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analyze-stats

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Use when data needs statistical analysis. Runs reproducible Python/R code for Table 1, diagnostic accuracy, agreement, regression, survival, propensity score, survey-weighted and repeated-measures models, with publication tables. Sample size is /calc-sample-size; pooling studies is /meta-analysis.

skills/analyze-stats/SKILL.md

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# Statistical Analysis Skill

Generate reproducible code (Python preferred, R when necessary) for medical research analyses,
run it, and produce publication-ready tables and figures from its output.

## Data Privacy Check

Before reading any data file, check whether it might contain Protected Health Information (PHI):

1. If `*_deidentified.*` files exist in the working directory, use those.
2. If only raw CSV/Excel files exist, ask the user whether the data contain patient identifiers
   (names, national ID / RRN, contact details); if so, have them de-identify it first with
   `/deidentify`.
3. Proceed once the user confirms the data are de-identified or contain no PHI.
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