Package: ospsuite 12.4.3.9015

Michael Sevestre

ospsuite: R package to manipulate OSPSuite Models

The ospsuite-R package provides the functionality of loading, manipulating, and simulating the simulations created in the Open Systems Pharmacology Software tools PK-Sim and MoBi.

Authors:Open-Systems-Pharmacology Community [cph, fnd], Michael Sevestre [aut, cre], Pavel Balazki [aut], Juri Solodenko [aut], Indrajeet Patil [aut], Felix MIL [aut]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ospsuite/json (API)

# Install 'ospsuite' in R:
install.packages('ospsuite', repos = c('https://open-systems-pharmacology.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/open-systems-pharmacology/ospsuite-r/issues

Pkgdown/docs site:https://www.open-systems-pharmacology.org

Datasets:

On CRAN:

Conda:

10.69 score 55 stars 4 packages 153 scripts 162 exports 71 dependencies

Last updated from:f5f251fd68 (on graceful-load-no-runtime). Checks:4 ERROR, 2 OK, 3 WARNING. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64ERROR217
source / vignettesOK359
linux-release-x86_64ERROR222
macos-release-arm64ERROR177
macos-oldrel-arm64ERROR160
windows-develWARNING387
windows-releaseWARNING437
windows-oldrelWARNING360
wasm-releaseOK257

Exports:addOutputIntervaladdOutputsaddResidualColumnaddUserDefinedPKParameterallAvailableDimensionsallPKParameterNamescalculatePKAnalysescalculateResidualsclearMemoryclearOutputIntervalsclearOutputsCompareByconvertSnapshotconvertUnitscreateDistributionscreateImporterConfigurationForFilecreateIndividualcreateIndividualCharacteristicscreatePopulationcreatePopulationCharacteristicscreateSimulationBatchDataAggregationMethodsDataCombinedDataErrorTypeDataImporterConfigurationDataSetdataSetsFromDataFramedataSetToDataFramedataSetToTibbleDefaultPlotConfigurationDotNetWrapperenumenumGetKeyenumGetValueenumHasKeyenumKeysenumPutenumRemoveenumValuesexportIndividualSimulationsexportPKAnalysesToCSVexportPopulationToCSVexportProjectToSnapshotexportResultsToCSVexportSensitivityAnalysisResultsToCSVexportSteadyStateToXLSGendergetAllContainerPathsIngetAllContainersMatchinggetAllMoleculePathsIngetAllMoleculesMatchinggetAllObserverPathsIngetAllParameterPathsIngetAllParametersForSensitivityAnalysisMatchinggetAllParametersMatchinggetAllQuantitiesMatchinggetAllQuantityPathsIngetAllStateVariableParametersPathsgetAllStateVariablesPathsgetBaseUnitgetContainergetDimensionByNamegetDimensionForUnitgetMoleculegetMolWeightForgetOSPSuiteSettinggetOutputValuesgetParametergetParameterDisplayPathsgetQuantitygetQuantityValuesByPathgetSimulationTreegetStandardMoleculeParametersgetSteadyStategetUnitsForDimensionhasDimensionhasUnitHumanPopulationimportPKAnalysesFromCSVimportResultsFromCSVimportSensitivityAnalysisResultsFromCSVIndividualCharacteristicsinitPKSimisExplicitFormulaByPathisSupportedUnitloadAgingDataFromCSVloadDataImporterConfigurationloadDataSetFromPKMLloadDataSetsFromExcelloadPopulationloadProjectFromSnapshotloadSimulationMoleculeOntogenyMoleculeParameterospDimensionsospsuiteSettingNamesospUnitsParameterRangepkAnalysesAsDataFramepkAnalysesToDataFramepkAnalysesToTibblepkParameterByNameplotGridPlotGridConfigurationplotIndividualTimeProfileplotObservedVsSimulatedplotPopulationTimeProfileplotPredictedVsObservedplotQuantileQuantilePlotplotResidualsAsHistogramplotResidualsVsCovariateplotResidualsVsSimulatedplotResidualsVsTimeplotTimeProfilepopulationAsDataFramePopulationCharacteristicspopulationFromDataFramepopulationToDataFramepopulationToTibblepotentialVariableParameterPathsForremoveAllUserDefinedPKParametersremoveSimulationFromCacheresetSimulationCacherunSensitivityAnalysisrunSimulationrunSimulationBatchesrunSimulationsrunSimulationsFromSnapshotsaveDataSetToPKMLsaveSimulationscaleParameterValuesSensitivityAnalysisSensitivityAnalysisRunOptionssetMoleculeInitialValuessetMoleculeScaleDivisorssetMoleculeValuesByPathsetOutputIntervalsetOutputssetParameterValuessetParameterValuesByPathsetQuantityValuesByPathSimulationBatchsimulationResultsToDataFramesimulationResultsToTibbleSimulationRunOptionsSnapshotParameterSpeciessplitPopulationFileStandardContainerStandardOntogenyStandardPathStandardPKParametertoBaseUnittoDisplayUnittoPathArraytoPathStringtoUnituniqueEntitiesupdatePKParametervalidateDimensionvalidateIsNamedListvalidateUnit

