Svetlana Freiberga 1, Georges Etté 1, Arnaud Gaby 1, Pēteris Prūsis 1, Joakim Hellner 1, Mounika Suddapalli 1
1 Pharmetheus (Uppsala, Sweden)
Objectives:
The process of creating analysis-ready data deliverables is a vital part of any pharmacometrics workflow, but is prone to being slow, repetitive, and full of manual steps. For every new study, programmers might often be required to rebuild the same fundamentals – specifications, folder structures, and report templates from scratch. This is time-consuming and makes it difficult to adhere to internal or industry standards. To support data programmers in this process, while enforcing adherence to standards and maintaining high quality, Pharmetheus has developed “rock”, an R Shiny application. “rock” streamlines everything from drafting data specifications to generating ready-to-use programming environments. It helps standardize workflows and ensures reproducibility and full traceability while retaining flexibility. “rock” brings programmers and modelers together in a shared, version-controlled framework that adapts to evolving project requirements. It’s not just about automation; it’s about building smart tools people actually want to use.
Methods:
Specification form – Users can create and customize data specifications using pre-defined templates for various analysis types. Variables can be added, edited, or removed, with detailed metadata including definitions, units, rounding, dependencies, and derivations.
Source data integration – Users can upload and manage different types of source data. The system tracks each variable’s origin, including study, file, and variable mappings, ensuring full transparency. When updated source files are received, the system allows for near-instant replacement. This rapid replacement mechanism is a key factor in ensuring reproducibility, allowing the user to simply update the source data and re-execute the entire programming process.
Data programming environment – “rock” generates a structured R/LaTeX environment with predefined directories, R script placeholders, and LaTeX templates for PDF report generation. This standardized framework allows documentation to be seamlessly integrated with the programming code and provides a structure which facilitates easier handover between team members.
Automated sanity checks – Provides quick overview of data and specification consistency.
Version control and traceability – All edits, derivations, and updates are tracked, maintaining a clear audit trail.
Results:
Using “rock” in project workflow has severely decreased time spent starting from drafting data specifications to generating ready-to-use programming environments as well as the quality control process of the analysis-ready data deliverables. Internal Pharmetheus estimates show that the efficiency of drafting data specifications and the quality control process for analysis-ready data deliverables has increased by ~50%. “rock” helps ensure that project adheres to necessary standards and maintains a high level of quality while allowing for complete reproducibility and traceability. “rock” is a practical solution designed around day-to-day challenges, making workflows more efficient, transparent, and scalable.
Conclusion:
Using “rock” as the foundation for creating deliverables provides a robust framework that eases the project lifecycle for data programmers, quality controllers as well as modelers. Its standardized structure simplifies collaboration and handovers, while strict adherence to principles of reproducibility ensures that deliverables can be reliably regenerated from updated source data. Furthermore, built-in version control contributes to full traceability, supporting transparency and accountability throughout the project development. “rock’s” extensible design allows teams to incorporate additional specification templates as needed, and its flexibility in supporting diverse programming report formats makes it adaptable to a wide range of project requirements. Together, these advantages make “rock” a powerful solution for consistent, traceable, and high-quality deliverable creation.
Reference: PAGE 34 (2026) Abstr 12091 [www.page-meeting.org/?abstract=12091]
Poster: Software Demonstration