Import a download requested from GBIF — import

This function imports a dataset downloaded from GBIF using a request key generated by the request_gbif() function. It optionally allows saving the imported occurrences to disk in CSV or GZIP format.

Usage

import_gbif(
  request_key,
  write_file = FALSE,
  output_dir = NULL,
  file.format = "gz",
  select_columns = TRUE,
  columns_to_import = NULL,
  overwrite = FALSE,
  ...
)

Arguments

request_key: an object of class 'request_key' returned by the request_gbif() function.
write_file: whether to save the downloaded occurrences to disk. Default is FALSE. If TRUE, you must specify the output_dir.
output_dir: (character) a directory to save the data downloaded from GBIF. Only applicable if write_file = TRUE. Default is NULL.
file.format: (character) the format to save the file. Options available are 'csv' (comma-separated values) and 'gz' (compressed GZIP). Only applicable if write_file = TRUE. Default is 'gz'.
select_columns: (logical) whether to import only specific columns (TRUE) or all columns (FALSE) from the occurrence table. Default is TRUE.
columns_to_import: (character) vector of column names to import. Default is NULL, meaning it will import the column names specified in RuHere::gbif_columns data.
overwrite: (logical) whether to overwrite the file in the 'output_dir' if it already exists. Default is FALSE.
...: other arguments passed to rgbif::occ_download_import().

Value

A data frame containing the GBIF occurrence records. If write_file = TRUE, the function also saves the dataset to disk in the specified format.

Note

This function requires an active internet connection.

Examples

 if (FALSE) { # \dontrun{
# Prepare data to request GBIF download
gbif_prepared <- prepare_gbif_download(species = "Araucaria angustifolia")
# Submit a request to download occurrences
gbif_requested <- request_gbif(gbif_info = gbif_prepared)
# Check progress
rgbif::occ_download_wait(gbif_requested)
# After succeeded, import data
occ_gbif <- import_gbif(request_key = gbif_requested)
} # }