Dependencies:backportsbitbit64checkmateclicliprcommonmarkcowplotcpp11crayoncurldata.tabledplyrfarverfitdistrplusfsgenericsggh4xggnewscaleggplot2ggtextgluegridtextgtablehmsisobandjpegjsonlitelabelinglatticelifecyclelitedownloggermagrittrmarkdownMASSMatrixopenxlsxospsuite.plotsospsuite.utilspatchworkpillarpkgconfigpngprettyunitsprogresspurrrR6RColorBrewerRcppreadrrlangrSharpS7scalesstringistringrsurvivaltibbletidyrtidyselecttlftzdbutf8vctrsviridisLitevroomwithrxfunxml2zip

Calculating PK parameters of simulation outputs
Calculating PK parameters | Extracting a dataframe | Import and export of PK-analyses | User-Defined PK Parameters | Examples | Calculate AUC between for a specific time interval. | Calculate CMax between the 4th and 5th application of a multiple applications simulation. | Calculate CMax between the 4th and 5th application of a multiple applications simulation and apply a time offset | Update Dimension of a standard parameter for correct visualization
Rendered frompk-analysis.Rmdusingknitr::rmarkdown

Last update: 2026-07-14
Started: 2020-05-20

Changing parameter and molecule start values
Changing initial values | Formula types | Changing parameters and molecules initial values
Rendered fromset-values.Rmdusingknitr::rmarkdown

Last update: 2026-07-14
Started: 2020-04-10

Creating individuals
Adding enzyme ontogenies
Rendered fromcreate-individual.Rmdusingknitr::rmarkdown

Last update: 2026-07-14
Started: 2020-04-10

Dimensions and Units
Unit conversion
Rendered fromunit-conversion.Rmdusingknitr::rmarkdown

Last update: 2026-07-14
Started: 2020-04-10

Efficient calculation
Life cycle of a simulation run | Running a single simulation once | Running a single simulation multiple times and varying some parameters/initial values between each run | Optimized loading for running simulations with predefined set of variable parameters | Varying state variable parameters with SimulationBatch
Rendered fromefficient-calculations.Rmdusingknitr::rmarkdown

Last update: 2026-07-14
Started: 2021-08-28

Getting Started with ospsuite
Overview | Quick Start: Basic Simulation | Step-by-Step Tutorial | Loading Simulations | Exploring Model Structure | Modifying Parameters | Customizing Simulation Settings | Running Simulations | Visualizing Results | Option 1: Built-in Plotting Functions | Option 2: Custom Plotting with ggplot2 | Complete Workflow Example | Understanding ospsuite Objects | Object-Oriented Approach | Key Classes | General Workflow Summary | Next Steps | Essential Next Steps: | Population Studies: | Analysis and Optimization: | Data Integration: | Advanced Topics: | General Information
Rendered fromospsuite.Rmdusingknitr::rmarkdown

