NMproject: Tidy, Reproducible, Script Based NONMEM projects in RStudio. A Step Toward Pharmacometric Industrialisation.
Sahota, Tarjinder (1), Ruau, David (2), Fox, Robert (3), Al-Huniti, Nidal (3)
(1) AstraZeneca, Quantitative Clinical Pharmacology, IMED, Cambridge, UK (2) AstraZeneca, Scientific Computing Solutions, GMD, Cambridge, UK (3) AstraZeneca, Quantitative Clinical Pharmacology, IMED, Gaithersburg, US.
Objectives: Modern computer systems should allow organisations and individuals to efficiently manage knowledge. Have you ever spent time implementing model code you later found out had already been implemented by someone else? Have you ever had to continue a colleague’s work but struggled to figure out what he/she did? Have you ever wasted time rerunning NONMEM and reproducing all post processing steps because of a small change to the dataset? Have you ever had trouble reproducing a plot because an R package may have been updated? We aim to develop an R package to overcome these challenges.
Methods: Two R packages have been created:
TidyProject: Directory and code management with a code repository interface.
NMproject: all functionality of TidyProject with a light interface to NONMEM from R for script based model development (requires installation of NONMEM and Perl speaks NONMEM (PsN)).
Installing NMproject will install both packages. They will soon be released on the Comprehensive R Archive Network (CRAN), but are currently available on GitHub via the following R command: devtools::install_github("tsahota/NMproject")
Results: AstraZeneca employees have successfully used NMproject to conduct NONMEM model development for over a year. Features include:
Tidy directory structure: Standardised, version controlled, directory structure for all NONMEM users.
Code library: Import NONMEM/R template scripts and functions into your project from a built-in code repository. Functionality to attach your own code repositories (can be simple directories of R scripts or NONMEM control streams). Search the code library using keywords, tags, or raw text search.
Private project library: Store R packages and version information alongside scripts in project directory. Aids in project reproducibility and portability.
Script based model development: Code your model development process using end-to-end R scripts. Switch between interactive and non-interactive mode.
Shiny run monitor: Shiny GUI interface for run management, monitoring and results comparison.
Conclusions: NMproject is a prototype of industrialised knowledge management for NONMEM and R users.