Package index • ospsuite.reportingengine

Working with Workflow objects

Functions and classes for creating and working with Workflow objects

MeanModelWorkflow: MeanModelWorkflow

PopulationWorkflow: PopulationWorkflow

QualificationWorkflow: QualificationWorkflow

activateWorkflowTasks(): activateWorkflowTasks

addStudyParameters(): addStudyParameters

addXParametersForDemographyPlot(): addXParametersForDemographyPlot

addXParametersForPKParametersPlot() addXParametersForPkParametersPlot(): addXParametersForPKParametersPlot

addYParametersForDemographyPlot(): addYParametersForDemographyPlot

addYParametersForPKParametersPlot() addYParametersForPkParametersPlot(): addYParametersForPKParametersPlot

checkTaskInputsExist(): checkTaskInputsExist

createWorkflowFromExcelInput(): createWorkflowFromExcelInput

getMeanSensitivityAnalysisResultsFileNames(): getMeanSensitivityAnalysisResultsFileNames

getOutputPathsInSimulationSet(): getOutputPathsInSimulationSet

getPKAnalysisResultsFileNames() getPkAnalysisResultsFileNames(): getPKAnalysisResultsFileNames

getPKParameterGroupsInOutput(): getPKParameterGroupsInOutput

getPKParametersInOutput(): getPKParametersInOutput

getPKParametersInSimulationSet(): getPKParametersInSimulationSet

getPopulationPKData(): getPopulationPKData

getPopulationPKMetaData(): getPopulationPKMetaData

getPopulationSensitivityAnalysisResultsFileNames(): getPopulationSensitivityAnalysisResultsFileNames

getSimulationDescriptor(): getSimulationDescriptor

getSimulationParameterDisplayPaths(): getSimulationParameterDisplayPaths

getSimulationResultFileNames(): getSimulationResultFileNames

getTaskInputs(): getTaskInputs

getWorkflowParameterDisplayPaths(): getWorkflowParameterDisplayPaths

getWorkflowReferencePopulationName(): getWorkflowReferencePopulationName

getXParametersForDemographyPlot(): getXParametersForDemographyPlot

getXParametersForPKParametersPlot() getXParametersForPkParametersPlot(): getXParametersForPKParametersPlot

getYParametersForDemographyPlot(): getYParametersForDemographyPlot

getYParametersForPKParametersPlot() getYParametersForPkParametersPlot(): getYParametersForPKParametersPlot

inactivateWorkflowTasks(): inactivateWorkflowTasks

setSimulationDescriptor(): setSimulationDescriptor

setWorkflowParameterDisplayPaths(): setWorkflowParameterDisplayPaths

setWorkflowParameterDisplayPathsFromFile(): setWorkflowParameterDisplayPathsFromFile

setXParametersForDemographyPlot(): setXParametersForDemographyPlot

setXParametersForPKParametersPlot() setXParametersForPkParametersPlot(): setXParametersForPKParametersPlot

setYParametersForDemographyPlot(): setYParametersForDemographyPlot

setYParametersForPKParametersPlot() setYParametersForPkParametersPlot(): setYParametersForPKParametersPlot

Simulation Sets and Outputs

Classes required for creating workflows

PopulationSimulationSet: PopulationSimulationSet

SimulationSet: SimulationSet

getOutputPathsInSimulationSet(): getOutputPathsInSimulationSet

getPKParametersInSimulationSet(): getPKParametersInSimulationSet

Output: Output

getPKParameterGroupsInOutput(): getPKParameterGroupsInOutput

getPKParametersInOutput(): getPKParametersInOutput

DataSource: DataSource

PkParameterInfo: PkParameterInfo

loadStudyDesign(): loadStudyDesign

Workflow tasks

Functions and classes for creating and working with workflow tasks

GofPlotTask: GofPlotTask

PlotTask: PlotTask

PopulationPlotTask: PopulationPlotTask

PopulationSensitivityAnalysisTask: PopulationSensitivityAnalysisTask

QualificationTask: QualificationTask

SensitivityAnalysisTask: SensitivityAnalysisTask

Task: Task

addUserDefinedTask(): addUserDefinedTask

loadCalculatePKParametersTask(): loadCalculatePKParametersTask

loadCalculateSensitivityTask(): loadCalculateSensitivityTask

loadGOFMergedTask(): loadGOFMergedTask

loadPlotAbsorptionTask(): loadPlotAbsorptionTask

loadPlotDDIRatioTask(): loadPlotDDIRatioTask

loadPlotDemographyTask(): loadPlotDemographyTask

loadPlotMassBalanceTask(): loadPlotMassBalanceTask

loadPlotPKParametersTask(): loadPlotPKParametersTask

loadPlotPKRatioTask(): loadPlotPKRatioTask

loadPlotSensitivityTask(): loadPlotSensitivityTask

loadPlotTimeProfilesAndResidualsTask(): loadPlotTimeProfilesAndResidualsTask

loadQualificationComparisonTimeProfileTask(): loadQualificationComparisonTimeProfileTask

loadQualificationTimeProfilesTask(): loadPlotTimeProfilesTask

loadSimulateTask(): loadSimulateTask

SensitivityPlotSettings: SensitivityPlotSettings

saveTaskResults(): saveTaskResults

Qualification Workflows

Functions and classes dedicated to Qualification Workflows

ConfigurationPlan: ConfigurationPlan

QualificationVersionInfo: QualificationVersionInfo

adjustTitlePage(): adjustTitlePage

loadConfigurationPlan(): loadConfigurationPlan

loadQualificationWorkflow(): loadQualificationWorkflow

startQualificationRunner(): startQualificationRunner

Writing and formatting reports

Functions for facilitating the writing and formatting of markdown and word reports

