Search CrossRef works (articles)

Usage

cr_works(
  dois = NULL,
  query = NULL,
  filter = NULL,
  offset = NULL,
  limit = NULL,
  sample = NULL,
  sort = NULL,
  order = NULL,
  facet = FALSE,
  cursor = NULL,
  cursor_max = 5000,
  .progress = "none",
  flq = NULL,
  select = NULL,
  async = FALSE,
  ...
)

cr_works_(
  dois = NULL,
  query = NULL,
  filter = NULL,
  offset = NULL,
  limit = NULL,
  sample = NULL,
  sort = NULL,
  order = NULL,
  facet = FALSE,
  cursor = NULL,
  cursor_max = 5000,
  .progress = "none",
  parse = FALSE,
  flq = NULL,
  select = NULL,
  async = FALSE,
  ...
)

Arguments

dois

Search by a single DOI or many DOIs. Note that using this parameter at the same time as the query, limit, select or flq parameter will result in an error.

query

Query terms

filter

Filter options. See examples for usage examples and filters for what filters are available. filter is available for use with cr_works and other crossref family functions with works=TRUE

offset

Number of record to start at. Minimum: 1. For cr_works, and any function setting works = TRUE, the maximum offset value is 10000. For larger requests use cursor.

limit

Number of results to return in the query. Not relavant when searching with specific dois. Default: 20. Max: 1000

sample

(integer) Number of random results to return. when you use the sample parameter, the rows and offset parameters are ignored. Ignored unless works=TRUE. Max: 100

sort

Field to sort on. Acceptable set of fields to sort on:

score OR relevance - Sort by relevance score
updated - Sort by date of most recent change to metadata. Currently the same as deposited.
deposited - Sort by time of most recent deposit
indexed - Sort by time of most recent index
published - Sort by publication date
published-print - Sort by print publication date
published-online - Sort by online publication date
issued - Sort by issued date (earliest known publication date)
is-referenced-by-count - Sort by number of times this DOI is referenced by other Crossref DOIs
references-count - Sort by number of references included in the references section of the document identified by this DOI

order

(character) Sort order, one of 'asc' or 'desc'

facet

(logical) Include facet results. Boolean or string with field to facet on. Valid fields are *, affiliation, funder-name, funder-doi, orcid, container-title, assertion, archive, update-type, issn, published, source, type-name, publisher-name, license, category-name, assertion-group. Default: FALSE

cursor

(character) Cursor character string to do deep paging. Default is None. Pass in '*' to start deep paging. Any combination of query, filters and facets may be used with deep paging cursors. While the limit parameter may be specified along with cursor, offset and sample cannot be used with the cursor. See https://github.com/CrossRef/rest-api-doc#deep-paging-with-cursors

cursor_max

(integer) Max records to retrieve. Only used when cursor param used. Because deep paging can result in continuous requests until all are retrieved, use this parameter to set a maximum number of records. Of course, if there are less records found than this value, you will get only those found. When cursor pagination is being used the limit parameter sets the chunk size per request.

.progress

Show a plyr-style progress bar? Options are "none", "text", "tk", "win", and "time". See create_progress_bar for details of each. Only used when passing in multiple ids (e.g., multiple DOIs, DOI prefixes, etc.), or when using the cursor param. When using the cursor param, this argument only accept a boolean, either TRUE or FALSE; any non-boolean is coerced to FALSE.

flq

field queries. One or more field queries. Acceptable set of field query parameters are:

query.container-title - Query container-title aka. publication name
query.author - Query author first and given names
query.editor - Query editor first and given names
query.chair - Query chair first and given names
query.translator - Query translator first and given names
query.contributor - Query author, editor, chair and translator first and given names
query.bibliographic - Query bibliographic information, useful for citation lookup. Includes titles, authors, ISSNs and publication years
query.affiliation - Query contributor affiliations

Note: query.title has been removed - use query.bibliographic as a replacement

select

(character) One or more field to return (only those fields are returned)

async

(logical) use async HTTP requests. Default: FALSE

...

Named parameters passed on to verb-GET

parse

(logical) Whether to output json FALSE or parse to list TRUE. Default: FALSE

Note

See the "Rate limiting" seciton in rcrossref to get into the "fast lane"

Deep paging (using the cursor)

When using the cursor, a character string called next-cursor is returned from Crossref that we use to do the next request, and so on. We use a while loop to get number of results up to the value of cursor_max. Since we are doing each request for you, you may not need the next-cursor string, but if you do want it, you can get to it by indexing into the result like x$meta$next_cursor

Note that you can pass in curl options when using cursor, via "..."

