Package index • ospsuite.reportingframework

Workflow support functions

ProjectConfigurationRF: ProjectConfiguration

createProjectConfiguration(): #' Create a `ProjectConfiguration`

getQCpassedEnvironmentVariable(): Get QC Passed Environment Variable

initProject(): Initialize Project Directory

setWorkflowOptions(): Sets options for a reporting frame work workflow.

exportRandomPopulations(): Export Random Populations

exportVirtualTwinPopulations(): Generate Virtual Twin Population

setupVirtualTwinPopConfig(): Setup Virtual Twin Population Configuration

calculatePKParameterForScenarios(): Calculate Pharmacokinetic (PK) Parameters

createScenarios.wrapped(): Create Scenario objects from `ScenarioConfiguration` objects

loadPKParameter(): Load Pharmacokinetic (PK) Parameters for Specified Scenarios

loadScenarioResultsToFramework(): Load existing scenario results

runAndSaveScenarios(): Run and save scenarios

runOrLoadScenarios(): Run or load scenarios

Data import

addBiometricsToConfig(): Add biometrics information to config

aggregateObservedDataGroups(): Aggregate Observed Data Groups

convertDataCombinedToDataTable(): Converts object of class `DataCombined` to data.table with attributes.

convertDataTableToDataCombined(): Converts data.table with observed data to `ospsuite::DataCombined` object

readObservedDataByDictionary(): Read data by dictionary

updateDataGroupId(): Update Data Group IDs in Project Configuration

updateOutputPathId(): Update Output Path IDs in Project Configuration

validateObservedData(): Validate Observed Data

Plot Functions

Functions to be used with runPlot

addDefaultConfigForPKForestPlots(): Add Default Configuration for PK Forest Plots

addDefaultConfigForTimeProfilePlots(): Add Default Configuration for Time Profile Plots

plotDistributionVsDemographics(): Plot Distribution vs Demographics

plotHistograms(): Plot Histograms

plotPKBoxwhisker(): Plot PK Box-and-Whisker

plotPKForestAggregatedAbsoluteValues(): PK Forest Plots

plotPKForestAggregatedRatios(): PK Forest Plots

plotPKForestPointEstimateOfAbsoluteValues(): PK Forest Plots

plotPKForestPointEstimateOfRatios(): PK Forest Plots

plotSensitivity(): Plot Sensitivity Function

plotTimeProfiles(): Generate Time Profile Panels

Plot Configuration helper

Functions which support the plot configuration

addDefaultConfigForDistributionsVsDemographics(): Add Default Configuration for for distribution vs demographics plots

addDefaultConfigForHistograms(): Add Default Configuration for Histograms

addDefaultConfigForPKBoxwhsikerPlots(): Add Default Configuration for Box-and-Whisker Plots

addDefaultConfigForPKForestPlots(): Add Default Configuration for PK Forest Plots

addDefaultConfigForTimeProfilePlots(): Add Default Configuration for Time Profile Plots

Plot Config validation

Functions to validate the plot configuration

validateDistributionVsDemographicsConfig(): Validate Distribution vs Demographics Configuration

validateHistogramsConfig(): Validate Histograms Configuration

validatePKBoxwhiskerConfig(): Validate PK Box-and-Whisker Configuration Table

validatePKForestAggregatedAbsoluteValuesConfig(): Validate PK Forest Absolute Values with Variance Configuration

validatePKForestAggregatedRatiosConfig(): Validate PK Forest Ratios with Variance Configuration

validatePKForestPointEstimateOfAbsoluteValuesConfig(): Validate PK Forest Absolute Values with Confidence Intervals Configuration

validatePKForestPointEstimateOfRatiosConfig(): Validate PK Forest Ratios with Confidence Intervals Configuration

validateSensitivityConfig(): Validate Sensitivity Configuration Table

validateTimeProfilesConfig(): Validation of config table for time profiles plots

Report generation

mergeRmds(): Creates Rmd file which include specified .Rmd s

renderWord(): converts .Rmd file to word

runPlot(): Run Plot Function

setExportAttributes(): Set Export Attributes for Plot and Table Objects

Electronic Package

exportSimulationWorkflowToEPackage(): Export Simulation Workflow

exportTLFWorkflowToEPackage(): Export TLF Workflow to E-Package

importWorkflow(): Import Workflow

Reading and writing to xlsx

setHeadersToLowerCase(): Convert Data Table Column Names to Lowercase

splitInputs(): Split the elements of a vector by comma

xlsxAddDataUsingTemplate(): Add new data to a config file using a template sheet

xlsxAddSheet(): Add a new sheet to a workbook with data

xlsxCloneAndSet(): Clone a sheet and set new content

xlsxReadData(): Read data from a worksheet

xlsxWriteData(): Write data to a worksheet, clearing existing content

Log-file management

addMessageToLog(): Used to add message to log file

captureLog(): function that catches messages, warnings, and errors. This function has to be initialized by `initLogfunction` function