addFigureChunk(): addFigureChunk

addTableChunk(): addTableChunk

addTextChunk(): addTextChunk

anchor(): anchor

copyReport(): copyReport

getAnchorName(): getAnchorName

getFigurePathsFromReport(): getFigurePathsFromReport

hasAnchor(): hasAnchor

mergeMarkdownFiles(): mergeMarkdownFiles

renderReport(): renderReport

renderWordReport(): renderWordReport

resetReport(): resetReport

trimFile(): trimFile

Enum Helpers

Enums listing available values for specific properties

AllAvailableTasks: AllAvailableTasks

ApplicationRanges: ApplicationRanges

DataSelectionKeys: DataSelectionKeys

PopulationWorkflowTypes: PopulationWorkflowTypes

ResidualScales: ResidualScales

StandardPlotTasks: StandardPlotTasks

StandardSimulationTasks: StandardSimulationTasks

StatisticsTypes: StatisticsTypes

reSettingsNames: reSettingsNames

Default Settings

Functions for defining default package or workflow settings.

setDefaultAutoAxisLimitMargin(): setDefaultAutoAxisLimitMargin

setDefaultBins(): setDefaultBins

setDefaultMCRandomSeed(): setDefaultMCRandomSeed

setDefaultMCRepetitions(): setDefaultMCRepetitions

setDefaultNumericFormat(): setDefaultNumericFormat

setDefaultPlotFormat(): setDefaultPlotFormat

setDefaultREErrorbarCapSize(): setDefaultREErrorbarCapSize

setDefaultStairstep(): setDefaultStairstep

setDefaultTheme(): setDefaultTheme

setDefaultThemeFromJson(): setDefaultThemeFromJson

setDefaultTimeProfileStatistics(): setDefaultTimeProfileStatistics

getDefaultDemographyXParameters(): getDefaultDemographyXParameters

getDefaultMCRandomSeed(): getDefaultMCRandomSeed

getDefaultMCRepetitions(): getDefaultMCRepetitions

getDefaultPKParametersXParameters() getDefaultPkParametersXParameters(): getDefaultPKParametersXParameters

getDefaultRETheme(): getDefaultRETheme

setPlotFormat(): setPlotFormat

getRESettings(): getRESettings

loadRESettings(): loadRESettings

saveRESettings(): saveRESettings Save the current reporting engine global settings in a .RData file

resetRESettingsToDefault(): resetRESettingsToDefault

Simulated and observed data helpers

Helper functions for working with simulated and observed data.

calculateArithmeticErrorRange(): calculateArithmeticErrorRange

calculateGeometricErrorRange(): calculateGeometricErrorRange

calculateGMFE(): calculateGMFE

displayConfigurationPlanPlotInfo(): displayConfigurationPlanPlotInfo

getResiduals(): getResiduals

measureValuesBetween(): measureValuesBetween

geomean(): geomean

geomeanDividedBySD(): geomeanDividedBySD

geomeanMultipliedBySD(): geomeanMultipliedBySD

getStatisticsFromType(): getStatisticsFromType

readObservedDataFile(): readObservedDataFile

lastPathElement(): lastPathElement

evalDataFilter(): evalDataFilter

getSelectedRows(): getSelectedRows

getSelectedData(): getSelectedData

loadSimulationWithUpdatedPaths(): loadSimulationWithUpdatedPaths

loadWorkflowPopulation(): loadWorkflowPopulation

getMolWeightForCompound(): getMolWeightForCompound

plotAbsorptionTimeProfile(): plotAbsorptionTimeProfile

plotDemographyHistogram(): plotDemographyHistogram

plotDemographyRange(): plotDemographyRange

plotMeanTimeProfile(): plotMeanTimeProfile

plotMeanTimeProfileLog(): plotMeanTimeProfileLog

plotPopTimeProfile(): plotPopTimeProfile

plotPopTimeProfileLog(): plotPopTimeProfileLog

ratioBoxplot(): ratioBoxplot

vpcParameterPlot(): vpcParameterPlot

addLineBreakToCaption(): addLineBreakToCaption

AggregationConfiguration: AggregationConfiguration

prettyCaption(): prettyCaption

removeForbiddenLetters(): removeForbiddenLetters

trimFileName(): trimFileName

Parallel computation helpers

Helper functions for working with parallel simulations and sensitivity analyses.

analyzeCoreSensitivity(): analyzeCoreSensitivity

analyzeSensitivity(): analyzeSensitivity

isLoadedPackage(): isLoadedPackage

isLoadedPopulation(): isLoadedPopulation

isLoadedSimulation(): isLoadedSimulation

generateResultFileNames(): generateResultFileNames

simulateModelOnCore(): simulateModelOnCore

updateSimulationIndividualParameters(): updateSimulationIndividualParameters

Logging system

Helper functions for working with workflow logs.

LogTypes: LogTypes

logInfo(): logInfo

logError(): logError

logDebug(): logDebug

logCatch(): logCatch

saveLogs(): saveLogs

saveLogsToJson(): saveLogsToJson

showLogMessages(): showLogMessages

displayDebugLogs(): displayDebugLogs

getReportingEngineInfo(): getReportingEngineInfo