popkinr

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

Installation

# 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')

Getting started with the applications

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()

PMXploit popkinr::nonmem_toolbox

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")

PMXecute popkinr::nonmem_monitor

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")

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PMXplore popkinr::dataset_exploration

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()

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