Last update: 2026-07-14
Started: 2021-10-01

Loading a simulation and accessing entities
Loading a simulation | Accessing entities of the model and their properties - the path concept | Loading simulation tree
Rendered fromload-get.Rmdusingknitr::rmarkdown

Last update: 2026-07-14
Started: 2020-04-10

Observed data
DataSet | Importing data
Rendered fromobserved-data.Rmdusingknitr::rmarkdown

Last update: 2026-07-14
Started: 2022-08-12

PK-Sim Installation
Not required for {ospsuite} version equal or above 12.1.0 | Versions below 12.1.0 | Install PK-Sim Globally | Install and use PK-Sim in a project
Rendered fromPKSim-installation.Rmdusingknitr::rmarkdown

Last update: 2026-07-14
Started: 2024-07-23

Plotting with ospsuite.plots
Introduction | Initial Setup | Setting up the data | Population Simulation Data | Time Profile Plots | Population Data Aggregation | Showing Individual Dataset Names | Custom Aesthetic Mappings | Predicted vs Observed Plots | Customizing Fold Distance | Swapping Axes | Scaling Options | Residuals vs Covariate Plots | Residuals vs Observed Values | Residuals vs Time | Residuals vs Predicted Values | Residual Scale Options | Residuals as Histogram | Quantile-Quantile (Q-Q) Plot | Automatic Unit Conversion | Specifying Units Directly | Handling Mixed Error Types | Using data.table Instead of DataCombined | Further Customization | Legend title | Legend position | Saving Plots
Rendered fromplotting-with-ospsuite-plots.Rmdusingknitr::rmarkdown

Last update: 2026-07-14
Started: 2026-03-17

Population simulations
Loading population file | Creating populations | Running population simulation
Rendered fromcreate-run-population.Rmdusingknitr::rmarkdown

Last update: 2026-07-14
Started: 2020-04-10

Running a simulation
Running individual simulation and retrieving the results | Running multiple individual simulations and retrieving the results | Adding new outputs | Changing simulation intervals | Adjusting solver settings
Rendered fromrun-simulation.Rmdusingknitr::rmarkdown

Last update: 2026-07-14
Started: 2020-04-10

Sensitivity analysis
Performing a sensitivity analysis | Understanding numberOfSteps and variationRange | Customizing sensitivity analysis settings | Import and export of sensitivity analysis results
Rendered fromsensitivity-analysis.Rmdusingknitr::rmarkdown

Last update: 2026-07-14
Started: 2020-05-25

Table parameters
Changing table parameter values
Rendered fromtable-parameters.Rmdusingknitr::rmarkdown

Last update: 2026-07-14
Started: 2020-04-10

Visualizations with DataCombined
Introduction | Time profile plots | Observed versus simulated scatter plot | Residuals versus time or vs simulated scatter plot | Customizing plots | Creating multi-panel plots | Saving plots | Implementation details
Rendered fromdata-combined-plotting.Rmdusingknitr::rmarkdown

Last update: 2026-07-14
Started: 2022-09-20

Working with DataCombined class
Introduction | Creating DataCombined object | Grouping | Transformations | Extracting a combined data frame | Further functionalities | Visualizations with DataCombined
Rendered fromdata-combined.Rmdusingknitr::rmarkdown

