occ_download_import {rgbif} | R Documentation |
Import a downloaded file from GBIF.
Description
Import a downloaded file from GBIF.
Usage
occ_download_import(
x = NULL,
key = NULL,
path = ".",
fill = FALSE,
encoding = "UTF-8",
...
)
as.download(path = ".", key = NULL)
## S3 method for class 'character'
as.download(path = ".", key = NULL)
## S3 method for class 'download'
as.download(path = ".", key = NULL)
Arguments
x |
The output of a call to |
key |
A key generated from a request, like that from
|
path |
Path to unzip file to. Default: |
fill |
(logical) (default: |
encoding |
(character) encoding to read in data; passed to
|
... |
parameters passed on to |
Details
You can provide either x as input, or both key and path. We use
data.table::fread()
internally to read data.
Value
a tibble (data.frame)
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.
countryCode result column and Namibia
The country code for Namibia is "NA"
. Unfortunately in R an "NA"
string
will be read in to R as an NA/missing. To avoid this, in this function
we read in the data, then convert an NA/missing values to the character
string "NA"
. When a country code is truly missing it will be an empty
string.
Note
see downloads for an overview of GBIF downloads methods
See Also
Other downloads:
download_predicate_dsl
,
occ_download_cached()
,
occ_download_cancel()
,
occ_download_dataset_activity()
,
occ_download_datasets()
,
occ_download_get()
,
occ_download_list()
,
occ_download_meta()
,
occ_download_queue()
,
occ_download_wait()
,
occ_download()
Examples
## Not run:
# 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)
## End(Not run)