## All functions

addOutputInterval()
Adds an interval to the output schema of the simulation
addOutputs()
Adds the quantities as output into the simulation. The quantities can either be specified using explicit instances or using paths.
addUserDefinedPKParameter()
Adds and returns a User-Defined PK-Parameter to the managed list of PK-Parameters
AgingData
AgingData
allAvailableDimensions()
List all available dimensions in the OSPSuite platform
allPKParameterNames()
Returns the name of all pk parameters defined in the system
Application
Application
calculatePKAnalyses()
Calculates the pkAnalyses for all output values available in results.
calculateResiduals()
Calculate residuals for datasets in DataCombined
clearMemory()
Clears the memory used by all underlying objects
clearOutputIntervals()
Removes all intervals as well as all single time points from the output schema defined in simulation
clearOutputs()
Removes all selected output from the given simulation
CompareBy
How should comparison of entities be performed
convertUnits()
Convert datasets in DataCombined to common units
createDistributions()
Creates the parameter distributions based on the given individual individualCharacteristics
createImporterConfigurationForFile()
Create a DataImporterConfiguration for an XLS sheet
createIndividual()
Creates an individual using the PK-Sim Database
createIndividualCharacteristics()
Creates an individual using the PK-Sim Database.
createPopulation()
Creates an population using the PK-Sim Database
createPopulationCharacteristics()
Creates the population characteristics used to create a population
createSimulationBatch()
Creates and returns an instance of a SimulationBatch that can be used to efficiently vary parameters and initial values in a simulation
DataColumn
DataColumn
DataCombined
Object combining simulated and observed data
DataErrorType
Supported types of the error
DataImporterConfiguration
DataImporterConfiguration
DataRepository
DataRepository
DataSet
DataSet
dataSetToDataFrame() dataSetToTibble()
Converts a list of DataSet objects to a data.frame
DefaultPlotConfiguration
Plot configuration for OSP plots
.expandPath()
Returns the expanded path for path and ensure that encoding is applied properly
.getConcurrentSimulationRunnerResults()
Get SimulationResults from ConcurrentSimulationRunner
.getDimensionTask()
Return an instance of the .NET Task DimensionTask This is purely for optimization purposes
.getPathToPKSimInstallDir()
Tries to find the installation path for a specific version of PK-Sim. Searching is done in the following order:
1. Search via Windows registry entry

2. Search via file system in a guessed installation folder from the base.search.folder (fallback 1)

.getPathToPKSimInstallDirFromRegistry()
Tries to find the installation path for a specific version of PK-Sim from an Windows registry entry.
.getQuantityDisplayPaths()
Retrieves the display path of the quantity defined by path in the simulation
.parameterValueListFrom()
Converts a list of .NET ParameterValue into a list with 2 entries: paths, values. A 3rd optional entry units will be defined if the parameter addUnits is set to TRUE. Note: Units are only available for .NET object of type ParameterValueWithUnit
.savePKAnalysesToCSV()
Saves the pK-analyses to csv file
.savePopulationToCSV()
Saves the population to csv file
.saveResultsToCSV()
Saves the simulation results to csv file
.saveSensitivityAnalysisResultsToCSV()
Saves the simulation analysis results to csv file
.scaleQuantityValues()
Scale current values of quantities using a factor
.setQuantityValues()
Set values of quantity
.validateHasUnit()
Check if quantity can be represented in the unit
DotNetWrapper
Wrapper class for .NET objects
Entity
Entity
exportIndividualSimulations()
Export simulation PKMLs for given individualIds. Each pkml file will contain the original simulation updated with parameters of the corresponding individual.