initLogfunction(): Initializing a Log Function

saveSessionInfo(): Save Session Info

setShowLogMessages(): Function to switch the display of log messages on the console on and off

writeTableToLog(): write a table to the logfile

writeToLog(): Writing to Log

Configuration identifier

Functions to retrieve configuration identifier

getDataGroups(): Load the Properties for Data Groups

getModelParameterDefinitions(): Load the Model Parameter Definitions

getOutputPathIds(): Load the Output Configurations

getScenarioDefinitions(): Load the Scenario Definitions

getTimeRangeTags(): Load the Time Range Tags

loadConfigTableEnvironment(): Load Configuration Tables

Addin support

Functions to support Addin

createDocumentFromTemplate(): Opens a template file a new document

createWorkflowTemplate(): Opens the workflow template as new document

openEPackageTemplate(): Opens the template for figure creation as new document

openFigureTemplate(): Opens the template for figure creation as new document

openWorkflowTemplate(): Opens the workflow template as new document

Miscellaneous

runSensitivityAnalysisForScenarios(): Run Sensitivity Analysis for Specified Scenarios

addSensitivityTable(): Add Sensitivity Table to Project Configuration

TestProjectBuilder: TestProjectBuilder

validateAtleastOneEntry(): check if at least one of the following columns is selected

validateConfigTablePlots(): validate types of plot configuration tables

validateDistributionVsDemographicsConfig(): Validate Distribution vs Demographics Configuration

validateGroupConsistency(): Validate Consistency of Values Within Groups

validateHeaders(): checks if config table header and plot rows are strict separated

validateHistogramsConfig(): Validate Histograms Configuration

validateNumericVectorColumns(): validate Numeric Range Columns

validateObservedData(): Validate Observed Data

validatePKBoxwhiskerConfig(): Validate PK Box-and-Whisker Configuration Table

validatePKForestAggregatedAbsoluteValuesConfig(): Validate PK Forest Absolute Values with Variance Configuration

validatePKForestAggregatedRatiosConfig(): Validate PK Forest Ratios with Variance Configuration

validatePKForestPointEstimateOfAbsoluteValuesConfig(): Validate PK Forest Absolute Values with Confidence Intervals Configuration

validatePKForestPointEstimateOfRatiosConfig(): Validate PK Forest Ratios with Confidence Intervals Configuration

validateSensitivityConfig(): Validate Sensitivity Configuration Table

validateTimeProfilesConfig(): Validation of config table for time profiles plots

formatPercentiles(): This function takes a numeric vector of percentiles and maps specific values to their corresponding labels. It also formats other numeric values based on whether they are integers or not.

Constants

Enumeration constants for OSPSuite.ReportingFrameworks options and scaling.

BIOMETRICUNITS: enumeration biometric units

DATACLASS: enumeration keys for `DataClass`

EXPORTDIR: enumeration keys for exportDirectories

TIMERANGE: enumeration keys for Time range shortcut

Markdown helpers

Functions that supports writing of a murkdown document

addFiguresAndTables(): Loop on figure keys, add figure or table

mdBullet(): Insert a bulleted item, making sure that there are sufficient newlines to build a bulleted list

mdBullet0(): Insert a bulleted item, making sure that there are sufficient newlines to build a bulleted list

mdCaption(): add Caption to .Rmd

mdFigure(): mdFigure

mdFootNote(): add footnote lines

mdHeading(): mdHeading

mdLink(): mdLink

mdNewline(): mdNewline

mdNewpage(): mdNewpage

mdPaste(): mdPaste

mdPaste0(): mdPaste0

mdTable(): mdTable

Temporary functions

Functions that will be moved to ospsuite.utils

ospsuite_plotPredictedVsObserved(): Plots predicted vs observed data, grouped by "group".

ospsuite_plotQuantileQuantilePlot(): Plots a Quantile-Quantile plot, grouped by "group".

ospsuite_plotResidualsAsHistogram(): Plots residuals as a histogram, grouped by "group".

ospsuite_plotResidualsVsObserved(): Plots residuals vs observed values, grouped by "group".

ospsuite_plotResidualsVsTime(): Plots residuals vs Time, grouped by "group".

ospsuite_plotTimeProfile(): Creates a time profile plot for given data.

addPredictedValues(): Interpolates observed data based on simulated data.