Last update: 2026-07-14
Started: 2022-09-20

Readme and manuals

Help Manual

Help pageTopics
Gather files and files from folders to one location.gatherFiles
Get SimulationResults from ConcurrentSimulationRunner.getConcurrentSimulationRunnerResults
get OSP Dimensions from OSPSuite.Dimensions.xml data.getOspDimensions
get OSP Units from OSPSuite.Dimensions.xml data.getOspUnits
Retrieves the display path of the quantity defined by path in the simulation.getQuantityDisplayPaths
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'.parameterValueListFrom
parse OSPSuite.Dimensions.xml containing dimensions and units.parseDimensionsXML
Saves the pK-analyses to csv file.savePKAnalysesToCSV
Saves the population to csv file.savePopulationToCSV
Saves the simulation results to csv file.saveResultsToCSV
Saves the simulation analysis results to csv file.saveSensitivityAnalysisResultsToCSV
Scale current values of quantities using a factor.scaleQuantityValues
Set end time of the simulation.setEndSimulationTime
Set values of quantity.setQuantityValues
Check if quantity can be represented in the unit.validateHasUnit
Adds an interval to the output schema of the simulationaddOutputInterval
Adds the quantities as output into the 'simulation'. The quantities can either be specified using explicit instances or using paths.addOutputs
Add a residual column to paired observed/predicted dataaddResidualColumn
Adds and returns a User-Defined PK-Parameter to the managed list of PK-ParametersaddUserDefinedPKParameter
AgingDataAgingData
List all available dimensions in the 'OSPSuite' platformallAvailableDimensions
Returns the name of all pk parameters defined in the systemallPKParameterNames
ApplicationApplication
Calculates the pkAnalyses for all output values available in 'results'.calculatePKAnalyses
Calculate residuals for datasets in 'DataCombined'calculateResiduals
Clears the memory used by all underlying objectsclearMemory
Removes all intervals as well as all single time points from the output schema defined in 'simulation'clearOutputIntervals
Removes all selected output from the given 'simulation'clearOutputs
How should comparison of entities be performedCompareBy
Convert between snapshot and project formatsconvertSnapshot
Convert datasets in 'DataCombined' to common unitsconvertUnits
Creates the parameter distributions based on the given individual 'individualCharacteristics'createDistributions
Create a 'DataImporterConfiguration' for an XLS sheetcreateImporterConfigurationForFile
Creates a set of parameter values describing an individual using the PK-Sim DatabasecreateIndividual
Create the characteristics of an individual using the PK-Sim Database.createIndividualCharacteristics
Creates an population using the PK-Sim DatabasecreatePopulation
Creates the population characteristics used to create a populationcreatePopulationCharacteristics
Creates and returns an instance of a 'SimulationBatch' that can be used to efficiently vary parameters and initial values in a simulationcreateSimulationBatch
Names of aggregation available for plotPopulationTimeProfile()DataAggregationMethods
DataColumnDataColumn
Object combining simulated and observed dataDataCombined
dataCombinedAciclovirdataCombinedAciclovir
Supported types of the errorDataErrorType
DataImporterConfigurationDataImporterConfiguration
DataRepositoryDataRepository
DataSetDataSet
Creates a list of 'DataSet' objects from a 'data.frame'dataSetsFromDataFrame
Converts a list of 'DataSet' objects to a data.framedataSetToDataFrame dataSetToTibble
Plot configuration for OSP plotsDefaultPlotConfiguration
Wrapper class for '.NET' objectsDotNetWrapper
EntityEntity
Export simulation PKMLs for given 'individualIds'. Each pkml file will contain the original simulation updated with parameters of the corresponding individual.exportIndividualSimulations
Saves the pK-analyses to csv fileexportPKAnalysesToCSV
Saves the population to csv fileexportPopulationToCSV
Export a project to a snapshotexportProjectToSnapshot
Saves the simulation results to csv fileexportResultsToCSV
Saves the simulation analysis results to csv fileexportSensitivityAnalysisResultsToCSV
Export steady-state to Excel in the format that can be imported in MoBi.exportSteadyStateToXLS
