Title: | Client for Various 'CrossRef' 'APIs' |
---|---|
Description: | Client for various 'CrossRef' 'APIs', including 'metadata' search with their old and newer search 'APIs', get 'citations' in various formats (including 'bibtex', 'citeproc-json', 'rdf-xml', etc.), convert 'DOIs' to 'PMIDs', and 'vice versa', get citations for 'DOIs', and get links to full text of articles when available. |
Authors: | Scott Chamberlain [aut],
Hao Zhu [aut],
Najko Jahn [aut, cre] |
Maintainer: | Najko Jahn <[email protected]> |
License: | MIT + file LICENSE |
Version: | 1.2.009 |
Built: | 2024-08-29 22:58:37 UTC |
Source: | https://github.com/ropensci/rcrossref |
R Client for Various CrossRef APIs.
rcrossref interacts with the main Crossref metadata search API at https://github.com/CrossRef/rest-api-doc, the old metadata search API at http://search.labs.crossref.org/, their DOI Content Negotiation service at http://citation.crosscite.org/docs.html, and the Text and Data Mining project http://tdmsupport.crossref.org/
Crossref's API issue tracker lives at https://gitlab.com/crossref/issues it's a good place to go ask them about things related to their API that go beyond the R interface here.
See rcrossref-deprecated and rcrossref-defunct for details.
When you use the cr_*()
functions in this package, you are using
the Crossref search API described at
https://github.com/CrossRef/rest-api-doc
When you search with query terms, on Crossref servers they are not searching
full text, or even abstracts of articles, but only what is available in the
data that is returned to you. That is, they search article titles, authors,
etc. For some discussion on this, see
https://gitlab.com/crossref/issues/issues/101
From time to time Crossref needs to impose rate limits to ensure that
the free API is usable by all. Any rate limits that are in effect will
be advertised in the X-Rate-Limit-Limit
and
X-Rate-Limit-Interval
HTTP headers.
This boils down to: they allow X number of requests per some time period.
The numbers can change so we can't give a rate limit that will always
be in effect. If you're curious pass in verbose = TRUE
to
your function call, and you'll get headers that will display these rate
limits.
Be nice and share your email with Crossref
The Crossref team encourage requests with appropriate contact information and will forward you to a dedicated API cluster for improved performance when you share your email address with them. https://github.com/CrossRef/rest-api-doc#good-manners–more-reliable-service
To pass your email address to Crossref via this client, simply store it
as environment variable in .Renviron
like this:
Open file:
file.edit("~/.Renviron")
Add email address to be shared with Crossref
crossref_email = [email protected]
Save the file and restart your R session
Don't wanna share your email any longer? Simply delete it from
~/.Renviron
All Crossref specific text mining functions are now deprecated, and
moved to a new package crminer
.
Another package fulltext is designed solely to do general purpose text mining involving Crossref and other sources of scholarly metadata and full text.
For the Crossref search API (the functions cr_funders()
,
cr_journals()
, cr_licenses()
,
cr_members()
, cr_prefixes()
, cr_types()
,
cr_works()
), there is a high level API and a low level. The
high level is accessible through those functions just listed (e.g.,
cr_works()
), whereas the low level is accessible via the same
fxn name with an underscore (e.g., cr_works_()
). The high level
API does data requests, and parses to data.frame's. Since the high level
API functions have been around a while, we didn't want to break their
behavior, so the low level API functions are separate, and only do the data
request, giving back json or a list, with no attempt to parse any further. The
low level API functions will be faster because there's much less parsing, and
therefore less prone to potential errors due to changes in the Crossref API
that could cause parsing errors. Note that cursor feature works with both
high and low level.
On installation of rcrossref you get an RStudio Addin. To use the Addin,
go to the top toolbar > Tools > Addins > Add Crossref Citations. You'll get a
window pop up that you can put in DOIs for. If the DOI is found, the bibtex
citations will be added to a file called crossref.bib
. New citations
will be appended to that file. Addin authored by Hao Zhu
https://github.com/haozhu233
Get abstract
cr_abstract(doi, ...)
cr_abstract(doi, ...)
doi |
(character) a DOI, required. |
... |
Named parameters passed on to |
## Not run: # abstract found cr_abstract('10.1109/TASC.2010.2088091') cr_abstract("10.1175//2572.1") cr_abstract("10.1182/blood.v16.1.1039.1039") # doi not found # cr_abstract(doi = '10.5284/1011335') # abstract not found, throws error # cr_abstract(doi = '10.1126/science.169.3946.635') # a random DOI # cr_abstract(cr_r(1)) ## End(Not run)
## Not run: # abstract found cr_abstract('10.1109/TASC.2010.2088091') cr_abstract("10.1175//2572.1") cr_abstract("10.1182/blood.v16.1.1039.1039") # doi not found # cr_abstract(doi = '10.5284/1011335') # abstract not found, throws error # cr_abstract(doi = '10.1126/science.169.3946.635') # a random DOI # cr_abstract(cr_r(1)) ## End(Not run)
Check the DOI minting agency on one or more dois
cr_agency(dois = NULL, .progress = "none", ...)
cr_agency(dois = NULL, .progress = "none", ...)
dois |
(character) One or more article or organization dois. |
.progress |
Show a |
... |
Named parameters passed on to |
Scott Chamberlain [email protected]
https://github.com/CrossRef/rest-api-doc
## Not run: cr_agency(dois = '10.13039/100000001') cr_agency( dois = c('10.13039/100000001','10.13039/100000015','10.5284/1011335')) ## End(Not run)
## Not run: cr_agency(dois = '10.13039/100000001') cr_agency( dois = c('10.13039/100000001','10.13039/100000015','10.5284/1011335')) ## End(Not run)
Get a citation count via CrossRef OpenURL
cr_citation_count( doi, url = "http://www.crossref.org/openurl/", key = "[email protected]", async = FALSE, ... )
cr_citation_count( doi, url = "http://www.crossref.org/openurl/", key = "[email protected]", async = FALSE, ... )
doi |
(character) One or more digital object identifiers. If
|
url |
(character) the url for the function (should be left to default) |
key |
your Crossref OpenURL email address, either enter, or loads
from |
async |
(logical) use async HTTP requests. Default: |
... |
Curl options passed on to |
See https://www.crossref.org/labs/openurl/ for more info on this Crossref API service.
This number is also known as cited-by
Note that this number may be out of sync/may not match that that the publisher is showing (if they show it) for the same DOI/article.
We've contacted Crossref about this, and they have confirmed this. Unfortunately, we can not do anything about this.
I would imagine it's best to use this data instead of from the publishers, and this data you can get programatically :)
a data.frame, with columns doi
and count
. The count column
has numeric values that are the citation count for that DOI, or NA
if
not found or no count available
When a DOI does not exist, we may not get a proper HTTP status code to throw a proper stop status, so we grep on the text itself, and throw a stop if only one DOI passed and not using async, or warning if more than one DOI passed or if using async.
