_pkgdown.yml

title: slendr
url: https://www.slendr.net

template:
  bootstrap: 5
  params:
  docsearch:
    api_key: a895c93f0e9eda05eb10b29a9921d586
    index_name: slendr

news:
  one_page: true

navbar:
  structure:
    left:  [home, reference, articles, news]
    right: [github, twitter]
  components:
    home:
      icon: fa-home
      href: index.html
    reference:
      icon: fa-question-circle
      text: Reference
      href: reference/index.html
    articles:
      icon: fa-book
      text: Articles
      menu:
        - text: Installation instructions
          href: articles/vignette-00-installation.html
        - text: Introduction and basic tutorial
          href: articles/vignette-01-tutorial.html
        - text: Demes on a regular spatial grid
          href: articles/vignette-02-grid-model.html
        - text: Programming dispersion dynamics
          href: articles/vignette-03-interactions.html
        - text: Traditional non-spatial models
          href: articles/vignette-04-nonspatial-models.html
        - text: Tree sequence processing and statistics
          href: articles/vignette-05-tree-sequences.html
        - text: Spatially annotated tree sequences
          href: articles/vignette-06-locations.html
        - text: Simulating data with SLiM and msprime backends
          href: articles/vignette-07-backends.html
        - text: Analyzing non-slendr tree sequences
          href: articles/vignette-08-nonslendr-tskit.html
        - text: Examples from the slendr paper
          href: articles/vignette-09-paper.html
        - text: Extracting true ancestry tracts
          href: articles/vignette-10-tracts.html
        - text: Extending models with custom SLiM code
          href: articles/vignette-11-extensions.html
    twitter:
      icon: fa-twitter
      href: https://twitter.com/fleventy5

reference:
  - title: Compiling and running population genetic models
    contents:
    - slim
    - msprime
    - compile_model
    - read_model
    - schedule_sampling
    - substitute_values

  - title: Installation and configuration of external dependencies
    contents:
    - setup_env
    - init_env
    - check_env
    - clear_env
    - get_env
    - check_dependencies

  - title: Model components
    contents:
    - population
    - world

  - title: Spatial population dynamics
    contents:
    - move
    - expand_range
    - shrink_range
    - set_range
    - set_dispersal

  - title: Non-spatial population dynamics
    contents:
    - gene_flow
    - resize

  - title: Manipulation of spatial objects
    contents:
    - region
    - join
    - overlap
    - subtract
    - reproject
    - distance
    - area

  - title: Model visualization and diagnostics
    contents:
    - plot_map
    - plot_model
    - animate_model
    - explore_model
    - print.slendr_map
    - print.slendr_region
    - print.slendr_pop
    - print.slendr_model
    - print.slendr_ts
    - summary.slendr_nodes
    - extract_parameters

  - title: Processing tree sequences
    contents:
    - ts_read
    - ts_write
    - ts_recapitate
    - ts_simplify
    - ts_mutate
    - ts_samples
    - ts_names
    - ts_coalesced
    - ts_save
    - ts_load

  - title: Tree sequence format conversion
    contents:
    - ts_genotypes
    - ts_eigenstrat
    - ts_vcf

  - title: Accessing tree sequence components
    contents:
    - ts_nodes
    - ts_edges
    - ts_table
    - ts_phylo
    - ts_tree
    - ts_draw
    - ts_metadata
    - ts_ancestors
    - ts_descendants

  - title: Tree sequence statistics
    contents:
    - ts_f2
    - ts_f3
    - ts_f4
    - ts_f4ratio
    - ts_afs
    - ts_divergence
    - ts_diversity
    - ts_fst
    - ts_tajima
    - ts_segregating
    - ts_ibd
    - ts_tracts