Files in Open-Systems-Pharmacology/OSPSuite-R
R package to manipulate OSPSuite Models

.Rbuildignore

.gitattributes

.github/.gitignore

.github/workflows/main-workflow.yaml

.github/workflows/update-core-files.yaml

.gitignore

.gitmodules

BinaryFiles

DESCRIPTION

LICENSE

NAMESPACE

NEWS.md R/aging-data.R R/api-config.R R/application.R R/cache.R R/container.R R/data-column.R R/data-combined.R R/data-importer-configuration.R R/data-repository.R R/data-set.R R/default-plot-configuration.R R/dot-net-wrapper.R R/entity.R R/formula.R R/get-net-task.R R/globals.R R/individual-characteristics.R R/init-package.R R/interval.R R/messages.R R/molecule-ontogeny.R R/molecule.R R/object-base.R R/ospsuite-env.R R/output-schema.R R/output-selections.R R/parameter-range.R R/parameter.R R/pk-parameter-sensitivity.R R/pk-parameter.R R/pk-sim.R R/plot-individual-time-profile.R R/plot-observed-vs-simulated.R R/plot-population-time-profile.R R/plot-residuals-vs-simulated.R R/plot-residuals-vs-time.R R/population-characteristics.R R/population.R R/quantity-pk-parameter.R R/quantity-selection.R R/quantity.R R/re-exports.R R/sensitivity-analysis-results.R R/sensitivity-analysis-run-options.R R/sensitivity-analysis.R R/simulation-batch-options.R R/simulation-batch-run-values.R R/simulation-batch.R R/simulation-pk-analyses.R R/simulation-results.R R/simulation-run-options.R R/simulation-settings.R R/simulation.R R/snapshot-parameter.R R/snapshots.R R/solver-settings.R R/standard-path.R R/table-formula.R R/tasks-env.R R/user-defined-pk-parameter.R R/utilities-container.R R/utilities-data-combined.R R/utilities-data-importer-configuration.R R/utilities-data-repository.R R/utilities-data-set.R R/utilities-dot-net.R R/utilities-entity.R R/utilities-file.R R/utilities-individual.R R/utilities-molecule.R R/utilities-output-schema.R R/utilities-output-selections.R R/utilities-parameter-value.R R/utilities-parameter.R R/utilities-path.R R/utilities-pk-analysis.R R/utilities-pk-parameter.R R/utilities-pksim.R R/utilities-plotting.R R/utilities-population.R R/utilities-quantity.R R/utilities-sensitivity-analysis.R R/utilities-simulation-results.R R/utilities-simulation.R R/utilities-units.R R/utilities.R R/value-point.R R/zzz.R R/zzz_deprecated.R README.Rmd README.md

_pkgdown.yml

codecov.yml

inst/WORDLIST

inst/extdata/Aciclovir.pkml

inst/extdata/CompiledDataSet.xlsx

inst/extdata/ObsDataAciclovir_1.pkml

inst/extdata/ObsDataAciclovir_2.pkml

inst/extdata/ObsDataAciclovir_3.pkml

inst/extdata/PKAnalyses.csv

inst/extdata/SAResult.csv

inst/extdata/SimResults.csv

inst/extdata/SimResults_pop.csv

inst/extdata/aging_data.csv

inst/extdata/dataImporterConfiguration.xml

inst/extdata/obs_data.pkml

inst/extdata/pop.csv

inst/extdata/res.csv

inst/extdata/sa.csv

inst/extdata/simple.pkml

inst/extdata/simple_pop.csv

inst/lib/Antlr3.Runtime.dll

inst/lib/Autofac.dll

inst/lib/BouncyCastle.Crypto.dll

inst/lib/Castle.Core.dll

inst/lib/Castle.Windsor.dll

inst/lib/ConsoleApp.deps.json

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inst/lib/ConsoleApp.dll.config

inst/lib/ConsoleApp.runtimeconfig.json

inst/lib/Dapper.dll

inst/lib/DevExpress.Data.v21.2.dll

inst/lib/FluentNHibernate.dll

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inst/lib/Iesi.Collections.dll

