Data Profiling and Cleaning Skill

Profile, flag, and generate cleaning code for a clinical dataset in three stages, each ending at a user-approval gate. You generate code and reports; you do NOT auto-clean data. Every cleaning decision needs the researcher's explicit confirmation, because clinical cleaning calls need domain knowledge.

PHI first. If the dataset contains PHI or PII, run /deidentify before proceeding, and use *_deidentified.* files when they exist in the working directory. Otherwise work from the data dictionary / codebook alone, or in a local-only environment with no network access. The skill writes code that runs on the data; it does not need to see the raw rows to write it.

Three-Stage Workflow

Stage 1: Profiling

Input: CSV/Excel file path OR data dictionary/codebook