Carl Boettiger [email protected], Scott Chamberlain
## Not run: cr_citation_count(doi="10.1371/journal.pone.0042793") cr_citation_count(doi="10.1016/j.fbr.2012.01.001") ## many dois <- c("10.1016/j.fbr.2012.01.001", "10.1371/journal.pone.0042793") cr_citation_count(doi = dois) # DOI not found cr_citation_count(doi="10.1016/j.fbr.2012") # asyc dois <- c("10.1016/j.fbr.2012.01.001", "10.1371/journal.pone.0042793", "10.1016/j.fbr.2012", "10.1109/tsp.2006.874779", "10.1007/bf02231542", "10.1007/s00277-016-2782-z", "10.1002/9781118339893.wbeccp020", "10.1177/011542659200700105", "10.1002/chin.197444438", "10.1002/9781118619599.ch4", "10.1007/s00466-012-0724-8", "10.1017/s0376892900029477", "10.1167/16.12.824") res <- cr_citation_count(doi = dois, async = TRUE) ## verbose curl res <- cr_citation_count(doi = dois, async = TRUE, verbose = TRUE) res ## time comparison system.time(cr_citation_count(doi = dois, async = TRUE)) system.time(cr_citation_count(doi = dois, async = FALSE)) # from a set of random DOIs cr_citation_count(cr_r(50), async = TRUE) ## End(Not run)
## Not run: cr_citation_count(doi="10.1371/journal.pone.0042793") cr_citation_count(doi="10.1016/j.fbr.2012.01.001") ## many dois <- c("10.1016/j.fbr.2012.01.001", "10.1371/journal.pone.0042793") cr_citation_count(doi = dois) # DOI not found cr_citation_count(doi="10.1016/j.fbr.2012") # asyc dois <- c("10.1016/j.fbr.2012.01.001", "10.1371/journal.pone.0042793", "10.1016/j.fbr.2012", "10.1109/tsp.2006.874779", "10.1007/bf02231542", "10.1007/s00277-016-2782-z", "10.1002/9781118339893.wbeccp020", "10.1177/011542659200700105", "10.1002/chin.197444438", "10.1002/9781118619599.ch4", "10.1007/s00466-012-0724-8", "10.1017/s0376892900029477", "10.1167/16.12.824") res <- cr_citation_count(doi = dois, async = TRUE) ## verbose curl res <- cr_citation_count(doi = dois, async = TRUE, verbose = TRUE) res ## time comparison system.time(cr_citation_count(doi = dois, async = TRUE)) system.time(cr_citation_count(doi = dois, async = FALSE)) # from a set of random DOIs cr_citation_count(cr_r(50), async = TRUE) ## End(Not run)
Get citations in various formats from CrossRef.
cr_cn( dois, format = "bibtex", style = "apa", locale = "en-US", raw = FALSE, .progress = "none", url = NULL, cache = FALSE, ... )
cr_cn( dois, format = "bibtex", style = "apa", locale = "en-US", raw = FALSE, .progress = "none", url = NULL, cache = FALSE, ... )
dois |
Search by a single DOI or many DOIs. |
format |
Name of the format. One of "rdf-xml", "turtle",
"citeproc-json", "citeproc-json-ish", "text", "ris", "bibtex" (default),
"crossref-xml", "datacite-xml","bibentry", or "crossref-tdm". The format
"citeproc-json-ish" is a format that is not quite proper citeproc-json.
Note that the package bibtex is required when |
style |
a CSL style (for text format only). See |
locale |
Language locale. See |
raw |
(logical) Return raw text in the format given by |
.progress |
Show a |
url |
(character) Base URL for the content negotiation request. Default: "https://doi.org" |
cache |
(logical) Should requests be cached and/or retrieved from the cache? Note that the cache only persists while the package is loaded. |
... |
Named parameters passed on to |
See http://citation.crosscite.org/docs.html for more info on the Crossref Content Negotiation API service.
DataCite DOIs: Some values of the format
parameter won't work with
DataCite DOIs, i.e. "citeproc-json", "crossref-xml", "crossref-tdm",
"onix-xml".
MEDRA DOIs only work with "rdf-xml", "turtle", "citeproc-json-ish", "ris", "bibtex", "bibentry", "onix-xml".
See examples below.
See cr_agency()
Note that the format type citeproc-json
uses the CrossRef API at
api.crossref.org
, while all others are content negotiated via
http://data.crossref.org
, http://data.datacite.org
or
http://data.medra.org
. DOI agency is checked first (see
cr_agency()
).
## Not run: cr_cn(dois="10.1126/science.169.3946.635") cr_cn(dois="10.1126/science.169.3946.635", "citeproc-json") cr_cn(dois="10.1126/science.169.3946.635", "citeproc-json-ish") cr_cn("10.1126/science.169.3946.635", "rdf-xml") cr_cn("10.1126/science.169.3946.635", "crossref-xml") cr_cn("10.1126/science.169.3946.635", "text") # return an R bibentry type cr_cn("10.1126/science.169.3946.635", "bibentry") cr_cn("10.6084/m9.figshare.97218", "bibentry") # return an apa style citation cr_cn("10.1126/science.169.3946.635", "text", "apa") cr_cn("10.1126/science.169.3946.635", "text", "harvard3") cr_cn("10.1126/science.169.3946.635", "text", "elsevier-harvard") cr_cn("10.1126/science.169.3946.635", "text", "ecoscience") cr_cn("10.1126/science.169.3946.635", "text", "heredity") cr_cn("10.1126/science.169.3946.635", "text", "oikos") # example with many DOIs dois <- cr_r(2) cr_cn(dois, "text", "apa") # Cycle through random styles - print style on each try stys <- get_styles() foo <- function(x){ cat(sprintf("<Style>:%s\n", x), sep = "\n\n") cat(cr_cn("10.1126/science.169.3946.635", "text", style=x)) } foo(sample(stys, 1)) # Using DataCite DOIs ## some formats don't work # cr_cn("10.5284/1011335", "crossref-xml") # cr_cn("10.5284/1011335", "crossref-tdm") ## But most do work cr_cn("10.5284/1011335", "text") cr_cn("10.5284/1011335", "datacite-xml") cr_cn("10.5284/1011335", "rdf-xml") cr_cn("10.5284/1011335", "turtle") cr_cn("10.5284/1011335", "citeproc-json-ish") cr_cn("10.5284/1011335", "ris") cr_cn("10.5284/1011335", "bibtex") cr_cn("10.5284/1011335", "bibentry") # Using Medra DOIs cr_cn("10.1430/8105", "onix-xml") # Get raw output cr_cn(dois = "10.1002/app.27716", format = "citeproc-json", raw = TRUE) # sometimes messy DOIs even work ## in this case, a DOI minting agency can't be found ## but we proceed anyway, just assuming it's "crossref" cr_cn("10.1890/0012-9615(1999)069[0569:EDILSA]2.0.CO;2") # Use a different base url cr_cn("10.1126/science.169.3946.635", "text", url = "http://dx.doi.org") cr_cn("10.1126/science.169.3946.635", "text", "heredity", url = "http://dx.doi.org") cr_cn("10.5284/1011335", url = "https://citation.crosscite.org/format", style = "oikos") cr_cn("10.5284/1011335", url = "https://citation.crosscite.org/format", style = "plant-cell-and-environment") # A temporary cache can be used to avoid sending the same request repeatedly # within the same R session. cr_cn("10.5284/1011335", cache = TRUE) ## End(Not run)
