Help for package rdatacite

Type:

Package

Title:

Client for the 'DataCite' API

Version:

0.5.4

Description:

Client for the web service methods provided by 'DataCite' (https://www.datacite.org/), including functions to interface with their 'RESTful' search API. The API is backed by 'Elasticsearch', allowing expressive queries, including faceting.

License:

MIT + file LICENSE

URL:

https://docs.ropensci.org/rdatacite/, https://github.com/ropensci/rdatacite

BugReports:

https://github.com/ropensci/rdatacite/issues

Imports:

crul (≥ 0.7.4), jsonlite, tibble, utils

Suggests:

testthat, vcr

Encoding:

UTF-8

RoxygenNote:

7.2.2

X-schema.org-applicationCategory:

Data

X-schema.org-isPartOf:

https://ropensci.org

X-schema.org-keywords:

data, scholarly, dataset, https, API, web-services

NeedsCompilation:

Packaged:

2023-01-02 23:04:00 UTC; Bianca

Author:

Scott Chamberlain

[aut], Bianca Kramer

[cre]

Maintainer:

Bianca Kramer <bianca.kramer@gmail.com>

Repository:

CRAN

Date/Publication:

2023-02-05 21:02:30 UTC

rdatacite

Description

DataCite R client

HTTP Requests

All HTTP requests are GET requests, and are sent with the following headers:

⁠Accept: application/vnd.api+json; version=2⁠
⁠User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(rdatacite/0.5.0)⁠
⁠X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(rdatacite/0.5.0)⁠

The user-agent strings change as the versions of each package change.

rdatacite defunct functions

dc_data_center
dc_data_centers
dc_facet
dc_member
dc_members
dc_mlt
dc_oai_getrecord
dc_oai_identify
dc_oai_listidentifiers
dc_oai_listmetadataformats
dc_oai_listrecords
dc_oai_listsets
dc_search
dc_stats
dc_work
dc_works

Content negotation

For content negotation see rcrossref::cr_cn(), which can be used for Crossref, DataCite and Medra DOIs

GraphGL API

rdatacite does not support the GraphGL API https://support.datacite.org/docs/datacite-graphql-api-guide - we suggest trying the ghql package (https://github.com/ropensci/ghql/)

Author(s)

Scott Chamberlain myrmecocystus@gmail.com

DataCite REST API: activities

Description

DataCite REST API: activities

Usage

dc_activities(
  ids = NULL,
  query = NULL,
  limit = 25,
  page = 1,
  cursor = NULL,
  ...
)

Arguments

ids

(character) one or more activity IDs

query

(character) Query string

limit

(numeric/integer) results per page

page

(numeric/integer) the page to get results for. default: 1

cursor

(character) page cursor (used instead of limit param). to use cursor pagination, set cursor = 1, then use the link in ⁠$links$next⁠

...

curl options passed on to crul::verb-GET

Details

for more info on the ⁠/activities⁠ route see https://support.datacite.org/docs/tracking-provenance

Examples

## Not run: 
if (dc_check()) {
x <- dc_activities()
x
# dc_activities(x$data$id[1]) # FIXME: doesn't work, returns no data
# dc_activities(query = "ecology") # FIXME: this thlimit a 500 error
}
## End(Not run)

check if the DataCite API is up or not

Description

check if the DataCite API is up or not

Usage

dc_check(...)

