Retrieve info from Dryad by URL
Arguments
- dryad_url
a Dryad dataset URL or DOI, or a table containing them (e.g., as created by
dryad_links())- id_col
the index or name of the column that contains Dryad URLs, if
dryad_urlis a table- pb
a progress bar passed from another function
- cache
if
TRUE, reuse a previously cached listing for a dataset already looked up (seerepo_info_cache_clear()) instead of re-querying Dryad's API. Off by default. Worth enabling for a corpus build likely to be interrupted and restarted, since Dryad's per-IP request quota is otherwise re-spent on every restart re-listing datasets nothing new needs fetching for.
Value
a data frame of information, one row per link, with the dataset's
metadata, its file records in the list column files, and
storage_size (the dataset's total size in bytes as Dryad reports it),
files_total (the number of files Dryad reports), and
files_incomplete (TRUE when fewer files could be listed than Dryad
reports; a warning is given too). A sharing link
(datadryad.org/stash/share/...) is followed to the dataset it leads to;
one that leads nowhere has its reason in error, as a dataset that
could not be found does.
Examples
# \donttest{
if (online("datadryad.org")) {
dryad_info("https://doi.org/10.5061/dryad.j1fd7")
}
#> No Dryad API key is set. Dryad dataset listings and metadata can be read without one, but downloading file CONTENTS from Dryad requires a key even for a fully public dataset -- every such download will fail with 'HTTP 401' until one is set. See ?dryad_pat or ?dryad_auth.
#> dryad_url dryad_doi
#> 1 https://doi.org/10.5061/dryad.j1fd7 10.5061/dryad.j1fd7
#> title doi
#> 1 Data from: Data archiving is a good investment doi:10.5061/dryad.j1fd7
#> publication_date updated_date
#> 1 2011-04-28 2020-06-24
#> authors
#> 1 Heather A. Piwowar, Todd J. Vision, Michael C. Whitlock
#> license
#> 1 https://spdx.org/licenses/CC0-1.0.html
#> files
#> 1 /api/v2/files/94868, /api/v2/datasets/doi%3A10.5061%2Fdryad.j1fd7, /api/v2/versions/26724, /api/v2/versions/26724/files, /api/v2/files/94868/download, stash, https://github.com/datadryad/dryad-app/blob/main/documentation/apis/link_relations.md#{rel}, true, PMC_reuse_of_2007_GEO_datasets.csv, 1842019, text/csv, created, 1bfc5f0f05efb9c4d8abe042ecd8a66f, md5, This is the raw data behind the analysis. It contains one row for every mention of a 2007 GEO dataset in PubMed Central. Each row identifies the mentioned GEO dataset, the PubMed Central article that mentions the dataset's accession number, whether the authors of the dataset and the attributing article overlap, and whether this is considered an instance of third-party data reuse., /api/v2/files/94869, /api/v2/datasets/doi%3A10.5061%2Fdryad.j1fd7, /api/v2/versions/26724, /api/v2/versions/26724/files, /api/v2/files/94869/download, stash, https://github.com/datadryad/dryad-app/blob/main/documentation/apis/link_relations.md#{rel}, true, README_for_PMC_reuse_of_2007_GEO_datasets.pdf, 747416, application/pdf, created, 8ebe9f0e0eef67d94d46a4f2d3dede56, md5, This is the raw data behind the analysis. It contains one row for every mention of a 2007 GEO dataset in PubMed Central. Each row identifies the mentioned GEO dataset, the PubMed Central article that mentions the dataset's accession number, whether the authors of the dataset and the attributing article overlap, and whether this is considered an instance of third-party data reuse., /api/v2/files/94870, /api/v2/datasets/doi%3A10.5061%2Fdryad.j1fd7, /api/v2/versions/26724, /api/v2/versions/26724/files, /api/v2/files/94870/download, stash, https://github.com/datadryad/dryad-app/blob/main/documentation/apis/link_relations.md#{rel}, true, tables.csv, 1176, text/csv, created, 76330f8572ab638692ce80a14f9ac977, md5, Aggregate table data behind the figures and results in the README associated with the main dataset. Includes Baseline metrics used for extrapolating PubMed Central (PMC) results to PubMed, Number of mentions of a 2007 GEO dataset by authors who submitted the dataset, and Number of mentions of a dataset by authors who DID NOT submit the dataset across 2007-2010.
#> storage_size files_total files_incomplete
#> 1 2590611 3 FALSE
# }