Package: ospsuite.reportingframework 1.0.1

Katrin Coboeken

ospsuite.reportingframework: Provides a framework for report generation with the ospsuite

The OSP Suite Reporting Framework, which is based on the esqlabsR package, is a robust tool designed to systematically define simulation scenarios, their inputs and outputs, and standardize data import and matching processes. These functionalities allow for easy and automatable model execution and plot generation, ultimately facilitating the generation of customizable reports for OSP physiologically-based pharmacokinetic (PBPK) models. As a result, this framework significantly enhances reporting efficiency, enabling researchers to create clear, tailored reports that effectively communicate complex modeling results.

Authors:Open-Systems-Pharmacology Community [cph], Katrin Coboeken [aut, cre]

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

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

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

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

On CRAN:

Conda:

2.26 score 12 scripts 109 exports 97 dependencies

Last updated from:d5b92de0e9 (on v1.0.1). Checks:8 ERROR, 1 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64ERROR283
source / vignettesERROR500
linux-release-x86_64ERROR324
macos-release-arm64ERROR222
macos-oldrel-arm64ERROR205
windows-develERROR230
windows-releaseERROR306
windows-oldrelERROR275
wasm-releaseFAIL370

Exports:addBiometricsToConfigaddDefaultConfigForDistributionsVsDemographicsaddDefaultConfigForHistogramsaddDefaultConfigForPKBoxwhsikerPlotsaddDefaultConfigForPKForestPlotsaddDefaultConfigForTimeProfilePlotsaddFiguresAndTablesaddMessageToLogaddPredictedValuesaddSensitivityTableaggregateObservedDataGroupsBIOMETRICUNITScalculatePKParameterForScenarioscaptureLogconvertDataCombinedToDataTableconvertDataTableToDataCombinedcreateDocumentFromTemplatecreateProjectConfigurationcreateScenarios.wrappedcreateWorkflowTemplateDATACLASSEXPORTDIRexportRandomPopulationsexportSimulationWorkflowToEPackageexportTLFWorkflowToEPackageexportVirtualTwinPopulationsformatPercentilesgetDataGroupsgetModelParameterDefinitionsgetOutputPathIdsgetQCpassedEnvironmentVariablegetScenarioDefinitionsgetTimeRangeTagsimportWorkflowinitLogfunctioninitProjectloadConfigTableEnvironmentloadPKParameterloadScenarioResultsToFrameworkmdBulletmdBullet0mdCaptionmdFiguremdHeadingmdLinkmdNewlinemdNewpagemdPastemdPaste0mdTablemergeRmdsopenEPackageTemplateopenFigureTemplateopenWorkflowTemplateospsuite_plotPredictedVsObservedospsuite_plotQuantileQuantilePlotospsuite_plotResidualsAsHistogramospsuite_plotResidualsVsObservedospsuite_plotResidualsVsTimeospsuite_plotTimeProfileplotDistributionVsDemographicsplotHistogramsplotPKBoxwhiskerplotPKForestAggregatedAbsoluteValuesplotPKForestAggregatedRatiosplotPKForestPointEstimateOfAbsoluteValuesplotPKForestPointEstimateOfRatiosplotSensitivityplotTimeProfilesProjectConfigurationRFreadObservedDataByDictionaryrenderWordrunAndSaveScenariosrunOrLoadScenariosrunPlotrunSensitivityAnalysisForScenariossaveSessionInfosetExportAttributessetHeadersToLowerCasesetShowLogMessagessetupVirtualTwinPopConfigsetWorkflowOptionssplitInputsTestProjectBuilderTIMERANGEupdateDataGroupIdupdateOutputPathIdvalidateAtleastOneEntryvalidateConfigTablePlotsvalidateDistributionVsDemographicsConfigvalidateGroupConsistencyvalidateHeadersvalidateHistogramsConfigvalidateNumericVectorColumnsvalidateObservedDatavalidatePKBoxwhiskerConfigvalidatePKForestAggregatedAbsoluteValuesConfigvalidatePKForestAggregatedRatiosConfigvalidatePKForestPointEstimateOfAbsoluteValuesConfigvalidatePKForestPointEstimateOfRatiosConfigvalidateSensitivityConfigvalidateTimeProfilesConfigwriteTableToLogwriteToLogxlsxAddDataUsingTemplatexlsxAddSheetxlsxCloneAndSetxlsxReadDataxlsxWriteData

