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Standardize country names

Source: R/standardize_countries.R
standardize_countries.Rd

This function standardizes country names using both names and codes present in a specified column.

Usage

standardize_countries(
  occ,
  country_column = "country",
  max_distance = 0.1,
  user_dictionary = NULL,
  lookup_na_country = FALSE,
  long = "decimalLongitude",
  lat = "decimalLatitude",
  return_dictionary = TRUE
)

Arguments

occ

(data.frame) a dataset with occurrence records, preferably standardized using format_columns().

country_column

(character) the column name containing the country information.

max_distance

(numeric) maximum allowed distance (as a fraction) when searching for suggestions for misspelled country names. Can be any value between 0 and 1. Higher values return more suggestions. See agrep() for details. Default is 0.1.

user_dictionary

(data.frame) optional data.frame with two columns: 'country_name' and 'country_suggested'. If provided, this dictionary will be combined with the package’s default country dictionary (RuHere::country_dictionary). Default is NULL.

lookup_na_country

(logical) whether to extract the country from coordinates when the country column has missing values. If TRUE, longitude and latitude columns must be provided. Default is FALSE.

long

(character) column name with longitude. Only applicable if lookup_na_country = TRUE. Default is "decimalLongitude".

lat

(character) column name with latitude. Only applicable if lookup_na_country = TRUE. Default is "decimalLatitude".

return_dictionary

(logical) whether to return the dictionary of countries that were (fuzzy) matched.

Value

A list with two elements:

data

The original occ data.frame with an additional column (country_suggested) containing the suggested country names based on exact match, fuzzy match, and/or coordinates.

dictionary

If return_dictionary = TRUE, a data.frame with the original country names and the suggested matches.

Details

Country names are first standardized by exact matching against a list of country names in several languages from rnaturalearthdata::map_units110. Any unmatched names are then processed using a fuzzy matching algorithm to find potential candidates for misspelled country names. If unmatched names remain and lookup_na_country = TRUE, the country is extracted from coordinates using a map retrieved from rnaturalearthdata::map_units110.

Examples

# Import and standardize GBIF
data("occ_gbif", package = "RuHere") #Import data example
gbif_standardized <- format_columns(occ_gbif, metadata = "gbif")
# Import and standardize SpeciesLink
data("occ_splink", package = "RuHere") #Import data example
splink_standardized <- format_columns(occ_splink, metadata = "specieslink")
# Import and standardize BIEN
data("occ_bien", package = "RuHere") #Import data example
bien_standardized <- format_columns(occ_bien, metadata = "bien")
# Import and standardize idigbio
data("occ_idig", package = "RuHere") #Import data example
idig_standardized <- format_columns(occ_idig, metadata = "idigbio")
# Merge all
all_occ <- bind_here(gbif_standardized, splink_standardized,
                     bien_standardized, idig_standardized)
# Standardize countries
occ_standardized <- standardize_countries(occ = all_occ)