RConsortium

RConsortium/pharma-skills

Settings file Claude Code

Agent settings declaring 17 allowed tools.

RConsortium/pharma-skills

Instructions file

Claude Code instructions for RConsortium/pharma-skills, covering pharmaskills — agent instructions, repository overview, directory structure, available skills and trigger phrases and agent guardrails.

RConsortium/pharma-skills

Skill Claude CodeCodex

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 performance", "eval the skills", or wants to measure whether a skill…

RConsortium/pharma-skills

Skill Claude CodeCodex

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 pattern analysis). Use this skill whenever the user asks to…

RConsortium/pharma-skills

Skill Claude CodeCodex

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.

RConsortium/pharma-skills

Skill Claude CodeCodex

Generate a concise weekly progress summary for the pharmaskills repository. Use this to summarize recent commits, PRs, and issues, then post the update to Slack and save it as a markdown file.

RConsortium/pharma-skills

Skill Claude CodeCodex

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 derivation workflows.

RConsortium/pharma-skills

Skill Claude CodeCodex

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, treatment-emergent flags, study day variables, baseline…

RConsortium/pharma-skills

Skill Claude CodeCodex

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 response, clinical benefit), or generate QC-ready R code…

RConsortium/pharma-skills

Skill Claude CodeCodex

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, population flags), or generate QC-ready R code following CDISC ADaM…

RConsortium/pharma-skills

Skill Claude CodeCodex

Derives an ADaM Time-to-Event Analysis Dataset (ADTTE) using the {admiral} R package. Use when a user needs to create ADTTE from SDTM event domains (AE, DS, CE) and ADSL, define event and censoring conditions, derive AVAL in days, and generate QC-ready R code following CDISC ADaM BDS-TTE conventions. Requires SDTM…

RConsortium/pharma-skills

Skill Claude CodeCodex

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, baseline values, change from baseline, visit windowing, or…

RConsortium/pharma-skills

Skill Claude CodeCodex

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 structural equations from ClinicalTrials.gov / literature…

RConsortium/pharma-skills

Skill Claude CodeCodex

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.

RConsortium/pharma-skills

Skill Claude CodeCodex

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, alpha spending, group sequential design, interim analysis…

RConsortium/pharma-skills

Skill Claude CodeCodex

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 framework. Produces executable, submission- ready R code with…

RConsortium/pharma-skills

Skill Claude CodeCodex

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 independent check of correctness, consistency, traceability…