Dependencies:backportsbase64encbitbit64bootbslibcachemcheckmateclicliprcodetoolscommonmarkcowplotcpp11crayoncurldata.tabledigestdoParalleldplyresqlabsRevaluatefarverfastmapfitdistrplusfontawesomeforeachfsgenericsggh4xggnewscaleggplot2ggsciggtextgluegridtextgtablehighrhmshtmltoolsisobanditeratorsjpegjquerylibjsonliteknitrlabelinglatticelifecyclelitedownloggermagrittrmarkdownMASSMatrixmemoisemimeopenxlsxospsuiteospsuite.plotsospsuite.utilspatchworkpillarpkgconfigpngprettyunitsprogresspurrrR6rappdirsRColorBrewerRcppreadrrlangrmarkdownrSharpS7sassscalesstringistringrsurvivaltibbletidyrtidyselecttinytextlftzdbutf8vctrsviridisLitevroomwithrxfunxml2yamlzip

Readme and manuals

Help Manual

Help pageTopics
Add biometrics information to configaddBiometricsToConfig
Add Default Configuration for for distribution vs demographics plotsaddDefaultConfigForDistributionsVsDemographics
Add Default Configuration for HistogramsaddDefaultConfigForHistograms
Add Default Configuration for Box-and-Whisker PlotsaddDefaultConfigForPKBoxwhsikerPlots
Add Default Configuration for PK Forest PlotsaddDefaultConfigForPKForestPlots
Add Default Configuration for Time Profile PlotsaddDefaultConfigForTimeProfilePlots
Loop on figure keys, add figure or tableaddFiguresAndTables
Used to add message to log fileaddMessageToLog
Interpolates observed data based on simulated data.addPredictedValues
Add Sensitivity Table to Project ConfigurationaddSensitivityTable
Aggregate Observed Data GroupsaggregateObservedDataGroups
enumeration biometric unitsBIOMETRICUNITS
Calculate Pharmacokinetic (PK) ParameterscalculatePKParameterForScenarios
function that catches messages, warnings, and errors. This function has to be initialized by `initLogfunction` functioncaptureLog
Converts object of class `DataCombined` to data.table with attributes.convertDataCombinedToDataTable
Converts data.table with observed data to `ospsuite::DataCombined` objectconvertDataTableToDataCombined
Opens a template file a new documentcreateDocumentFromTemplate
#' Create a `ProjectConfiguration`createProjectConfiguration
Create Scenario objects from `ScenarioConfiguration` objectscreateScenarios.wrapped
Opens the workflow template as new documentcreateWorkflowTemplate
enumeration keys for `DataClass`DATACLASS
enumeration keys for exportDirectoriesEXPORTDIR
Export Random PopulationsexportRandomPopulations
Export Simulation WorkflowexportSimulationWorkflowToEPackage
Export TLF Workflow to E-PackageexportTLFWorkflowToEPackage
Generate Virtual Twin PopulationexportVirtualTwinPopulations
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.formatPercentiles
Load the Properties for Data GroupsgetDataGroups
Load the Model Parameter DefinitionsgetModelParameterDefinitions
Load the Output ConfigurationsgetOutputPathIds
Get QC Passed Environment VariablegetQCpassedEnvironmentVariable
Load the Scenario DefinitionsgetScenarioDefinitions
Load the Time Range TagsgetTimeRangeTags
Import WorkflowimportWorkflow
Initializing a Log FunctioninitLogfunction
Initialize Project DirectoryinitProject
Load Configuration TablesloadConfigTableEnvironment
Load Pharmacokinetic (PK) Parameters for Specified ScenariosloadPKParameter
Load existing scenario resultsloadScenarioResultsToFramework
Insert a bulleted item, making sure that there are sufficient newlines to build a bulleted listmdBullet
Insert a bulleted item, making sure that there are sufficient newlines to build a bulleted listmdBullet0
add Caption to .RmdmdCaption
mdFiguremdFigure
add footnote linesmdFootNote
mdHeadingmdHeading
mdLinkmdLink
mdNewlinemdNewline
mdNewpagemdNewpage
mdPastemdPaste
mdPaste0mdPaste0
mdTablemdTable
Creates Rmd file which include specified .Rmd smergeRmds
