_pkgdown.yml

url: https://gilead-biostats.github.io/gsm

template:
  bootstrap: 5
  bootswatch: yeti
  includes:
    in_header: '<link href="pkgdown/extra.css" rel="stylesheet">'

navbar:
  structure:
    left: [articles, Reports, reference, news]
    right: [search, github]
  components:
    Reports:
      text: Sample Reports
      menu:
        - text: Site Report
          href: report_kri_site.html
        - text: Country Report
          href: report_kri_country.html

articles:
  - title: "Workflows"
    navbar: "Workflows"
    contents:
      - DataModel
      - Cookbook
      - DataAnalysis
      - DataReporting
      - gsmExtensions
      - articles/KRIMethod
  - title: "Quality"
    navbar: "Quality"
    contents:
      - articles/QualificationWorkflow
      - articles/Qualification
      - articles/ContributorGuidelines

reference:
  - title: Visualize
    desc: Generate a visualization from the Assessment results
  - contents:
      - starts_with("Visualize_")
      - starts_with("Widget_")
      - Analyze_NormalApprox_PredictBounds
      - Analyze_Poisson_PredictBounds

  - title: Analyze
    desc: Conduct statistical analysis based on input data
  - contents:
      - Analyze_NormalApprox
      - Analyze_Identity
      - Analyze_Fisher
      - Analyze_Poisson

  - title: Data Pipeline
    desc: Create site-level summary, analyzed, and flagged data for an assessment
  - contents:
      - Input_Rate
      - Transform_Count
      - Transform_Rate
      - Flag
      - Flag_NormalApprox
      - Flag_Poisson
      - Summarize

  - title: Reporting
    desc: Creates summary tables and HTML objects to create a report
  - contents:
      - Report_FlagOverTime
      - Report_FormatFlag
      - Report_KRI
      - Report_MetricCharts
      - Report_MetricTable
      - Report_StudyInfo


  - title: Utility
    desc: Utility functions for use within the Data Model
  - contents:
     -  ApplySpec
     -  BindResults
     -  cli_fmt
     -  CalculatePercentage
     -  CheckSpec
     -  CombineSpecs
     -  FilterByLatestSnapshotDate
     -  FilterByFlags
     -  GetStrFunctionIfNamespaced
     -  Ingest
     -  LogMessage
     -  MakeBounds
     -  MakeCharts
     -  MakeMetric
     -  MakeMetricTable
     -  MakeLongMeta
     -  MakeParamLabels
     -  MakeParamLabelsList
     -  MakeStudyInfo
     -  MakeWideGroups
     -  MakeWorkflowList
     -  ParseThreshold
     -  RenderRmd
     -  RunStep
     -  RunQuery
     -  RunWorkflow
     -  RunWorkflows
     -  SetLogger
     -  stop_if
     -  UseClindata

  - title: Sample Data
    desc: data used for examples and testing
  - contents:
      - analyticsInput
      - analyticsSummary
      - reportingBounds
      - reportingGroups
      - reportingMetrics
      - reportingResults
      - reportingBounds_country
      - reportingGroups_country
      - reportingMetrics_country
      - reportingResults_country