CLAUDE.md          # project instructions (see references/claude-md-template.md)
└── .gitignore

Run git init, generate .gitignore (R/data patterns), create CLAUDE.md from template customized with planning session outputs. Optionally invoke /setup-snakemake-pipeline. Create config.yaml with random seeds. Initialize renv.

Done when: Directory structure exists, CLAUDE.md written, pipeline runnable.

Quick Reference

Common Mistakes