From 125062aa69428e559230e1e3f10f4fa69f015bc9 Mon Sep 17 00:00:00 2001 From: Andrew Santulli Date: Sat, 30 Mar 2024 11:16:52 -0400 Subject: [PATCH] update readme --- README.Rmd | 62 +++++++++++++++++++++++++++++++++++ README.md | 96 ++++++++++++++++++++++++++++++++++++++++++++++++++++-- 2 files changed, 155 insertions(+), 3 deletions(-) create mode 100644 README.Rmd diff --git a/README.Rmd b/README.Rmd new file mode 100644 index 0000000..4af44af --- /dev/null +++ b/README.Rmd @@ -0,0 +1,62 @@ +--- +title: "nonmem2mrgsolve" +output: github_document +--- + +```{r setup, include=FALSE} +knitr::opts_chunk$set(warning=FALSE, message=FALSE, eval=FALSE) # echo = FALSE +``` + +## 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: +```{r} +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: +```{r} +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)](https://mrgsolve.org/blog/posts/2023-update-validation.html). + +## Usage Statement + +```{r} +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](https://github.com/Andy00000000000/nonmem2mrgsolve/issues) or to reach out for help on the [Discussion Board](https://github.com/Andy00000000000/nonmem2mrgsolve/discussions). + +## Our Team + +[Enhanced Pharmacodynamics, LLC (ePD)](https://www.epd-llc.com/) 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](https://www.linkedin.com/in/don-mager-2652615/) and [Dr. Scott A. Van Wart](https://www.linkedin.com/in/scott-van-wart-2b6002a/). + +[Finch Studio](https://finchstudio.io/) 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](https://www.linkedin.com/in/mohamed-ismail-bb54a367/). + +nonmem2mrgsolve was developed at ePD by [Andrew Santulli](https://www.linkedin.com/in/andrew-santulli-219034156/). diff --git a/README.md b/README.md index d0ba1ad..be4d931 100644 --- a/README.md +++ b/README.md @@ -1,3 +1,93 @@ -# nonmem2mrgsolve -# Run the command below within R to install: -# devtools::install_github("Andy00000000000/nonmem2mrgsolve") +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: + +``` r +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: + +``` r +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)](https://mrgsolve.org/blog/posts/2023-update-validation.html). + +## Usage Statement + +``` r +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](https://github.com/Andy00000000000/nonmem2mrgsolve/issues) or +to reach out for help on the [Discussion +Board](https://github.com/Andy00000000000/nonmem2mrgsolve/discussions). + +## Our Team + +[Enhanced Pharmacodynamics, LLC (ePD)](https://www.epd-llc.com/) 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](https://www.linkedin.com/in/don-mager-2652615/) +and [Dr. Scott A. Van +Wart](https://www.linkedin.com/in/scott-van-wart-2b6002a/). + +[Finch Studio](https://finchstudio.io/) 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](https://www.linkedin.com/in/mohamed-ismail-bb54a367/). + +nonmem2mrgsolve was developed at ePD by [Andrew +Santulli](https://www.linkedin.com/in/andrew-santulli-219034156/).