Research

Fills all [FILL:] placeholders across the template to initialize a new research project. Use when setting up a freshly cloned project.

Writes a session handoff report to handoffs/ with project state, work done, decisions, and next steps. Use at session end or after significant work.

Checks whether registered notebooks have current, stale, or missing outputs. Use before rendering or to verify freshness.

Generates an HTML gallery of all project figures with captions and source notebooks. Use when reviewing figures.

Executes all registered notebooks, strips noisy cell metadata, and syncs Jupytext pairs. Use when asked to re-run notebooks or refresh outputs.

Captures tool versions, packages, and kernel info as a reproducibility record in notes/. Use when documenting the environment.

Drafts academic prose for a manuscript section from bullet points or an outline. Use when writing or expanding a section.

Scans notebooks for data file references and verifies each file exists on disk. Use when checking for broken data paths.

Auto-generates a Markdown codebook from a dataset (CSV, DTA, Excel, Parquet) with types and summary statistics. Use when documenting variables.

Finds a paper by title, author, or DOI, adds BibTeX to references.bib, and shows citation syntax. Use when adding a reference.

Verifies required tools (Quarto, uv, Python, R, Stata, TeX) and Jupyter kernels are installed. Use when setting up or troubleshooting.

Cross-checks citation keys in index.qmd against references.bib, reporting missing, orphaned, and duplicate entries. Use when verifying citations.

Reads the manuscript and notebooks to generate a structured abstract. Use when writing or updating the abstract.

Run the R code review protocol on R scripts. Checks code quality, reproducibility, domain correctness, and professional standards. Produces a report without editing files.

Comprehensive manuscript review covering argument structure, econometric specification, citation completeness, and potential referee objections

Generate structured research questions, testable hypotheses, and empirical strategies from a topic or dataset

Run a full 6-phase autonomous replication of a biomedical/epidemiology paper against UK Biobank or similar cohort data, producing Python and R scripts plus a validated replication report. Use when asked to replicate a paper end-to-end, or when invoked as /replicate-paper [paper.pdf] [data.csv|dta].

Run the proofreading protocol on lecture files. Checks grammar, typos, overflow, consistency, and academic writing quality. Produces a report without editing files.

Structured literature search and synthesis with citation extraction and gap identification

Interactive interview to formalize a research idea into a structured specification with hypotheses and empirical strategy

Challenge a slide deck design with 5-7 specific pedagogical questions. Checks ordering, prerequisites, gaps, alternatives, notation conflicts, cognitive load, and book readiness.

Render Quarto slides and sync to docs/ for GitHub Pages deployment. Use when deploying lecture slides after making changes.

End-to-end R data analysis workflow from exploration through regression to publication-ready tables and figures

Thoroughly verify all code, tables, figures, modeling decisions, and quantitative claims in an academic paper against its source R scripts and output files. Use this skill whenever you need to audit, replicate, or verify an academic research paper - including cross-checking LaTeX tables against R output, validating econometric modeling choices, ensuring sample sizes are consistent, building a verification manifest, and running automated replication tests. Trigger this skill for any mention of...