The ospsuite-R package provides the functionality of loading, manipulating, and simulating the simulations created in the Open Systems Pharmacology Software tools PK-Sim and MoBi.
Please refer to the online documentation for more details on the package
The ospsuite-R package is compatible with version 3.6.x AND version 4.x.x of R. One of its dependency, rClr needs to be installed specifically for the targeted R version. Please follow the installation instructions below.
ospsuite requires following packages to be installed:
The release version of the package comes as a binary *.zip and can be downloaded from here.
The package also requires the Visual C++ Runtime that is installed with OSPS and can be manually downloaded here.
The ospsuite package has been tested under Linux distributions CentOS 7 and Ubuntu 18. Some functionality, such as creating individuals, is not available under Linux. Installation under Linux requires several prerequisites, the detailed instructions can be found in the Wiki. For other Linux distributions Docker containers can be used (Dockerfiles based on CentOS 7 and Ubuntu 18 are available under https://github.com/Open-Systems-Pharmacology/OSPSuite-R/releases )
You can clone the GIT repository and build the package from source.
git submodule update --init --recursiveto install all submodules
- Make sure you have ruby install and that it is available in your path
rake postcleanor simply double click on
postclean.bat. This will update all nuget packages and copy the dependencies in the package
In general, every workflow starts with loading a simulation that has been exported to the
*.pkml format. The method
loadSimulation() returns the corresponding simulation that is used as input of other methods. The user can then change values of parameters and initial conditions, run the simulation, and retrieve the simulated results.
library(ospsuite) # Load a simulation simFilePath <- system.file("extdata", "Aciclovir.pkml", package = "ospsuite") sim <- loadSimulation(simFilePath) # Get the parameter "Dose" doseParamPath <- "Applications|IV 250mg 10min|Application_1|ProtocolSchemaItem|Dose" doseParam <- getParameter(doseParamPath, sim) # Change the dose to 350mg. The values has to be converted to base unit, first newValue <- toBaseUnit(quantity = doseParam, values = 350, unit = "mg") setParameterValues(parameters = doseParam, values = newValue) # Simulate simResults <- runSimulation(simulation = sim) # Retrieve the results simulatedValues <- getOutputValues(simulationResults = simResults) # Plot time-concentration profile plot(simulatedValues$data$Time, simulatedValues$data$`Organism|PeripheralVenousBlood|Aciclovir|Plasma (Peripheral Venous Blood)`, type = "l", xlab = "Time [min]", ylab = "Concentration [µmol/l]")
More detailed description of the methods and the typical workflows can be found in the vignettes. You can see the list of all vignettes available for ospsuite by calling
vignette(package = "ospsuite")
To open a specific vignette, call
# Insert the name of the vignette you want to view as the argument vignette("introduction-ospsuite")
RStudio crashes when trying to load a workspace. The ospsuite package uses the features implemented in PK-Sim and MoBi by creating .NET objects (e.g. a simulation) and using them from R. These objects cannot be saved as part of the workspace and reloaded on next start. When trying to do so, RStudio simply crashes. There is no possibility to overcome this limitation. To prevent RStudio from crashing, make sure to disable the check-box “Restore .RData into workspace at startup” in the options of RStudio. Keep in mind that you can also change this setting for specific projects.
Everyone interacting in the Open Systems Pharmacology community (codebases, issue trackers, chat rooms, mailing lists etc…) is expected to follow the Open Systems Pharmacology code of conduct.
We encourage contribution to the Open Systems Pharmacology community. Before getting started please read the contribution guidelines. If you are contributing code, please be familiar with the coding standards.
OSPSuite-R is released under the GPLv2 License.
All trademarks within this document belong to their legitimate owners.