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inst/lib/MPFitLib.dll

inst/lib/MarkdownLog.dll

inst/lib/MathNet.Numerics.dll

inst/lib/Microsoft.DotNet.PlatformAbstractions.dll

inst/lib/Microsoft.Extensions.Configuration.Abstractions.dll

inst/lib/Microsoft.Extensions.Configuration.Binder.dll

inst/lib/Microsoft.Extensions.Configuration.dll

inst/lib/Microsoft.Extensions.DependencyInjection.Abstractions.dll

inst/lib/Microsoft.Extensions.DependencyInjection.dll

inst/lib/Microsoft.Extensions.DependencyModel.dll

inst/lib/Microsoft.Extensions.Logging.Abstractions.dll

inst/lib/Microsoft.Extensions.Logging.dll

inst/lib/Microsoft.Extensions.Options.dll

inst/lib/Microsoft.Extensions.Primitives.dll

inst/lib/Microsoft.Win32.SystemEvents.dll

inst/lib/NHibernate.dll

inst/lib/NPOI.OOXML.dll

inst/lib/NPOI.OpenXml4Net.dll

inst/lib/NPOI.OpenXmlFormats.dll

inst/lib/NPOI.dll

inst/lib/Newtonsoft.Json.Schema.dll

inst/lib/Newtonsoft.Json.dll

inst/lib/OSPSuite.Assets.Images.dll

inst/lib/OSPSuite.Assets.dll

inst/lib/OSPSuite.Core.dll

inst/lib/OSPSuite.Dimensions.xml

inst/lib/OSPSuite.FuncParser.dll

inst/lib/OSPSuite.FuncParserNative.dll

inst/lib/OSPSuite.Infrastructure.Autofac.dll

inst/lib/OSPSuite.Infrastructure.Castle.dll

inst/lib/OSPSuite.Infrastructure.Export.dll

inst/lib/OSPSuite.Infrastructure.Import.dll

inst/lib/OSPSuite.Infrastructure.Reporting.dll

inst/lib/OSPSuite.Infrastructure.Serialization.dll

inst/lib/OSPSuite.Infrastructure.dll

inst/lib/OSPSuite.PKParameters.xml

inst/lib/OSPSuite.Presentation.Serialization.dll

inst/lib/OSPSuite.Presentation.dll

inst/lib/OSPSuite.R.dll

inst/lib/OSPSuite.Serializer.dll

inst/lib/OSPSuite.SimModel.dll

inst/lib/OSPSuite.SimModelNative.dll

inst/lib/OSPSuite.SimModelSolver_CVODES.dll

inst/lib/OSPSuite.TeXReporting.dll

inst/lib/OSPSuite.Utility.dll

inst/lib/PKSim.Assets.Images.dll

inst/lib/PKSim.Assets.dll

inst/lib/PKSim.CLI.Core.dll

inst/lib/PKSim.Core.dll

inst/lib/PKSim.Infrastructure.dll

inst/lib/PKSim.Presentation.dll

inst/lib/PKSim.R.dll

inst/lib/PKSimDB.sqlite

inst/lib/Remotion.Linq.EagerFetching.dll

inst/lib/Remotion.Linq.dll

inst/lib/SQLite.Interop.dll

inst/lib/Serilog.Extensions.Logging.File.dll

inst/lib/Serilog.Extensions.Logging.dll

inst/lib/Serilog.Formatting.Compact.dll

inst/lib/Serilog.Sinks.Async.dll

inst/lib/Serilog.Sinks.File.dll

inst/lib/Serilog.Sinks.RollingFile.dll

inst/lib/Serilog.dll

inst/lib/System.Configuration.ConfigurationManager.dll

inst/lib/System.Data.SQLite.dll

inst/lib/System.Diagnostics.PerformanceCounter.dll

inst/lib/System.Drawing.Common.dll

inst/lib/System.Resources.Extensions.dll

inst/lib/System.Security.Cryptography.ProtectedData.dll

inst/lib/System.Security.Permissions.dll

inst/lib/System.Windows.Extensions.dll

inst/lib/libOSPSuite.FuncParserNative.dylib

inst/lib/libOSPSuite.FuncParserNative.so

inst/lib/libOSPSuite.SimModelNative.dylib

inst/lib/libOSPSuite.SimModelNative.so

