_pkgdown.yml

url: https://www.open-systems-pharmacology.org/OSPSuite.ReportingEngine/

template:
  bootstrap: 5

development:
  mode: !expr Sys.getenv('PKGDOWN_MODE')

reference:
- title: "Working with Workflow objects"
  desc: "Functions and classes for creating and working with Workflow objects"
  contents: 
  - has_concept("workflows")
  - has_concept("workflow helpers")
  - matches("createWorkflowFromExcelInput")
- title: "Simulation Sets and Outputs"
  desc: "Classes required for creating workflows"
  contents: 
  - matches("SimulationSet")
  - matches("PopulationSimulationSet")
  - matches("Output")
  - matches("DataSource")
  - matches("PkParameterInfo")
  - matches("loadStudyDesign")
- title: "Workflow tasks"
  desc: "Functions and classes for creating and working with workflow tasks"
  contents: 
  - has_concept("workflow tasks")
  - matches("SensitivityPlotSettings")
  - matches("saveTaskResults")
- title: "Qualification Workflows"
  desc: "Functions and classes dedicated to Qualification Workflows"
  contents: 
  - has_concept("qualification workflow")
  - matches("QualificationVersionInfo")  
- title: "Writing and formatting reports"
  desc: "Functions for facilitating the writing and formatting of markdown and word reports"
  contents: 
  - has_concept("reporting")
- title: "Enum Helpers"
  desc: "Enums listing available values for specific properties"
  contents: 
  - has_concept("enum helpers")
- title: "Default Settings"
  desc: "Functions for defining default package or workflow settings."
  contents:
  - starts_with("setDefault")
  - matches("setWatermarkConfiguration")
  - starts_with("getDefault")
  - matches("setPlotFormat")
  - ends_with("RESettings")
  - matches("resetRESettingsToDefault")
- title: "Simulated and observed data helpers"
  desc: "Helper functions for working with simulated and observed data."
  contents:
  - matches("calculateArithmeticErrorRange")
  - matches("calculateGeometricErrorRange")
  - matches("calculateGMFE")
  - matches("calculateResiduals")
  - matches("displayConfigurationPlanPlotInfo")
  - matches("getResiduals")
  - matches("isBetween")
  - matches("measureValuesBetween")
  - matches("geomean")
  - matches("geomeanDividedBySD")
  - matches("geomeanMultipliedBySD")
  - matches("getStatisticsFromType")
  - matches("readObservedDataFile")
  - matches("lastPathElement")
  - matches("evalDataFilter")
  - matches("getSelectedRows")
  - matches("getSelectedData")
  - matches("loadSimulationWithUpdatedPaths")
  - matches("loadWorkflowPopulation")
  - matches("getMolWeightForCompound")
  - matches("plotAbsorptionTimeProfile")
  - matches("plotDemographyHistogram")
  - matches("plotDemographyRange")
  - matches("plotMassBalanceCumulativeTimeProfile")
  - matches("plotMassBalancePieChart")
  - matches("plotMassBalanceTimeProfile")
  - matches("plotMeanObsVsPred")
  - matches("plotMeanResVsPred")
  - matches("plotMeanResVsTime")
  - matches("plotMeanTimeProfile")
  - matches("plotPopTimeProfile")
  - matches("plotPopTimeProfileLog")
  - matches("plotResidualsHistogram")
  - matches("plotResidualsQQPlot")
  - matches("ratioBoxplot")
  - matches("vpcParameterPlot")
  - matches("addLineBreakToCaption")
  - matches("AggregationConfiguration")
  - matches("prettyCaption")
  - matches("removeForbiddenLetters")
  - matches("trimFileName")
- title: "Parallel computation helpers"
  desc: "Helper functions for working with parallel simulations and sensitivity analyses."
  contents:
  - matches("analyzeCoreSensitivity")
  - matches("analyzeSensitivity")
  - starts_with("isLoaded")
  - matches("generateResultFileNames")
  - matches("simulateModelOnCore")
  - matches("updateSimulationIndividualParameters")
- title: "Logging system"
  desc: "Helper functions for working with workflow logs."
  contents:
  - matches("LogTypes")
  - matches("logInfo")
  - matches("logError")
  - matches("logDebug")
  - matches("logCatch")
  - matches("saveLogs")
  - matches("saveLogsToJson")
  - matches("showLogMessages")
  - matches("displayDebugLogs")
  - matches("getReportingEngineInfo")