_pkgdown.yml

template:
  params:
    ganalytics: UA-53797708-7
  includes:
    before_title: '<a href="https://www.usgs.gov/"><img src="logo.png" id="logo" alt="Home" style="padding: 0px 50px 0px 0px;"></a>'
  bootstrap: 5
  theme: atom-one-light
  bslib:
    bg: "white"
    fg: "#283140"
    navbar-brand-color: "white"
    navbar-light-color: "white"
    nav-link-color: "white"
    nav-link-hover-color: "#a9a9a9"
    navbar-light-brand-hover-color: "white"
    navbar-light-hover-color: "white"
    text-muted: "white"
    pkgdown-nav-height: 125px
navbar:
  left:
  - text: Background
    href: articles/Introduction.html
  - text: Basic Workflow
    href: articles/basicWorkflow.html
  - text: Function Help
    href: reference/index.html
  - text: Data Preparation
    href: articles/PrepareData.html
  - text: Articles
    menu:
      - text: Shiny App
        href: articles/shinyApp.html
      - text: Exploring Benchmarks
        href: articles/benchmarks.html
      - text: Prepare Data in R
        href: articles/pivot.html
      - text: Dose Response Curves
        href: articles/dose_curves.html
      - text: Chemical Names
        href: articles/Chemical_names.html
      - text: How to Contribute
        href: articles/Contributing.html
  - text: Bibliograpy
    href: articles/bibliography.html
  right:
  - icon: fa-gitlab fa-lg
    href: https://code.usgs.gov/water/toxEval
reference:
  - title: Import Data
    contents:
      - create_toxEval
  - title: ToxCast Data
    desc: Data provided in the package from ToxCast database.
    contents:
      - end_point_info
      - ToxCast_ACC
      - tox_chemicals
      - flags
  - title: Clean Data
    desc:  Functions to prepare data for analysis
    contents:
      - clean_endPoint_info
      - get_ACC
      - get_chemical_summary
      - get_concentration_summary
      - remove_flags
      - filter_groups
      - side_by_side_data
  - title: Visualize Data
    desc: Functions to create graphs and tables of output.
    contents:
      - plot_tox_boxplots
      - plot_tox_endpoints
      - plot_tox_stacks
      - plot_tox_heatmap
      - hits_summary
      - hits_by_groupings
      - rank_sites
      - endpoint_hits
      - make_tox_map
      - explore_endpoints
      - plot_tox_endpoints2
  - title: Utility Functions
    desc: Functions to help
    contents:
      - toxEval-package 
      - summary.toxEval
      - as.toxEval