_pkgdown.yml

navbar:
  structure:
    left:
    - home
    - FATE
    - RFate
    - reference
    right:
    - download
    - github
  components:
    home:
      icon: fa-home fa-lg
      href: index.html
    reference:
      text: Reference
      icon: fa-book fa-lg
      href: reference/index.html
    FATE:
      text: FATE
      icon: fab fa-pagelines
      menu:
        - text: "---------"
        - text: Publications
          href: articles/fate_tutorial_0_publications.html
        - text: Modelling framework
          href: articles/fate_tutorial_0_modelling_framework.html
        - text: "---------"
        - text: a. Principle of PFG
          href: articles/fate_tutorial_1_PFG.html
        - text: b. Run a FATE simulation
          href: articles/fate_tutorial_2_RUN_SIMULATION.html
        - text: c. Use a FATE module
          href: articles/fate_tutorial_3_MODULES.html
    RFate:
      text: RFate
      icon: fas fa-toolbox
      menu:
        - text: "---------"
        - text: Build PFG
          icon: fa-battery-quarter
          href: articles/rfate_tutorial_1_PFG.html
        - text: Build parameter files
          icon: fa-battery-half
          href: articles/rfate_tutorial_2_params.html
        - text: Build graphics
          icon: fa-battery-three-quarters
          href: articles/rfate_tutorial_3_graphics.html
        - text: "---------"
    Interface:
      text: SHINY interface
      icon: fas fa-desktop
      href: articles/interface_tutorial_0_presentation.html
    articles:
    download:
      text: 'Download Current Version'
      icon: fa-rocket fa-lg
      href: archive/RFate_0.2.0.9000.tar.gz
    github:
      icon: fa-github fa-lg
      href: https://github.com/MayaGueguen/RFate.git
      

reference:
  - title: Datasets
    desc:  Used in the examples.
    contents:
      - "DATASET_Bauges_PFG"
  - title: Interface
    desc:  Graphical User Interface (shiny application)
    contents:
      - "RFATE.run"
  - title: Build Plant Functional Groups (PFG)
    desc:  Functions to select dominant species, compute functional distance between species and build clusters.
    contents:
      - "PRE_FATE.abundBraunBlanquet"
      - "PRE_FATE.selectDominant"
      - "PRE_FATE.speciesDistance"
      - "PRE_FATE.speciesClustering_step1"
      - "PRE_FATE.speciesClustering_step2"
      - "PRE_FATE.speciesClustering_step3"
  - title: Create FATE parameter files
    desc:  Create user-friendly directory tree, parameter and simulation files for FATE simulation.
    contents:
      - "PRE_FATE.skeletonDirectory"
      - "PRE_FATE.params_PFGsuccession"
      - "PRE_FATE.params_PFGlight"
      - "PRE_FATE.params_PFGsoil"
      - "PRE_FATE.params_PFGdispersal"
      - "PRE_FATE.params_PFGdisturbance"
      - "PRE_FATE.params_PFGdrought"
      - "PRE_FATE.params_changingYears"
      - "PRE_FATE.params_savingYears"
      - "PRE_FATE.params_globalParameters"
      - "PRE_FATE.params_simulParameters"
      - "PRE_FATE.params_multipleSet"
  - title: Run FATE simulation
    contents:
      - "FATE.run"
  - title: Analyze FATE outputs
    desc:  Evalute predicted maps, produce summary and dynamic graphics.
    contents:
      - "POST_FATE.graphics"
      - "POST_FATE.temporalEvolution"
      - "POST_FATE.graphic_evolutionCoverage"
      - "POST_FATE.graphic_evolutionPixels"
      - "POST_FATE.graphic_evolutionStability"
      - "POST_FATE.relativeAbund"
      - "POST_FATE.graphic_validationStatistics"
      - "POST_FATE.binaryMaps"
      - "POST_FATE.graphic_mapPFGvsHS"
      - "POST_FATE.graphic_mapPFG"
  - title: Save FATE simulation
    contents:
      - "SAVE_FATE.step1_PFG"
      - "SAVE_FATE.step2_parameters"
  - title: Tool box
    desc:  Utility functions.
    contents:
      - ".getOS"
      - ".getParam"
      - ".setParam"
      - ".setPattern"
      - ".adaptMaps"
      - ".upscaleMaps"
      - ".getCutoff"
      - ".unzip_ALL"