rdryad is a package to interface with the Dryad data repository.
- General Dryad API documentation: http://wiki.datadryad.org/Data_Access
- Solr API (http://wiki.datadryad.org/API#SOLR_search_access)
- OAI-PMH (Open Archives Initiative Protocol for Metadata Harvesting) interface; Dryad OAI-PMH description. Description of OAI-PMH in general
Installation
Install Dryad from CRAN
install.packages("rdryad")
Or install development version of rdryad from GitHub:
devtools::install_github("ropensci/rdryad")
library('rdryad')
Examples
Solr search interface
Basic search, restricting to certain fields for brevity
d_solr_search(q="Galliard", fl='handle,dc.title_sort') #> # A tibble: 10 x 2 #> handle dc.title_sort #> <chr> <chr> #> 1 252539 <NA> #> 2 10255/dryad.88… Data from: Inconsistency between different measures of… #> 3 10255/dryad.86… Data from: Quantification of correlational selection o… #> 4 10255/dryad.36… Data from: Patterns and processes of dispersal behavio… #> 5 10255/dryad.15… Data from: Water restriction causes an intergeneration… #> 6 10255/dryad.84… Data from: An experimental test of density-dependent s… #> 7 10255/dryad.34… Data from: Population and life-history consequences of… #> 8 10255/dryad.17… Data from: Reduction of baseline corticosterone secret… #> 9 10255/dryad.13… Data from: Sex-specific density-dependent secretion of… #> 10 10255/dryad.10… Data from: Climate and habitat interacts to shape the …
Dryad data based on an article DOI:
d_solr_search(q="dc.relation.isreferencedby:10.1038/nature04863", fl="dc.identifier,dc.title_ac") #> # A tibble: 1 x 2 #> dc.identifier dc.title_ac #> <chr> <chr> #> 1 doi:10.5061/dryad.8426doi:10.5061/d… Data from: Minimal ProtoHox cluste…
All terms in the dc.subject facet, along with their frequencies:
d_solr_facet(q="location:l2", facet.field="dc.subject_filter", facet.minCount=1, facet.limit=10) #> $facet_queries #> NULL #> #> $facet_fields #> $facet_fields$dc.subject_filter #> # A tibble: 10 x 2 #> term value #> <chr> <chr> #> 1 adaptation|||Adaptation 809 #> 2 population genetics - empirical|||Population Genetics - Empirical 594 #> 3 speciation|||Speciation 493 #> 4 ecological genetics|||Ecological Genetics 394 #> 5 climate change|||climate change 387 #> 6 phylogeography|||Phylogeography 379 #> 7 hybridization|||Hybridization 350 #> 8 phylogeny|||phylogeny 316 #> 9 conservation genetics|||Conservation Genetics 304 #> 10 insects|||Insects 290 #> #> #> $facet_pivot #> NULL #> #> $facet_dates #> NULL #> #> $facet_ranges #> NULL
Article DOIs associated with all data published in Dryad over the past 90 days:
d_solr_search(q="dc.date.available_dt:[NOW-90DAY/DAY TO NOW]", fl="dc.relation.isreferencedby", rows=10) #> # A tibble: 5 x 1 #> dc.relation.isreferencedby #> <chr> #> 1 doi:10.3389/fevo.2018.00138 #> 2 doi:10.1002/ece3.4479 #> 3 doi:10.7554/elife.35949 #> 4 doi:10.1007/s10592-018-1106-3 #> 5 doi:10.1212/wnl.0000000000006116
OAI-PMH interface
Identify the service
dr_identify() #> repositoryName baseURL #> 1 Dryad Digital Repository http://api.datadryad.org/oai/request #> protocolVersion adminEmail earliestDatestamp deletedRecord #> 1 2.0 [email protected] 2001-01-01T00:00:00Z persistent #> granularity compression compression.1 #> 1 YYYY-MM-DDThh:mm:ssZ gzip deflate #> description #> 1 OCLC's OAICat Repository FrameworkJeffrey A. [email protected]://alcme.oclc.org/oaicat/oaicat_icon.gifhttp://www.oclc.org/research/software/oai/cat.shtm
