{ "_id": "6a578beeff0138dec5d71478", "Package": "ospsuite.reportingframework", "Type": "Package", "Title": "Provides a framework for report generation with the ospsuite", "Version": "1.0.1", "Authors@R": "c(person(given = \"Open-Systems-Pharmacology Community\",\nrole = \"cph\"),\nperson(given = \"Katrin\",\nfamily = \"Coboeken\",\nrole = c(\"aut\", \"cre\"),\nemail = \"katrin.coboeken@bayer.com\"))", "Description": "The OSP Suite Reporting Framework, which is based on the\nesqlabsR package, is a robust tool designed to systematically\ndefine simulation scenarios, their inputs and outputs, and\nstandardize data import and matching processes. These\nfunctionalities allow for easy and automatable model execution\nand plot generation, ultimately facilitating the generation of\ncustomizable reports for OSP physiologically-based\npharmacokinetic (PBPK) models. As a result, this framework\nsignificantly enhances reporting efficiency, enabling\nresearchers to create clear, tailored reports that effectively\ncommunicate complex modeling results.", "URL": "https://www.open-systems-pharmacology.org/OSPSuite.ReportingFramework/", "License": "GPL-2 | file LICENSE", "Language": "en-US", "Encoding": "UTF-8", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "RoxygenNote": "7.3.1", "Remotes": [ "ospsuite.utils=Open-Systems-Pharmacology/OSPSuite.RUtils", "ospsuite.plots=Open-Systems-Pharmacology/OSPSuite.Plots", "ospsuite=Open-Systems-Pharmacology/OSPSuite-R", "esqlabsR=esqLABS/esqlabsR" ], "Config/pak/sysreqs": "cmake dotnet-runtime-8.0 git make libgit2-dev\nlibicu-dev libjpeg-dev libpng-dev libuv1-dev libxml2-dev\nlibssl-dev libx11-dev zlib1g-dev", "Repository": "https://open-systems-pharmacology.r-universe.dev", "Date/Publication": "2025-10-09 06:15:07 UTC", "RemoteUrl": 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configuration helper function" ], "topics": [ "addDefaultConfigForDistributionsVsDemographics" ] }, { "page": "addDefaultConfigForHistograms", "title": "Add Default Configuration for Histograms", "concept": [ "functions to generate plots displaying distribution vs demographics", "plot configuration helper function" ], "topics": [ "addDefaultConfigForHistograms" ] }, { "page": "addDefaultConfigForPKBoxwhsikerPlots", "title": "Add Default Configuration for Box-and-Whisker Plots", "concept": [ "functions to generate box whisker plots", "plot configuration helper function" ], "topics": [ "addDefaultConfigForPKBoxwhsikerPlots" ] }, { "page": "addDefaultConfigForPKForestPlots", "title": "Add Default Configuration for PK Forest Plots", "concept": [ "functions to generate forest plots", "plot configuration helper function", "plot functions" ], "topics": [ "addDefaultConfigForPKForestPlots" ] }, { "page": "addDefaultConfigForTimeProfilePlots", "title": "Add Default Configuration for Time Profile Plots", "concept": [ "plot configuration helper function", "plot functions" ], "topics": [ "addDefaultConfigForTimeProfilePlots" ] }, { "page": "addFiguresAndTables", "title": "Loop on figure keys, add figure or table", "concept": [ "markdown helper function" ], "topics": [ "addFiguresAndTables" ] }, { "page": "addMessageToLog", "title": "Used to add message to log file", "concept": [ "log file management" ], "topics": [ "addMessageToLog" ] }, { "page": "addPredictedValues", "title": "Interpolates observed data based on simulated data.", "topics": [ "addPredictedValues" ] }, { "page": "addSensitivityTable", "title": "Add Sensitivity Table to Project Configuration", "topics": [ "addSensitivityTable" ] }, { "page": "aggregateObservedDataGroups", "title": "Aggregate Observed Data Groups", "concept": [ "observed data processing" ], "topics": [ "aggregateObservedDataGroups" ] }, { "page": "BIOMETRICUNITS", "title": "enumeration biometric units", "concept": [ "enumerations" ], "topics": [ "BIOMETRICUNITS" ] }, { "page": "calculatePKParameterForScenarios", "title": "Calculate Pharmacokinetic (PK) Parameters", "concept": [ "scenario management" ], "topics": [ "calculatePKParameterForScenarios" ] }, { "page": "captureLog", "title": "function