exportPKAnalysesToCSV()
Saves the pK-analyses to csv file
exportPopulationToCSV()
Saves the population to csv file
exportResultsToCSV()
Saves the simulation results to csv file
exportSensitivityAnalysisResultsToCSV()
Saves the simulation analysis results to csv file
Formula TableFormula
Formula
Gender
Default genders defined in PK-Sim
getAllContainerPathsIn()
Retrieves the path of all containers defined in the container and all its children
getAllContainersMatching()
Retrieve all sub containers of a parent container (simulation or container instance) matching the given path criteria
getAllMoleculePathsIn()
Retrieves the paths of all molecules defined in the container and all its children
getAllMoleculesMatching()
Retrieve all molecules of a container (simulation or container instance) matching the given path criteria
getAllObserverPathsIn()
Retrieves the path of all observers defined in the container and all its children
getAllParameterPathsIn()
Retrieves the path of all parameters defined in the container and all its children
getAllParametersForSensitivityAnalysisMatching()
Retrieve all parameters of the given simulation matching the given path criteria and also potential candidate for sensitivity variation
getAllParametersMatching()
Retrieve all parameters of a container (simulation or container instance) matching the given path criteria
getAllQuantitiesMatching()
Retrieve all quantities of a container (simulation or container instance) matching the given path criteria
getAllQuantityPathsIn()
Retrieves the path of all quantities defined in the container and all its children
getAllStateVariableParametersPaths()
Get the paths of all state variable parameters of the simulation
getAllStateVariablesPaths()
Get the paths of all state variable quantities of the simulation
getBaseUnit()
Get base unit of a dimension
getContainer()
Retrieve a single container by path under the given container
getDimensionByName()
Get dimension by name
getDimensionForUnit()
Get dimension for a given unit
getMolecule()
Retrieve a single molecule by path in the given container
getOSPSuiteSetting()
Get the value of a global ospsuite-R setting.
getOutputValues()
Extracting simulated values
getParameter()
Retrieve a single parameter by path in the given container
getParameterDisplayPaths()
Retrieves the display path of the parameters defined by paths in the simulation
getQuantity()
Retrieve a single quantity by path in the given container
getQuantityValuesByPath()
Get the values of quantities in the simulation by path
getSimulationTree()
Get simulation tree
getStandardMoleculeParameters()
Returns a list containing all standard global parameters defined in a simulation for given moleculeName. These parameters are typically located directly under the container named after the moleculeName. For the list of standard parameters
getUnitsForDimension()
Get units for a given dimension
hasDimension()
Dimension existence
hasUnit()
Unit existence
HumanPopulation
Default human population defined in PK-Sim
importPKAnalysesFromCSV()
Loads the pK-analyses from csv file
importResultsFromCSV()
Imports the simulation results from one or more csv files
importSensitivityAnalysisResultsFromCSV()
Imports the simulation analysis results from one or more csv files
IndividualCharacteristics
IndividualCharacteristics
initPKSim()
Loads the PKSim.R that will enable create individual and create population workflows.
isExplicitFormulaByPath()
Is the value defined by an explicit formula
loadAgingDataFromCSV()
Loads aging data (typically generated from PK-Sim) i
loadDataImporterConfiguration()
Load DataImporterConfiguration from XML file.
loadDataSetFromPKML()
Loads data (typically observed data) from a PKML file and creates a DataSet from it. The pkml files are typically exported from PK-Sim or MoBi.
loadDataSetsFromExcel()
Load data sets from excel
loadPopulation()
Loads a population from a csv file and returns the population.
