pharma-skills

In the author's own words, from each skill's SKILL.md.

• admiral

  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.

  admiral/SKILL.md on GitHub (opens in a new tab)

• clinical-trial-ipd-sim

  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 priors, runs an R6 forward simulator, and calibrates marginal statistics to the publ…

  clinical-trial-ipd-sim/SKILL.md on GitHub (opens in a new tab)

• clinical-trial-simulation

  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.

  clinical-trial-simulation/SKILL.md on GitHub (opens in a new tab)

• group-sequential-design

  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 planning, or enrollment/event timeline prediction for clinical trials.

  group-sequential-design/SKILL.md on GitHub (opens in a new tab)

• rounding

  Audit R code that prepares CSR/TLF statistics for SAS-compatible rounding compliance (ties away from zero, round-once-at-display, fixed trailing-zero precision). Make sure to use this skill whenever the user asks to review, check, verify, or fix rounding, mentions SAS rounding, half-away-from-zero, display precision, trailing zeros, early rounding, mock tables showing 76 not 76.00, percentages of…

  rounding/SKILL.md on GitHub (opens in a new tab)

• sdtm-oak

  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 controlled terminology recoding, ISO 8601 date derivation, sequence numbering, and st…

  sdtm-oak/SKILL.md on GitHub (opens in a new tab)

• statistical-reviewer

  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, or data realism. Reviews denominators, populations, endpoints, multiplicity, saf…

  statistical-reviewer/SKILL.md on GitHub (opens in a new tab)

• benchmark-runner

  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 improves output quality.

  _automation/benchmark-runner/SKILL.md on GitHub (opens in a new tab)

• benchmark-summary

  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 update the benchmark summary, generate the benchmark analysis, summarize skill vs n…

  _automation/benchmark-summary/SKILL.md on GitHub (opens in a new tab)

• issue-to-eval

  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.

  _automation/issue-to-eval/SKILL.md on GitHub (opens in a new tab)

• weekly-summary

  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.

  _automation/weekly-summary/SKILL.md on GitHub (opens in a new tab)

• admiral-adae

  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 flags), or generate QC-ready R code following CDISC ADaM conventions. Requires SDTM…

  admiral/admiral-adae/SKILL.md on GitHub (opens in a new tab)

• admiral-adrs

  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 following CDISC ADaM and oncology conventions. Requires SDTM RS input data, ADSL wit…

  admiral/admiral-adrs/SKILL.md on GitHub (opens in a new tab)

• admiral-adsl

  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 conventions. Requires SDTM input data and an ADaM spec.

  admiral/admiral-adsl/SKILL.md on GitHub (opens in a new tab)

• admiral-adtte

  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 source domains, a completed ADSL, and an ADaM ADTTE specification that defines the…

  admiral/admiral-adtte/SKILL.md on GitHub (opens in a new tab)

• admiral-bds

  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 analysis flags, following CDISC ADaM conventions. Requires SDTM input data, an ADaM BD…

  admiral/admiral-bds/SKILL.md on GitHub (opens in a new tab)

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