_pkgdown.yml

template:
  params:
    bootswatch: cosmo
    
home:
  links:
  - text: Ask a question
    href: http://forums.ohdsi.org
    
navbar:
  structure:
    left:
    - home
    - intro
    - videos
    - reference
    - articles
    - tutorial
    - bestpractice
    - news
    right: [hades, github]
  components:
    home:
      icon: fa-home fa-lg
      href: index.html
    reference:
      text: Reference
      href: reference/index.html
    intro:
      text: Get started
      href: articles/InstallationGuide.html
    videos:
      text: Videos
      href: articles/Videos.html
    bestpractice:
      text: Best Practices
      href: articles/BestPractices.html
    news:
      text: Changelog
      href: news/index.html
    tutorial:
      text: Tutorial
      href: https://www.ohdsi.org/past-events/patient-level-prediction/
    github:
      icon: fa-github fa-lg
      href: https://github.com/OHDSI/PatientLevelPrediction
    hades:
      text: hadesLogo
      href: https://ohdsi.github.io/Hades

reference:
  - title: "Extracting data from the OMOP CDM database"
    desc: >
      Functions for getting the necessary data from the database in Common Data Model and saving/loading.
    contents:
      - createDatabaseDetails
      - createRestrictPlpDataSettings
      - getPlpData
      - savePlpData
      - loadPlpData   
  - title: "Settings for designing a prediction models"
    desc: >
      Design settings required when developing a model.
    contents:
      - createStudyPopulationSettings
      - createDefaultSplitSetting
      - createSampleSettings
      - createFeatureEngineeringSettings
      - createPreprocessSettings
  - title: "Execution settings when developing a model"
    desc: >
      Execution settings required when developing a model.
    contents:
      - createLogSettings
      - createExecuteSettings
  - title: "Binary Classification Models"
    desc: >
      Functions for setting binary classifiers and their hyper-parameter search.
    contents:
      - setAdaBoost
      - setDecisionTree
      - setGradientBoostingMachine
      - setKNN
      - setLassoLogisticRegression
      - setMLP
      - setNaiveBayes
      - setRandomForest
      - setSVM
  - title: "Survival Models"
    desc: >
      Functions for setting survival models and their hyper-parameter search.
    contents:
      - setCoxModel
  - title: "Single Patient-Level Prediction Model"
    desc: >
      Functions for training/evaluating/applying a single patient-level-prediction model
    contents:
      - runPlp
      - externalValidateDbPlp
      - savePlpModel
      - loadPlpModel
      - savePlpResult
      - loadPlpResult
  - title: "Multiple Patient-Level Prediction Models"
    desc: >
      Functions for training mutliple patient-level-prediction model in an efficient way.
    contents:
      - createModelDesign
      - runMultiplePlp  
      - validateMultiplePlp
      - savePlpAnalysesJson 
      - loadPlpAnalysesJson
  - title: "Saving results into database"
    desc: >
      Functions for saving the prediction model and performances into a database.
    contents:
      - createPlpResultTables
      - populatePlpResultTables     
  - title: "Shiny Viewers"
    desc: >
      Functions for viewing results via a shiny app
    contents:
      - viewPlp
      - viewMultiplePlp
      - viewDatabaseResultPlp
  - title: "Plotting"
    desc: >
      Functions for various performance plots
    contents:
      - plotPlp
      - plotSparseRoc
      - plotSmoothCalibration
      - plotSparseCalibration
      - plotSparseCalibration2
      - plotDemographicSummary
      - plotF1Measure
      - plotGeneralizability
      - plotPrecisionRecall
      - plotPredictedPDF
      - plotPreferencePDF
      - plotPredictionDistribution
      - plotVariableScatterplot
  - title: "Learning Curves"
    desc: >
      Functions for creating and plotting learning curves
    contents:
      - createLearningCurve
      - plotLearningCurve
  - title: "Simulation"
    desc: >
      Functions for simulating cohort method data objects.
    contents:
      - simulatePlpData