## Not run: cr_cn(dois="10.1126/science.169.3946.635") cr_cn(dois="10.1126/science.169.3946.635", "citeproc-json") cr_cn(dois="10.1126/science.169.3946.635", "citeproc-json-ish") cr_cn("10.1126/science.169.3946.635", "rdf-xml") cr_cn("10.1126/science.169.3946.635", "crossref-xml") cr_cn("10.1126/science.169.3946.635", "text") # return an R bibentry type cr_cn("10.1126/science.169.3946.635", "bibentry") cr_cn("10.6084/m9.figshare.97218", "bibentry") # return an apa style citation cr_cn("10.1126/science.169.3946.635", "text", "apa") cr_cn("10.1126/science.169.3946.635", "text", "harvard3") cr_cn("10.1126/science.169.3946.635", "text", "elsevier-harvard") cr_cn("10.1126/science.169.3946.635", "text", "ecoscience") cr_cn("10.1126/science.169.3946.635", "text", "heredity") cr_cn("10.1126/science.169.3946.635", "text", "oikos") # example with many DOIs dois <- cr_r(2) cr_cn(dois, "text", "apa") # Cycle through random styles - print style on each try stys <- get_styles() foo <- function(x){ cat(sprintf("<Style>:%s\n", x), sep = "\n\n") cat(cr_cn("10.1126/science.169.3946.635", "text", style=x)) } foo(sample(stys, 1)) # Using DataCite DOIs ## some formats don't work # cr_cn("10.5284/1011335", "crossref-xml") # cr_cn("10.5284/1011335", "crossref-tdm") ## But most do work cr_cn("10.5284/1011335", "text") cr_cn("10.5284/1011335", "datacite-xml") cr_cn("10.5284/1011335", "rdf-xml") cr_cn("10.5284/1011335", "turtle") cr_cn("10.5284/1011335", "citeproc-json-ish") cr_cn("10.5284/1011335", "ris") cr_cn("10.5284/1011335", "bibtex") cr_cn("10.5284/1011335", "bibentry") # Using Medra DOIs cr_cn("10.1430/8105", "onix-xml") # Get raw output cr_cn(dois = "10.1002/app.27716", format = "citeproc-json", raw = TRUE) # sometimes messy DOIs even work ## in this case, a DOI minting agency can't be found ## but we proceed anyway, just assuming it's "crossref" cr_cn("10.1890/0012-9615(1999)069[0569:EDILSA]2.0.CO;2") # Use a different base url cr_cn("10.1126/science.169.3946.635", "text", url = "http://dx.doi.org") cr_cn("10.1126/science.169.3946.635", "text", "heredity", url = "http://dx.doi.org") cr_cn("10.5284/1011335", url = "https://citation.crosscite.org/format", style = "oikos") cr_cn("10.5284/1011335", url = "https://citation.crosscite.org/format", style = "plant-cell-and-environment") # A temporary cache can be used to avoid sending the same request repeatedly # within the same R session. cr_cn("10.5284/1011335", cache = TRUE) ## End(Not run)
Search the CrossRef Fundref API
cr_funders( dois = NULL, query = NULL, filter = NULL, offset = NULL, limit = NULL, sample = NULL, sort = NULL, order = NULL, facet = FALSE, works = FALSE, cursor = NULL, cursor_max = 5000, .progress = "none", flq = NULL, select = NULL, ... ) cr_funders_( dois = NULL, query = NULL, filter = NULL, offset = NULL, limit = NULL, sample = NULL, sort = NULL, order = NULL, facet = FALSE, works = FALSE, cursor = NULL, cursor_max = 5000, .progress = "none", parse = FALSE, flq = NULL, select = NULL, ... )
cr_funders( dois = NULL, query = NULL, filter = NULL, offset = NULL, limit = NULL, sample = NULL, sort = NULL, order = NULL, facet = FALSE, works = FALSE, cursor = NULL, cursor_max = 5000, .progress = "none", flq = NULL, select = NULL, ... ) cr_funders_( dois = NULL, query = NULL, filter = NULL, offset = NULL, limit = NULL, sample = NULL, sort = NULL, order = NULL, facet = FALSE, works = FALSE, cursor = NULL, cursor_max = 5000, .progress = "none", parse = FALSE, flq = NULL, select = NULL, ... )
dois |
Search by a single DOI or many DOIs. |
query |
Query terms |
filter |
Filter options. See examples for usage examples
and |
offset |
Number of record to start at. Minimum: 1. For
|
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 |
sort |
Field to sort on. Acceptable set of fields to sort on:
|
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: |
works |
(logical) If |
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 |
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 |
.progress |
Show a |
flq |
field queries. One or more field queries. Acceptable set of field query parameters are:
Note: |
select |
(character) One or more field to return (only those fields are returned) |
... |
Named parameters passed on to |
parse |
(logical) Whether to output json |
BEWARE: The API will only work for CrossRef DOIs.
This function name changing to cr_funders
in the next version -
both work for now
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 "..."
Funders without IDs don't show up on the /funders route, and in this function. Some funders don't have assigned IDs in Crossref's system, so won't show up in searches.
See the "Rate limiting" seciton in rcrossref to get into the "fast lane"
https://github.com/CrossRef/rest-api-doc
Other crossref:
cr_journals()
,
cr_licenses()
,
cr_members()
,
cr_prefixes()
,
cr_types()
,
cr_works()
## Not run: cr_funders(query="NSF", limit=1) cr_funders(query="NSF") cr_funders(dois='10.13039/100000001') out <- cr_funders(dois=c('10.13039/100000001','10.13039/100000015')) out['10.13039/100000001'] out[['10.13039/100000001']] cr_funders(dois='10.13039/100000001') cr_funders(dois='10.13039/100000001', works=TRUE, limit=5) cr_funders(dois=c('10.13039/100000001','10.13039/100000015')) cr_funders(dois=c('10.13039/100000001','10.13039/100000015'), works=TRUE) ## get facets back cr_funders("10.13039/100000001", works=TRUE, facet=TRUE, limit = 0) cr_funders("10.13039/100000001", works=TRUE, facet="license:*", limit = 0) cr_funders('100000001', works = TRUE, cursor = "*", cursor_max = 500, limit = 100, facet=TRUE) # Curl options cr_funders(dois='10.13039/100000001', verbose = TRUE) # If not found, and > 1 DOI given, those not found dropped cr_funders(dois=c("adfadfaf","asfasf")) cr_funders(dois=c("adfadfaf","asfasf"), works=TRUE) cr_funders(dois=c("10.13039/100000001","asfasf")) cr_funders(dois=c("10.13039/100000001","asfasf"), works=TRUE) # Use the cursor for deep paging cr_funders('100000001', works = TRUE, cursor = "*", cursor_max = 500, limit = 100) cr_funders(c('100000001', '100000002'), works = TRUE, cursor = "*", cursor_max = 300, limit = 100) ## with optional progress bar cr_funders('100000001', works = TRUE, cursor = "*", cursor_max = 500, limit = 100, .progress = TRUE) # Low level function - does no parsing to data.frame, get json or a