## 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()

Returns the name of all available dimensions defined in the OSPSuite platform

AllMatchingMethod

Names of the .NET container tasks of the type "AllXXXMatching"

AllPathsInMethod

Names of the .NET container tasks of the type "AllXXXPathsIn"

allPKParameterNames()

Returns the name of all pk parameters defined in the system

ApiConfig

ApiConfig

Application

Application

Cache

Cache

calculatePKAnalyses()

Calculates the pkAnalyses for all output values available in results.

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

Container

Container

createDistributions()

Creates the parameter distributions based on the given individual individualCharacteristics

createIndividual()

Creates an individual using the PKSim Database

createIndividualCharacteristics()

Creates an individual using the PKSim Database.

createPopulation()

Creates an population using the PKSim 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

DataErrorType

Supported types of the error

DataImporterConfiguration

DataImporterConfiguration

DataRepository

DataRepository

DataSet

DataSet

dataSetToDataFrame()

Converts a list of DataSet objects to a data.frame

.getConcurrentSimulationRunnerResults()

Get SimulationResults from ConcurrentSimulationRunner

.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 filesystem in a guessed installation folder from the base.search.folder (fallback 1)

.getPathToPKSimInstallDirFromFileSystem()

Tries to find the installation path for a specific version of PK-Sim via the filesystem. Searching is done in the following order:

1. Search via filesystem in a guessed installation folder from the base.search.folder

2. Search via filesystem for PKSim.exe recursively from the defined base.search.folder (fallback)

.getPathToPKSimInstallDirFromRegistry()

Tries to find the installation path for a specific version of PK-Sim from an Windows registry entry.

.ImporterErrorTypeToDataSetErrorType

Mapping of string representation for the error types supported by DataSet to the values supported in the importer configuration

.loadDataRepositoryFromPKML()

Loads a data repository (typically observed data) from a PKML file and returns the loaded observed data. The pkml files are typically exported from PK-Sim or MoBi

DotNetWrapper

DotNetRwapper

encodeUnit()

This is required to ensure that we have no issue using the mu symbol in different OS See https://github.com/Open-Systems-Pharmacology/OSPSuite-R/issues/476 for details

Entity

Entity

enum()

Create an enumeration to be used instead of arbitrary values in code.

enumGetValue()

Return the value that is stored under the given key. If the key is not present, an error is thrown.

enumHasKey()

Check if an enum has a certain key.

enumKeys()

Return all keys of an enum

enumPut()

Add a new key-value pairs to an enum.

enumRemove()

Remove an entry from the enum.

enumValues()

Return the values stored in an enum

expandPath()

Returns the expanded path for path and ensure that encoding is applied properly

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

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

getAllEntitiesMatching()

Retrieves all entities of a container (simulation or container instance) matching the given path criteria.

getAllEntityPathsIn()

Retrieves all path of entities defined within the container (simulation or container instance)

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

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

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()

Returns the an instance of the dimension with the given name if found or NULL otherwise

getDimensionForUnit()

Returns the name of dimension that can be used to support the given unit or null if the dimension cannot be found

getDimensionsEnum()

#'Function to return an enum of all available dimensions

getDimensionTask()

Return an instance of the .NET Task DimensionTask This is purely for optimization purposes

getEntity()

Retrieve a single entity by path in the given container

getEnumKey()

Get the key mapped to the given value in an enum

getMolecule()

Retrieve a single molecule by path in the given container

getNetTask()

Returns an instance of the specified .NET Task

getOSPSuiteSetting()

Get the value of a global ospsuite-R setting.

getOutputValues()

Returns the simulated values for the selected outputs (e.g molecules or parameters)

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

getPropertyValue()

Returns the value of property named propertyName from .NET object instance netObject

getPropertyValues()

Returns a list containing all properties propertyName from the .NET objects netObjects

getQuantity()

Retrieve a single quantity by path in the given container

getQuantityDisplayPaths()

Retrieves the display path of the quantity defined by path in the simulation

getSimulationTree()

Given a simulation file path or an instance of a simulation, traverses the simulation structure and returns a tree like structure allowing for intuitive navigation in the 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

getUnitsEnum()

Loop through dimensions and build a list containing an enum of all units available for each dimension

getUnitsForDimension()

Returns a vector containing all units defined in the dimension

hasDimension()

Dimension existence

hasUnit()

Unit existence

HumanPopulation

Default human population defined in PK-Sim

ifNotNull()

ifnotnull

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

initPackage()

Load the OSPSuite R to .NET Binding

initPKSim()

Loads the PKSim.R that will enable create individual and create population workflows.

Interval

Interval

isOfType()

Check if the provided object is of certain type

loadAgingDataFromCSV()

Loads aging data (typically generated from PK-Sim) i

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()

loadPopulation()

Loads a population from a csv file and returns the population.

loadSimulation()

Loads a simulation from a pkml file and returns the simulation. If the passed simulation file has been loaded before, the simulation is not loaded again but a cached object is returned. This behavior can be overridden.

Molecule

Molecule

MoleculeOntogeny

MoleculeOntogeny

MoleculeParameter

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

netEnumName()

Retrieves the name of the constant in the specified enumeration that has the specified value.

ObjectBase

ObjectBase

ospDimensions

Supported dimensions defined as a named list

ospUnits

Supported units defined as a named list of lists

OutputSchema

OutputSchema

OutputSelections

OutputSelections

Parameter

Parameter

ParameterRange

ParameterRange

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

pkAnalysesAsDataFrame()

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

Population

Population

populationAsDataFrame()

Creates a data.frame containing one column for each parameter defined in the population

PopulationCharacteristics

PopulationCharacteristics

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

Printable

Printable

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()

runSensitivityAnalysis()

Runs a sensitivity analysis

runSimulation()

DEPRECATED runSimulations should be used in favor of runSimulation. The latter will be removed in future releases Runs one simulation (individual or population) and returns a SimulationResults object containing all results of the simulation.

runSimulationBatches()

Run simulation batches

runSimulations()

Runs one simulation (individual or population) and returns a SimulationResults object containing all results of the simulation. Alternatively if multiple simulations are provided, they will be run concurrently. This feature is only supported for individual simulation

saveDataSetToPKML()

Save the DataSet to pkml

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

saveSimulation()

Saves a simulation to pkml file

scaleParameterValues()

Scale current values of parameters using a factor

scaleQuantityValues()

Scale current values of quantities 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

setQuantityValues()

Set values of quantity

setQuantityValuesByPath()

Set the values of parameters in the simulation by path

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

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()

Converts a value given in base unit of a quantity into the display unit of a quantity

toList()

Make sure the object is a list

toObjectType()

Transforms a single .NET object or a list of .NET Object to their corresponding wrapper class in R. Note that if the object is a single object, NULL will be returned if the .NET object is null. This allows semantic equivalence between .NET and R

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

validateEnumValue()

Check if value is in the given enum. If not, stops with an error.

validateIsOfType()

Check if the provided object is of certain type. If not, stop with an error.

validateUnit()

Validate unit

ValuePoint

ValuePoint