Opens the template for figure creation as new documentopenEPackageTemplate
Opens the template for figure creation as new documentopenFigureTemplate
Opens the workflow template as new documentopenWorkflowTemplate
Plots predicted vs observed data, grouped by "group".ospsuite_plotPredictedVsObserved
Plots a Quantile-Quantile plot, grouped by "group".ospsuite_plotQuantileQuantilePlot
Plots residuals as a histogram, grouped by "group".ospsuite_plotResidualsAsHistogram
Plots residuals vs observed values, grouped by "group".ospsuite_plotResidualsVsObserved
Plots residuals vs Time, grouped by "group".ospsuite_plotResidualsVsTime
Creates a time profile plot for given data.ospsuite_plotTimeProfile
Plot Distribution vs DemographicsplotDistributionVsDemographics
Plot HistogramsplotHistograms
Plot PK Box-and-WhiskerplotPKBoxwhisker
PK Forest PlotsplotPKForestAggregatedAbsoluteValues
PK Forest PlotsplotPKForestAggregatedRatios
PK Forest PlotsplotPKForestPointEstimateOfAbsoluteValues
PK Forest PlotsplotPKForestPointEstimateOfRatios
Plot Sensitivity FunctionplotSensitivity
Generate Time Profile PanelsplotTimeProfiles
ProjectConfigurationProjectConfigurationRF
Read data by dictionaryreadObservedDataByDictionary
converts .Rmd file to wordrenderWord
Run and save scenariosrunAndSaveScenarios
Run or load scenariosrunOrLoadScenarios
Run Plot FunctionrunPlot
Run Sensitivity Analysis for Specified ScenariosrunSensitivityAnalysisForScenarios
Save Session InfosaveSessionInfo
Set Export Attributes for Plot and Table ObjectssetExportAttributes
Convert Data Table Column Names to LowercasesetHeadersToLowerCase
Function to switch the display of log messages on the console on and offsetShowLogMessages
Setup Virtual Twin Population ConfigurationsetupVirtualTwinPopConfig
Sets options for a reporting frame work workflow.setWorkflowOptions
Split the elements of a vector by commasplitInputs
TestProjectBuilderTestProjectBuilder
enumeration keys for Time range shortcutTIMERANGE
Update Data Group IDs in Project ConfigurationupdateDataGroupId
Update Output Path IDs in Project ConfigurationupdateOutputPathId
check if at least one of the following columns is selectedvalidateAtleastOneEntry
validate types of plot configuration tablesvalidateConfigTablePlots
Validate Distribution vs Demographics ConfigurationvalidateDistributionVsDemographicsConfig
Validate Consistency of Values Within GroupsvalidateGroupConsistency
checks if config table header and plot rows are strict separatedvalidateHeaders
Validate Histograms ConfigurationvalidateHistogramsConfig
validate Numeric Range ColumnsvalidateNumericVectorColumns
Validate Observed DatavalidateObservedData
Validate PK Box-and-Whisker Configuration TablevalidatePKBoxwhiskerConfig
Validate PK Forest Absolute Values with Variance ConfigurationvalidatePKForestAggregatedAbsoluteValuesConfig
Validate PK Forest Ratios with Variance ConfigurationvalidatePKForestAggregatedRatiosConfig
Validate PK Forest Absolute Values with Confidence Intervals ConfigurationvalidatePKForestPointEstimateOfAbsoluteValuesConfig
Validate PK Forest Ratios with Confidence Intervals ConfigurationvalidatePKForestPointEstimateOfRatiosConfig
Validate Sensitivity Configuration TablevalidateSensitivityConfig
Validation of config table for time profiles plotsvalidateTimeProfilesConfig
write a table to the logfilewriteTableToLog
Writing to LogwriteToLog
Add new data to a config file using a template sheetxlsxAddDataUsingTemplate
Add a new sheet to a workbook with dataxlsxAddSheet
Clone a sheet and set new contentxlsxCloneAndSet
Read data from a worksheetxlsxReadData
Write data to a worksheet, clearing existing contentxlsxWriteData