RFate/_pkgdown.yml at master · leca-dev/RFate · GitHub

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authors:
  Isabelle Boulangeat:
    href: https://iboulangeat.github.io/
  Maya Guéguen:
    href: https://mayagueguen.github.io
  Wilfried Thuiller:
    href: http://www.will.chez-alice.fr/


navbar:
  structure:
    left:
    - home
    - FATE
    - RFate
    - interface
    - reference
    right:
    - manual
    - news
    - github
  components:
    home:
      icon: fa-house
      href: index.html
    reference:
      text: Reference
      icon: fa-book
      href: reference/index.html
    FATE:
      text: FATE
      icon: 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: 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: fa-desktop
      href: articles/interface_tutorial_0_presentation.html
    articles:
    manual:
      text: 'Manual & Examples'
      icon: fa-stethoscope
      href: articles/manual.html
    news:
      text: 'News'
      icon: fa-newspaper
      href: articles/news.html
    github:
      icon: fa-github
      href: https://github.com/leca-dev/RFate.git


reference:
  - title: Datasets
    desc:  Used in the examples.
    contents:
      - ".loadData"
  - title: Interface
    desc:  Graphical User Interface (shiny application)
    contents:
      - "RFATE"
  - title: Build Plant Functional Groups
    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.speciesDistanceOverlap"
      - "PRE_FATE.speciesDistanceTraits"
      - "PRE_FATE.speciesDistanceCombine"
      - "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"
  - 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"
      - ".scaleMaps"
      - ".getCutoff"
      - ".unzip_ALL"