RuHere (version 1.0.1)

import_gbif: Import a download requested from GBIF

Description

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,
  ...
)

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.

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().

Examples

 if (FALSE) {
# 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)
}