_pkgdown.yml

destination: docs

template:
  params:
    bootswatch: flatly

navbar:
  structure:
    left:
    - home
    - intro
    - reference
    - articles
    - tutorials
    right:
    - news
    - github
    - twitter
  components:
    home:
      icon: fa-home fa-lg
      href: index.html
    reference:
      text: Reference
      href: reference/index.html
    articles:
      text: Vignettes
      menu:
      - text: WExT Statistics
        href: articles/statistics.html
      - text: Computing the Weighted Exclusivity Test (WExT)
        href: articles/computing_probabilities.html
      - text: Simple Example (the hard way)
        href: articles/simpleexample-hardway.html
    news:
      text: Changelog
      href: news/index.html
    github:
      icon: fa-github fa-lg
      href: https://github.com/jhrcook/wext
    twitter:
      icon: fab fa-twitter fa-lg
      href: https://twitter.com/JoshDoesa


reference:
- title: The WExT package
  desc: >
    General information about the package
  contents:
  - '`wext`'

- title: Statistical functions
  desc: >
    Functions that underpin the statistics for the Weighted Exclusivity
    Test (WExT)
  contents:
  - '`calculate_row_exclusivity_weights`'
  - '`calculate_row_col_exclusivity_weights`'
  - '`calculate_weighted_row_exclusivity_weights`'
  - '`rc_test`'
  - '`calculate_events`'

- title: Edge swapping
  desc: >
    Functions used for the edge swap algorithm to sample possible matrices in
    the Row-Column-Exclusivity test
  contents:
  - '`bipartite_edge_swap`'
  - '`bipartite_edge_swap2`'
  - '`bipartite_edge_swap3`'
  - '`swap_an_edge`'
  - '`swap_an_edge2`'
  - '`swap_an_edgeC`'
  - '`random_edge_nodes`'
  - '`remove_edge`'

- title: Utilities
  desc: utilitiy functions used throughout
  contents:
  - '`bipartite_edgelist`'
  - '`matrix_to_tibble`'
  - '`get_node_index`'
  - '`check_gr`'
  - '`make_sample_gene_bipartite`'
  - '`filter_by_mutation_frequency`'
  - '`results_tracker`'

- title: Example data sets
  desc: Small data sets used for examples and testing
  contents:
  - '`simple_dataset`'