list cr_funders_(query = 'nsf') cr_funders_('10.13039/100000001') cr_funders_(query = 'science', parse=TRUE) cr_funders_('10.13039/100000001', works = TRUE, cursor = "*", cursor_max = 300, limit = 100) cr_funders_('10.13039/100000001', works = TRUE, cursor = "*", cursor_max = 300, limit = 100, parse = TRUE) # field queries ## query.container-title cr_funders('10.13039/100000001', works = TRUE, flq = c(`query.container-title` = 'Ecology')) # select only certain fields to return res <- cr_funders('10.13039/100000001', works = TRUE, select = c('DOI', 'title')) names(res$data) ## End(Not run)
## Not run: cr_funders(query="NSF", limit=1) cr_funders(query="NSF") cr_funders(dois='10.13039/100000001') out <- cr_funders(dois=c('10.13039/100000001','10.13039/100000015')) out['10.13039/100000001'] out[['10.13039/100000001']] cr_funders(dois='10.13039/100000001') cr_funders(dois='10.13039/100000001', works=TRUE, limit=5) cr_funders(dois=c('10.13039/100000001','10.13039/100000015')) cr_funders(dois=c('10.13039/100000001','10.13039/100000015'), works=TRUE) ## get facets back cr_funders("10.13039/100000001", works=TRUE, facet=TRUE, limit = 0) cr_funders("10.13039/100000001", works=TRUE, facet="license:*", limit = 0) cr_funders('100000001', works = TRUE, cursor = "*", cursor_max = 500, limit = 100, facet=TRUE) # Curl options cr_funders(dois='10.13039/100000001', verbose = TRUE) # If not found, and > 1 DOI given, those not found dropped cr_funders(dois=c("adfadfaf","asfasf")) cr_funders(dois=c("adfadfaf","asfasf"), works=TRUE) cr_funders(dois=c("10.13039/100000001","asfasf")) cr_funders(dois=c("10.13039/100000001","asfasf"), works=TRUE) # Use the cursor for deep paging cr_funders('100000001', works = TRUE, cursor = "*", cursor_max = 500, limit = 100) cr_funders(c('100000001', '100000002'), works = TRUE, cursor = "*", cursor_max = 300, limit = 100) ## with optional progress bar cr_funders('100000001', works = TRUE, cursor = "*", cursor_max = 500, limit = 100, .progress = TRUE) # Low level function - does no parsing to data.frame, get json or a list cr_funders_(query = 'nsf') cr_funders_('10.13039/100000001') cr_funders_(query = 'science', parse=TRUE) cr_funders_('10.13039/100000001', works = TRUE, cursor = "*", cursor_max = 300, limit = 100) cr_funders_('10.13039/100000001', works = TRUE, cursor = "*", cursor_max = 300, limit = 100, parse = TRUE) # field queries ## query.container-title cr_funders('10.13039/100000001', works = TRUE, flq = c(`query.container-title` = 'Ecology')) # select only certain fields to return res <- cr_funders('10.13039/100000001', works = TRUE, select = c('DOI', 'title')) names(res$data) ## End(Not run)
Search CrossRef journals
cr_journals( issn = NULL, query = NULL, filter = NULL, offset = NULL, limit = NULL, sample = NULL, sort = NULL, order = NULL, facet = FALSE, works = FALSE, cursor = NULL, cursor_max = 5000, .progress = "none", flq = NULL, select = NULL, ... ) cr_journals_( issn = NULL, query = NULL, filter = NULL, offset = NULL, limit = NULL, sample = NULL, sort = NULL, order = NULL, facet = FALSE, works = FALSE, cursor = NULL, cursor_max = 5000, .progress = "none", parse = FALSE, flq = NULL, select = NULL, ... )
cr_journals( issn = NULL, query = NULL, filter = NULL, offset = NULL, limit = NULL, sample = NULL, sort = NULL, order = NULL, facet = FALSE, works = FALSE, cursor = NULL, cursor_max = 5000, .progress = "none", flq = NULL, select = NULL, ... ) cr_journals_( issn = NULL, query = NULL, filter = NULL, offset = NULL, limit = NULL, sample = NULL, sort = NULL, order = NULL, facet = FALSE, works = FALSE, cursor = NULL, cursor_max = 5000, .progress = "none", parse = FALSE, flq = NULL, select = NULL, ... )
issn |
(character) One or more ISSN's. Format: XXXX-XXXX. |
query |
Query terms |
filter |
Filter options. See examples for usage examples
and |
offset |
Number of record to start at. Minimum: 1. For
|
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 |
sort |
Field to sort on. Acceptable set of fields to sort on:
|
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: |
works |
(logical) If |
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 |
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 |
.progress |
Show a |
flq |
field queries. One or more field queries. Acceptable set of field query parameters are:
Note: |
select |
(character) One or more field to return (only those fields are returned) |
... |
Named parameters passed on to |
parse |
(logical) Whether to output json |
BEWARE: The API will only work for CrossRef DOIs.
Note that some parameters are ignored unless works=TRUE
: sample, sort,
order, filter
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 "..."
backfile_dois: Back file records have a publication date older than two years ago.
current_dois: Current records are anything published in the last two years.
See the "Rate limiting" seciton in rcrossref to get into the "fast lane"
https://github.com/CrossRef/rest-api-doc
Other crossref:
cr_funders()
,
cr_licenses()
,
cr_members()
,
cr_prefixes()
,
cr_types()
,
cr_works()
## Not run: cr_journals(issn="2167-8359") cr_journals() cr_journals(issn="2167-8359", works=TRUE) cr_journals(issn=c('1803-2427','2326-4225')) cr_journals(query="ecology") cr_journals(issn="2167-8359", query='ecology', works=TRUE, sort='score', order="asc") cr_journals(issn="2167-8359", query='ecology', works=TRUE, sort='score', order="desc") cr_journals(issn="2167-8359", works=TRUE, filter=c(from_pub_date='2014-03-03')) cr_journals(query="peerj") cr_journals(issn='1803-2427', works=TRUE) cr_journals(issn='1803-2427', works=TRUE, sample=1) cr_journals(limit=2) ## get facets back cr_journals('1803-2427', works=TRUE, facet=TRUE) cr_journals('1803-2427', works=TRUE, facet="published:*", limit = 0) cr_journals(issn=c('1803-2427','2326-4225'), works=TRUE, facet="published:*", limit = 10) # Use the cursor for deep paging cr_journals(issn='1932-6203', works = TRUE, cursor = "*", cursor_max = 500, limit = 100) cr_journals(c('1932-6203', '0028-0836'), works = TRUE, cursor = "*", cursor_max = 300, limit = 100) ## with optional progress bar cr_journals(issn='1932-6203', works = TRUE, cursor = "*", cursor_max = 90, limit = 30, .progress = TRUE) # fails, if you want works, you must give an ISSN # cr_journals(query = "ecology", filter=c(has_full_text = TRUE), # works = TRUE) # Low level function - does no parsing to data.frame, get json or a list cr_journals_(query = 'ecology') cr_journals_("2167-8359") cr_journals_(query = 'ecology', parse=TRUE) cr_journals_("2167-8359", works = TRUE, cursor = "*", cursor_max = 300, limit = 100) cr_journals_("2167-8359", works = TRUE, cursor = "*", cursor_max = 300, limit = 100, parse = TRUE) # field queries ## query.author cr_journals("2167-8359", works = TRUE, flq = c(`query.author` = 'Jane')) # select only certain fields to return res <- cr_journals('2167-8359', works = TRUE, select = c('DOI', 'title')) names(res$data) ## End(Not run)
## Not run: cr_journals(issn="2167-8359") cr_journals() cr_journals(issn="2167-8359", works=TRUE) cr_journals(issn=c('1803-2427','2326-4225')) cr_journals(query="ecology") cr_journals(issn="2167-8359", query='ecology', works=TRUE, sort='score', order="asc") cr_journals(issn="2167-8359", query='ecology', works=TRUE, sort='score', order="desc") cr_journals(issn="2167-8359", works=TRUE, filter=c(from_pub_date='2014-03-03')) cr_journals(query="peerj") cr_journals(issn='1803-2427', works=TRUE) cr_journals(issn='1803-2427', works=TRUE, sample=1) cr_journals(limit=2) ## get facets back cr_journals('1803-2427', works=TRUE, facet=TRUE) cr_journals('1803-2427', works=TRUE, facet="published:*", limit = 0) cr_journals(issn=c('1803-2427','2326-4225'), works=TRUE, facet="published:*", limit = 10) # Use the cursor for deep paging cr_journals(issn='1932-6203', works = TRUE, cursor = "*", cursor_max = 500, limit = 100) cr_journals(c('1932-6203', '0028-0836'), works = TRUE, cursor = "*", cursor_max = 300, limit = 100) ## with optional progress bar cr_journals(issn='1932-6203', works = TRUE, cursor = "*", cursor_max = 90, limit = 30, .progress = TRUE) # fails, if you want works, you must give an ISSN # cr_journals(query = "ecology", filter=c(has_full_text = TRUE), # works = TRUE) # Low level function - does no parsing to data.frame, get json or a list cr_journals_(query = 'ecology') cr_journals_("2167-8359") cr_journals_(query = 'ecology', parse=TRUE) cr_journals_("2167-8359", works = TRUE, cursor = "*", cursor_max = 300, limit = 100) cr_journals_("2167-8359", works = TRUE, cursor = "*", cursor_max = 300, limit = 100, parse = TRUE) # field queries ## query.author cr_journals("2167-8359", works = TRUE, flq = c(`query.author` = 'Jane')) # select only certain fields to return res <- cr_journals('2167-8359', works = TRUE, select = c('DOI', 'title')) names(res$data) ## End(Not run)
Search CrossRef licenses
cr_licenses( query = NULL, offset = NULL, limit = NULL, sort = NULL, order = NULL, .progress = "none", ... ) cr_licenses_( query = NULL, offset = NULL, limit = NULL, sort = NULL, order = NULL, .progress = "none", parse = FALSE, ... )
cr_licenses( query = NULL, offset = NULL, limit = NULL, sort = NULL, order = NULL, .progress = "none", ... ) cr_licenses_( query = NULL, offset = NULL, limit = NULL, sort = NULL, order = NULL, .progress = "none", parse = FALSE, ... )
query |
Query terms |
offset |
Number of record to start at, from 1 to infinity. |
limit |
Number of results to return in the query. Not relavant when searching with specific dois. Default: 20. Max: 1000 |
sort |
Field to sort on. Acceptable set of fields to sort on:
|
order |
(character) Sort order, one of 'asc' or 'desc' |
.progress |
Show a |
... |
Named parameters passed on to |
parse |
(logical) Whether to output json |
BEWARE: The API will only work for CrossRef DOIs.
NOTE: The API route behind this function does not support filters
any more, so the filter
parameter has been removed.
https://github.com/CrossRef/rest-api-doc
Other crossref:
cr_funders()
,
cr_journals()
,
cr_members()
,
cr_prefixes()
,
cr_types()
,
cr_works()
## Not run: cr_licenses() # query for something, e.g. a publisher cr_licenses(query = 'elsevier') # Low level function - does no parsing to data.frame, get json or a list cr_licenses_() cr_licenses_(query = "elsevier") cr_licenses_(query = "elsevier", parse=TRUE) ## End(Not run)
## Not run: cr_licenses() # query for something, e.g. a publisher cr_licenses(query = 'elsevier') # Low level function - does no parsing to data.frame, get json or a list cr_licenses_() cr_licenses_(query = "elsevier") cr_licenses_(query = "elsevier", parse=TRUE) ## End(Not run)
Search CrossRef members
cr_members( member_ids = NULL, query = NULL, filter = NULL, offset = NULL, limit = NULL, sample = NULL, sort = NULL, order = NULL, facet = FALSE, works = FALSE, cursor = NULL, cursor_max = 5000, .progress = "none", flq = NULL, select = NULL, ... ) cr_members_( member_ids = NULL, query = NULL, filter = NULL, offset = NULL, limit = NULL, sample = NULL, sort = NULL, order = NULL, facet = FALSE, works = FALSE, cursor = NULL, cursor_max = 5000, .progress = "none", parse = FALSE, flq = NULL, select = NULL, ... )
cr_members( member_ids = NULL, query = NULL, filter = NULL, offset = NULL, limit = NULL, sample = NULL, sort = NULL, order = NULL, facet = FALSE, works = FALSE, cursor = NULL, cursor_max = 5000, .progress = "none", flq = NULL, select = NULL, ... ) cr_members_( member_ids = NULL, query = NULL, filter = NULL, offset = NULL, limit = NULL, sample = NULL, sort = NULL, order = NULL, facet = FALSE, works = FALSE, cursor = NULL, cursor_max = 5000, .progress = "none", parse = FALSE, flq = NULL, select = NULL, ... )
member_ids |
One or more member ids. See examples. Alternatively, you can query for them using the query parameter. |
query |
Query terms |
filter |
Filter options. See examples for usage examples
and |
offset |
Number of record to start at. Minimum: 1. For
|
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 |
sort |
Field to sort on. Acceptable set of fields to sort on:
|
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: |
works |
(logical) If |
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 |
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 |
.progress |
Show a |
flq |
field queries. One or more field queries. Acceptable set of field query parameters are:
Note: |
select |
(character) One or more field to return (only those fields are returned) |
... |
Named parameters passed on to |
parse |
(logical) Whether to output json |
BEWARE: The API will only work for CrossRef DOIs.
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 "..."
