ospsuite R Documentation
The ospsuite package
The ospsuite package (repository OSPSuite-R) provides the functionality of loading, manipulating, and simulating the simulations created in the software tools PK-Sim and MoBi. Starting with version 13, it also offers a MoBi® interface for scripted work with MoBi projects, modules, and building blocks (e.g. loadMoBiProject, createMoBiModule, loadModuleFromPKML, createIndividualBuildingBlock, createExpressionProfileBuildingBlock).
The documentation of the package can be found here: https://www.open-systems-pharmacology.org/OSPSuite-R/
Installing the ospsuite package
The package requires R version 4.4 or higher (64bit). Installation instructions are provided here: https://www.open-systems-pharmacology.org/OSPSuite-R/#installation
Articles
Specific workflows and details regarding the ospsuite package can be found here: https://www.open-systems-pharmacology.org/OSPSuite-R/articles/
A typical scripted simulation workflow uses the following functions:
Load a simulation exported to *.pkml
loadSimulation
Find and modify model entities
getParameter, getAllParametersMatching, setParameterValues, getMolecule, getAllMoleculesMatching
Define the simulated outputs
addOutputs, clearOutputs
Run one or several simulations
runSimulation, runSimulations
Calculate PK parameters
calculatePKAnalyses, pkAnalysesAsDataFrame
Combine simulated and observed data for plotting
DataCombined, DefaultPlotConfiguration, plotIndividualTimeProfile, plotPopulationTimeProfile
Create individuals and populations
createIndividual, createPopulation
Work with MoBi projects and building blocks
loadMoBiProject, createMoBiModule, loadModuleFromPKML, createIndividualBuildingBlock, createExpressionProfileBuildingBlock
References
The list of functions defined in the package can be found here: https://www.open-systems-pharmacology.org/OSPSuite-R/reference/
Last updated