Introduction
The following packages are maintained and supported under Metrum Research Group (MetrumRG)’s software development lifecycle (SDLC). Every MetrumRG package is linked with its respective user guide, website, vignettes, repository, and additional learning material. An introductory page is linked if the package is used extensively throughout the Expo.
All of our tools are free and open-source; however, they are built and optimized for use on our Metworx platform.
Torsten
Stan functions for Bayesian (Bayes) population pharmacokinetic (popPK) and pharmacokinetic and pharmacodynamic (PKPD) modeling.
Torsten is a fork of Stan containing additional Stan language functions to facilitate implementation of pharmacometric models. It plays a role analogous to prediction for popPK (PREDPP) for NONMEM® models. Given an event schedule and an ODE system, Torsten’s functions calculate amounts in each compartment. The current version includes:
- Specific linear compartment models:
- One compartment model with first order absorption.
- Two compartment model with elimination from and first order absorption into central compartment
- General linear compartment model described by a system of first-order linear ODEs.
- General compartment model described by a system of first order ODEs.
- Coupled model with PK forcing function described by a linear one or two compart- ment model and PD components solved by numerical ODE integration.
The models and data format are based on NONMEM®/NMTRAN/PREDPP conventions.
Torsten is currently intended for investigational purposes only. Validation testing is underway. A Torsten version validated for production use is expected to be released soon.
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MPN (MetrumRG Package Network) and pkgr
Create and manage curated, reproducible R package environments.
MPN is an open repository of ~1000 packages specific to PMX sourced from CRAN and GitHub which is freely available and accessible to all. pkgr is a command line tool to help project collaborators quickly identify and install all the packages relevant to a given project.
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bbr
Manage, track, and report modeling activities through simple R objects with a user-friendly interface between R and NONMEM®.
bbr is used to submit models, consume outputs and diagnostics, and iterate through models during development. It also provides simple model tagging options and model inheritance trees to support the replication and external review of your work.
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bbr.bayes
Manage, track, and report modeling activities through simple R objects with a user-friendly interface between R and NONMEM®.
bbr.bayes is used to create and submit NONMEM® models that use Bayesian estimation, create model summaries, and iterate through models during development. It also provides simple model tagging options and model inheritance trees to support the replication and external review of your work.
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mrgsolve
Simulate from ODE-based population PK/PD and quantitative systems pharmacology (QSP) models in R.
mrgsolve is used to create a model specification file consisting of R and C++ code that is parsed, compiled, and dynamically loaded into the R session. Input data is passed in and simulated data is returned as R objects, so disk access is never required during the simulation cycle after compiling. The resulting computational efficiency facilitates model exploration and application during both model development and decision-making phases of a drug development program.
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pmforest
Create forest plots for pharmacometrics to visualize variables of interest.
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pmplots
Create exploratory and diagnostic plots for pharmacometrics.
pmplots provides light wrappers around ggplot2, plotting code tailored for pharmacometric applications.
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pmtables
Create summary tables commonly used in pharmacometrics and turn any R table into a highly customized, publication-quality tex table.
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yspec
Data specification, wrangling, and documentation for pharmacometrics.
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