pg_data: Download data from Pangaea.

In pangaear: Client for the 'Pangaea' Database

Description

Grabs data as a dataframe or list of dataframes from a Pangaea data repository URI; see: https://www.pangaea.de/

Usage

pg_data(doi, overwrite = TRUE, mssgs = TRUE, ...)

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

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.

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()

Author(s)

Naupaka Zimmerman, Scott Chamberlain

References

https://www.pangaea.de

Examples

## Not run: 
# 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")

## End(Not run)

pangaear documentation built on May 14, 2021, 9:05 a.m.