that catches messages, warnings, and errors. This function has to be initialized by `initLogfunction` function", "concept": [ "log file management" ], "topics": [ "captureLog" ] }, { "page": "convertDataCombinedToDataTable", "title": "Converts object of class `DataCombined` to data.table with attributes.", "concept": [ "observed data processing" ], "topics": [ "convertDataCombinedToDataTable" ] }, { "page": "convertDataTableToDataCombined", "title": "Converts data.table with observed data to `ospsuite::DataCombined` object", "concept": [ "observed data processing" ], "topics": [ "convertDataTableToDataCombined" ] }, { "page": "createDocumentFromTemplate", "title": "Opens a template file a new document", "concept": [ "Addins Support" ], "topics": [ "createDocumentFromTemplate" ] }, { "page": "createProjectConfiguration", "title": "#' Create a `ProjectConfiguration`", "concept": [ "project initialization" ], "topics": [ "createProjectConfiguration" ] }, { "page": "createScenarios.wrapped", "title": "Create Scenario objects from `ScenarioConfiguration` objects", "concept": [ "scenario management" ], "topics": [ "createScenarios.wrapped" ] }, { "page": "createWorkflowTemplate", "title": "Opens the workflow template as new document", "concept": [ "Addins Support" ], "topics": [ "createWorkflowTemplate" ] }, { "page": "DATACLASS", "title": "enumeration keys for `DataClass`", "concept": [ "enumerations" ], "topics": [ "DATACLASS" ] }, { "page": "EXPORTDIR", "title": "enumeration keys for exportDirectories", "concept": [ "enumerations" ], "topics": [ "EXPORTDIR" ] }, { "page": "exportRandomPopulations", "title": "Export Random Populations", "concept": [ "population export" ], "topics": [ "exportRandomPopulations" ] }, { "page": "exportSimulationWorkflowToEPackage", "title": "Export Simulation Workflow", "concept": [ "electronic package" ], "topics": [ "exportSimulationWorkflowToEPackage" ] }, { "page": "exportTLFWorkflowToEPackage", "title": "Export TLF Workflow to E-Package", "concept": [ "electronic package" ], "topics": [ "exportTLFWorkflowToEPackage" ] }, { "page": "exportVirtualTwinPopulations", "title": "Generate Virtual Twin Population", "concept": [ "population export" ], "topics": [ "exportVirtualTwinPopulations" ] }, { "page": "formatPercentiles", "title": "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.", "topics": [ "formatPercentiles" ] }, { "page": "getDataGroups", "title": "Load the Properties for Data Groups", "concept": [ "get identifier" ], "topics": [ "getDataGroups" ] }, { "page": "getModelParameterDefinitions", "title": "Load the Model Parameter Definitions", "concept": [ "get identifier" ], "topics": [ "getModelParameterDefinitions" ] }, { "page": "getOutputPathIds", "title": "Load the Output Configurations", "concept": [ "get identifier" ], "topics": [ "getOutputPathIds" ] }, { "page": "getQCpassedEnvironmentVariable", "title": "Get QC Passed Environment Variable", "concept": [ "project initialization" ], "topics": [ "getQCpassedEnvironmentVariable" ] }, { "page": "getScenarioDefinitions", "title": "Load the Scenario Definitions", "concept": [ "get identifier" ], "topics": [ "getScenarioDefinitions" ] }, { "page": "getTimeRangeTags", "title": "Load the Time Range Tags", "concept": [ "get identifier" ], "topics": [ "getTimeRangeTags" ] }, { "page": "importWorkflow", "title": "Import Workflow", "concept": [ "electronic package" ], "topics": [ "importWorkflow" ] }, { "page": "initLogfunction", "title": "Initializing a Log Function", "concept": [ "log file management" ], "topics": [ "initLogfunction" ] }, { "page": "initProject", "title": "Initialize Project Directory", "concept": [ "project initialization" ], "topics": [ "initProject" ] }, { "page": "loadConfigTableEnvironment", "title": "Load Configuration Tables", "concept": [ "get identifier" ], "topics": [ "loadConfigTableEnvironment" ] }, { "page": "loadPKParameter", "title": "Load Pharmacokinetic (PK) Parameters for Specified Scenarios", "concept": [ "scenario management" ], "topics": [ "loadPKParameter" ] }, { "page": "loadScenarioResultsToFramework", "title": "Load