inst/lib/libOSPSuite.SimModelSolver_CVODES.dylib

inst/lib/libOSPSuite.SimModelSolver_CVODES.so

inst/lib/libSQLite.Interop.dll

man-roxygen/simulation_results.R man/AgingData.Rd man/AllMatchingMethod.Rd man/AllPathsInMethod.Rd man/ApiConfig.Rd man/Application.Rd man/Cache.Rd man/CompareBy.Rd man/Container.Rd man/DataAggregationMethods.Rd man/DataColumn.Rd man/DataCombined.Rd man/DataErrorType.Rd man/DataImporterConfiguration.Rd man/DataRepository.Rd man/DataSet.Rd man/DefaultPlotConfiguration.Rd man/DotNetWrapper.Rd man/Entity.Rd man/Formula.Rd man/Gender.Rd man/HumanPopulation.Rd man/IndividualCharacteristics.Rd man/Interval.Rd man/Molecule.Rd man/MoleculeOntogeny.Rd man/MoleculeParameter.Rd man/ObjectBase.Rd man/OutputSchema.Rd man/OutputSelections.Rd man/PKParameter.Rd man/PKParameterSensitivity.Rd man/Parameter.Rd man/ParameterRange.Rd man/Population.Rd man/PopulationCharacteristics.Rd man/Quantity.Rd man/QuantityPKParameter.Rd man/QuantitySelection.Rd man/SensitivityAnalysis.Rd man/SensitivityAnalysisResults.Rd man/SensitivityAnalysisRunOptions.Rd man/Simulation.Rd man/SimulationBatch.Rd man/SimulationBatchOptions.Rd man/SimulationBatchRunValues.Rd man/SimulationPKAnalyses.Rd man/SimulationResults.Rd man/SimulationRunOptions.Rd man/SimulationSettings.Rd man/SnapshotParameter.Rd man/SolverSettings.Rd man/Species.Rd man/StandardContainer.Rd man/StandardOntogeny.Rd man/StandardPKParameter.Rd man/StandardPath.Rd man/UserDefinedPKParameter.Rd man/ValuePoint.Rd man/addOutputInterval.Rd man/addOutputs.Rd man/addUserDefinedPKParameter.Rd man/allAvailableDimensions.Rd man/allPKParameterNames.Rd man/calculatePKAnalyses.Rd man/calculateResiduals.Rd man/clearMemory.Rd man/clearOutputIntervals.Rd man/clearOutputs.Rd man/convertSnapshot.Rd man/convertUnits.Rd man/createDistributions.Rd man/createImporterConfigurationForFile.Rd man/createIndividual.Rd man/createIndividualCharacteristics.Rd man/createPopulation.Rd man/createPopulationCharacteristics.Rd man/createSimulationBatch.Rd man/dataSetToDataFrame.Rd man/dot-ImporterErrorTypeToDataSetErrorType.Rd man/dot-addMissingGroupings.Rd man/dot-cleanVectorArgs.Rd man/dot-convertGeneralToSpecificPlotConfiguration.Rd man/dot-createAxesLabels.Rd man/dot-encodeUnit.Rd man/dot-expandPath.Rd man/dot-extractAggregatedSimulatedData.Rd man/dot-extractMostFrequentUnit.Rd man/dot-extractResidualsToTibble.Rd man/dot-gatherFiles.Rd man/dot-geoRange.Rd man/dot-getAllEntitiesMatching.Rd man/dot-getAllEntityPathsIn.Rd man/dot-getConcurrentSimulationRunnerResults.Rd man/dot-getDimensionsEnum.Rd man/dot-getEntity.Rd man/dot-getNetTask.Rd man/dot-getNetTaskFromCache.Rd man/dot-getOspDimensions.Rd man/dot-getOspUnits.Rd man/dot-getParentContainerByType.Rd man/dot-getPropertyValue.Rd man/dot-getPropertyValues.Rd man/dot-getQuantityDisplayPaths.Rd man/dot-getUnitsEnum.Rd man/dot-initPackage.Rd man/dot-loadDataRepositoryFromPKML.Rd man/dot-makeDataFrameColumn.Rd man/dot-netEnumName.Rd man/dot-normRange.Rd man/dot-parameterValueListFrom.Rd