See the "Rate limiting" seciton in rcrossref to get into the "fast lane"
https://github.com/CrossRef/rest-api-doc
Other crossref:
cr_funders()
,
cr_journals()
,
cr_licenses()
,
cr_prefixes()
,
cr_types()
,
cr_works()
## Not run: cr_members(member_ids=98) cr_members(member_ids=340) cr_members(member_ids=98, works=TRUE) cr_members(member_ids=c(10,98,45,1,9)) cr_members(member_ids=c(10,98,45,1,9), works=TRUE) cr_members(query='hindawi') cr_members(query='ecology') # facets cr_members(member_ids=98, works=TRUE, facet=TRUE, limit = 0) cr_members(member_ids=98, works=TRUE, facet="license:*", limit = 0) # curl options cr_members(member_ids=98, verbose = TRUE) # Use the cursor for deep paging cr_members(member_ids=98, works = TRUE, cursor = "*", cursor_max = 500, limit = 100) cr_members(member_ids=c(10, 98, 45), works = TRUE, cursor = "*", cursor_max = 200, limit = 100) ## with optional progress bar cr_members(member_ids=98, works = TRUE, cursor = "*", cursor_max = 500, limit = 100, .progress = TRUE) # data not found # cr_members(query="adfdf") # cr_members(member_ids=c(323234343434,3434343434), works=TRUE, facet=TRUE) # cr_members(member_ids=c(323234343434,3434343434,98), works=TRUE,facet=TRUE) # Low level function - does no parsing to data.frame, get json or a list cr_members_(query = 'hindawi') cr_members_(member_ids = 98) cr_members_(query = 'hindawi', parse=TRUE) cr_members_(member_ids = 98, works = TRUE, cursor = "*", cursor_max = 300, limit = 100) cr_members_(member_ids = 98, works = TRUE, cursor = "*", cursor_max = 300, limit = 100, parse=TRUE) # field queries ## query.container-title cr_members(98, works = TRUE, flq = c(`query.container-title` = 'Ecology')) # select only certain fields to return res <- cr_members(98, works = TRUE, select = c('DOI', 'title')) names(res$data) # Passing a filter parameter as named value to query for index updates ## Using backtick escaped CrossRef documented filter in list of named values cr_members(1988, works=TRUE, filter=list(`from-index-date`='2023-02-06')) ## Using rcrossref naming convention in named character vector cr_members(1988, works=TRUE, filter=c(from_index_date='2023-02-06')) ## End(Not run)
## Not run: cr_members(member_ids=98) cr_members(member_ids=340) cr_members(member_ids=98, works=TRUE) cr_members(member_ids=c(10,98,45,1,9)) cr_members(member_ids=c(10,98,45,1,9), works=TRUE) cr_members(query='hindawi') cr_members(query='ecology') # facets cr_members(member_ids=98, works=TRUE, facet=TRUE, limit = 0) cr_members(member_ids=98, works=TRUE, facet="license:*", limit = 0) # curl options cr_members(member_ids=98, verbose = TRUE) # Use the cursor for deep paging cr_members(member_ids=98, works = TRUE, cursor = "*", cursor_max = 500, limit = 100) cr_members(member_ids=c(10, 98, 45), works = TRUE, cursor = "*", cursor_max = 200, limit = 100) ## with optional progress bar cr_members(member_ids=98, works = TRUE, cursor = "*", cursor_max = 500, limit = 100, .progress = TRUE) # data not found # cr_members(query="adfdf") # cr_members(member_ids=c(323234343434,3434343434), works=TRUE, facet=TRUE) # cr_members(member_ids=c(323234343434,3434343434,98), works=TRUE,facet=TRUE) # Low level function - does no parsing to data.frame, get json or a list cr_members_(query = 'hindawi') cr_members_(member_ids = 98) cr_members_(query = 'hindawi', parse=TRUE) cr_members_(member_ids = 98, works = TRUE, cursor = "*", cursor_max = 300, limit = 100) cr_members_(member_ids = 98, works = TRUE, cursor = "*", cursor_max = 300, limit = 100, parse=TRUE) # field queries ## query.container-title cr_members(98, works = TRUE, flq = c(`query.container-title` = 'Ecology')) # select only certain fields to return res <- cr_members(98, works = TRUE, select = c('DOI', 'title')) names(res$data) # Passing a filter parameter as named value to query for index updates ## Using backtick escaped CrossRef documented filter in list of named values cr_members(1988, works=TRUE, filter=list(`from-index-date`='2023-02-06')) ## Using rcrossref naming convention in named character vector cr_members(1988, works=TRUE, filter=c(from_index_date='2023-02-06')) ## End(Not run)
Search CrossRef prefixes
cr_prefixes( prefixes, query = NULL, filter = NULL, offset = NULL, limit = NULL, sample = NULL, sort = NULL, order = NULL, facet = FALSE, works = FALSE, cursor = NULL, cursor_max = 5000, .progress = "none", flq = NULL, select = NULL, ... ) cr_prefixes_( prefixes, query = NULL, filter = NULL, offset = NULL, limit = NULL, sample = NULL, sort = NULL, order = NULL, facet = FALSE, works = FALSE, cursor = NULL, cursor_max = 5000, .progress = "none", parse = FALSE, flq = NULL, select = NULL, ... )
cr_prefixes( prefixes, query = NULL, filter = NULL, offset = NULL, limit = NULL, sample = NULL, sort = NULL, order = NULL, facet = FALSE, works = FALSE, cursor = NULL, cursor_max = 5000, .progress = "none", flq = NULL, select = NULL, ... ) cr_prefixes_( prefixes, query = NULL, filter = NULL, offset = NULL, limit = NULL, sample = NULL, sort = NULL, order = NULL, facet = FALSE, works = FALSE, cursor = NULL, cursor_max = 5000, .progress = "none", parse = FALSE, flq = NULL, select = NULL, ... )
prefixes |
(character) Publisher prefixes, one or more in a vector or list. Required. |
query |
Query terms |
filter |
Filter options. See examples for usage examples
and |
offset |
Number of record to start at. Minimum: 1. For
|
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 |
sort |
Field to sort on. Acceptable set of fields to sort on:
|
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: |
works |
(logical) If |
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 |
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 |
.progress |
Show a |
flq |
field queries. One or more field queries. Acceptable set of field query parameters are:
Note: |
select |
(character) One or more field to return (only those fields are returned) |
... |
Named parameters passed on to |
parse |
(logical) Whether to output json |
BEWARE: The API will only work for CrossRef DOIs.
Note that any one publisher can have more than one DOI. If you want to
search on all DOIs for a publisher, pass in all DOIs, or see
cr_members()
, and pass in the member_ids
parameter.
Notes from CrossRef (quoting them):
The prefix of a CrossRef DOI does NOT indicate who currently owns the DOI.
It only reflects who originally registered the DOI. CrossRef metadata has
an owner_prefix
element that records the current owner of the
CrossRef DOI in question.
CrossRef also has member IDs for depositing organisations. A single member may control multiple owner prefixes, which in turn may control a number of DOIs. When looking at works published by a certain organisation, member IDs and the member routes should be used.
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 "..."
See the "Rate limiting" seciton in rcrossref to get into the "fast lane"
https://github.com/CrossRef/rest-api-doc
Other crossref:
cr_funders()
,
cr_journals()
,
cr_licenses()
,
cr_members()
,
cr_types()
,
cr_works()
## Not run: cr_prefixes(prefixes="10.1016") cr_prefixes(prefixes="10.1016", works=TRUE) cr_prefixes(prefixes=c('10.1016','10.1371','10.1023','10.4176','10.1093')) cr_prefixes(prefixes=c('10.1016','10.1371'), works=TRUE) cr_prefixes(prefixes="10.1016", works=TRUE, filter=c(has_full_text=TRUE), limit=5) cr_prefixes(prefixes="10.1016", works=TRUE, query='ecology', limit=4) cr_prefixes(prefixes="10.1016", works=TRUE, query='ecology', limit=4) # facets - only avail. when works=TRUE cr_prefixes(prefixes="10.1016", works=TRUE, facet=TRUE) cr_prefixes(prefixes="10.1016", works=TRUE, facet="license:*", limit=0) cr_prefixes(prefixes=c('10.1016','10.1371'), works=TRUE, facet=TRUE, limit=0) # Use the cursor for deep paging cr_prefixes("10.1016", works = TRUE, cursor = "*", cursor_max = 500, limit = 100) cr_prefixes(c('10.1016', '10.1371'), works = TRUE, cursor = "*", cursor_max = 300, limit = 100) ## with optional progress bar cr_prefixes("10.1016", works = TRUE, cursor = "*", cursor_max = 500, limit = 100, .progress = TRUE) # Low level function - does no parsing to data.frame, get json or a list cr_prefixes_("10.1016") cr_prefixes_(c('10.1016', '10.1371')) cr_prefixes_("10.1016", works = TRUE, query = 'ecology', limit = 10) cr_prefixes_("10.1016", works = TRUE, query = 'ecology', parse=TRUE, limit = 10) cr_prefixes_("10.1016", works = TRUE, cursor = "*", cursor_max = 300, limit = 100) cr_prefixes_("10.1016", works = TRUE, cursor = "*", cursor_max = 300, limit = 100, parse = TRUE) # field queries ## query.container-title cr_prefixes("10.1016", works = TRUE, flq = c(`query.container-title` = 'Ecology')) # select only certain fields to return res <- cr_prefixes("10.1016", works = TRUE, select = c('DOI', 'title')) names(res$data) ## End(Not run)
## Not run: cr_prefixes(prefixes="10.1016") cr_prefixes(prefixes="10.1016", works=TRUE) cr_prefixes(prefixes=c('10.1016','10.1371','10.1023','10.4176','10.1093')) cr_prefixes(prefixes=c('10.1016','10.1371'), works=TRUE) cr_prefixes(prefixes="10.1016", works=TRUE, filter=c(has_full_text=TRUE), limit=5) cr_prefixes(prefixes="10.1016", works=TRUE, query='ecology', limit=4) cr_prefixes(prefixes="10.1016", works=TRUE, query='ecology', limit=4) # facets - only avail. when works=TRUE cr_prefixes(prefixes="10.1016", works=TRUE, facet=TRUE) cr_prefixes(prefixes="10.1016", works=TRUE, facet="license:*", limit=0) cr_prefixes(prefixes=c('10.1016','10.1371'), works=TRUE, facet=TRUE, limit=0) # Use the cursor for deep paging cr_prefixes("10.1016", works = TRUE, cursor = "*", cursor_max = 500, limit = 100) cr_prefixes(c('10.1016', '10.1371'), works = TRUE, cursor = "*", cursor_max = 300, limit = 100) ## with optional progress bar cr_prefixes("10.1016", works = TRUE, cursor = "*", cursor_max = 500, limit = 100, .progress = TRUE) # Low level function - does no parsing to data.frame, get json or a list cr_prefixes_("10.1016") cr_prefixes_(c('10.1016', '10.1371')) cr_prefixes_("10.1016", works = TRUE, query = 'ecology', limit = 10) cr_prefixes_("10.1016", works = TRUE, query = 'ecology', parse=TRUE, limit = 10) cr_prefixes_("10.1016", works = TRUE, cursor = "*", cursor_max = 300, limit = 100) cr_prefixes_("10.1016", works = TRUE, cursor = "*", cursor_max = 300, limit = 100, parse = TRUE) # field queries ## query.container-title cr_prefixes("10.1016", works = TRUE, flq = c(`query.container-title` = 'Ecology')) # select only certain fields to return res <- cr_prefixes("10.1016", works = TRUE, select = c('DOI', 'title')) names(res$data) ## End(Not run)
Get a random set of DOI's through CrossRef.