List sets
dr_list_sets() #> # A tibble: 8 x 2 #> setSpec setName #> <chr> <chr> #> 1 hdl_10255_dryad.148 BIRDD #> 2 hdl_10255_2 Dryad Data Files #> 3 hdl_10255_3 Dryad Data Packages #> 4 hdl_10255_dryad.7872 DryadLab Activities #> 5 hdl_10255_dryad.7871 DryadLab Packages #> 6 hdl_10255_dryad.2027 KNB #> 7 hdl_10255_dryad.2171 TreeBASE #> 8 hdl_10255_1 Main
Get records
dr_get_records(ids = 'oai:secundus.datadryad.org:10255/dryad.8820') #> $`oai:secundus.datadryad.org:10255/dryad.8820` #> $`oai:secundus.datadryad.org:10255/dryad.8820`$header #> # A tibble: 1 x 3 #> identifier datestamp setSpec #> <chr> <chr> <chr> #> 1 oai:secundus.datadryad.org:10255/dryad.8… 2015-10-29T06:27:5… hdl_10255… #> #> $`oai:secundus.datadryad.org:10255/dryad.8820`$metadata #> # A tibble: 1 x 9 #> title creator subject date type identifier relation coverage rights #> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> #> 1 NEXUS… Janies,… Echinod… 2011… Data… doi:10.50… doi:10.… World's… http:…
Get download URLs from a Dryad identifier (DOI)
dryad_files('10.5061/dryad.1758') #> [1] "http://datadryad.org/bitstream/handle/10255/dryad.1759/dataset.csv?sequence=1" #> [2] "http://datadryad.org/bitstream/handle/10255/dryad.1759/README.txt?sequence=2"
Download a file
Does not read file into, just a helper to get data files
dryad_fetch(dryad_files('10.5061/dryad.1758'))
By default dryad_fetch() will download to temporary files (note that these are cleaned up at the end of your R session). Check out the documentation for other options.
Get file DOIs from a package DOI
dryad_package_dois('10.5061/dryad.60699') #> [1] "10.5061/dryad.60699/1" "10.5061/dryad.60699/2" "10.5061/dryad.60699/3" #> [4] "10.5061/dryad.60699/4" "10.5061/dryad.60699/5" "10.5061/dryad.60699/6"
Get metadata for a DOI
Works for both package DOIs and for DOIs for files within packages
dryad_metadata('10.5061/dryad.9t0n8') #> $desc #> # A tibble: 25 x 6 #> text qualifier confidence mdschema element authority #> <chr> <chr> <chr> <chr> <chr> <chr> #> 1 Lawing, A. Michelle author NOVALUE dc contri… <NA> #> 2 Eronen, Jussi T. author NOVALUE dc contri… <NA> #> 3 Blois, Jessica L. author NOVALUE dc contri… <NA> #> 4 Graham, Catherine H. author NOVALUE dc contri… <NA> #> 5 Polly, P. David author NOVALUE dc contri… <NA> #> 6 2016-05-18T15:17:33Z accession… <NA> dc date <NA> #> 7 2016-05-18T15:17:33Z available <NA> dc date <NA> #> 8 2016-04-27 issued <NA> dc date <NA> #> 9 doi:10.5061/dryad.9t0… <NA> <NA> dc identi… <NA> #> 10 Lawing AM, Eronen JT,… citation <NA> dc identi… <NA> #> # ... with 15 more rows #> #> $files #> # A tibble: 0 x 0 #> #> $attributes #> # A tibble: 9 x 2 #> attr text #> <chr> <chr> #> 1 PROFILE DSPACE METS SIP Profile 1.0 #> 2 LABEL DSpace Item #> 3 OBJID /handle/10255/dryad.116170 #> 4 ID hdl:10255/dryad.116170 #> 5 OBJEDIT /admin/item?itemID=159223 #> 6 xmlns:mets http://www.loc.gov/METS/ #> 7 xmlns:xlink http://www.w3.org/TR/xlink/ #> 8 xmlns:xsi http://www.w3.org/2001/XMLSchema-instance #> 9 xmlns:dim http://www.dspace.org/xmlns/dspace/dim #> #> $structMap #> $structMap$div #> list() #> attr(,"DMDID") #> [1] "dmd_1" #> attr(,"TYPE") #> [1] "DSpace Item" #> #> attr(,"LABEL") #> [1] "DSpace" #> attr(,"TYPE") #> [1] "LOGICAL"
Meta
- Please report any issues or bugs.
- License: MIT
- Get citation information for
rdryadin R doingcitation(package = 'rdryad') - Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.
