rdatacite tutorial


for v0.1.0


rdatacite provides programmatic accesses to DataCite metadata

Installation

install.packages("rdatacite")

Or development version from GitHub

install.packages("devtools")
devtools::install_github("ropensci/rdatacite")
library("rdatacite")

Usage

OAI-PMH

Ping the service

dc_oai_identify()
#>   repositoryName                     baseURL protocolVersion
#> 1   DataCite MDS http://oai.datacite.org/oai             2.0
#>           adminEmail    earliestDatestamp deletedRecord
#> 1 [email protected] 2011-01-01T00:00:00Z    persistent
#>            granularity compression compression.1
#> 1 YYYY-MM-DDThh:mm:ssZ        gzip       deflate
#>                                      description
#> 1 oaioai.datacite.org:oai:oai.datacite.org:12425

List metadata formats

dc_oai_listmetadataformats(id = "56225")
#> $`56225`
#> NULL

List identifiers

dc_oai_listidentifiers(from = '2011-06-01T', until = '2011-07-01T')
#> # A tibble: 5 x 4
#>                   identifier            datestamp setSpec setSpec.1
#>                        <chr>                <chr>   <chr>     <chr>
#> 1 oai:oai.datacite.org:32153 2011-06-08T08:57:11Z     TIB  TIB.WDCC
#> 2 oai:oai.datacite.org:32200 2011-06-20T08:12:41Z     TIB TIB.DAGST
#> 3 oai:oai.datacite.org:32220 2011-06-28T14:11:08Z     TIB TIB.DAGST
#> 4 oai:oai.datacite.org:32241 2011-06-30T13:24:45Z     TIB TIB.DAGST
#> 5 oai:oai.datacite.org:32255 2011-07-01T12:09:24Z     TIB TIB.DAGST

Get records

dc_oai_getrecord(id = "56225")
#> $`oai:oai.datacite.org:56225`
#> $`oai:oai.datacite.org:56225`$header
#> # A tibble: 1 x 3
#>                   identifier            datestamp   setSpec
#>                        <chr>                <chr>     <chr>
#> 1 oai:oai.datacite.org:56225 2014-06-03T12:03:28Z BL;BL.ADS
#> 
#> $`oai:oai.datacite.org:56225`$metadata
#> # A tibble: 1 x 12
#>                                                                         title
#>                                                                         <chr>
#> 1 Land at Hill Barton, Clyst St Mary, Devon (NGR SY 0002 9083) Hill Barton In
#> # ... with 11 more variables: creator <chr>, publisher <chr>, date <chr>,
#> #   identifier <chr>, relation <chr>, subject <chr>, language <chr>,
#> #   type <chr>, format <chr>, rights <chr>, coverage <chr>

You can pass in more than one identifier to id parameter.

Search API

This is the API for the same query interface you’d use on the DataCite website.

Search for the term laser

dc_search(q = "laser", fl = c('doi','publicationYear'), rows = 5)
#> # A tibble: 5 x 2
#>                          doi publicationYear
#>                        <chr>           <chr>
#> 1             10.7283/R3ZW26            2016
#> 2 10.17035/D.2016.0008119129            2016
#> 3             10.7283/R3V30K            2016
#> 4      10.2314/GBV:667365621            2010
#> 5      10.2314/GBV:72192168X            2012

Another search: published between 2000 and 2005

dc_search(q = "publicationYear:[2000 TO 2005]", fl = c('doi', 'publicationYear'), rows = 5)
#> # A tibble: 5 x 2
#>                   doi publicationYear
#>                 <chr>           <chr>
#> 1 10.17192/Z2003.0408            2003
#> 2        10.17617/1.5            2000
#> 3        10.17617/1.6            2004
#> 4  10.17617/2.2250118            2005
#> 5   10.17617/2.492916            2004

Facet

dc_facet(q = "wind", facet.field = 'publisher_facet', facet.limit = 5)
#> $facet_queries
#> NULL
#> 
#> $facet_fields
#> $facet_fields$publisher_facet
#> # A tibble: 5 x 2
#>                                                         term value
#>                                                        <chr> <chr>
#> 1 PANGAEA - Data Publisher for Earth & Environmental Science 32377
#> 2                       Defense Technical Information Center  2382
#> 3                                                   Figshare  1533
#> 4                                                Unpublished  1186
#> 5                                                     Zenodo   594
#> 
#> 
#> $facet_pivot
#> NULL
#> 
#> $facet_dates
#> NULL
#> 
#> $facet_ranges
#> NULL

Stats

dc_stats(q = "ecology", stats.field = 'date')
#> $data
#>                          min                max  count missing
#> date 01-Jan-2007/29-Nov-2010 September 30, 2015 153476    5366
#> 
#> $facet
#> NULL

More-like-this

dc_mlt(q = "ecology", mlt.fl = 'title', mlt.count = 2, fl = 'doi')
#> $docs
#> # A tibble: 10 x 1
#>                            doi
#>                          <chr>
#>  1         10.7892/BORIS.79067
#>  2         10.7892/BORIS.16589
#>  3         10.7892/BORIS.16333
#>  4      10.13140/2.1.3940.8968
#>  5      10.1594/PANGAEA.745038
#>  6      10.1594/PANGAEA.745039
#>  7      10.1594/PANGAEA.745049
#>  8 10.6084/M9.FIGSHARE.1540730
#>  9 10.6084/M9.FIGSHARE.1541138
#> 10 10.6084/M9.FIGSHARE.1178080
#> 
#> $mlt
#> $mlt$`8103779`
#> # A tibble: 1 x 2
#>   numFound start
#>      <int> <int>
#> 1        0     0
#> 
#> $mlt$`7245706`
#> # A tibble: 2 x 3
#>   numFound start                         doi
#>      <int> <int>                       <chr>
#> 1      591     0 10.7925/DRS1.DUCHAS_5141541
#> 2      591     0            10.7282/T3P55KJ4
#> 
#> $mlt$`5704684`
#> # A tibble: 1 x 2
#>   numFound start
#>      <int> <int>
#> 1        0     0
#> 
#> $mlt$`4647415`
#> # A tibble: 1 x 2
#>   numFound start
#>      <int> <int>
#> 1        0     0
#> 
#> $mlt$`536251`
#> # A tibble: 1 x 2
#>   numFound start
#>      <int> <int>
#> 1        0     0
#> 
#> $mlt$`536252`
#> # A tibble: 1 x 2
#>   numFound start
#>      <int> <int>
#> 1        0     0
#> 
#> $mlt$`536260`
#> # A tibble: 1 x 2
#>   numFound start
#>      <int> <int>
#> 1        0     0
#> 
#> $mlt$`6743504`
#> # A tibble: 1 x 2
#>   numFound start
#>      <int> <int>
#> 1        0     0
#> 
#> $mlt$`6746350`
#> # A tibble: 1 x 2
#>   numFound start
#>      <int> <int>
#> 1        0     0
#> 
#> $mlt$`4013379`
#> # A tibble: 1 x 2
#>   numFound start
#>      <int> <int>
#> 1        0     0

Citing

To cite rdatacite in publications use:


Scott Chamberlain (2016). rdatacite: ‘DataCite’ Client for ‘OAI-PMH’ Methods and their Search ‘API’. R package version 0.1.0. https://cran.rstudio.com/package=rdatacite

License and bugs

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