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Standardize state names

Source: R/standardize_states.R
standardize_states.Rd

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

Usage

standardize_states(
  occ,
  state_column = "stateProvince",
  country_column = "country_suggested",
  max_distance = 0.1,
  lookup_na_state = FALSE,
  long = "decimalLongitude",
  lat = "decimalLatitude",
  return_dictionary = TRUE
)

Arguments

occ

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

state_column

(character) the column name containing the state information.

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 state names. Can be any value between 0 and 1. Higher values return more suggestions. See agrep() for details. Default is 0.1.

lookup_na_state

(logical) whether to extract the state from coordinates when the state 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_state = TRUE. Default is "decimalLongitude".

lat

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

return_dictionary

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

Value

A list with two elements:

data

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

dictionary

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

Details

States names are first standardized by exact matching against a list of state names in several languages from rnaturalearthdata::states50. Any unmatched names are then processed using a fuzzy matching algorithm to find potential candidates for misspelled state names. If unmatched names remain and lookup_na_state = TRUE, the state is extracted from coordinates using a map retrieved from rnaturalearthdata::states50.

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)
# Standardize states
occ_standardized2 <- standardize_states(occ = occ_standardized$occ)