Clean GBIF Occurrence Records — clean

This function cleans species occurrence records downloaded using the download_gbif_records() function from this package. It applies filters based on coordinate precision, uncertainty, and geographic buffers, removes records with low precision or uncertainty, excludes records near country, capital, and zoo/herbaria centroids using methods from the CoordinateCleaner package, and eliminates duplicates based on longitude, latitude, speciesKey, and datasetKey. Additionally, it removes records that do not contain species or year information.

Usage

clean_gbif(
  df,
  coordinatePrecision = NULL,
  coordinateUncertaintyInMeters = NULL,
  buffer_centroid_countries = NULL,
  buffer_centroid_capitals = NULL,
  buffer_centroid_zoo_herbaria = NULL,
  decimalLongitude = "decimalLongitude",
  decimalLatitude = "decimalLatitude",
  speciesKey = "speciesKey",
  datasetKey = "datasetKey",
  year = "year",
  species = "species",
  duplicate = FALSE
)

Arguments

df: A data frame containing species occurrence records, typically downloaded using the download_gbif_records() function from this package.
coordinatePrecision: Numeric. Remove records below this precision.
coordinateUncertaintyInMeters: Numeric. Remove records below this uncertainty or specific common values (301, 3036, 999, 9999).
buffer_centroid_countries: Numeric. Buffer size for removing records near country centroids.
buffer_centroid_capitals: Numeric. Buffer size for removing records near capital centroids.
buffer_centroid_zoo_herbaria: Numeric. Buffer size for removing records near zoo or herbaria centroids.
decimalLongitude: String. Column name for longitude. Default is "decimalLongitude".
decimalLatitude: String. Column name for latitude. Default is "decimalLatitude".
speciesKey: String. Column name for species key. Default is "speciesKey".
datasetKey: String. Column name for dataset key. Default is "datasetKey".
year: String. Column name for the year of occurrence. Default is "year".
species: String. Column name for the species. Default is "species".
duplicate: Logical. Default is FALSE. Whether or not to remove duplicates that have the same longitude, latitude, speciesKey, and datasetKey.

Value

A cleaned data frame with species occurrences.

Details

The function uses the following methods from the CoordinateCleaner package:

cc_cen(): Removes records near country centroids.
cc_cap(): Removes records near capital centroids.
cc_inst(): Removes records near zoo or herbaria centroids.

Examples

# Example usage
df <- download_gbif_records(...)
#> Error: '...' used in an incorrect context
cleaned_df <- clean_gbif(df, coordinatePrecision = 0.01,
                         coordinateUncertaintyInMeters = 100,
                         buffer_centroid_countries = 10,
                         buffer_centroid_capitals = 10,
                         buffer_centroid_zoo_herbaria = 10,
                         decimalLongitude = "decimalLongitude",
                         decimalLatitude = "decimalLatitude",
                         speciesKey = "speciesKey",
                         datasetKey = "datasetKey",
                         year = "year",
                         species = "species")
#> Error in clean_gbif(df, coordinatePrecision = 0.01, coordinateUncertaintyInMeters = 100,     buffer_centroid_countries = 10, buffer_centroid_capitals = 10,     buffer_centroid_zoo_herbaria = 10, decimalLongitude = "decimalLongitude",     decimalLatitude = "decimalLatitude", speciesKey = "speciesKey",     datasetKey = "datasetKey", year = "year", species = "species"): Missing required columns: decimalLongitude, decimalLatitude, speciesKey, datasetKey, year, species