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Prepare Synthetic Data Table

prepare_table.Rd

Prepare Synthetic Benthic Data Table

Usage

prepare_table(data_fixed_locs_points)

Arguments

data_fixed_locs_points

An sf object containing synthetic fine-scale point or quadrat data generated by sampling_design_fine_scale_points() or equivalent. Must include:

  • Reef, Site, Transect, Year, Date

  • Depth, Latitude, Longitude

  • For points: POINT_NO, Group

  • For quadrats/cover: Value, Quad, Group

  • Geometry column

data_type

A string specifying the structure of the input dataset:

  • "points" – raw point-level classifications (HCC, SC, MA, etc.)

  • "cover" – aggregated quadrat or percentage cover measurements

Value

A processed data.frame containing:

  • Project, site, transect and survey metadata

  • Coordinates and depth

  • Either:

    • Point identifiers and benthic class (for data_type = "points")

    • Quadrat numbers and numeric cover (for data_type = "cover")

  • Reef and site identifiers extracted and standardised

  • Final benthic metrics (COUNT, COVER, COVER_TRUE) after reef selection and processing by select_process_reefs()

Details

Converts synthetic point- or cover-based benthic sampling observations into a standardised data table suitable for downstream processing and ReefCloud-style export. The function harmonises identifiers (site, transect, survey), formats benthic attributes, and then applies reef-selection and cover calculations via select_process_reefs().

The function:

  • Creates consistent project, site, survey, and transect identifiers

  • Adds point-level or quadrat-level variables depending on data_type

  • Selects only the variables required for synthetic export

  • Calls select_process_reefs() to:

    • Select a subset of reefs according to config_lrge

    • Compute TRUE and selected cover values

    • Extract and standardise reef and site codes

    • Attach year and benthic cover metrics

See also

select_process_reefs()

Author

Murray/Julie