_pkgdown.yml

authors:
  Wilfried Thuiller:
    href: http://www.will.chez-alice.fr/
  Maya Gueguen:
    href: https://mayagueguen.github.io

navbar:
  structure:
    left:
    - home
    - videos
    - presentation
    - examples
    - reference
    right:
    - news
    - github
  components:
    home:
      icon: fa-home fa-lg
      href: index.html
    videos:
      text: Videos
      icon: fas fa-video
      href: articles/vignette_videos.html
    presentation:
      text: Presentation
      icon: fas fa-graduation-cap
      href: articles/vignette_presentation.html
    examples:
      text: Examples
      icon: fas fa-stethoscope
      menu:
        - text: Main functions
          href: articles/examples_1_mainFunctions.html
        - text: Secundary functions
          href: articles/examples_2_secundaryFunctions.html
        - text: "---------"
        - text: Data preparation
          href: articles/vignette_dataPreparation.html
        - text: Pseudo-absences
          href: articles/vignette_pseudoAbsences.html
        - text: Cross-validation
          href: articles/vignette_crossValidation.html
        - text: Modeling options
          href: articles/vignette_modelingOptions.html
        - text: Variability in results
          href: articles/vignette_variability.html
        - text: Abundance modelling
          href: articles/vignette_Abundance.html
    reference:
      text: Reference
      icon: fa-book fa-lg
      href: reference/index.html
    news:
      text: News
      icon: fas fa-newspaper
      href: articles/news.html
    github:
      icon: fa-github fa-lg
      href: https://github.com/biomodhub/biomod2.git


reference:
  - title: Modeling species distributions
  - subtitle: Main functions
    contents:
      - "BIOMOD_FormatingData"
      - "BIOMOD_Modeling"
      - "BIOMOD_Projection"
      - "BIOMOD_EnsembleModeling"
      - "BIOMOD_EnsembleForecasting"
      - "BIOMOD_RangeSize"
      - "BIOMOD_LoadModels"
  - subtitle: Secundary functions
    contents:
      - "bm_MakeFormula"
      - "bm_SampleBinaryVector"
      - "bm_SampleFactorLevels"
      - "bm_PseudoAbsences"
      - "bm_CrossValidation"
      - "bm_ModelingOptions"
      - "bm_Tuning"
      - "bm_RunModelsLoop"
      - "bm_SRE"
      - "bm_FindOptimStat"
      - "bm_BinaryTransformation"
      - "bm_VariablesImportance"
      - "bm_PlotEvalMean"
      - "bm_PlotEvalBoxplot"
      - "bm_PlotVarImpBoxplot"
      - "bm_PlotResponseCurves"
      - "bm_PlotRangeSize"
  - title: Toolbox
  - subtitle: Objects
    contents:
      - "BIOMOD.formated.data"
      - "BIOMOD.formated.data.PA"
      - "plot,BIOMOD.formated.data,missing-method"
      - "summary,BIOMOD.formated.data-method"
      - "BIOMOD.options.default"
      - "BIOMOD.options.dataset"
      - "BIOMOD.models.options"
      - "BIOMOD.stored.data"
      - "biomod2_model"
      - "biomod2_ensemble_model"
      - "BIOMOD.models.out"
      - "BIOMOD.projection.out"
      - "BIOMOD.ensemble.models.out"
  - subtitle: Getters
    contents:
      - "load_stored_object"
      - "getters.bm"
      - "getters.out"
      - "predict.bm"
      - "predict.em"
  - title: Data
  - subtitle: Models options
    contents:
      - "ModelsTable"
      - "OptionsBigboss"
  - subtitle: Species data
    contents:
      - "DataSpecies"
  - subtitle: Environmental data
    contents:
      - "bioclim_current"
      - "bioclim_future"