Value

boolean

DataCite REST API: client prefixes

Description

DataCite REST API: client prefixes

Usage

dc_client_prefixes(
  query = NULL,
  year = NULL,
  client_id = NULL,
  prefix_id = NULL,
  sort = NULL,
  include = NULL,
  limit = 25,
  page = 1,
  cursor = NULL,
  ...
)

Arguments

query

(character) Query string

year

(integer/numeric/character) a year

client_id

a client ID

prefix_id

a prefix ID

sort

(character) variable to sort by

include

(character) vector of fields to return

limit

(numeric/integer) results per page

page

(numeric/integer) the page to get results for. default: 1

cursor

(character) page cursor (used instead of limit param). to use cursor pagination, set cursor = 1, then use the link in ⁠$links$next⁠

...

curl options passed on to crul::verb-GET

Examples

## Not run: 
if (dc_check()) {
x <- dc_client_prefixes()
x
}
## End(Not run)

DataCite REST API: clients

Description

DataCite REST API: clients

Usage

dc_clients(
  ids = NULL,
  query = NULL,
  year = NULL,
  provider_id = NULL,
  software = NULL,
  include = NULL,
  limit = 25,
  page = 1,
  cursor = NULL,
  ...
)

Arguments

ids

(character) one or more client IDs

query

(character) Query string

year

(integer/numeric/character) a year

provider_id

a provider ID

software

no idea what should go here, anyone?

include

(character) vector of fields to return

limit

(numeric/integer) results per page

page

(numeric/integer) the page to get results for. default: 1

cursor

(character) page cursor (used instead of limit param). to use cursor pagination, set cursor = 1, then use the link in ⁠$links$next⁠

...

curl options passed on to crul::verb-GET

Examples

## Not run: 
if (dc_check()) {
x <- dc_clients()
x
dc_clients(x$data$id[1])
dc_clients(x$data$id[1:2], verbose = TRUE)
}
## End(Not run)

DataCite content negotation

Description

DataCite content negotation

Usage

dc_cn(dois, format = "bibtex", style = "apa", locale = "en-US", ...)

Arguments

dois

(character) one or more DOIs

format

Name of the format. One of "rdf-xml", "turtle", "citeproc-json", "schemaorg", "codemeta", "text", "ris", "bibtex" (default), "datacite-xml", "datacite-json", "bibentry", or "jats".

style

a CSL style (for text format only). See ‘rcrossref::get_styles()’ for options. Default: 'apa'. If there's a style that DataCite doesn't support you'll get a (500) Internal Server Error

locale

Language locale. See ‘?Sys.getlocale’

...

curl options passed on to crul::verb-GET

References

https://support.datacite.org/docs/datacite-content-resolver

Examples

## Not run: 
dc_cn("10.5281/zenodo.50213")
dc_cn(c("10.5281/zenodo.50213", "10.5281/zenodo.57081"), "text")
dc_cn(c("a-bad-doi", "10.5281/zenodo.50213", "10.5281/zenodo.57081"), "text")

## End(Not run)

DataCite REST API: dois

Description

DataCite REST API: dois

Usage

dc_dois(
  ids = NULL,
  query = NULL,
  created = NULL,
  registered = NULL,
  provider_id = NULL,
  client_id = NULL,
  person_id = NULL,
  resource_type_id = NULL,
  subject = NULL,
  schema_version = NULL,
  random = NULL,
  sample_size = NULL,
  sample_group = NULL,
  include = NULL,
  sort = NULL,
  limit = 25,
  page = 1,
  cursor = NULL,
  ...
)

Arguments

ids

(character) one or more DOIs

query

(character) Query string. See Querying below.

created

(character) metadata where year of DOI creation is created. See Filtering Responses below.

registered

(character) metadata where year of DOI registration is year. See Filtering Responses below.

provider_id

(character) metadata associated with a specific DataCite provider. See Filtering Responses below.

client_id

(character) metadata associated with a specific DataCite client. See Filtering Responses below.

person_id

(character) metadata associated with a specific person's ORCID iD. See Filtering Responses below.

resource_type_id

(character) metadata for a specific resourceTypeGeneral. See Filtering Responses below.

subject

(character)

schema_version

(character) metadata where schema version of the deposited metadata is schema-version. See Filtering Responses below.

random

(logical) return random set of results, can be combined with any kind of query. default: FALSE.

