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

Usage

check_states(
  occ,
  long = "decimalLongitude",
  lat = "decimalLatitude",
  state_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_states().
long: (character) column name with longitude. Default is 'decimalLongitude'.
lat: lat (character) column name with latitude. Default is 'decimalLatitude'.
state_column: (character) column name containing the state information.
distance: (numeric) maximum distance (in kilometers) a record can fall outside the state assigned in the state_column. Default is 5.
try_to_fix: (logical) whether to check if coordinates are inverted or transposed (see fix_states() 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_state) indicating whether each record falls within the state 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
# Subset occurrences for Araucaria angustifolia
occ <- occurrences[occurrences$species == "Araucaria angustifolia", ]
# Standardize country names
occ_country <- standardize_countries(occ = occ,
                                     return_dictionary = FALSE)
# Standardize state names
occ_state <- standardize_states(occ = occ_country,
                                country_column = "country_suggested",
                                return_dictionary = FALSE)
# Check whether records fall within assigned states
occ_state_checked <- check_states(occ = occ_state,
                                    state_column = "state_suggested")
#> Warning: The following states listed in the 'state_suggested' column were absent in the world map used for validation: NA, mexico
#> Testing states...
#> 13 records fall in wrong states