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Identify and remove invalid coordinates

Source: R/remove_invalid_coordinates.R
remove_invalid_coordinates.Rd

This function identifies and removes invalid geographic coordinates, including non-numeric values, NA or empty values, and coordinates outside the valid range for Earth (latitude > 90 or < -90, and longitude > 180 or < -180).

Usage

remove_invalid_coordinates(
  occ,
  long = "decimalLongitude",
  lat = "decimalLatitude",
  return_invalid = TRUE,
  save_invalid = FALSE,
  output_dir = NULL,
  overwrite = FALSE,
  output_format = ".gz",
  verbose = FALSE
)

Arguments

occ

(data.frame or data.table) a dataset with occurrence records.

long

(character) column name in occ with the longitude.

lat

(character) column name in occ with the latitude.

return_invalid

(logical) whether to return a list containing records that passed and failed this test. Default is TRUE.

save_invalid

(logical) whether to save the records that failed this test (i.e., flagged as FALSE). If TRUE, an output_dir must be provided. Default is FALSE.

output_dir

(character) path to an existing directory where records flagged as FALSE will be saved. Only used when save_invalid = TRUE.

overwrite

(logical) whether to overwrite existing files in output_dir. Only used when save_invalid = TRUE. Default is FALSE.

output_format

(character) output format for saving flagged records. Options are ".csv" or ".gz". Only used when save_invalid = TRUE. Default is ".gz".

verbose

(logical) whether to print messages about function progress. Default is TRUE.

Value

The input data.frame with an additional logical column indicating whether each record passed (TRUE) or failed (FALSE) the coordinate quality check (i.e., is not missing, non-numeric, or outside the possible range for Earth: latitude between -90 and 90, longitude between -180 and 180). 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().

If return_invalid = FALSE, returns the occurrence dataset containing only records flagged as TRUE. If return_invalid = TRUE (default), returns a list with two elements:

  • valid – the dataset with records flagged as TRUE.

  • invalid – the dataset with records flagged as FALSE.

Examples

# Create fake data example
occ <- data.frame("species" = "spp",
                  "decimalLongitude" = c(10, -190, 20, 50, NA),
                  "decimalLatitude" = c(20, 20, 240, 50, NA))
# Split valid and invalid coordinates
occ_valid <- remove_invalid_coordinates(occ)