sample_size

(character)

sample_group

(character)

include

(character) vector of fields to return

sort

(character) variable to sort by

limit

(numeric/integer) results per page

page

(numeric/integer) the page to get results for. default: 1

cursor

(character) page cursor (used instead of limit param). to use cursor pagination, set cursor = 1, then use the link in ⁠$links$next⁠

...

curl options passed on to crul::verb-GET

Querying

See https://support.datacite.org/docs/api-queries for details

Filtering Responses

See https://support.datacite.org/docs/api-queries#section-filtering-list-responses for details

Examples

## Not run: 
if (dc_check()) {
x <- dc_dois()
x
dc_dois(query = "birds")
dc_dois(query = "climate change")
dc_dois(query = "publicationYear:2016")
x <- dc_dois(query = "creators.familyName:mil*", verbose = TRUE)
lapply(x$data$attributes$creators, "[[", "familyName")
x <- dc_dois(query = "titles.title:climate +change")
lapply(x$data$attributes$titles, "[[", "title")
dc_dois(client_id = "dryad.dryad")
dc_dois(x$data$id[1])
dc_dois(x$data$id[1:3])
dc_dois("10.5281/zenodo.1308060")

# pagination
dc_dois(limit = 1)
x <- dc_dois(cursor = 1)
x$links$`next`
}
## End(Not run)

DataCite REST API: events

Description

DataCite REST API: events

Usage

dc_events(
  ids = NULL,
  query = NULL,
  subj_id = NULL,
  obj_id = NULL,
  doi = NULL,
  orcid = NULL,
  prefix = NULL,
  subtype = NULL,
  subject = NULL,
  source_id = NULL,
  registrant_id = NULL,
  relation_type_id = NULL,
  issn = NULL,
  publication_year = NULL,
  year_month = NULL,
  include = NULL,
  sort = NULL,
  limit = 25,
  page = 1,
  cursor = NULL,
  ...
)

Arguments

ids

(character) one or more event IDs

query

(character) Query for any event information

subj_id

(character) The identifier for the event subject, expressed as a URL. For example: ⁠https://doi.org/10.7272/q6qn64nk⁠

obj_id

(character) The identifier for the event object, expressed as a URL. For example: ⁠https://doi.org/10.7272/q6qn64nk⁠

doi

(character) The subj-id or obj-id of the event, expressed as a DOI. For example: 10.7272/q6qn64nk

orcid

(character) an ORCID, presumably

prefix

(character) The DOI prefix of the subj-id or obj-id of the event. For example: 10.7272

subtype

(character) xxx

subject

(character) xxx

source_id

(character) a source ID. See Details

registrant_id

(character)

relation_type_id

(character) a relation-type ID. See Details

issn

(character) an ISSN, presumably

publication_year

(character) the publication year

year_month

(character) The year and month in which the event occurred, in the format YYYY-MM. For example 2018-08

include

(character) vector of fields to return

sort

(character) variable to sort by

limit

(numeric/integer) results per page

page

(numeric/integer) the page to get results for. default: 1

cursor

(character) page cursor (used instead of limit param). to use cursor pagination, set cursor = 1, then use the link in ⁠$links$next⁠

...

curl options passed on to crul::verb-GET

Details

See https://support.datacite.org/docs/eventdata-guide for details on possible values for parameters

Examples

## Not run: 
if (dc_check()) {
# dc_events(query = "birds")
}
## End(Not run)

DataCite REST API: prefixes

Description

DataCite REST API: prefixes

Usage

dc_prefixes(include = NULL, limit = 25, page = 1, cursor = NULL, ...)

Arguments

include

(character) vector of fields to return

limit

(numeric/integer) results per page

page

(numeric/integer) result page, the record to start at

cursor

(character) page cursor (used instead of limit param)

...

curl options passed on to crul::HttpClient

Examples

## Not run: 
if (dc_check()) {
x <- dc_prefixes()
x
dc_prefixes(limit = 3)
}
## End(Not run)

DataCite REST API: provider prefixes

Description

DataCite REST API: provider prefixes

Usage

dc_provider_prefixes(include = NULL, limit = 25, page = 1, cursor = NULL, ...)

