Check if the records fall in the country assigned in the metadata

Usage

check_countries(
  occ,
  long = "decimalLongitude",
  lat = "decimalLatitude",
  country_column,
  distance = 5,
  try_to_fix = FALSE,
  progress_bar = FALSE,
  verbose = TRUE
)

Arguments

occ: (data.frame) a dataset with occurrence records, preferably with country information standardized using standardize_countries().
long: (character) column name with longitude. Default is 'decimalLongitude'.
lat: lat (character) column name with latitude. Default is 'decimalLatitude'.
country_column: (character) column name containing the country information.
distance: (numeric) maximum distance (in kilometers) a record can fall outside the country assigned in the country_column. Default is 5.
try_to_fix: (logical) whether to check if coordinates are inverted or transposed (see fix_countries() for details). If TRUE, coordinates identified as inverted or transposed will be corrected. Default is FALSE.
progress_bar: (logical) whether to display a progress bar during processing. If TRUE, the 'pbapply' package must be installed. Default is FALSE.
verbose: (logical) whether to print messages about function progress. Default is TRUE.

Value

The original occ data.frame with an additional column (correct_country) indicating whether each record falls within the country specified in the metadata (TRUE) or not (FALSE). As with all other flagging functions in RuHere, TRUE indicates that the record passed this test and is eligible for retention; FALSE indicates it failed and is flagged as potentially problematic, and can be removed using remove_flagged().

Examples

# Load example data
data("occurrences", package = "RuHere") #Import data example
# Standardize country names
occ_country <- standardize_countries(occ = occurrences,
                                     return_dictionary = FALSE)
# Check whether records fall within assigned countries
occ_country_checked <- check_countries(occ = occ_country,
                                       country_column = "country_suggested")
#> Warning: The following countries listed in the 'country_suggested' column were absent in the world map used for validation: NA
#> Warning: GDAL Message 1: +init=epsg:XXXX syntax is deprecated. It might return a CRS with a non-EPSG compliant axis order.
#> Testing countries...
#> 54 records fall in wrong countries