bio-clinical-biostatistics-cdisc-data

Installation
SKILL.md

Version Compatibility

Reference examples tested with: pyreadstat 1.2+, pandas 2.1+, numpy 1.26+. CDISC standards referenced: SDTM 2.0 / SDTMIG 3.4 (SDTM 3.0 / SDTMIG 4.0 in public review through April 2026); ADaMIG v1.3 (2021); OCCDS v1.1 (Nov 2021); BDS-for-TTE v1.0; Define-XML 2.1 (FDA-recommended for studies starting on/after March 15, 2023); Dataset-JSON v1.1 (Dec 2024; FDA Federal Register notice April 2025); Pinnacle 21 Community 4.0+; CORE (CDISC Open Rules Engine, 2021). Define-XML 2.1 FDA support began March 15, 2021 and is required for studies starting on/after March 15, 2023.

Before using code patterns, verify installed versions match. If versions differ:

  • Python: pip show <package> then help(module.function) to check signatures
  • R packages cited (essential for ADaM derivation): admiral (Roche/openpharma), metacore, metatools, xportr

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

CDISC SDTM and ADaM Data Handling

"Load clinical trial data" -> Parse CDISC SDTM domain files; build or consume ADaM analysis-ready datasets; preserve subject-level and event-level structure; respect traceability and validation expectations for regulatory submission.

  • Python: pyreadstat.read_xport(), pd.read_sas(), pd.merge()
  • R: haven::read_xpt(), admiral for ADaM derivation, Pinnacle21 or CORE for validation

Aggregation Strategy Taxonomy -- Choose the Right Question

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