_pkgdown.yml

url: https://microbiomer.vallenderlab.org/
template:
  params:
    bootswatch: yeti

development:
  mode: unreleased

authors:
  Robert Gilmore:
    href: https://github.com/grabear
  Shaurita Hutchins:
    href: https://www.shauritahutchins.com

navbar:
  title: MicrobiomeR
  left:
    - text: "Home"
      href: index.html
    - text: "Vignettes"
      menu:
      - text: "Introduction"
        href: articles/introduction.html
      - text: "Data Wrangling"
        href: articles/data-wrangling.html
      - text: "Data Filtering"
        href: articles/filtering.html
      - text: "Data Analysis"
        href: articles/analysis.html
      - text: "Color Palettes"
        href: articles/color-palettes.html
    - text: "Functions"
      href: reference/index.html
    - text: "Publication"
      href: articles/paper.html
    - text: "Changelog"
      href: news/index.html
  right:
    - text: "About"
      href: articles/about.html
    - icon: fa-twitter
      href: https://twitter.com/datasnakes
    - icon: fa-github
      href: https://github.com/vallenderlab/MicrobiomeR

reference:
- title: Import
  contents:
  - create_phyloseq
  - create_metacoder
  - parse_taxonomy_default
  - parse_taxonomy_silva_128
  - parse_taxonomy_greengenes
  - parse_taxonomy_qiime
  - has_concept("Phylogenetic Tree Manipulators")

- title: Formatting
  contents:
  - has_concept("Formatting")

- title: Statistics
  contents:
  - alpha_diversity_measures
  - permanova

- title: Validation
  contents:
  - has_concept("Validation")

- title: Basic Filtering
  contents:
  - has_concept("Basic Metacoder Filters")

- title: Advanced Filtering
  contents:
  - has_concept("Advanced Metacoder Filters")

- title: Other Filtering
  contents:
  - has_concept("Data Manipulators")

- title: Visualization
  contents:
  - output_dir
  - has_concept("Visualizations")

- title: Color Palettes
  contents:
  - has_concept("Color Palettes")

- title: Miscellaneous
  contents:
  - create_pub_table