Grabs data as a dataframe or list of dataframes from a Pangaea data repository URI; see: https://www.pangaea.de/
Arguments
- doi
DOI of Pangaeae single dataset, or of a collection of datasets. Expects either just a DOI of the form
10.1594/PANGAEA.746398, or with the URL part in front, like https://doi.pangaea.de/10.1594/PANGAEA.746398- overwrite
(logical) Ovewrite a file if one is found with the same name
- mssgs
(logical) print information messages. Default:
TRUE- ...
Curl options passed on to crul::verb-GET
Value
One or more items of class pangaea, each with the doi, parent doi
(if many dois within a parent doi), url, citation, path, and data object.
Data object depends on what kind of file it is. For tabular data, we print
the first 10 columns or so; for a zip file we list the files in the zip
(but leave it up to the user to dig unzip and get files from the zip file);
for png files, we point the user to read the file in with png::readPNG()
Details
Data files are stored in an operating system appropriate location.
Run pg_cache$cache_path_get() to get the storage location
on your machine. See pg_cache for more information, including how to
set a different base path for downloaded files.
Some files/datasets require the user to be logged in. For now we just pass on these - that is, give back nothing other than metadata.
Examples
if (FALSE) { # \dontrun{
# a single file
(res <- pg_data(doi='10.1594/PANGAEA.807580'))
res[[1]]$doi
res[[1]]$citation
res[[1]]$data
res[[1]]$metadata
# another single file
pg_data(doi='10.1594/PANGAEA.807584')
# Many files
(res <- pg_data(doi='10.1594/PANGAEA.761032'))
res[[1]]
res[[2]]
# Manipulating the cache
## list files in the cache
pg_cache$list()
## clear all data
# pg_cache$delete_all()
pg_cache$list()
## clear a single dataset by DOI
pg_data(doi='10.1594/PANGAEA.812093')
pg_cache$list()
path <- grep("PANGAEA.812093", pg_cache$list(), value = TRUE)
pg_cache$delete(path)
pg_cache$list()
# search for datasets, then pass in DOIs
(searchres <- pg_search(query = 'birds', count = 20))
pg_data(searchres$doi[1])
# png file
pg_data(doi = "10.1594/PANGAEA.825428")
# zip file
pg_data(doi = "10.1594/PANGAEA.860500")
# login required
## we skip file download
pg_data("10.1594/PANGAEA.788547")
} # }