R-package installation and initialization

In this page, we explain the installation procedure of the R-package that allows to run Monolix from R.

Prerequisites

R version 3.0.0 or higher is required to use lixoftConnectors.

The lixoftConnectors package depends on the RJSONIO, gridExtra and ggplot2 packages that need to be installed from CRAN first using:

install.packages('RJSONIO')
install.packages('ggplot2')
install.packages('gridExtra')

Installation

The R package lixoftConnectors is located in the installation directory as tar.gz archive. It can be installed directly using Rstudio (Tools > Install packages > from package archive file) or with the following R command:

install.packages(packagePath, repos = NULL, type="source", INSTALL_opts ="--no-multiarch")

with the packagePath = ‘<installDirectory>/connectors/lixoftConnectors.tar.gz’ where <installDirectory> is the MonolixSuite installation directory.

With the default installation directory, the command is:

# for Windows OS
install.packages("C:/Program Files/Lixoft/MonolixSuite2024R1/connectors/lixoftConnectors.tar.gz", 
                 repos = NULL, type="source", INSTALL_opts ="--no-multiarch")

# for Mac OS
install.packages("/Applications/MonolixSuite2024R1.app/Contents/Resources/\
                  monolixSuite/connectors/lixoftConnectors.tar.gz",
                  repos = NULL, type="source", INSTALL_opts ="--no-multiarch")

Note that for MonolixSuite version 2023 and earlier, the path to use for Windows OS is different:

# for Windows OS (MonolixSuite version 2023)
install.packages("C:/ProgramData/Lixoft/MonolixSuite2023R1/connectors/lixoftConnectors.tar.gz", 
                 repos = NULL, type="source", INSTALL_opts ="--no-multiarch")

Note that for MonolixSuite version 2018, the R package is called MlxConnectors.

Initializing

When starting a new R session, you need to load the library and initialize the connectors with the following commands, specifying either “monolix”, “simulx”, or “pkanalix” for the software argument.

library(lixoftConnectors)
initializeLixoftConnectors(software = "monolix")

In some cases, it may be necessary to specify the path to the installation directory of the Lixoft suite. If no path is given, the one written in the <user home>/lixoft/lixoft.ini file is used (usually “C:/Program Files/Lixoft/MonolixSuite2024R1” for Windows or “C:/ProgramData/Lixoft/MonolixSuiteXXXX” where XXXX corresponds to the version of MonolixSuite for earlier versions)

library(lixoftConnectors) 
initializeLixoftConnectors(software = "monolix", path = "/path/to/MonolixSuite/")

When you initialize the connectors with one application (e.g. “monolix”) and then initialize it again with another one (e.g. “simulx”), there is a security check asking you to agree with the switch. To bypass this check and avoid having to answer “yes” manually, you can specify the option “force = TRUE”:

library(lixoftConnectors) 
initializeLixoftConnectors(software = "monolix", force = TRUE)

Verifying the installation is correct

To test if the installation is correct, you can load and run a demo project as shown:

demoPath <- getDemoPath()
loadProject(file.path(demoPath, "1.creating_and_using_models", "1.1.libraries_of_models", "theophylline_project.mlxtran"))
runScenario()
getEstimatedPopulationParameters()

These three commands should output the estimated population parameters (ka_pop, V_pop, Cl_pop, omega_ka, omega_V, omega_Cl, a, and b).