FormulaFormula TableFormula
Default genders defined in PK-SimGender
Retrieves the path of all containers defined in the container and all its childrengetAllContainerPathsIn
Retrieve all sub containers of a parent container (simulation or container instance) matching the given path criteriagetAllContainersMatching
Retrieves the paths of all molecules defined in the container and all its childrengetAllMoleculePathsIn
Retrieve all molecules of a container (simulation or container instance) matching the given path criteriagetAllMoleculesMatching
Retrieves the path of all observers defined in the container and all its childrengetAllObserverPathsIn
Retrieves the path of all parameters defined in the container and all its childrengetAllParameterPathsIn
Retrieve all parameters of the given simulation matching the given path criteria and also potential candidate for sensitivity variationgetAllParametersForSensitivityAnalysisMatching
Retrieve all parameters of a container (simulation or container instance) matching the given path criteriagetAllParametersMatching
Retrieve all quantities of a container (simulation or container instance) matching the given path criteriagetAllQuantitiesMatching
Retrieves the path of all quantities defined in the container and all its childrengetAllQuantityPathsIn
Get the paths of all state variable parameters of the simulationgetAllStateVariableParametersPaths
Get the paths of all state variable quantities of the simulationgetAllStateVariablesPaths
Get base unit of a dimensiongetBaseUnit
Retrieve a single container by path under the given containergetContainer
Get dimension by namegetDimensionByName
Get dimension for a given unitgetDimensionForUnit
Retrieve a single molecule by path in the given containergetMolecule
Retrieve molecular weight for a quantity's moleculegetMolWeightFor
Get the value of a global ospsuite-R setting.getOSPSuiteSetting
Extracting simulated valuesgetOutputValues
Retrieve a single parameter by path in the given containergetParameter
Retrieves the display path of the parameters defined by paths in the simulationgetParameterDisplayPaths
Retrieve a single quantity by path in the given containergetQuantity
Get the values of quantities in the simulation by pathgetQuantityValuesByPath
Get simulation treegetSimulationTree
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 parametersgetStandardMoleculeParameters
Get the steady-state values of species and state variable parameters.getSteadyState
Get units for a given dimensiongetUnitsForDimension
Dimension existencehasDimension
Unit existencehasUnit
Default human population defined in PK-SimHumanPopulation
Loads the pK-analyses from csv fileimportPKAnalysesFromCSV
Imports the simulation results from one or more csv filesimportResultsFromCSV
Imports the simulation analysis results from one or more csv filesimportSensitivityAnalysisResultsFromCSV
IndividualCharacteristicsIndividualCharacteristics
Loads the 'PKSim.R' dll that will enable create individual and create population workflows.initPKSim
Is the value defined by an explicit formulaisExplicitFormulaByPath
Check if unit is supported in the OSPSuite platformisSupportedUnit
Loads aging data (typically generated from PK-Sim) iloadAgingDataFromCSV
Load 'DataImporterConfiguration' from XML file.loadDataImporterConfiguration
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.loadDataSetFromPKML
Load data sets from excelloadDataSetsFromExcel
Loads a population from a csv file and returns the population.loadPopulation
Load a project from a snapshotloadProjectFromSnapshot
Load a simulation from a pkml fileloadSimulation
List of functions and strings used to signal error messages Extends the 'messages' list from ospsuite.utilsmessages
MoleculeOntogenyMoleculeOntogeny
Standard molecule parameter names typically available in an endogenous molecule (enzyme, transporter etc...) coming from PK-SimMoleculeParameter
Supported dimensions defined as a named listospDimensions
Deprecated functionsospsuite_deprecated pkAnalysesAsDataFrame populationAsDataFrame
Names of the settings stored in ospsuiteEnv. Can be used with 'getOSPSuiteSetting()'ospsuiteSettingNames
Supported units defined as a named list of listsospUnits
OutputSchemaOutputSchema
OutputSelectionsOutputSelections
