In this page, we present the installation procedure of the R-package lixoftConnectors that allow to run PKanalix 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 by the following R command:
install.packages(packagePath, repos = NULL, type="source", INSTALL_opts ="--no-multiarch")
with 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 and ggplot2 packages that may need to be installed from CRAN first using:
install.packages('RJSONIO')
install.packages('ggplot2')
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 = "pkanalix")
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 = "pkanalix", 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:
demoPath = '<userFolder>/lixoft/pkanalix/pkanalix2019R1/demos/1.basic_examples/' loadProject(paste0(demoPath ,'project_ivbolus.pkx')) runNCAEstimation() getNCAIndividualParameters()
where <userFolder> is the user’s home folder (on windows C:/Users/toto if toto is your username). These three commands should output the estimated NCA parameters.
