Package index • ospsuite

All functions

AgingData: AgingData

Application: Application

CompareBy: How should comparison of entities be performed

DataAggregationMethods: Names of aggregation available for plotPopulationTimeProfile()

DataColumn: DataColumn

DataCombined: Object combining simulated and observed data

DataErrorType: Supported types of the error

DataImporterConfiguration: DataImporterConfiguration

DataRepository: DataRepository

DataSet: DataSet

DefaultPlotConfiguration: Plot configuration for OSP plots

DotNetWrapper: Wrapper class for .NET objects

Entity: Entity

Formula TableFormula: Formula

Gender: Default genders defined in PK-Sim

HumanPopulation: Default human population defined in PK-Sim

IndividualCharacteristics: IndividualCharacteristics

MoleculeOntogeny: MoleculeOntogeny

MoleculeParameter: Standard molecule parameter names typically available in an endogenous molecule (enzyme, transporter etc...) coming from PK-Sim

OutputSchema: OutputSchema

OutputSelections: OutputSelections

PKParameter: PKParameter

PKParameterSensitivity: PKParameterSensitivity

Parameter: Parameter

ParameterRange: ParameterRange

Population: Population

PopulationCharacteristics: PopulationCharacteristics

Quantity: Quantity

QuantityPKParameter: QuantityPKParameter

QuantitySelection: QuantitySelection

SensitivityAnalysis: SensitivityAnalysis

SensitivityAnalysisResults: SensitivityAnalysisResults

SensitivityAnalysisRunOptions: SensitivityAnalysisRunOptions

Simulation: Simulation

SimulationBatch: SimulationBatch

SimulationBatchOptions: SimulationBatchOptions

SimulationBatchRunValues: SimulationBatchRunValues

SimulationPKAnalyses: SimulationPKAnalyses

SimulationResults: SimulationResults

SimulationRunOptions: SimulationRunOptions

SimulationSettings: SimulationSettings

SnapshotParameter: SnapshotParameter

SolverSettings: SolverSettings

Species: Default species defined in PK-Sim

StandardContainer: Standard containers typically available in a PBPK simulation

StandardOntogeny: List of ontogeny supported in PK-Sim

StandardPKParameter: Standard PK-Parameters types defined in OSPSuite This is only used to defined how a user defined PK Parameter should be calculated

StandardPath: Standard parameter paths typically available in a PBPK simulation

UserDefinedPKParameter: UserDefinedPKParameter

ValuePoint: ValuePoint

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

allAvailableDimensions(): List all available dimensions in the OSPSuite platform

allPKParameterNames(): Returns the name of all pk parameters defined in the system

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

convertSnapshot(): Convert between snapshot and project formats

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

dataSetToDataFrame() dataSetToTibble(): Converts a list of DataSet objects to a data.frame

.expandPath(): Returns the expanded path for path and ensure that encoding is applied properly

.gatherFiles(): Gather files and files from folders to one location

.getConcurrentSimulationRunnerResults(): Get SimulationResults from ConcurrentSimulationRunner

.getOspDimensions(): get OSP Dimensions from OSPSuite.Dimensions.xml data

.getOspUnits(): get OSP Units from OSPSuite.Dimensions.xml data

.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

.parseDimensionsXML(): parse OSPSuite.Dimensions.xml containing dimensions and units

.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

.setEndSimulationTime(): Set end time of the simulation

.setQuantityValues(): Set values of quantity

.validateHasUnit(): Check if quantity can be represented in the unit

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

exportSteadyStateToXLS(): Export steady-state to Excel in the format that can be imported in MoBi.

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

getMolWeightFor(): Retrieve molecular weight for a quantity's molecule

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

getSteadyState(): Get the steady-state values of species and state variable parameters.

getUnitsForDimension(): Get units for a given dimension

hasDimension(): Dimension existence

hasUnit(): Unit existence

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

initPKSim(): Loads the PKSim.R dll 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

ospDimensions: Supported dimensions defined as a named list

ospUnits: Supported units defined as a named list of lists

ospsuiteSettingNames: Names of the settings stored in ospsuiteEnv. Can be used with getOSPSuiteSetting()

pkAnalysesAsDataFrame() populationAsDataFrame(): Deprecated functions

pkAnalysesToDataFrame() pkAnalysesToTibble(): Convert the pk-Analysis to data frame

pkParameterByName(): Returns an instance of a PK-Parameter by name or NULL if the parameter by name is not found

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

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

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

runSimulationBatches(): Run simulation batches

runSimulations(): Runs multiple simulations concurrently.

runSimulationsFromSnapshot(): Run Simulations From Snapshot Files

saveDataSetToPKML(): Save the DataSet to pkml

saveSimulation(): Saves a simulation to pkml file

scaleParameterValues(): Scale current values of parameters using a factor

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.

setOutputs(): Set outputs

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

simulationResultsToDataFrame() simulationResultsToTibble(): Converts a SimulationResults objects to a data.frame

splitPopulationFile(): Loads a population from the csvPopulationFile and split the loaded population according to numberOfCores.

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)

validateDimension(): Validate dimension

validateUnit(): Validate unit