isabella232 / rnmimport

Tools for importing and manipulating NONMEM data

RNMImport

NONMEM is a FORTRAN application for fitting mixed effects models. NONMEM licenses are available from ICON Development Solutions. Models are specified as plain text files called control files. The control file contains blocks corresponding to components of the model. Model results are presented as plain text files. These input and output files can be imported into R by RNMImport to facilitate model modification, model diagnostics, model interpretation and reporting.

# install devtools for devtools::install_github
install.packages("devtools")
library(devtools)
# install RNMImport
install_github("MangoTheCat/RNMImport")
library(RNMImport)

A NONMEM execution including both input files and results files can be read using importNm. The imported object is S4 class 'NMRun'. Various methods are available for extracting the model information.

theo1 <- importNm(conFile = "theoph.con", 
    path = system.file(package = "RNMImport", "examples", "theoph"))
slotNames(theo1)

The dataset can be extracted using nmData. This contains the input data, and the model residuals and other records requested when defining the model.

head(nmData(theo1))

Model parameters can be extracted using methods corresponding to the parameter type.

getThetas(theo1)
getOmegas(theo1)
getSigmas(theo1)