Arguments

include

(character) vector of fields to return

limit

(numeric/integer) results per page

page

(numeric/integer) result page, the record to start at

cursor

(character) page cursor (used instead of limit param)

...

curl options passed on to crul::HttpClient

Examples

## Not run: 
if (dc_check()) {
x <- dc_provider_prefixes()
x
dc_provider_prefixes(limit = 3)
}
## End(Not run)

DataCite REST API: providers

Description

DataCite REST API: providers

Usage

dc_providers(
  ids = NULL,
  query = NULL,
  year = NULL,
  region = NULL,
  organization_type = NULL,
  focus_area = NULL,
  include = NULL,
  limit = 25,
  page = 1,
  cursor = NULL,
  ...
)

Arguments

ids

(character) one or more provider IDs

query

(character) query string

year

(character) year

region

(character) region name

organization_type

(character) organization type

focus_area

(character) focus area

include

(character) vector of fields to return

limit

(numeric/integer) results per page

page

(numeric/integer) result page, the record to start at

cursor

(character) page cursor (used instead of limit param)

...

curl options passed on to crul::HttpClient

Examples

## Not run: 
if (dc_check()) {
x <- dc_providers()
x
dc_providers(limit = 3)
dc_providers(ids = x$data$id[1:5])
}
## End(Not run)

DataCite REST API: reports

Description

DataCite REST API: reports

Usage

dc_reports(
  ids = NULL,
  platform = NULL,
  report_name = NULL,
  report_id = NULL,
  release = NULL,
  created = NULL,
  created_by = NULL,
  include = NULL,
  limit = 25,
  page = 1,
  ...
)

Arguments

ids

(character) one or more report IDs

platform

(character) Name of the Platform the usage is being requested for. This can be omitted if the service provides usage for only one platform.

report_name

(character) The long name of the report

report_id

(character) The report ID or code or shortname. Typically this will be the same code provided in the Report parameter of the request

release

(character) The release or version of the report

created

(character) Time the report was prepared. Format as defined by date-time - RFC3339

created_by

(character) Name of the organization producing the report

include

(character) vector of fields to return

limit

(numeric/integer) results per page

page

(numeric/integer) result page, the record to start at

...

curl options passed on to crul::HttpClient

Examples

## Not run: 
if (dc_check()) {
x <- dc_reports()
x
dc_reports(created = "2019-08-01T07:00:00.000Z")
dc_reports(created_by = "urn:node:GOA")
dc_reports(limit = 3)
# dc_reports(ids = x$reports$id[1:3]) # FIXME: doesn't work
}
## End(Not run)

DataCite REST API: status of the API

Description

DataCite REST API: status of the API

Usage

dc_status(...)

Arguments

...

curl options passed on to crul::HttpClient

Examples

## Not run: 
if (dc_check()) {
dc_status()
}
## End(Not run)

rdatacite

Description

HTTP Requests

Methods in the package

rdatacite defunct functions

Content negotation

GraphGL API

Author(s)

DataCite REST API: activities

Description

Usage

Arguments

Details

Examples

check if the DataCite API is up or not

Description

Usage

Value

DataCite REST API: client prefixes

Description

Usage

Arguments

Examples

DataCite REST API: clients

Description

Usage

Arguments

Examples

DataCite content negotation

Description

Usage

Arguments

References

See Also

Examples

DataCite REST API: dois

Description

Usage

Arguments

Querying

Filtering Responses

Examples

DataCite REST API: events

Description

Usage

Arguments

Details

Examples

DataCite REST API: prefixes

Description

Usage

Arguments

Examples

DataCite REST API: provider prefixes

Description

Usage

Arguments

Examples

DataCite REST API: providers

Description

Usage

Arguments

Examples

DataCite REST API: reports

Description

Usage

Arguments

Examples

DataCite REST API: status of the API

Description

Usage

Arguments

Examples