_pkgdown.yml

url: https://januarharianto.github.io/respR

template:
  params:
    bootstrap: 5
    bootswatch: cosmo

code:
  width: 999

reference:
  - title: "Pre-processing"
    desc: >
      Functions for importing, processing, visualising and inspecting data:
    contents:
    - '`import_file`'
    - '`format_time`'
    - '`inspect`'
    - '`inspect.ft`'
    - '`subsample`'
    - '`subset_data`'

  - title: "Analytical"
    desc: >
      Functions for calculating rates of oxygen consumption or production:
    contents:
    - '`auto_rate`'
    - '`auto_rate.int`'
    - '`calc_rate`'
    - '`calc_rate.int`'
    - '`calc_rate.bg`'
    - '`calc_rate.ft`'
    - '`oxy_crit`'

  - title: "Adjust"
    desc: >
      Functions for rate adjustments:
    contents:
    - '`adjust_rate`'
    - '`adjust_rate.ft`'

  - title: "Convert"
    desc: >
      Functions for rate and unit conversions:
    contents:
    - '`convert_rate`'
    - '`convert_rate.ft`'
    - '`convert_DO`'
    - '`convert_MR`'
    - '`convert_val`'
    - '`unit_args`'

  - title: "Summarise"
    desc: >
      Functions for rate filtering and summarising:
    contents:
    - '`select_rate`'

  - title: "Data"
    desc: >
      Example data files:
    contents:
    - '`algae.rd`'
    - '`background_con.rd`'
    - '`background_exp.rd`'
    - '`background_lin.rd`'
    - '`flowthrough.rd`'
    - '`flowthrough_mult.rd`'
    - '`flowthrough_sim.rd`'
    - '`intermittent.rd`'
    - '`sardine.rd`'
    - '`squid.rd`'
    - '`urchins.rd`'
    - '`zeb_intermittent.rd`'

navbar:
  type: inverse

  left:
    - icon: fa-home
      href: index.html

    - text: "Getting Started"
      href: articles/respR.html

    - text: "Documentation"
      href: reference/index.html

    - text: Vignettes
      menu:
      - text: "---- Complete Workflows ----"
      - text: "Closed-chamber respirometry"
        href: articles/closed.html
      - text: "Intermittent-flow respirometry: Short experiment"
        href: articles/intermittent_short.html
      - text: "Intermittent-flow respirometry: Long experiment"
        href: articles/intermittent_long.html
      - text: "Flowthrough respirometry"
        href: articles/flowthrough.html
      - text: "Critical oxygen values (PCrit)"
        href: articles/oxycrit.html
      - text: "Oxygen production respirometry"
        href: articles/oxy_production.html
      - text: "---- Function Guides ----"
      - text: "inspect: Inspecting data"
        href: articles/inspecting.html
      - text: "subset_data: Subset data by time, row, or oxygen ranges"
        href: articles/subset_data.html
      - text: "calc_rate: Manually select and calculate rates"
        href: articles/calc_rate.html
      - text: "calc_rate.int: Manual extraction of rates in intermittent-flow respirometry"
        href: articles/calc_rate.int.html
      - text: "auto_rate: Automatic detection of linear rates"
        href: articles/auto_rate.html
      - text: "auto_rate.int: Automatic extraction of rates in intermittent-flow respirometry"
        href: articles/auto_rate.int.html
      - text: "adjust_rate: Adjusting rates for background"
        href: articles/adjust_rate.html
      - text: "select_rate: Exploring and filtering results"
        href: articles/select_rate.html
      - text: "format_time: Convert date-time data to numeric time"
        href: articles/format_time.html
      - text: "convert_DO: Convert between units of dissolved oxygen"
        href: articles/convert_DO.html
      - text: "---- Miscellaneous ----"
      - text: "Importing files from oxygen probe systems"
        href: articles/importing.html
      - text: "Two-point rate calculation"
        href: articles/twopoint.html
      - text: "Thin larger datasets"
        href: articles/subsample.html
      - text: "Integration with the tidyverse"
        href: articles/tidyverse.html
      - text: "Reporting reproducibile analyses"
        href: articles/reproducibility.html

    - text: More
      menu:
      - text: "Contact"
        href: articles/contact.html
      - text: "Release Notes"
        href: articles/release_notes.html
      - text: "respR Citations"
        href: articles/citations.html
      - text: "Future Features"
        href: articles/future.html
      - text: "References"
        href: articles/refs.html
      - text: Archived
        menu:
        - text: "Intermittent-flow respirometry: Alternative approaches"
          href: articles/archive/intermittent_old.html
        - text: "v2.0: Code changes"
          href: articles/archive/v2_code_change.html
        - text: "v1.1: How to install and run older code"
          href: articles/archive/v1_code.html
        - text: "auto_rate: Performance"
          href: articles/archive/auto_rate_performance.html
        - text: "auto_rate: Comparisons with LoLinR"
          href: articles/archive/auto_rate_comp.html
        - text: "oxy_crit: Comparisons with other packages"
          href: articles/archive/oxy_crit_comp.html
        - text: "oxy_crit: Discussion of Pcrit estimation methods"
          href: articles/archive/oxy_crit_disc.html
        - text: "respR: Comparisons with other R packages"
          href: articles/archive/packages_comp.html
        - text: "respR: When to use respR"
          href: articles/archive/usage.html