Skip to contents

Select and Process Synthetic Reefs

select_process_reefs.Rd

Select Reefs and Prepare Synthetic Benthic Data

Usage

select_process_reefs(reef_data_synthetic)

Arguments

reef_data_synthetic

A data frame containing synthetic reef survey data. Must include columns such as site_name, survey_depth, survey_start_date, survey_transect_number, and point_machine_classification. If data_type = "cover", it should also include cover.

data_type

A string specifying the type of data to process:

  • "points" – process raw point-based benthic classifications

  • "cover" – process aggregated percentage cover values

Value

A processed data frame containing:

  • reef – reef identifier

  • site – standardized site name ("Site X")

  • year – survey year extracted from survey_start_date

  • COUNT – selected point counts (for points data)

  • COVER – benthic cover (%) for selected reefs

Details

Processes a synthetic reef dataset to select a subset of reefs for survey and prepares benthic cover data either at the point level or aggregated cover level. Reef and site identifiers are extracted, and site names are standardized.

The function:

  • Randomly selects reefs based on config_lrge$n_locs

  • Aggregates point-based counts or cover values depending on data_type

  • Extracts year, reef, and site identifiers from site_name

  • Standardizes site names from "S1" to "Site 1"

  • Assigns NA to reefs not selected for survey

Author

Julie