existing scenario results", "concept": [ "scenario management" ], "topics": [ "loadScenarioResultsToFramework" ] }, { "page": "mdBullet", "title": "Insert a bulleted item, making sure that there are sufficient newlines to build a bulleted list", "concept": [ "markdown helper function" ], "topics": [ "mdBullet" ] }, { "page": "mdBullet0", "title": "Insert a bulleted item, making sure that there are sufficient newlines to build a bulleted list", "concept": [ "markdown helper function" ], "topics": [ "mdBullet0" ] }, { "page": "mdCaption", "title": "add Caption to .Rmd", "concept": [ "markdown helper function" ], "topics": [ "mdCaption" ] }, { "page": "mdFigure", "title": "mdFigure", "concept": [ "markdown helper function" ], "topics": [ "mdFigure" ] }, { "page": "mdFootNote", "title": "add footnote lines", "concept": [ "markdown helper function" ], "topics": [ "mdFootNote" ] }, { "page": "mdHeading", "title": "mdHeading", "concept": [ "markdown helper function" ], "topics": [ "mdHeading" ] }, { "page": "mdLink", "title": "mdLink", "concept": [ "markdown helper function" ], "topics": [ "mdLink" ] }, { "page": "mdNewline", "title": "mdNewline", "concept": [ "markdown helper function" ], "topics": [ "mdNewline" ] }, { "page": "mdNewpage", "title": "mdNewpage", "concept": [ "markdown helper function" ], "topics": [ "mdNewpage" ] }, { "page": "mdPaste", "title": "mdPaste", "concept": [ "markdown helper function" ], "topics": [ "mdPaste" ] }, { "page": "mdPaste0", "title": "mdPaste0", "concept": [ "markdown helper function" ], "topics": [ "mdPaste0" ] }, { "page": "mdTable", "title": "mdTable", "concept": [ "markdown helper function" ], "topics": [ "mdTable" ] }, { "page": "mergeRmds", "title": "Creates Rmd file which include specified .Rmd s", "concept": [ "functions called by workflow script" ], "topics": [ "mergeRmds" ] }, { "page": "openEPackageTemplate", "title": "Opens the template for figure creation as new document", "concept": [ "Addins Support" ], "topics": [ "openEPackageTemplate" ] }, { "page": "openFigureTemplate", "title": "Opens the template for figure creation as new document", "concept": [ "Addins Support" ], "topics": [ "openFigureTemplate" ] }, { "page": "openWorkflowTemplate", "title": "Opens the workflow template as new document", "concept": [ "Addins Support" ], "topics": [ "openWorkflowTemplate" ] }, { "page": "ospsuite_plotPredictedVsObserved", "title": "Plots predicted vs observed data, grouped by \"group\".", "topics": [ "ospsuite_plotPredictedVsObserved" ] }, { "page": "ospsuite_plotQuantileQuantilePlot", "title": "Plots a Quantile-Quantile plot, grouped by \"group\".", "topics": [ "ospsuite_plotQuantileQuantilePlot" ] }, { "page": "ospsuite_plotResidualsAsHistogram", "title": "Plots residuals as a histogram, grouped by \"group\".", "topics": [ "ospsuite_plotResidualsAsHistogram" ] }, { "page": "ospsuite_plotResidualsVsObserved", "title": "Plots residuals vs observed values, grouped by \"group\".", "topics": [ "ospsuite_plotResidualsVsObserved" ] }, { "page": "ospsuite_plotResidualsVsTime", "title": "Plots residuals vs Time, grouped by \"group\".", "topics": [ "ospsuite_plotResidualsVsTime" ] }, { "page": "ospsuite_plotTimeProfile", "title": "Creates a time profile plot for given data.", "topics": [ "ospsuite_plotTimeProfile" ] }, { "page": "plotDistributionVsDemographics", "title": "Plot Distribution vs Demographics", "concept": [ "functions to generate plots displaying distribution vs demographics", "plot functions" ], "topics": [ "plotDistributionVsDemographics" ] }, { "page": "plotHistograms", "title": "Plot Histograms", "concept": [ "functions to generate histograms", "plot functions" ], "topics": [ "plotHistograms" ] }, { "page": "plotPKBoxwhisker", "title": "Plot PK Box-and-Whisker", "concept": [ "functions to generate box whisker plots", "plot functions" ], "topics": [ "plotPKBoxwhisker" ] }, { "page": "plotPKForestAggregatedAbsoluteValues", "title": "PK Forest Plots", "concept": [ "functions to generate forest plots", "plot functions" ], "topics": [ "plotPKForestAggregatedAbsoluteValues" ] }, { "page": "plotPKForestAggregatedRatios", "title": "PK Forest Plots", "concept": [ "functions to generate forest plots", "plot functions" ], "topics": [ "plotPKForestAggregatedRatios" ] }, { "page": "plotPKForestPointEstimateOfAbsoluteValues", "title": "PK Forest Plots", "concept": [ "functions to generate forest plots", "plot functions" ], "topics": [ "plotPKForestPointEstimateOfAbsoluteValues" ] }, { "page": "plotPKForestPointEstimateOfRatios", "title": "PK Forest Plots", "concept": [ "functions to generate forest plots", "plot functions" ], "topics": [ "plotPKForestPointEstimateOfRatios" ] }, { "page": "plotSensitivity", "title": "Plot Sensitivity Function", "concept": [ "plot functions" ], "topics": [ "plotSensitivity" ] }, { "page": "plotTimeProfiles", "title": "Generate Time Profile Panels", "concept": [ "plot functions" ], "topics": [ "plotTimeProfiles" ] }, { "page": "ProjectConfigurationRF", "title": "ProjectConfiguration", "concept": [ "project initialization" ], "topics": [ "ProjectConfigurationRF" ] }, { "page": "readObservedDataByDictionary", "title": "Read data by dictionary", "concept": [ "observed data processing" ], "topics": [ "readObservedDataByDictionary" ] }, { "page": "renderWord", "title": "converts .Rmd file to word", "topics": [ "renderWord" ] }, { "page": "runAndSaveScenarios", "title": "Run and save scenarios", "concept": [ "scenario management" ], "topics": [ "runAndSaveScenarios" ] }, { "page": "runOrLoadScenarios", "title": "Run or load scenarios", "concept": [ "scenario management" ], "topics": [ "runOrLoadScenarios" ] }, { "page": "runPlot", "title": "Run Plot Function", "topics": [ "runPlot" ] }, { "page": "runSensitivityAnalysisForScenarios", "title": "Run Sensitivity Analysis for Specified Scenarios", "topics": [ "runSensitivityAnalysisForScenarios" ] }, { "page": "saveSessionInfo", "title": "Save Session Info", "concept": [ "log file management" ], "topics": [ "saveSessionInfo" ] }, { "page": "setExportAttributes", "title": "Set Export Attributes for Plot and Table Objects", "topics": [ "setExportAttributes" ] }, { "page": "setHeadersToLowerCase", "title": "Convert Data Table Column Names to Lowercase", "concept": [ "function to read from and write to xlsx" ], "topics": [ "setHeadersToLowerCase" ] }, { "page": "setShowLogMessages", "title": "Function to switch the display of log messages on the console on and off", "concept": [ "log file management" ], "topics": [ "setShowLogMessages" ] }, { "page": "setupVirtualTwinPopConfig", "title": "Setup Virtual Twin Population Configuration", "concept": [ "population export" ], "topics": [ "setupVirtualTwinPopConfig" ] }, { "page": "setWorkflowOptions", "title": "Sets options for a reporting frame work workflow.", "concept": [ "project initialization" ], "topics": [ "setWorkflowOptions" ] }, { "page": "splitInputs", "title": "Split the elements of a vector by comma", "concept": [ "function to read from and write to xlsx" ], "topics": [ "splitInputs" ] }, { "page": "TestProjectBuilder", "title": "TestProjectBuilder", "topics": [ "TestProjectBuilder" ] }, { "page": "TIMERANGE", "title": "enumeration keys for Time range shortcut", "concept": [ "enumerations" ], "topics": [ "TIMERANGE" ] }, { "page": "updateDataGroupId", "title": "Update Data Group IDs in Project Configuration", "concept": [ "observed data processing" ], "topics": [ "updateDataGroupId" ] }, { "page": "updateOutputPathId", "title": "Update Output Path IDs in Project Configuration", "concept": [ "observed data processing" ], "topics": [ "updateOutputPathId" ] }, { "page": "validateAtleastOneEntry", "title": "check if at least one of the following columns is selected", "topics": [ "validateAtleastOneEntry" ] }, { "page": "validateConfigTablePlots", "title": "validate types of plot configuration tables", "topics": [ "validateConfigTablePlots" ] }, { "page": "validateDistributionVsDemographicsConfig", "title": "Validate Distribution vs Demographics Configuration", "concept": [ "functions 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