cr_r(sample = 10, ...)
cr_r(sample = 10, ...)
sample |
The number of returned random DOIs. Maximum: 100. Default: 20. |
... |
Further args passed on to |
A character vector of DOIs
Scott Chamberlain [email protected]
## Not run: # Default search gets 10 random DOIs cr_r() # Get 30 DOIs cr_r(30) ## End(Not run)
## Not run: # Default search gets 10 random DOIs cr_r() # Get 30 DOIs cr_r(30) ## End(Not run)
Search CrossRef types
cr_types( types = NULL, query = NULL, filter = NULL, offset = NULL, limit = NULL, sample = NULL, sort = NULL, order = NULL, facet = FALSE, works = FALSE, cursor = NULL, cursor_max = 5000, .progress = "none", flq = NULL, select = NULL, ... ) cr_types_( types = NULL, query = NULL, filter = NULL, offset = NULL, limit = NULL, sample = NULL, sort = NULL, order = NULL, facet = FALSE, works = FALSE, cursor = NULL, cursor_max = 5000, .progress = "none", parse = FALSE, flq = NULL, select = NULL, ... )
cr_types( types = NULL, query = NULL, filter = NULL, offset = NULL, limit = NULL, sample = NULL, sort = NULL, order = NULL, facet = FALSE, works = FALSE, cursor = NULL, cursor_max = 5000, .progress = "none", flq = NULL, select = NULL, ... ) cr_types_( types = NULL, query = NULL, filter = NULL, offset = NULL, limit = NULL, sample = NULL, sort = NULL, order = NULL, facet = FALSE, works = FALSE, cursor = NULL, cursor_max = 5000, .progress = "none", parse = FALSE, flq = NULL, select = NULL, ... )
types |
(character) Type identifier, e.g., journal |
query |
Query terms |
filter |
Filter options. See examples for usage examples
and |
offset |
Number of record to start at. Minimum: 1. For
|
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 |
sort |
Field to sort on. Acceptable set of fields to sort on:
|
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: |
works |
(logical) If |
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 |
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 |
.progress |
Show a |
flq |
field queries. One or more field queries. Acceptable set of field query parameters are:
Note: |
select |
(character) One or more field to return (only those fields are returned) |
... |
Named parameters passed on to |
parse |
(logical) Whether to output json |
BEWARE: The API will only work for CrossRef DOIs.
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 "..."
See the "Rate limiting" seciton in rcrossref to get into the "fast lane"
https://github.com/CrossRef/rest-api-doc
Other crossref:
cr_funders()
,
cr_journals()
,
cr_licenses()
,
cr_members()
,
cr_prefixes()
,
cr_works()
## Not run: cr_types() cr_types("monograph") cr_types("monograph", works=TRUE) cr_types(c('monograph', 'book-set', 'book', 'book-track')) cr_types(c('monograph', 'book-set'), works=TRUE) ## get facets back cr_types("journal-article", works=TRUE, facet=TRUE)$facets cr_types("monograph", works=TRUE, facet="license:*", limit = 0) cr_types(c('monograph', 'book-set'), works=TRUE, facet=TRUE) # Use the cursor for deep paging cr_types("journal-article", works = TRUE, cursor = "*", cursor_max = 500, limit = 100) cr_types(c('monograph', 'book-set'), works = TRUE, cursor = "*", cursor_max = 300, limit = 100) ## with optional progress bar cr_types("journal-article", works = TRUE, cursor = "*", cursor_max = 500, limit = 100, .progress = TRUE) # query doesn't work unless using works=TRUE ### you get results, but query param is silently dropped cr_types(query = "ecology") # print progress - only works when passing more than one type cr_types(c('monograph', 'book-set'), works=TRUE, .progress='text') # Low level function - does no parsing to data.frame, get json or a list cr_types_('monograph') cr_types_('monograph', parse = TRUE) cr_types_("journal-article", works = TRUE, cursor = "*", cursor_max = 300, limit = 100) # field queries ## query.container-title cr_types("journal-article", works = TRUE, flq = c(`query.container-title` = 'Ecology')) # select only certain fields to return res <- cr_types("journal-article", works = TRUE, select = c('DOI', 'title')) names(res$data) ## End(Not run)
## Not run: cr_types() cr_types("monograph") cr_types("monograph", works=TRUE) cr_types(c('monograph', 'book-set', 'book', 'book-track')) cr_types(c('monograph', 'book-set'), works=TRUE) ## get facets back cr_types("journal-article", works=TRUE, facet=TRUE)$facets cr_types("monograph", works=TRUE, facet="license:*", limit = 0) cr_types(c('monograph', 'book-set'), works=TRUE, facet=TRUE) # Use the cursor for deep paging cr_types("journal-article", works = TRUE, cursor = "*", cursor_max = 500, limit = 100) cr_types(c('monograph', 'book-set'), works = TRUE, cursor = "*", cursor_max = 300, limit = 100) ## with optional progress bar cr_types("journal-article", works = TRUE, cursor = "*", cursor_max = 500, limit = 100, .progress = TRUE) # query doesn't work unless using works=TRUE ### you get results, but query param is silently dropped cr_types(query = "ecology") # print progress - only works when passing more than one type cr_types(c('monograph', 'book-set'), works=TRUE, .progress='text') # Low level function - does no parsing to data.frame, get json or a list cr_types_('monograph') cr_types_('monograph', parse = TRUE) cr_types_("journal-article", works = TRUE, cursor = "*", cursor_max = 300, limit = 100) # field queries ## query.container-title cr_types("journal-article", works = TRUE, flq = c(`query.container-title` = 'Ecology')) # select only certain fields to return res <- cr_types("journal-article", works = TRUE, select = c('DOI', 'title')) names(res$data) ## End(Not run)
Search CrossRef works (articles)
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, ... )
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, ... )
dois |
Search by a single DOI or many DOIs. Note that using this
parameter at the same time as the |
query |
Query terms |
filter |
Filter options. See examples for usage examples
and |
offset |
Number of record to start at. Minimum: 1. For
|
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 |
sort |
Field to sort on. Acceptable set of fields to sort on:
|
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: |
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 |
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 |
.progress |
Show a |
flq |
field queries. One or more field queries. Acceptable set of field query parameters are:
Note: |
select |
(character) One or more field to return (only those fields are returned) |
async |
(logical) use async HTTP requests. Default: |
... |
Named parameters passed on to |
parse |
(logical) Whether to output json |
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 "..."
