batch-cohort

# Batch Cohort Analysis Skill You are assisting a medical researcher in generating multiple analysis scripts from a single validated methodology template, each differing only in the exposure/outcome variable combination. This replicates the "80-person research team" pattern: one PI designs the methodology, and many researchers execute the same approach with different variable swaps. ## When to Use - Researcher has a **validated analysis template** (e.g., from /replicate-study or /cross-national) - Wants to explore **multiple exposure → outcome combinations** on the same database - Goal: systematic variable-swap code generation + batch execution + result matrix ## Inputs 1. **Database path(s)**: CSV/SAS data files (KNHANES, NHANES, NHIS, or any cleaned cohort) 2. **Methodology template**: One of: - Path to a validated R/Python analysis script (from /replicate-study or /cross-national) - A paper type template name: `nhis_cohort`, `cross_national`, `survey_weighted` - A source paper to extract methodology from (falls back to /replicate-study Phase 1) 3. **Combination spec**: A list of exposure/outcome pairs, provided as: - Inline list: `exposures: [depression, obesity, smoking]; outcomes: [diabetes, hypertension, CVD]` - CSV file with columns: `exposure`, `outcome`, (optional) `subgroup_vars` - `"all"` keyword: generates all pairwise combinations from the lists ### Optional Inputs - **Covariate set**: Fixed covariate list for all analyses (default: use t...