nonmem2mrgsolve

Purpose

Provide an R package that automates NONMEM to mrgsolve translation to reduce human errors and improve efficiency.

Introduction

Pharmacometricians often utilize multiple software, with NONMEM (ICON plc, Dublin, Ireland) widely regarded as the current gold standard for population pharmacokinetic (PK) and pharmacokinetic-pharmacodynamic (PK-PD) modeling. While NONMEM has the ability to simulate, it is often more convenient and practical to perform simulations using free open-source software such as R which can also perform post-processing of the output.A popular pharmacometrics-orientated R package for solving ODE systems is mrgsolve. Although mrgsolve has built-in functionality to streamline translation, to the best of our knowledge a previously-developed and publicly-available R package for fully automated NONMEM to mrgsolve translation does not exist.

Installation

If not already installed, install R. Then within R run the following command:

devtools::install_github("Andy00000000000/nonmem2mrgsolve")

Getting Started

Full work-through examples will be created shortly, but in the meantime assume that a NONMEM run has finished estimating and has explicitly-defined ODEs. The ctl and ext files are both named pbpk-101 and are located at C:/Documents/NONMEM/Project.

Load R and run:

setwd("C:/Documents/NONMEM/Project") # set the working directory to where the NONMEM files are located
library(nonmem2mrgsolve)             # load the nonmem2mrgsolve package
nonmem2mrgsolve("pbpk-101")          # run the nonmem2mrgsolve function with default settings

The resulting mrgsolve code will be wrote to mrgsolve-code-V0_pbpk-101.R within the C:/Documents/NONMEM/Project folder. The user should then validate the translation, for which there is an intuitive and established framework (Here).

Usage Statement

nonmem2mrgsolve::nonmem2mrgsolve(
  filename = "nonmem-model.ctl", # String of the NONMEM model name with or without the .ctl extension
  dir = "./folder",              # String of the directory path to the NONMEM files (if not already given in the file name input or the working directory already set)
  sigdig = NULL,                 # Numeric of the number of significant digits to round non-fixed thetas and etas to; default NULL for no rounding
  write = T,                     # [T or F] for whether to write the resulting mrgsolve code to an R file
  return.orig = F,               # [T or F] for whether to return the original NONMEM ctl and ext (or cnv) files to the R environment
  out.filename = NULL,           # String of the name for the mrgsolve output file without the .R extension; NULL for default naming
  use.cnv = F                    # [T or F] for whether to use the NONMEM cnv file for parameter estimates instead of the ext file
)

Getting Help

Please feel free to report problems using the Issue Tracker or to reach out for help on the Discussion Board.

Our Team

Enhanced Pharmacodynamics, LLC (ePD) is a contract research organization that assists clients with the design and implementation of model-informed drug development strategies in a broad range of therapeutic areas. The executive management team is led by Dr. Donald E. Mager and Dr. Scott A. Van Wart.

Finch Studio is an integrated modeling environment for pharmacometricians, clinical pharmacologists, and other team members to visualize, develop, and organize PK/PD models and data. It includes a modern NONMEM code editor and workbench, interactive data tables and visualizations, and a PK/PD model library. The development team is led by Dr. Mohamed Ismail.

nonmem2mrgsolve was developed at ePD by Andrew Santulli.

Andy00000000000 / nonmem2mrgsolve