loadSimulation()
Load a simulation from a pkml file
messages
List of functions and strings used to signal error messages Extends the messages list from ospsuite.utils
MoleculeOntogeny
MoleculeOntogeny
MoleculeParameter
Standard molecule parameter names typically available in an endogenous molecule (enzyme, transporter etc...) coming from PK-Sim
ospDimensions
Supported dimensions defined as a named list
ospsuiteSettingNames
Names of the settings stored in ospsuiteEnv. Can be used with getOSPSuiteSetting()
pkAnalysesAsDataFrame() populationAsDataFrame()
Deprecated functions
ospUnits
Supported units defined as a named list of lists
OutputSchema
OutputSchema
OutputSelections
OutputSelections
Parameter
Parameter
ParameterRange
ParameterRange
pkAnalysesToDataFrame() pkAnalysesToTibble()
Convert the pk-Analysis to data frame
PKParameter
PKParameter
pkParameterByName()
Returns an instance of a PK-Parameter by name or NULL if the parameter by name is not found
PKParameterSensitivity
PKParameterSensitivity
plotIndividualTimeProfile()
Time-profile plot of individual data
plotObservedVsSimulated()
Observed versus predicted/simulated scatter plot
plotPopulationTimeProfile()
Time-values profile plot for population simulations
plotResidualsVsSimulated()
Residuals versus time scatter plot
plotResidualsVsTime()
Residuals versus time scatter plot
Population
Population
PopulationCharacteristics
PopulationCharacteristics
populationToDataFrame() populationToTibble()
Creates a data.frame containing one column for each parameter defined in the population
potentialVariableParameterPathsFor()
Returns an array of parameter path with one entry for each parameter that is used in the simulation and can potentially be used for sensitivity analysis
Quantity
Quantity
QuantityPKParameter
QuantityPKParameter
QuantitySelection
QuantitySelection
removeAllUserDefinedPKParameters()
Removes all User-Defined PK-Parameters that may have been added to the system
removeSimulationFromCache()
Removes a simulation from simulations cache.
resetSimulationCache()
Clears cache of loaded simulations
runSensitivityAnalysis()
Runs a sensitivity analysis
runSimulation()
Run a single simulation
runSimulationBatches()
Run simulation batches
runSimulations()
Runs multiple simulations concurrently.
saveDataSetToPKML()
Save the DataSet to pkml
saveSimulation()
Saves a simulation to pkml file
scaleParameterValues()
Scale current values of parameters using a factor
SensitivityAnalysis
SensitivityAnalysis
SensitivityAnalysisResults
SensitivityAnalysisResults
SensitivityAnalysisRunOptions
SensitivityAnalysisRunOptions
setMoleculeInitialValues()
Set molecule start values
setMoleculeScaleDivisors()
Set molecule scale divisors
setMoleculeValuesByPath()
Set molecule start values in the simulation by path
setOutputInterval()
Clears the output interval from the simulation and adds a new one.
setParameterValues()
Set values of parameters
setParameterValuesByPath()
Set the values of parameters in the simulation by path
setQuantityValuesByPath()
Set the values of quantities in the simulation by path
Simulation
Simulation
SimulationBatch
SimulationBatch
SimulationBatchOptions
SimulationBatchOptions
SimulationBatchRunValues
SimulationBatchRunValues
SimulationPKAnalyses
SimulationPKAnalyses
SimulationResults
SimulationResults
simulationResultsToDataFrame() simulationResultsToTibble()
Converts a SimulationResults objects to a data.frame
SimulationRunOptions
SimulationRunOptions
SimulationSettings
SimulationSettings
SnapshotParameter
SnapshotParameter
SolverSettings
SolverSettings
Species
Default species defined in PK-Sim
splitPopulationFile()
Loads a population from the csvPopulationFile and split the loaded population according to numberOfCores.
StandardContainer
Standard containers typically available in a PBPK simulation
StandardOntogeny
List of ontogeny supported in PK-Sim
StandardPath
Standard parameter paths typically available in a PBPK simulation
StandardPKParameter
Standard PK-Parameters types defined in OSPSuite This is only used to defined how a user defined PK Parameter should be calculated
toBaseUnit()
Converts a value given in a specified unit into the base unit of a quantity
toDisplayUnit()
Convert base unit to display unit
toPathArray()
Convert a path defined as string to a path array
toPathString()
Convert a path array to a path as string with entries separated by '|'
toUnit()
Converts a value given in base unit of a quantity into a target unit
uniqueEntities()
Extract Unique Elements of type 'Entity'
updatePKParameter()
Updates some properties of a PK-Parameter (displayName and displayUnit)
UserDefinedPKParameter
UserDefinedPKParameter
validateDimension()
Validate dimension
validateUnit()
Validate unit
ValuePoint
ValuePoint