man/dot-parseDimensionsXML.Rd man/dot-removeEmptyDataFrame.Rd man/dot-removeUnpairableDatasets.Rd man/dot-savePKAnalysesToCSV.Rd man/dot-savePopulationToCSV.Rd man/dot-saveResultsToCSV.Rd man/dot-saveSensitivityAnalysisResultsToCSV.Rd man/dot-scaleQuantityValues.Rd man/dot-setEndSimulationTime.Rd man/dot-setQuantityValues.Rd man/dot-toObjectType.Rd man/dot-unitConverter.Rd man/dot-validateHasUnit.Rd man/dot-validateScalarDataCombined.Rd man/exportIndividualSimulations.Rd man/exportPKAnalysesToCSV.Rd man/exportPopulationToCSV.Rd man/exportResultsToCSV.Rd man/exportSensitivityAnalysisResultsToCSV.Rd man/exportSteadyStateToXLS.Rd man/getAllContainerPathsIn.Rd man/getAllContainersMatching.Rd man/getAllMoleculePathsIn.Rd man/getAllMoleculesMatching.Rd man/getAllObserverPathsIn.Rd man/getAllParameterPathsIn.Rd man/getAllParametersForSensitivityAnalysisMatching.Rd man/getAllParametersMatching.Rd man/getAllQuantitiesMatching.Rd man/getAllQuantityPathsIn.Rd man/getAllStateVariableParametersPaths.Rd man/getAllStateVariablesPaths.Rd man/getBaseUnit.Rd man/getContainer.Rd man/getDimensionByName.Rd man/getDimensionForUnit.Rd man/getMolWeightFor.Rd man/getMolecule.Rd man/getOSPSuiteSetting.Rd man/getOutputValues.Rd man/getParameter.Rd man/getParameterDisplayPaths.Rd man/getQuantity.Rd man/getQuantityValuesByPath.Rd man/getSimulationTree.Rd man/getStandardMoleculeParameters.Rd man/getSteadyState.Rd man/getUnitsForDimension.Rd man/hasDimension.Rd man/hasUnit.Rd man/importPKAnalysesFromCSV.Rd man/importResultsFromCSV.Rd man/importSensitivityAnalysisResultsFromCSV.Rd man/initPKSim.Rd man/isExplicitFormulaByPath.Rd man/loadAgingDataFromCSV.Rd man/loadDataImporterConfiguration.Rd man/loadDataSetFromPKML.Rd man/loadDataSetsFromExcel.Rd man/loadPopulation.Rd man/loadSimulation.Rd man/messages.Rd man/ospDimensions.Rd man/ospUnits.Rd man/ospsuiteSettingNames.Rd man/ospsuite_deprecated.Rd man/pkAnalysesToDataFrame.Rd man/pkParameterByName.Rd man/plotIndividualTimeProfile.Rd man/plotObservedVsSimulated.Rd man/plotPopulationTimeProfile.Rd man/plotResidualsVsSimulated.Rd man/plotResidualsVsTime.Rd man/populationToDataFrame.Rd man/potentialVariableParameterPathsFor.Rd man/reexports.Rd man/removeAllUserDefinedPKParameters.Rd man/removeSimulationFromCache.Rd man/resetSimulationCache.Rd man/runSensitivityAnalysis.Rd man/runSimulation.Rd man/runSimulationBatches.Rd man/runSimulations.Rd man/runSimulationsFromSnapshot.Rd man/saveDataSetToPKML.Rd man/saveSimulation.Rd man/scaleParameterValues.Rd man/setMoleculeInitialValues.Rd man/setMoleculeScaleDivisors.Rd man/setMoleculeValuesByPath.Rd man/setOutputInterval.Rd man/setOutputs.Rd man/setParameterValues.Rd man/setParameterValuesByPath.Rd man/setQuantityValuesByPath.Rd man/simulationResultsToDataFrame.Rd man/splitPopulationFile.Rd man/toBaseUnit.Rd man/toDisplayUnit.Rd man/toPathArray.Rd man/toPathString.Rd man/toUnit.Rd man/uniqueEntities.Rd man/updatePKParameter.Rd man/validateDimension.Rd man/validateUnit.Rd

