rdryad
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.8872 Data from: Inconsistency between different measures…
#> 3 10255/dryad.86943 Data from: Quantification of correlational selectio…
#> 4 10255/dryad.36217 Data from: Patterns and processes of dispersal beha…
#> 5 10255/dryad.159843 Data from: Water restriction causes an intergenerat…
#> 6 10255/dryad.84720 Data from: An experimental test of density-dependen…
#> 7 10255/dryad.34100 Data from: Population and life-history consequences…
#> 8 10255/dryad.135812 Data from: Sex-specific density-dependent secretion…
#> 9 10255/dryad.177079 Data from: Reduction of baseline corticosterone sec…
#> 10 10255/dryad.102424 Data from: Climate and habitat interacts to shape t…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:1… Data from: Minimal ProtoHox cluster inferr…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 791
#> 2 population genetics - empirical|||Population Genetics - Empirical 581
#> 3 speciation|||Speciation 482
#> 4 ecological genetics|||Ecological Genetics 390
#> 5 phylogeography|||Phylogeography 380
#> 6 climate change|||climate change 359
#> 7 hybridization|||Hybridization 340
#> 8 conservation genetics|||Conservation Genetics 301
#> 9 phylogeny|||phylogeny 300
#> 10 insects|||Insects 284
#>
#>
#> $facet_pivot
#> NULL
#>
#> $facet_dates
#> NULL
#>
#> $facet_ranges
#> NULLArticle 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: 7 x 1
#> dc.relation.isreferencedby
#> <chr>
#> 1 doi:10.1111/oik.05215
#> 2 doi:10.1086/693781
#> 3 doi:10.1111/jav.01643
#> 4 doi:10.1002/2017jf004462
#> 5 doi:10.1111/jav.01633
#> 6 doi:10.1111/jav.01685
#> 7 doi:10.1111/ecog.03632OAI-PMH interface
Identify the service
dr_identify()
#> repositoryName baseURL
#> 1 Dryad Data Repository https://www.datadryad.org/oai/request
#> protocolVersion adminEmail earliestDatestamp deletedRecord
#> 1 2.0 admin@datadryad.org 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. Youngjyoung@oclc.orgOCLC1.5.48http://alcme.oclc.org/oaicat/oaicat_icon.gifhttp://www.oclc.org/research/software/oai/cat.shtmList 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 MainGet records
dr_get_records(ids = 'oai:datadryad.org:10255/dryad.8820')
#> $`oai:datadryad.org:10255/dryad.8820`
#> $`oai:datadryad.org:10255/dryad.8820`$header
#> # A tibble: 1 x 3
#> identifier datestamp setSpec
#> <chr> <chr> <chr>
#> 1 oai:datadryad.org:10255/dryad.8820 2015-10-29T06:27:53Z hdl_10255_2
#>
#> $`oai:datadryad.org:10255/dryad.8820`$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 accessio… <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.9t0n8 <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.
Data provided by...
Data is provided from the Dryad API.