Type: Package
Title: Client for the Open Citations Corpus
Description: Client for the Open Citations Corpus (http://opencitations.net/). Includes a set of functions for getting one identifier type from another, as well as getting references and citations for a given identifier.
Version: 0.3.0
License: MIT + file LICENSE
URL: https://github.com/ropenscilabs/citecorp (devel), https://docs.ropensci.org/citecorp/ (docs)
BugReports: https://github.com/ropenscilabs/citecorp/issues
Encoding: UTF-8
Language: en-US
LazyData: yes
Imports: crul (≥ 0.7.0), data.table, fauxpas (≥ 0.5.0), jsonlite
Suggests: testthat, vcr, webmockr
RoxygenNote: 7.1.0
X-schema.org-applicationCategory: Literature
X-schema.org-keywords: doi, metadata, citation, opencitations, bibtex
X-schema.org-isPartOf: https://ropensci.org
NeedsCompilation: no
Packaged: 2020-04-16 15:09:33 UTC; sckott
Author: Scott Chamberlain ORCID iD [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Repository: CRAN
Date/Publication: 2020-04-16 15:20:02 UTC

citecorp

Description

Client for the Open Citations Corpus http://opencitations.net/

Author(s)

Scott Chamberlain myrmecocystus@gmail.com

COCI: OpenCitations Index of Crossref open DOI-to-DOI references

Description

AFAICT this API is a REST wrapper around the SPARQL service

Usage

oc_coci_refs(doi, exclude = NULL, filter = NULL, sort = NULL, ...)

oc_coci_cites(doi, exclude = NULL, filter = NULL, sort = NULL, ...)

oc_coci_meta(doi, exclude = NULL, filter = NULL, sort = NULL, ...)

oc_coci_citation(oci, ...)

Arguments

doi

(character) one or more Digital Object Identifiers (DOIs)

exclude

(character) a field_name; all the rows that have an empty value in the field_name specified are removed from the result set

filter

⁠=<field_name>:<operator><value>:⁠ only the rows compliant with ⁠<value>⁠ are kept in the result set. The parameter ⁠<operation>⁠ is not mandatory. If ⁠<operation>⁠ is not specified, ⁠<value>⁠ is interpreted as a regular expression, otherwise it is compared by means of the specified operation. Possible operators are "=", "<", and ">". For instance, ⁠filter=title:semantics?⁠ returns all the rows that contain the string "semantic" or "semantics" in the field title, while ⁠filter=date:>2016-05⁠ returns all the rows that have a date greater than May 2016.

sort

⁠=<order>(<field_name>):⁠ sort in ascending (⁠<order>⁠ set to "asc") or descending (⁠<order>⁠ set to "desc") order the rows in the result set according to the values in ⁠<field_name>⁠. For instance, sort=desc(date) sorts all the rows according to the value specified in the field date in descending order.

...

curl options passed on to crul::verb-GET

oci

(character) one or more Open Citation Identifiers (OCIs)

Value

data.frame, see http://opencitations.net/index/coci/api/v1 for explanation of the resulting columns

References

http://opencitations.net/index/coci/api/v1, https://github.com/opencitations/api-coci

Examples

doi1 <- "10.1108/jd-12-2013-0166"
doi2 <- "10.1371/journal.pgen.1005937"
oci1 <-
 "02001010806360107050663080702026306630509-0200101080636102704000806"
oci2 <-
 "0200101000836191363010263020001036300010606-020010003083604090301050910"

if (
crul::ok(
"http://opencitations.net/index/coci/api/v1/references/10.1108/jd-12-2013-0166",
timeout_ms = 1000L)
) {
try(
  oc_coci_cites(doi1),
  silent = TRUE
)
}

### More examples
## Not run: 
# references
oc_coci_refs(doi1, exclude = "oci")
oc_coci_refs(doi1, filter = "date:>2016-05", verbose = TRUE)
oc_coci_refs(doi2)
oc_coci_refs(c(doi1, doi2))

# citations
oc_coci_cites(doi1, exclude = "oci")
oc_coci_cites(doi2)
oc_coci_cites(c(doi1, doi2))

# metadata
oc_coci_meta(doi2)
oc_coci_meta(c(doi1, doi2))

# citation - an OCI instead of a DOI
oc_coci_citation(oci1)
oc_coci_citation(c(oci1, oci2))

## End(Not run)

Vector of 25 DOIs (Digital Object Identifiers)

Description

To be used in examples, etc. for oc_lookup and oc_coci methods

Methods for getting IDs from other IDs

Description

Methods for getting IDs from other IDs

Usage

oc_doi2ids(id, ...)

oc_pmid2ids(id, ...)

oc_pmcid2ids(id, ...)

Arguments

id

One or more digital object identifiers (DOI), PMID, or PMCID, depending on the function

...

curl options passed on to crul::verb-GET

Value

data.frame, with four columns:

An empty data.frame (no columns or rows) when no results found

Column order will always be the same; note though that some columns may be missing if, for example, there's no PMID for a DOI search.

Examples

if (oc_lookup_check()) {
try(
  oc_doi2ids("10.1097/igc.0000000000000609", timeout_ms=10),
  silent = TRUE
)
}

### More examples
## Not run: 
oc_doi2ids('10.1093/biomet/80.3.527')
oc_doi2ids('10.1093/biomet/79.3.531')
oc_pmid2ids("26645990")
oc_pmcid2ids("PMC4679344")

oc_doi2ids(id = oc_dois[1:3])
oc_pmid2ids(id = oc_pmids[1:3])
oc_pmcid2ids(id = oc_pmcids[1:3])

## End(Not run)

oc_lookup checker

Description

oc_lookup checker

Usage

oc_lookup_check()

Vector of 8 PMCIDs (PubMed Central Identifiers)

Description

To be used in examples, etc. for oc_lookup and oc_coci methods

Vector of 24 PMIDs (PubMed Identifiers)

Description

To be used in examples, etc. for oc_lookup and oc_coci methods