ReadCrossRef {RefManageR}

Search CrossRef for citations.

Description

Provides an interface to the CrossRef API, searching for citations given a string query. Results are written to a bib file, read back into R using WriteBib, and returned as a BibEntry object.

Usage

ReadCrossRef(
  query = "",
  filter = list(),
  limit = 5,
  offset = 0,
  sort = "relevance",
  year = NULL,
  min.relevance = 2,
  temp.file = tempfile(fileext = ".bib"),
  delete.file = TRUE,
  verbose = FALSE,
  use.old.api = FALSE
)

Arguments

query

string; search term

filter

named list of possible filters; see Details and References; ignored if use.old.api = TRUE

limit

numeric; maximum number of entries to return

offset

numeric; CrossRef will not return the first offset results (default 0); ignored if use.old.api = TRUE

sort

string; how specifying how the results from CrossRef should be sorted. Possible values when use.old.api = FALSE are "score" (default; same as "relevance"), "updated", "deposited", "indexed", or "published"; see the references

year

numeric; if specified, only results from this year will be returned.

min.relevance

numeric; only results with a CrossRef-assigned relevance score at least this high will be returned.

temp.file

string; file name to use for storing Bibtex information returned by CrossRef.

delete.file

boolean; should the bib file be deleted on exit?

verbose

boolean; if TRUE, additional messages are output regarding the results of the query.

use.old.api

boolean; should the older CrossRef API be used for the search? NO LONGER SUPPORTED, all queries need to use the new API.

Details

When use.old.api = TRUE, the query HTTP request only returns DOIs, which are then used to make HTTP requests for the corresponding BibTeX entries from CrossRef; when use.old.api = FALSE, the query HTTP request is parsed to create the BibEntry object (i.e. there are less HTTP requests when using the new API).

CrossRef assigns a score between 0 and 100 based on how relevant a reference seems to be to your query. The old API documentation warns that while false negatives are unlikely, the search can be prone to false positives. Hence, setting min.revelance to a high value may be necessary if use.old.api = TRUE. In some instances with the old API, no score is returned, if this happens, the entries are added with a message indicating that no score was available.

Possible values for the names in filter are "has-funder", "funder", "prefix", "member", "from-index-date", "until-index-date", "from-deposit-date", "until-deposit-date", "from-update-date", "until-update-date", "from-created-date", "until-created-date", "from-pub-date", "until-pub-date", "has-license", "license.url", "license.version", "license.delay", "has-full-text", "full-text.version", "full-text.type", "public-references", "has-references", "has-archive", "archive", "has-orcid", "orcid", "issn", "type", "directory", "doi", "updates", "is-update", "has-update-policy", "container-title", "publisher-name", "category-name", "type-name", "award.number", "award.funder", "assertion-group", "assertion", "affiliation", "has-affiliation", "alternative-id", and "article-number". See the first reference for a description of their meanings.

Value

An object of class BibEntry.

Note

The entries returned by Crossref are frequently missing fields required by BibTeX, if you want the entries to be returned anyway, set BibOptions()$check.entries to FALSE or "warn"

Fields "score" (the relevancy score) and "license" will be returned when use.old.api = FALSE.

References

Newer API: https://github.com/CrossRef/rest-api-doc/blob/master/rest_api.md, Older API: https://search.crossref.org/help/api

See Also

ReadZotero, BibEntry, package rcrossref for larger queries and deep paging

Other pubmed: GetPubMedByID(), GetPubMedRelated(), LookupPubMedID(), ReadPubMed()

Examples

if (interactive() && !httr::http_error("https://search.crossref.org/")){
  BibOptions(check.entries = FALSE)
  ## 3 results from the American Statistical Association involving "regression"
  ReadCrossRef("regression", filter = list(prefix="10.1198"), limit = 3)

  ## Some JRSS-B papers published in 2010 or later, note the quotes for filter
  ##   names with hypens
  ReadCrossRef(filter = list(issn = "1467-9868", "from-pub-date" = 2010),
               limit = 2, min.relevance = 0)

  ## Articles published by Institute of Mathematical Statistics
  ReadCrossRef(filter = list(prefix = "10.1214"), limit = 5, min.relevance = 0)

  ## old API
  ReadCrossRef(query = 'rj carroll measurement error', limit = 2, sort = "relevance",
    min.relevance = 80, use.old.api = TRUE)

  ReadCrossRef(query = 'carroll journal of the american statistical association',
    year = 2012, limit = 2, use.old.api = TRUE)
}