codiv/_pkgdown.yml at main · SprockettLab/codiv · GitHub

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url: https://www.sprockettlab.com/codiv/

template:
  bootstrap: 5
  bootswatch: morph

home:
  title: codiv - Host-Microbe Codiversification Analysis
  description: >
    Perform codiversification scans between phylogenetic trees of hosts and
    their microbial symbionts using statistical methods including Hommola, PACo,
    and ParaFit.

navbar:
  structure:
    left:  [intro, reference, articles]
    right: [search, github]
  components:
    articles:
      text: Articles
      menu:
      - text: "Getting Started"
        href: articles/codiv.html
      - text: "-------"
      - text: "Simulation & validation"
        href: articles/simulation-and-validation.html
      - text: "Secondary analyses"
        href: articles/secondary-analyses.html

reference:
  - title: "Main Functions"
    desc: "Core codiversification analysis"
    contents:
      - codiv
      - check_inputs
      - codiv_null_scans
      - host_codiv_summary
  - title: "Working with Results"
    desc: "Methods for the codiv result object"
    contents:
      - print.codiv
      - summary.codiv
      - as.data.frame.codiv
      - filter_results
  - title: "Codiversification Methods"
    desc: "Statistical methods used at each node"
    contents:
      - hommola
      - hommola_wf
      - paco_wf
      - topology_wf
  - title: "Helper Functions"
    desc: "Tree and data manipulation utilities"
    contents:
      - collapse_monophyletic
      - host_symbiont_links
  - title: "Secondary Analyses"
    desc: "Robustness, interpretation, and visualization"
    contents:
      - loo_host_analysis
      - sensitivity_analysis
      - molecular_clock
      - plot_codiv_trees
  - title: "Simulation"
    desc: "Generate host/symbiont data with known co-diversification"
    contents:
      - simulate_codiv_data

development:
  mode: auto