ospsuite.Rproj

tests/data/CompiledDataSet.xlsx

tests/data/CompiledDataSetStevens2012.xlsx

tests/data/CompiledDataSetStevens2012v2.xlsx

tests/data/CompiledDataSet_oneSheet.xlsx

tests/data/ImporterConfiguration.xml

tests/data/MinimalModel.pkml

tests/data/S1.pkml

tests/data/Stevens_2012_placebo_indiv_results.csv

tests/data/Stevens_2012_placebo_pop_results.csv

tests/data/amount_based.pkml

tests/data/baby.csv

tests/data/baby_aging.csv

tests/data/concentration_based.pkml

tests/data/create_and_save_data_combined_objects.R

tests/data/customDPC

tests/data/dataImporterConfiguration.xml

tests/data/dataImporterConfiguration_UnitFromColumn.xml

tests/data/dataImporterConfiguration_noSheets.xml

tests/data/junk.csv

tests/data/manyObsDC

tests/data/manyObsSimDC

tests/data/manySimDC

tests/data/molecules.pkml

tests/data/obs_data.pkml

tests/data/obs_data_no_error.pkml

tests/data/oneObsDC

tests/data/oneObsGeometricDC

tests/data/oneObsSimDC

tests/data/oneSimDC

tests/data/pop.csv

tests/data/pop_5_spared_id.csv

tests/data/res_10.csv

tests/data/res_11-20.csv

tests/data/sa.csv

tests/data/sa_1.csv

tests/data/sa_2.csv

tests/data/simple.pkml

tests/data/test_project.pksim5

tests/data/test_snapshot.json

tests/data/unicode.pkml

tests/dev/script-benchmark-unitConversion.R tests/dev/script-create-individual.R tests/dev/script-create-population.R tests/dev/script-data-repository.R tests/dev/script-data-set.R tests/dev/script-demography.R tests/dev/script-molecules.R tests/dev/script-outputs.R tests/dev/script-pk-analyses.R tests/dev/script-population.R tests/dev/script-sensitivity-analysis.R tests/dev/script-simulation-batch.R tests/dev/script.R tests/testthat.R tests/testthat/_snaps/data-combined.md

tests/testthat/_snaps/plot-individual-time-profile/both-custom.svg

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tests/testthat/_snaps/plot-individual-time-profile/no-lloq.svg

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tools/check.env

update_core_files.R

vignettes/.gitignore

vignettes/PKSim-installation.Rmd vignettes/create-individual.Rmd vignettes/create-run-population.Rmd vignettes/data-combined-plotting.Rmd vignettes/data-combined.Rmd vignettes/efficient-calculations.Rmd

vignettes/images/batch_simulation.drawio.png

vignettes/images/iterative_simulation.drawio.png

vignettes/images/parallel_simulation.drawio.png

vignettes/images/simple_simulation.drawio.png

vignettes/images/simulation_lifecycle_flowcharts.drawio

vignettes/load-get.Rmd vignettes/observed-data.Rmd vignettes/ospsuite.Rmd vignettes/pk-analysis.Rmd vignettes/run-simulation.Rmd vignettes/sensitivity-analysis.Rmd vignettes/set-values.Rmd vignettes/table-parameters.Rmd vignettes/unit-conversion.Rmd

Open-Systems-Pharmacology/OSPSuite-R documentation built on Feb. 14, 2025, 4:48 p.m.

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Open-Systems-Pharmacology/OSPSuite-R
R package to manipulate OSPSuite Models

Files in Open-Systems-Pharmacology/OSPSuite-R
R package to manipulate OSPSuite Models

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Open-Systems-Pharmacology/OSPSuite-R R package to manipulate OSPSuite Models

Files in Open-Systems-Pharmacology/OSPSuite-R R package to manipulate OSPSuite Models

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Open-Systems-Pharmacology/OSPSuite-R
R package to manipulate OSPSuite Models

Files in Open-Systems-Pharmacology/OSPSuite-R
R package to manipulate OSPSuite Models