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Extract and Format FAO Taxonomic Groups

get_fao_groups.Rd

Filters and formats taxonomic information from the FAO ASFIS list for specified FAO 3-alpha codes, excluding miscellaneous ("MZZ") and unknown ("UNKN") categories.

Usage

get_fao_groups(fao_codes = NULL, asfis_list = NULL)

Arguments

fao_codes

A character vector of FAO 3-alpha codes to extract. If NULL, returns empty dataset.

asfis_list

A data frame containing the FAO ASFIS list with required columns:

  • Alpha3_Code - FAO 3-alpha code

  • Scientific_Name - Scientific name of taxon

  • English_name - Common name in English

  • Family - Family name

  • Order - Order name

  • ISSCAAP_Group - FAO ISSCAAP group number

Value

A tibble with standardized column names containing taxonomic information:

  • a3_code - FAO 3-alpha code

  • scientific_name - Scientific name

  • english_name - Common name in English

  • family - Family name

  • order - Order name

  • taxon_group - ISSCAAP group number

Details

The function:

  1. Filters ASFIS list for specified FAO codes

  2. Standardizes column names for consistency

  3. Removes miscellaneous ("MZZ") and unknown ("UNKN") categories

  4. Preserves the taxonomic hierarchy information

Note

  • Requires dplyr package

  • MZZ (Miscellaneous marine fishes) and UNKN (Unknown) are automatically excluded

  • Column names are standardized for consistency with other functions

Examples

# Example ASFIS data
asfis <- data.frame(
  Alpha3_Code = c("TUN", "MZZ", "RAG"),
  Scientific_Name = c("Thunnini", "Marine fishes nei", "Rastrelliger kanagurta"),
  English_name = c("Tunas", "Marine fishes", "Indian mackerel"),
  Family = c("SCOMBRIDAE", NA, "SCOMBRIDAE"),
  Order = c("PERCIFORMES", NA, "PERCIFORMES"),
  ISSCAAP_Group = c(36, 39, 37)
)

# Get taxonomic information for specific codes
fao_taxa <- get_fao_groups(c("TUN", "RAG"), asfis)