Beware

The API will only work for CrossRef DOIs.

Functions

cr_works() - Does data request and parses to data.frame for easy downstream consumption
cr_works_() - Does data request, and gives back json (default) or lists, with no attempt to parse to data.frame's

Explanation of some data fields

score: a term frequency, inverse document frequency score that comes from the Crossref Solr backend, based on bibliographic metadata fields title, publication title, authors, ISSN, publisher, and date of publication.

References

https://github.com/CrossRef/rest-api-doc

Examples

if (FALSE) { # \dontrun{
# Works funded by the NSF
cr_works(query="NSF")

# Works that include renear but not ontologies
cr_works(query="renear+-ontologies")

# Filter
cr_works(query="global state", filter=c(has_orcid=TRUE), limit=3)
# Filter by multiple fields
cr_works(filter=c(has_orcid=TRUE, from_pub_date='2004-04-04'))
# Only full text articles
cr_works(filter=c(has_full_text = TRUE))
# has affilitation data
cr_works(filter=c(has_affiliation = TRUE))
# has abstract
cr_works(filter=c(has_abstract = TRUE))
# has clinical trial number
cr_works(filter=c(has_clinical_trial_number = TRUE))

# Querying dois
cr_works(dois='10.1063/1.3593378')
cr_works('10.1371/journal.pone.0033693')
cr_works(dois='10.1007/12080.1874-1746')
cr_works(dois=c('10.1007/12080.1874-1746','10.1007/10452.1573-5125',
   '10.1111/(issn)1442-9993'))

# progress bar
cr_works(dois=c('10.1007/12080.1874-1746','10.1007/10452.1573-5125'),
   .progress="text")

# Include facetting in results
cr_works(query="NSF", facet=TRUE)
## Get facets only, by setting limit=0
cr_works(query="NSF", facet=TRUE, limit=0)
## you can also set facet to a query
cr_works(facet = "license:*", limit=0)

# Sort results
cr_works(query="ecology", sort='relevance', order="asc")
res <- cr_works(query="ecology", sort='score', order="asc")
res$data$score
cr_works(query="ecology", sort='published')
x=cr_works(query="ecology", sort='published-print')
x=cr_works(query="ecology", sort='published-online')

# Get a random number of results
cr_works(sample=1)
cr_works(sample=10)

# You can pass in dot separated fields to filter on specific fields
cr_works(filter=c(award.number='CBET-0756451',
   award.funder='10.13039/100000001'))

# Use the cursor for deep paging
cr_works(query="NSF", cursor = "*", cursor_max = 300, limit = 100)
cr_works(query="NSF", cursor = "*", cursor_max = 300, limit = 100,
   facet = TRUE)
## with optional progress bar
x <- cr_works(query="NSF", cursor = "*", cursor_max = 1200, limit = 200, 
  .progress = TRUE)

# Low level function - does no parsing to data.frame, get json or a list
cr_works_(query = "NSF")
cr_works_(query = "NSF", parse=TRUE)
cr_works_(query="NSF", cursor = "*", cursor_max = 300, limit = 100)
cr_works_(query="NSF", cursor = "*", cursor_max = 300, limit = 100,
   parse=TRUE)

# field queries
## query.author
res <- cr_works(query = "ecology", flq = c(query.author = 'Boettiger'))

## query.container-title
res <- cr_works(query = "ecology",
  flq = c(`query.container-title` = 'Ecology'))

## query.author and query.bibliographic
res <- cr_works(query = "ecology",
  flq = c(query.author = 'Smith', query.bibliographic = 'cell'))

# select only certain fields to return
res <- cr_works(query = "NSF", select = c('DOI', 'title'))
names(res$data)

# asyc
queries <- c("ecology", "science", "cellular", "birds", "European",
  "bears", "beets", "laughter", "hapiness", "funding")
res <- cr_works(query = queries, async = TRUE)
res_json <- cr_works_(query = queries, async = TRUE)
unname(vapply(res_json, class, ""))
jsonlite::fromJSON(res_json[[1]])

queries <- c("ecology", "science", "cellular")
res <- cr_works(query = queries, async = TRUE, verbose = TRUE)
res

# time
queries <- c("ecology", "science", "cellular", "birds", "European",
  "bears", "beets", "laughter", "hapiness", "funding")
system.time(cr_works(query = queries, async = TRUE))
system.time(lapply(queries, function(z) cr_works(query = z)))
} # }