Man pages for Open-Systems-Pharmacology/OSPSuite-R
R package to manipulate OSPSuite Models
| addOutputInterval | Adds an interval to the output schema of the simulation |
| addOutputs | Adds the quantities as output into the 'simulation'. The... |
| addUserDefinedPKParameter | Adds and returns a User-Defined PK-Parameter to the managed... |
| AgingData | AgingData |
| allAvailableDimensions | List all available dimensions in the 'OSPSuite' platform |
| AllMatchingMethod | Names of the '.NET' container tasks of the type... |
| AllPathsInMethod | Names of the '.NET' container tasks of the type... |
| 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... |
| 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... |
| clearOutputs | Removes all selected output from the given 'simulation' |
| CompareBy | How should comparison of entities be performed |
| Container | Container |
| convertUnits | Convert datasets in 'DataCombined' to common units |
| createDistributions | Creates the parameter distributions based on the given... |
| 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... |
| createSimulationBatch | Creates and returns an instance of a 'SimulationBatch' that... |
| DataAggregationMethods | Names of aggregation available for... |
| DataColumn | DataColumn |
| DataCombined | Object combining simulated and observed data |
| DataErrorType | Supported types of the error |
| DataImporterConfiguration | DataImporterConfiguration |
| DataRepository | DataRepository |
| DataSet | DataSet |
| dataSetToDataFrame | Converts a list of 'DataSet' objects to a data.frame |
| DefaultPlotConfiguration | Plot configuration for OSP plots |
| dot-addMissingGroupings | Replace missing groupings with dataset names |
| dot-cleanVectorArgs | Validate arguments provided as vectors |
| dot-convertGeneralToSpecificPlotConfiguration | Create plot-specific 'tlf::PlotConfiguration' object |
| dot-createAxesLabels | Create axes labels |
| dot-encodeUnit | Encoding mu symbol |
| dot-expandPath | Returns the expanded path for 'path' and ensure that encoding... |
| dot-extractAggregatedSimulatedData | Extract aggregated simulated data |
| dot-extractMostFrequentUnit | Find the most common units |
| dot-extractResidualsToTibble | Created observed versus simulated paired data |
| dot-geoRange | Geometric Range |
| dot-getAllEntitiesMatching | Retrieve all entities of a container (simulation or container... |
| dot-getAllEntityPathsIn | Retrieves all path of entities defined within the container... |
| dot-getConcurrentSimulationRunnerResults | Get SimulationResults from ConcurrentSimulationRunner |
| dot-getDimensionsEnum | Function to return an enum of all available dimensions |
| dot-getEntity | Retrieve a single entity by path in the given container |
| dot-getNetTask | .getNetTask |
| dot-getNetTaskFromCache | .getNetTaskFromCache |
| dot-getOspDimensions | get OSP Dimensions from OSPSuite.Dimensions.xml data |
| dot-getOspUnits | get OSP Units from OSPSuite.Dimensions.xml data |
| dot-getPathToPKSimInstallDir | Tries to find the installation path for a specific version of... |
| dot-getPathToPKSimInstallDirFromFileSystem | Tries to find the installation path for a specific version of... |
| dot-getPathToPKSimInstallDirFromRegistry | Tries to find the installation path for a specific version of... |
| dot-getPropertyValue | Returns the value of property named 'propertyName' from .NET... |
| dot-getPropertyValues | Returns a list containing all properties 'propertyName' from... |
| dot-getQuantityDisplayPaths | Retrieves the display path of the quantity defined by path in... |
| dot-getUnitsEnum | Create a list of all units available for each dimension |
| dot-ImporterErrorTypeToDataSetErrorType | Mapping of string representation for the error types... |
| dot-initPackage | Load the OSPSuite R to .NET Binding |
| dot-loadDataRepositoryFromPKML | Loads a data repository (typically observed data) from a PKML... |
| dot-makeDataFrameColumn | Create a vector of the right length for a certain property of... |
| dot-netEnumName | Retrieves the name of the constant in the specified... |
| DotNetWrapper | Wrapper class for '.NET' objects |
| dot-normRange | Normal Range |
| dot-parameterValueListFrom | Converts a list of .NET 'ParameterValue' into a list with 2... |
| dot-parseDimensionsXML | parse OSPSuite.Dimensions.xml containing dimensions and units |
| dot-removeEmptyDataFrame | Remove empty data frames from a list of data frames |
| dot-removeUnpairableDatasets | Remove unpairable datasets for computing residuals |
| dot-savePKAnalysesToCSV | Saves the pK-analyses to csv file |
| dot-savePopulationToCSV | Saves the population to csv file |
| dot-saveResultsToCSV | Saves the simulation results to csv file |
| dot-saveSensitivityAnalysisResultsToCSV | Saves the simulation analysis results to csv file |
| dot-scaleQuantityValues | Scale current values of quantities using a factor |
