Clinical Trial Analysis: SDTM to ADaM Pipeline

A full end-to-end CDISC-compliant clinical trial analysis pipeline built in R using the pharmaverse admiral package.

🔗 Live Report

👉 View the full rendered analysis here

Overview

This project demonstrates a production-ready ADaM dataset construction pipeline and regulatory-standard TLF generation for a Phase III clinical trial.

ADaM Datasets Constructed

Dataset	Description	Key Derivations
ADSL	Subject-Level Analysis	Treatment vars, population flags, study dates, age groups
ADAE	Adverse Events	TEAE flag, seriousness, severity grade, study day
ADVS	Vital Signs	Baseline, change from baseline, % change

Tables, Listings & Figures (TLFs)

• Table 1 — Demographic & Baseline Characteristics
• Table 2 — Treatment-Emergent Adverse Events by System Organ Class
• Table 3 — SAE Seriousness & Severity Summary
• Figure 1 — TEAE Incidence by SOC and Treatment Group
• Figure 2 — Mean Change from Baseline in Systolic Blood Pressure
• Figure 3 — Kaplan–Meier Time to First TEAE

Tech Stack

• R + Quarto
• admiral — ADaM derivations
• haven — SAS .xpt read/write
• gtsummary — Clinical summary tables
• survival + survminer — Kaplan–Meier curves
• ggplot2 — Figures

Project Structure

clinical-trial-adam/
├── clinical_trial_adam.qmd   # Full analysis source
├── index.html                # Rendered report (GitHub Pages)
├── R/
│   ├── derive_adsl.R
│   ├── derive_adae.R
│   └── derive_advs.R
└── data/                     # Not committed — patient data stays local
    ├── sdtm/
    └── adam/

Standards Compliance

• CDISC ADaM Implementation Guide
• CDISC SDTM Implementation Guide
• FDA Study Data Technical Conformance Guide
• Pharmaverse ecosystem

Author

Ndoh Penn