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SkillsMP has collected 14 skills from RConsortium/pharma-skills. Open a skill to review its source and details.
Showing 14 of 14 collected skills.
Derives CDISC SDTM domains from raw clinical (EDC/eCRF) data using the {sdtm.oak} R package. Use when a user needs to map raw study data to SDTM Events (AE, CM, MH), Findings (VS, LB, EG), or Interventions (EX) domains following the sdtm.oak algorithm…
Derives an ADaM Tumor Response Analysis Dataset (ADRS) using the {admiral} and {admiralonco} R packages. Use when a user needs to create ADRS from SDTM RS domain data, derive RECIST 1.1 response parameters (overall response, confirmed response, best overall…
Parent skill for the admiral ADaM derivation family. Covers shared conventions used across all admiral child skills: library setup, pipe style, date derivation rules, flag variable conventions, and QC patterns. Route to a child skill for dataset-specific…
Generate a concise weekly progress summary for the pharma_skills repository. Use this to summarize recent commits, PRs, and issues, then post the update to Slack and save it as a markdown file.
End-to-end R workflow to simulate individual patient data (IPD) for a registered clinical trial using a g-formula causal-DAG simulator. Given an NCT ID with posted results and a protocol PDF, derives CRFs, builds an evidence-based causal DAG, parameterizes…
Simulates an independent statistical reviewer auditing a clinical trial submission package (SDTM, ADaM, TLG/TLF, SAP, CSR). Use when the user provides clinical trial datasets, tables, listings, figures, analysis outputs, or submission materials and wants an…
Derives an ADaM Subject-Level Analysis Dataset (ADSL) using the {admiral} R package and pharmaverse ecosystem. Use when a user needs to create ADSL from SDTM domains, derive standard subject-level variables (treatment dates, disposition, demographics,…
Design and simulate clinical trials using the TrialSimulator R package and produce a QC-ready build-order-spine report that pairs each block of code with rationale, parameters, and operating characteristics.
Auto-discover all skills with evals in RConsortium/pharma-skills, benchmark each with vs. without skill using matched isolated sessions, and post scored results to the linked GitHub issue. Use whenever someone says "run benchmarks", "compare skill…
Converts one or more GitHub Issues into standardized benchmark data using automated scripts. Use when a user provides an issue number or URL and wants to add it to the evaluation suite.
Derives ADaM Basic Data Structure (BDS) datasets using the {admiral} R package. Initial scope covers ADVS (vital signs) and ADLB (laboratory values). Use when a user needs to create a BDS findings dataset from SDTM domains, derive parameter assignments,…
Derives an ADaM Adverse Events Analysis Dataset (ADAE) using the {admiral} R package and pharmaverse ecosystem. Use when a user needs to create ADAE from SDTM AE and supporting domains, derive standard adverse event analysis variables (severity, seriousness,…
Design group sequential clinical trials for survival endpoints (OS, PFS, DFS) with interim analyses, spending functions, boundaries, multiplicity, and event/enrollment prediction. Triggers on: Phase 3 trial design, sample size/events for survival endpoints,…
Generate a combined benchmark analysis for the group-sequential-design skill by reading all benchmark GitHub issues, selecting the latest completed run per issue, and producing a structured three-section report (summary table + overall scorecard + failure…