rbabylon is an R interface for running babylon. babylon is (will be) a complete solution for managing projects involving modeling and simulation with a number of software solutions used in pharmaceutical sciences. Currently, only NONMEM modeling is supported, though there are plans to add Stan and other modeling software as well. You can get more detailed information on babylon (the underlying CLI tool) here.
rbabylon is intended to help scientists manage the entire modeling workflow from within R. Users can submit models, consume outputs and diagnostics, and iterate on models. Furthermore, workflow tools–like simple tagging of models and model inheritence trees–make reproducibility and external review much more streamlined.
Installation
You can install the latests released version of rbabylon via MPN snapshots from any snapshot date after 2020-03-07.
You can also install development versions of rbabylon by downloading the source files for the latest version from https://s3.amazonaws.com/mpn.metworx.dev/releases/rbabylon/ or get the latest development version from GitHub with:
# install.packages("devtools")
devtools::install_github("metrumresearchgroup/rbabylon", ref = "develop")Documentation
You can find documentation and a “Getting Started” vignette that shows users how to set up rbabylon and demonstrates the basic modeling workflow here.
There are several other vignettes, and more are being added as new functionality is rolled out. A complete list can be found here.
Featured Vignettes
-
Getting Started with rbabylon – Some basic scenarios for modeling with NONMEM using
rbabylon, introducing you to its standard workflow and functionality. -
Using the based_on field – How to use the
based_onfield to track a model’s ancestry through the model development process, as well how to leverageconfig_log()to check whether older models are still up-to-date. -
Creating a Model Summary Log – How to use
summary_log()to extract model diagnostics like the objective function value, condition number, and parameter counts.
Development
rbabylon uses pkgr to manage development dependencies and renv to provide isolation. To replicate this environment,
clone the repo
install pkgr
run
pkgr install
Then, launch R with the repo as the working directory (open the project in RStudio). renv will activate and find the project library.
