In this page, we present the installation procedure of the R-package that allow to run Simulx from R.
Installation
The R package lixoftConnectors is located in the installation directory as tar.gz ball. 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:/ProgramData/Lixoft/MonolixSuite2023R1/connectors/lixoftConnectors.tar.gz",
repos = NULL, type="source", INSTALL_opts ="--no-multiarch")
# for Mac OS
install.packages("/Applications/MonolixSuite2023R1.app/Contents/Resources/\
monolixSuite/connectors/lixoftConnectors.tar.gz",
repos = NULL, type="source", INSTALL_opts ="--no-multiarch")
The lixoftConnectors package depends on the RJSONIO package that may need to be installed from CRAN first using:
install.packages('RJSONIO')
R version 3.0.0 or higher is required to install lixoftConnectors.
Initializing
When starting a new R session, you need to load the library and initialize the connectors with the following commands
library(lixoftConnectors) initializeLixoftConnectors(software = "simulx")
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:/ProgramData/Lixoft/MonolixSuiteXXXX” for Windows). where XXXX corresponds to the version of MonolixSuite
library(lixoftConnectors) initializeLixoftConnectors(software = "simulx", path = "/path/to/MonolixSuite/")
Making sure the installation is ok
To test if the installation is ok, you can load and run a project from the demos as on the following:
# load and initialize the API library(lixoftConnectors) initializeLixoftConnectors(software="simulx") # Get the project. <UserName> is the user's home folder (on windows C:/Users/toto if toto is your username). demoPath = '<UserName>/lixoft/simulx/simulx2020R1/demos/' project <- paste0(demoPath, "2.models/longitudinal.smlx") loadProject(projectFile = project) # Run the simulation runSimulation() # The results are accessible through the function getSimulationResults() # The results for the output is the list res and TS is one of the outputs head(getSimulationResults()$res$TS) id time TS 1 1 0 10.00000 2 1 1 11.04939 3 1 2 12.20862 4 1 3 13.48915 5 1 4 14.90359 6 1 5 16.46585
