_pkgdown.yml

url: https://iiasa.github.io/ibis.iSDM/

development:
  mode: auto

template:
  bootstrap: 5
  bootswatch: zephyr
  bslib:
    pkgdown-nav-height: 80px
  opengraph:
    twitter:
      creator: "@Martin_Ecology"
      site: "@IIASAVienna"
      card: summary

home:
  title: A R-package for Integrated Biodiversity distribution modelling
  description: Help and tutorial for building integrated species distribution models.
  sidebar:
    structure: [links, citation, license, authors, dev]
  links:
    - text: Learn about contributing
      href: articles/contributing.html
    - text: IIASA BEC group
      href: https://iiasa.ac.at/programs/biodiversity-and-natural-resources/biodiversity-ecology-and-conservation

navbar:
  structure:
    left:  [home, intro, reference, articles, faq, contributing, news]
    right: [search, github]
  components:
    articles:
      text: Articles
      menu:
        - text: 1. Helper functions to prepare inputs
          href: articles/01_data_preparationhelpers.html
        - text: 2. Train a model
          href: articles/02_train_simple_model.html
        - text: 3. Integrate data
          href: articles/03_integrate_data.html
        - text: 4. Biodiversity projections
          href: articles/04_biodiversity_projections.html
        - text: 5. Simulating mechanisms
          href: articles/05_mechanistic_estimation.html
        - text: 6. Engine comparison
          href: articles/06_engine_comparison.html
        - text: 7. Other packages
          href: articles/07_package_comparison.html
    faq:
      text: FAQ
      href: articles/08_frequently-asked-questions.html
    contributing:
      text: Contributing
      href: articles/contributing.html

reference:
  - title: Setting up and train models
    desc: >
      Key functions for setting up species distribution models and adding information to them. Start with
      distribution() and see articles examples on how to build a model from there. Also includes functions
      to specify priors for a model.
    contents:
        - distribution
        - has_keyword("priors")
        - has_concept("priors")
        - matches("Prior")
        - priors
        - pseudoabs_settings
        - train

  - title: Add or modify data and parameters
    desc: >
      Functions to add or modify data and parameters in a distribution object. These can be
      used to add or remove biodiversity, covariates and priors in various forms.
    contents:
      - starts_with("add_")
      - starts_with("set_")
      - starts_with("sel_")
      - starts_with("rm_")
      - starts_with("get_")
      - has_keyword("control")


  - title: Engines
    desc: >
      Statistical models used for estimation of species distributions.
    contents:
      - starts_with("engine_")

  - title: Create spatial-temporal projections
    desc: >
      After a model has been trained, the functions in here can be used to
      create projections with scenario() objects. Constraints can be on such scenarios
      to limit extrapolations.
    contents:
      - scenario
      - project
      - simulate_population_steps
      - starts_with("add_constrain")
      - has_keyword("scenarios")

  - title: Model summary and validation
    desc: Key functions to summarize, validate or extract information from trained models.
    contents:
      - plot
      - bivplot
      - nicheplot
      - print
      - summary
      - coef
      - validate
      - similarity
      - effects
      - partial
      - spartial
      - partial_density
      - limiting
      - threshold
      - ensemble
      - ensemble_partial
      - ensemble_spartial
      - has_keyword("partial")

  - title: Utility functions
    desc: >
      These functions are used by engines or spatial processing in the package. Most
      of them are for internal use, but can be of use if input needs to be reformatted.
    contents:
      - posterior_predict_stanfit
      - alignRasters
      - emptyraster
      - get_ngbvalue
      - get_rastervalue
      - predictor_transform
      - predictor_derivate
      - predictor_filter
      - interpolate_gaps
      - objects_size
      - run_stan
      - wrap_stanmodel
      - sanitize_names
      - get_data
      - combine_formulas
      - starts_with("stancode")
      - starts_with("write_")
      - starts_with("load_")
      - has_keyword("utils")

  - title: Class definitions and methods
    desc: >
     These pages document the package's internal data structures and functions
     for manipulating them---they contain information that is really only
     useful when adding new functionality to the package.
    contents:
      - BiodiversityDataset
      - BiodiversityDatasetCollection
      - BiodiversityDistribution
      - BiodiversityScenario
      - DistributionModel
      - Engine
      - Prior
      - PriorList
      - Settings
      - PredictorDataset
      - Log
      - has_keyword("classes")

  - title: Parallel processing
    desc: >
      Functions to enable or set up parallel processing
    contents:
      - ibis_future
      - ibis_enable_parallel
      - ibis_set_strategy
      - ibis_set_threads
      - run_parallel

  - title: Miscellaneous functions
    desc: >
     Other functions only relevant for development
    contents:
      - as.Id
      - is.Id
      - check
      - has_keyword("misc")
      - print
      - myLog
      - modal
      - new_id
      - new_waiver
      - ibis_options
      - ibis_dependencies