rconsortium/pharma-skills
13 skills
$npx skills add rconsortium/pharma-skillsSkillInstalls
admiralParent 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 QCadmiral-adaeDerives 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 standaradmiral-adslDerives 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 varadmiral-bdsDerives 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 datbenchmark-runnerAuto-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 whenevebenchmark-summaryGenerate 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-sectclinical-trial-ipd-simEnd-to-end R/pharmaverse 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 protocol + results, dericlinical-trial-simulationDesign 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 charactergroup-sequential-designDesign group sequential clinical trials for survival endpoints (OS, PFS, DFS) with interim analyses, spending functions, boundaries, multiplicity, and event/enrollment prediction. Triggers on: Phase 3issue-to-evalConverts 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.sdtm-oakDerives 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 Intervenstatistical-reviewerSimulates 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, figureweekly-summaryGenerate 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.