PopkinR is an R package aiming at facilitating the development of non-linear mixed effects models with NONMEM.
It contains interactive web-applications based on shiny for:
- Post-processing of NONMEM runs results (
PMXploit) - Launch of NONMEM runs and editing control files (
PMXecute) - Exploration of NONMEM-like datasets (
PMXplore)
Reference: PopkinR: a suite of Shiny applications focused on the pharmacometrics workflow presented at PAGE 2018
# Install the latest version from GitHub
# install.packages('devtools')
# Install pmxploit package first
devtools::install_github('pnolain/pmxploit')
# Install PopkinR
devtools::install_github('pnolain/popkinr')library(popkinr)
# PMXploit
nonmem_toolbox()
# PMXploit with VPC feature
nonmem_toolbox(nonmem_exe = "/path/to/nonmem/run/nmfe74",
nmcheck_exe = "/path/to/nonmem/tr/NMTRAN.exe")
# PMXecute
nonmem_monitor(nonmem_exe = "/path/to/nonmem/run/nmfe74",
nmcheck_exe = "/path/to/nonmem/tr/NMTRAN.exe",
nonmem_parafile = "/path/to/nonmem/runfiles/mpilinux8.pnm")
# PMXecute (with PsN execute)
nonmem_monitor(nonmem_exe = "/usr/local/bin/execute",
nonmem_call = "{nonmem_exe} {control_file} -nodes={n_nodes}",
nmcheck_exe = "/path/to/nonmem/tr/NMTRAN.exe")
# PMXplore
dataset_exploration()
Together with the pmxploit package, brings interactivity to NONMEM runs post-processing analysis.
Dynamically generates corresponding R-code to most of the plots and tables provided by the application so it can be embedded in any R script.
library(popkinr)
# PMXploit
nonmem_toolbox()
# PMXploit with VPC feature
nonmem_toolbox(nonmem_exe = "/path/to/nonmem/run/nmfe74",
nmcheck_exe = "/path/to/nonmem/tr/NMTRAN.exe")
Application for launching and monitoring NONMEM runs on a local setup.
Provides control file generation functionalities for models with $PRIOR, $CHAIN processing or bootstrapping.
library(popkinr)
# PMXecute
nonmem_monitor(nonmem_exe = "/path/to/nonmem/run/nmfe74",
nmcheck_exe = "/path/to/nonmem/tr/NMTRAN.exe",
nonmem_parafile = "/path/to/nonmem/runfiles/mpilinux8.pnm")
# PMXecute (with PsN execute)
nonmem_monitor(nonmem_exe = "/usr/local/bin/execute",
nonmem_call = "{nonmem_exe} {control_file} -nodes={n_nodes}",
nmcheck_exe = "/path/to/nonmem/tr/NMTRAN.exe")Gif preview...
Application for exploratory data analysis of NONMEM-like datasets.
Provides interactive visualizations and summaries of dependent variables, dosing regimens and covariates (distributions, longitudinal evolution) and dataset manipulation functionalities.
library(popkinr)
# PMXplore
dataset_exploration()Gif preview...
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