Skip to contents

Map Survey Labels to Standardized Taxa, Gear, and Vessel Names

map_surveys.Rd

Converts local species, gear, and vessel labels from surveys to standardized names using Airtable reference tables. Handles two survey form types: the standard form which uses catch_taxon, and the KEFs v2 form which uses priority_species and sample_species. Replaces local names with scientific names and alpha3 codes, and standardizes gear, vessel, and site names.

Usage

map_surveys(
  data = NULL,
  taxa_mapping = NULL,
  gear_mapping = NULL,
  vessels_mapping = NULL,
  sites_mapping = NULL,
  kefs_v2 = FALSE
)

Arguments

data

A data frame with preprocessed survey data. For standard surveys, must contain catch_taxon, gear, vessel_type, and landing_site columns. For KEFs v2 surveys, must contain priority_species, sample_species, gear, vessel_type, and landing_site columns.

taxa_mapping

A data frame from Airtable taxa table with survey_label, alpha3_code, and scientific_name columns.

gear_mapping

A data frame from Airtable gears table with survey_label and standard_name columns.

vessels_mapping

A data frame from Airtable vessels table with survey_label and standard_name columns.

sites_mapping

A data frame from Airtable landing_sites table with site_code and site columns.

kefs_v2

Logical. If TRUE, processes data from the KEFs v2 survey form which uses priority_species and sample_species columns. If FALSE (default), processes standard survey forms with catch_taxon column.

Value

A tibble with survey labels replaced by standardized names:

  • For standard surveys: catch_taxon replaced by scientific_name and alpha3_code

  • For KEFs v2 surveys: priority_species replaced by priority_scientific_name and priority_alpha3_code; sample_species replaced by sample_scientific_name and sample_alpha3_code

  • gear and vessel_type replaced by standardized names

  • landing_site replaced by the full site name

Records without matches will have NA values.

Details

This function is called within preprocess_landings() after processing raw survey data. The mapping tables are retrieved from Airtable frame base and filtered by form ID before being passed to this function.

The KEFs v2 survey form captures both priority species (target catch) and sample species (for biological sampling), requiring separate taxonomic mappings for each.