Import a downloaded file from GBIF.

occ_download_import(
  x = NULL,
  key = NULL,
  path = ".",
  fill = FALSE,
  encoding = "UTF-8",
  ...
)

as.download(path = ".", key = NULL)

# S3 method for character
as.download(path = ".", key = NULL)

# S3 method for download
as.download(path = ".", key = NULL)

Arguments

x

The output of a call to occ_download_get

key

A key generated from a request, like that from occ_download

path

Path to unzip file to. Default: "." Writes to folder matching zip file name

fill

(logical) (default: FALSE). If TRUE then in case the rows have unequal length, blank fields are implicitly filled. passed on to fill parameter in data.table::fread.

encoding

(character) encoding to read in data; passed to data.table::fread(). default: "UTF-8". other allowed options: "Latin-1" and "unknown". see ?data.table::fread docs

...

parameters passed on to data.table::fread()

Value

a tibble (data.frame)

Details

You can provide either x as input, or both key and path. We use data.table::fread() internally to read data.

Note

see downloads for an overview of GBIF downloads methods

Problems reading data

You may run into errors when using occ_download_import(); most often these are due to data.table::fread() not being able to parse the occurrence.txt file correctly. The fill parameter passes down to data.table::fread() and the ... allows you to pass on any other parameters that data.table::fread() accepts. Read the docs for fread for help.

See also

Examples

if (FALSE) { # First, kick off at least 1 download, then wait for the job to be complete # Then use your download keys res <- occ_download_get(key="0000066-140928181241064", overwrite=TRUE) occ_download_import(res) occ_download_get(key="0000066-140928181241064", overwrite = TRUE) %>% occ_download_import # coerce a file path to the right class to feed to occ_download_import # as.download("0000066-140928181241064.zip") # as.download(key = "0000066-140928181241064") # occ_download_import(as.download("0000066-140928181241064.zip")) # download a dump that has a CSV file # res <- occ_download_get(key = "0001369-160509122628363", overwrite=TRUE) # occ_download_import(res) # occ_download_import(key = "0001369-160509122628363") # download and import a species list (in csv format) # x <- occ_download_get("0000172-190415153152247") # occ_download_import(x) }