ParameterParameter
ParameterRangeParameterRange
Convert the pk-Analysis to data framepkAnalysesToDataFrame pkAnalysesToTibble
PKParameterPKParameter
Returns an instance of a PK-Parameter by name or NULL if the parameter by name is not foundpkParameterByName
PKParameterSensitivityPKParameterSensitivity
Time-profile plot of individual dataplotIndividualTimeProfile
Observed versus predicted/simulated scatter plotplotObservedVsSimulated
Time-values profile plot for population simulationsplotPopulationTimeProfile
Plot Predicted vs Observed ValuesplotPredictedVsObserved
Plot Quantile-Quantile PlotplotQuantileQuantilePlot
Plot Residuals HistogramplotResidualsAsHistogram
Plot Residuals vs CovariateplotResidualsVsCovariate
Residuals versus time scatter plotplotResidualsVsSimulated
Residuals versus time scatter plotplotResidualsVsTime
Create Time Profile PlotplotTimeProfile
PopulationPopulation
PopulationCharacteristicsPopulationCharacteristics
Creates a 'Population' object from a data.framepopulationFromDataFrame
Creates a data.frame containing one column for each parameter defined in the populationpopulationToDataFrame populationToTibble
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 analysispotentialVariableParameterPathsFor
QuantityQuantity
QuantityPKParameterQuantityPKParameter
QuantitySelectionQuantitySelection
Removes all User-Defined PK-Parameters that may have been added to the systemremoveAllUserDefinedPKParameters
Removes a simulation from simulations cache.removeSimulationFromCache
Clears cache of loaded simulationsresetSimulationCache
Runs a sensitivity analysisrunSensitivityAnalysis
Run simulation batchesrunSimulationBatches
Runs multiple simulations concurrently.runSimulations
Run Simulations From Snapshot FilesrunSimulationsFromSnapshot
Save the 'DataSet' to pkmlsaveDataSetToPKML
Saves a simulation to pkml filesaveSimulation
Scale current values of parameters using a factorscaleParameterValues
SensitivityAnalysisSensitivityAnalysis
SensitivityAnalysisResultsSensitivityAnalysisResults
SensitivityAnalysisRunOptionsSensitivityAnalysisRunOptions
Set molecule start valuessetMoleculeInitialValues
Set molecule scale divisorssetMoleculeScaleDivisors
Set molecule start values in the simulation by pathsetMoleculeValuesByPath
Clears the output interval from the simulation and adds a new one.setOutputInterval
Set outputs of a simulationsetOutputs
Set values of parameterssetParameterValues
Set the values of parameters in the simulation by pathsetParameterValuesByPath
Set the values of quantities in the simulation by pathsetQuantityValuesByPath
SimulationSimulation
SimulationBatchSimulationBatch
SimulationBatchOptionsSimulationBatchOptions
SimulationBatchRunValuesSimulationBatchRunValues
SimulationPKAnalysesSimulationPKAnalyses
SimulationResultsSimulationResults
Converts a 'SimulationResults' objects to a data.framesimulationResultsToDataFrame simulationResultsToTibble
SimulationRunOptionsSimulationRunOptions
SimulationSettingsSimulationSettings
SnapshotParameterSnapshotParameter
SolverSettingsSolverSettings
Default species defined in PK-SimSpecies
Loads a population from the 'csvPopulationFile' and split the loaded population according to 'numberOfCores'.splitPopulationFile
Standard containers typically available in a PBPK simulationStandardContainer
List of ontogeny supported in PK-SimStandardOntogeny
Standard parameter paths typically available in a PBPK simulationStandardPath
Standard PK-Parameters types defined in OSPSuite This is only used to defined how a user defined PK Parameter should be calculatedStandardPKParameter
Converts a value given in a specified unit into the base unit of a quantitytoBaseUnit
Convert base unit to display unittoDisplayUnit
Convert a path defined as string to a path arraytoPathArray
Convert a path array to a path as string with entries separated by '|'toPathString
Converts values from one unit to anothertoUnit
Extract Unique Elements of type 'Entity'uniqueEntities
Updates some properties of a PK-Parameter (displayName and displayUnit)updatePKParameter
UserDefinedPKParameterUserDefinedPKParameter
Validate dimensionvalidateDimension
Validate that an object is a named listvalidateIsNamedList
Validate unitvalidateUnit
ValuePointValuePoint