| dot-setEndSimulationTime | Set end time of the simulation |
| dot-setQuantityValues | Set values of quantity |
| dot-toObjectType | Convert '.NET' object to wrapper class in R |
| dot-unitConverter | Convert a data frame to common units |
| dot-validateHasUnit | Check if quantity can be represented in the unit |
| dot-validateScalarDataCombined | Validate that single instance of 'DataCombined' |
| Entity | Entity |
| exportIndividualSimulations | Export simulation PKMLs for given 'individualIds'. Each pkml... |
| 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... |
| Formula | Formula |
| Gender | Default genders defined in PK-Sim |
| getAllContainerPathsIn | Retrieves the path of all containers defined in the container... |
| getAllContainersMatching | Retrieve all sub containers of a parent container (simulation... |
| getAllMoleculePathsIn | Retrieves the paths of all molecules defined in the container... |
| getAllMoleculesMatching | Retrieve all molecules of a container (simulation or... |
| getAllObserverPathsIn | Retrieves the path of all observers defined in the container... |
| getAllParameterPathsIn | Retrieves the path of all parameters defined in the container... |
| getAllParametersForSensitivityAnalysisMatching | Retrieve all parameters of the given simulation matching the... |
| getAllParametersMatching | Retrieve all parameters of a container (simulation or... |
| getAllQuantitiesMatching | Retrieve all quantities of a container (simulation or... |
| getAllQuantityPathsIn | Retrieves the path of all quantities defined in the container... |
| getAllStateVariableParametersPaths | Get the paths of all state variable parameters of the... |
| getAllStateVariablesPaths | Get the paths of all state variable quantities of the... |
| 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... |
| 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... |
| getSteadyState | Get the steady-state values of species and state variable... |
| 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... |
| IndividualCharacteristics | IndividualCharacteristics |
| initPKSim | Loads the 'PKSim.R' that will enable create individual and... |
| Interval | Interval |
| 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... |
| loadDataSetsFromExcel | Load data sets from excel |
| loadPopulation | Loads a population from a csv file and returns the... |
| loadSimulation | Load a simulation from a pkml file |
| messages | List of functions and strings used to signal error messages... |
| Molecule | Molecule |
| MoleculeOntogeny | MoleculeOntogeny |
| MoleculeParameter | Standard molecule parameter names typically available in an... |
| ObjectBase | ObjectBase |
| ospDimensions | Supported dimensions defined as a named list |
| ospsuite_deprecated | Deprecated functions |
| ospsuiteSettingNames | Names of the settings stored in ospsuiteEnv. Can be used with... |
| ospUnits | Supported units defined as a named list of lists |
| OutputSchema | OutputSchema |
| OutputSelections | OutputSelections |
| Parameter | Parameter |
| ParameterRange | ParameterRange |
| pkAnalysesToDataFrame | Convert the pk-Analysis to data frame |
| PKParameter | PKParameter |
| pkParameterByName | Returns an instance of a PK-Parameter by name or NULL if the... |
| 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 | Creates a data.frame containing one column for each parameter... |
| potentialVariableParameterPathsFor | Returns an array of parameter path with one entry for each... |
| Quantity | Quantity |
| QuantityPKParameter | QuantityPKParameter |
| QuantitySelection | QuantitySelection |
| reexports | Objects exported from other packages |
| removeAllUserDefinedPKParameters | Removes all User-Defined PK-Parameters that may have been... |
| 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... |
| 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 |
| Simulation | Simulation |
| SimulationBatch | SimulationBatch |
| SimulationBatchOptions | SimulationBatchOptions |
| SimulationBatchRunValues | SimulationBatchRunValues |
| SimulationPKAnalyses | SimulationPKAnalyses |
| SimulationResults | SimulationResults |
| simulationResultsToDataFrame | 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... |
| 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... |
| StandardPKParameter | Standard PK-Parameters types defined in OSPSuite This is only... |
| toBaseUnit | Converts a value given in a specified unit into the base unit... |
| 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... |
| toUnit | Converts a value given in base unit of a quantity into a... |
| uniqueEntities | Extract Unique Elements of type 'Entity' |
| updatePKParameter | Updates some properties of a PK-Parameter (displayName and... |
| UserDefinedPKParameter | UserDefinedPKParameter |
| validateDimension | Validate dimension |
| validateUnit | Validate unit |
| ValuePoint | ValuePoint |
