_pkgdown.yml

url: https://globalarchivemanual.github.io/CheckEM/
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reference:
- title: Functions for data formatting
  desc: Essential functionality for formatting stereo-video annotation
  contents:
  - clean_names
  - create_cti
  - standardize_tibble
  - has_special_characters
  - read_metadata
  - read_points
  - read_counts
  - read_TM
  - find_lw
  - find_tl
  - plot_transformations
  - read_em_length
  - read_gen_length
  - read_periods
  - expand_life_history
  - create_min_max
  - load_rds_from_github
  - add_zeros_count
  - add_zeros_length
- title: Shiny App
  desc: Functions for shiny app
  contents: runCheckEM
- title: GlobalArchive API
  desc: Essential functionality for accessing data through the GlobalArchive API
  contents:
  - ga_api_set_token
  - ga_api_all_data
  - ga_api_count
  - ga_api_habitat
  - ga_api_relief
  - ga_api_length
  - ga_api_metadata
  - ga_api_species_list
  - ga_api_benthic_list
- title: Data
  desc: Datasets included with CheckEM
  contents:
  - australia_life_history
  - global_life_history
  - aus_regions
  - world_regions
  - imcra_regions
  - aus_synonyms
  - catami
  - maturity
- title: Investigating maximum sizes of fish
  desc: Functions to plot and investigate size frequency and maximum sizes of fish
  contents:
  - plot_species_hdi
  - hdi_table
navbar:
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  type: default
  right:
  - icon: fa-github
    href: https://github.com/GlobalArchiveManual/CheckEM
    text: GitHub
  - href: https://www.nespmarinecoastal.edu.au/
    html: '<img src=''man/figures/mac.svg'' width=''200'' alt=''National Environmental
      Science Program: Marine and Coastal''/>'
    text: ARDC
  left:
  - text: User Guides
    menu:
    - text: '-------'
    - text: Field Manuals
    - text: Baited Remote Underwater Stereo-video (stereo-BRUVs)
      href: https://benthic-bruvs-field-manual.github.io/
    - text: Diver Operated Stereo-video (stereo-DOVs)
      href: https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.13189
    - text: '-------'
    - text: Annotation Guides
    - text: Fish annotation guide (EventMeasure)
      href: articles/manuals/EventMeasure_annotation_guide.html
    - text: Benthos annotation guide (TransectMeasure)
      href: articles/manuals/TransectMeasure_annotation_guide.html
    - text: '-------'
    - text: CheckEM Guides
    - text: CheckEM PDF user manual
      href: articles/manuals/CheckEM_user_guide.html
    - text: CheckEM instructional video
      href: articles/manuals/CheckEM_video.html
  - text: R Workflows
    menu:
    - text: '-------'
    - text: Create sampling design
    - text: Create a spatially-balanced sampling design using GRTS
      href: articles/r-workflows/sampling-design.html
    - text: '-------'
    - text: Check Data
    - text: Check habitat data from TransectMeasure
      href: articles/r-workflows/check-habitat.html
    - text: Check fish data from single point based methods
      href: articles/r-workflows/check-fish-point.html
    - text: Check fish data from transect based methods
      href: articles/r-workflows/check-fish-transect.html
    - text: '-------'
    - text: Format Data
    - text: Generate spatial layers for modelling
      href: articles/r-workflows/spatial-layers.html
    - text: Format & visualise habitat data
      href: articles/r-workflows/format-visualise-habitat.html
    - text: Format & visualise fish data
      href: articles/r-workflows/format-visualise-fish.html
    - text: '-------'
    - text: Modelling
    - text: Generate spatial predictions of habitat using FSSgam
      href: articles/r-workflows/habitat-modelling.html
    - text: Select top models for fish using FSSgam
      href: articles/r-workflows/fish-modelling.html
    - text: Generate Generalized Additive Model predictions of fish
      href: articles/r-workflows/fish-predictions.html
    - text: Spatially predict fish distributions
      href: articles/r-workflows/fish-spatial-prediction.html
  - text: Improve CheckEM - Contribute to Species Records
    href: articles/community-updates
  - text: Functions
    href: reference
authors:
  footer:
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    text: '<img src=''https://ardc.edu.au/wp-content/uploads/2022/09/ardc-logo.svg''
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      height=''70'' alt=''National Environmental Science Program: Marine and Coastal''/>  &nbsp;
      &nbsp; Package developed by '
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