knitr::opts_chunk$set(collapse = TRUE, comment = "#>", fig.path = 'man/figures/', fig.align = 'center', out.width = '80%', dev = 'png', dev.args = list(type = 'cairo'))
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:
PMXploit
)PMXecute
)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()
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")
popkinr::nonmem_monitor
Application for launching and monitoring NONMEM runs on a local setup.
Provides control file generation functionalities for models with $PRIOR and for $SIMULATION.
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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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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