The API will only work for CrossRef DOIs.
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
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.
See the "Rate limiting" seciton in rcrossref to get into the "fast lane"
https://github.com/CrossRef/rest-api-doc
Other crossref:
cr_funders()
,
cr_journals()
,
cr_licenses()
,
cr_members()
,
cr_prefixes()
,
cr_types()
## Not run: # 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$data) # asyc queries <- c("ecology", "science", "cellular", "birds", "European", "bears", "beets", "laughter", "hapiness", "funding") res <- cr_works(query = queries, async = TRUE) res_json <- cr_works_(query = queries, async = TRUE) unname(vapply(res_json, class, "")) jsonlite::fromJSON(res_json[[1]]) queries <- c("ecology", "science", "cellular") res <- cr_works(query = queries, async = TRUE, verbose = TRUE) res # time queries <- c("ecology", "science", "cellular", "birds", "European", "bears", "beets", "laughter", "hapiness", "funding") system.time(cr_works(query = queries, async = TRUE)) system.time(lapply(queries, function(z) cr_works(query = z))) ## End(Not run)
## Not run: # Works funded by the NSF cr_works(query="NSF") # Works that include renear but not ontologies cr_works(query="renear+-ontologies") # Filter cr_works(query="global state", filter=c(has_orcid=TRUE), limit=3) # Filter by multiple fields cr_works(filter=c(has_orcid=TRUE, from_pub_date='2004-04-04')) # Only full text articles cr_works(filter=c(has_full_text = TRUE)) # has affilitation data cr_works(filter=c(has_affiliation = TRUE)) # has abstract cr_works(filter=c(has_abstract = TRUE)) # has clinical trial number cr_works(filter=c(has_clinical_trial_number = TRUE)) # Querying dois cr_works(dois='10.1063/1.3593378') cr_works('10.1371/journal.pone.0033693') cr_works(dois='10.1007/12080.1874-1746') cr_works(dois=c('10.1007/12080.1874-1746','10.1007/10452.1573-5125', '10.1111/(issn)1442-9993')) # progress bar cr_works(dois=c('10.1007/12080.1874-1746','10.1007/10452.1573-5125'), .progress="text") # Include facetting in results cr_works(query="NSF", facet=TRUE) ## Get facets only, by setting limit=0 cr_works(query="NSF", facet=TRUE, limit=0) ## you can also set facet to a query cr_works(facet = "license:*", limit=0) # Sort results cr_works(query="ecology", sort='relevance', order="asc") res <- cr_works(query="ecology", sort='score', order="asc") res$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))) ## End(Not run)
Get filter details and names.
filter_names() filter_details(x = NULL)
filter_names() filter_details(x = NULL)
x |
(character) Optional filter name. If not given, all filters returned. |
Note that all filter names in this package have periods and dashes replaced with underscores as they both cause problems in an R console.
filter_names() filter_details() filter_details()$has_authenticated_orcid filter_details()$has_authenticated_orcid$possible_values filter_details()$has_authenticated_orcid$description filter_details("issn") filter_details("iss") filter_details(c("issn", "alternative_id"))
filter_names() filter_details() filter_details()$has_authenticated_orcid filter_details()$has_authenticated_orcid$possible_values filter_details()$has_authenticated_orcid$description filter_details("issn") filter_details("iss") filter_details(c("issn", "alternative_id"))
Get list of styles from github.com/citation-style-language/styles
get_styles(...)
get_styles(...)
... |
Named parameters passed on to crul::HttpClient |
## Not run: x <- get_styles() x[1:10] ## End(Not run)
## Not run: x <- get_styles() x[1:10] ## End(Not run)
Get a PMID from a DOI, and vice versa.
id_converter(x, type = NULL, ...)
id_converter(x, type = NULL, ...)
x |
(character) One or more of: doi, pmid, pmcid, or manuscript id, see examples. required. |
type |
(character) one of doi, pmid, pmcid, or manuscript id |
... |
Curl args passed on to crul::verb-GET |
https://www.ncbi.nlm.nih.gov/pmc/tools/id-converter-api/
## Not run: # get a pmid/pmcid from a doi id_converter("10.1038/ng.590") # pmid to doi/pmcid id_converter("20495566", "pmid") id_converter("20495566") # id_converter("20495566", "doi") #error # pmcid to doi/pmid id_converter("PMC2883744", "pmcid") id_converter("PMC2883744") # manuscript id id_converter("NIHMS311352") # more than 1 ID id_converter(c("PMC3531190","PMC3245039")) # error, wrong type passed for id given # id_converter("PMC2883744", "doi") # error, 200 ids or less # ids <- cr_r(100) # id_converter(c(ids, ids, ids)) ## End(Not run)
## Not run: # get a pmid/pmcid from a doi id_converter("10.1038/ng.590") # pmid to doi/pmcid id_converter("20495566", "pmid") id_converter("20495566") # id_converter("20495566", "doi") #error # pmcid to doi/pmid id_converter("PMC2883744", "pmcid") id_converter("PMC2883744") # manuscript id id_converter("NIHMS311352") # more than 1 ID id_converter(c("PMC3531190","PMC3245039")) # error, wrong type passed for id given # id_converter("PMC2883744", "doi") # error, 200 ids or less # ids <- cr_r(100) # id_converter(c(ids, ids, ids)) ## End(Not run)
These functions are gone, no longer available.
cr_citation()
: Crossref is trying to sunset their
OpenURL API, which this function uses. So this function is now removed.
See the function cr_cn()
, which does the same things, but with
more functionality, using the new Crossref API.
pmid2doi()
and doi2pmid()
: The API behind
these functions is down for good, see id_converter()
for
similar functionality.
cr_search()
: The functionality of this function can
be achieved with the new Crossref API. See functions cr_works()
et al.
cr_search_free()
: The functionality of this function can
be achieved with the new Crossref API. See functions cr_works()
et al.
crosscite()
: The functionality of this function can be
achieved with cr_cn()
cr_fundref()
: Crossref changed their name "fundref"
to "funders", so we've changed our function, see cr_funders()
cr_ft_text()
: This function and other text mining
functions are incorporated in a new package crminer
.
cr_ft_links()
: This function and other text mining
functions are incorporated in a new package crminer
.
cr_ft_pdf()
: This function and other text mining
functions are incorporated in a new package crminer
.
cr_ft_plain()
: This function and other text mining
functions are incorporated in a new package crminer
.
cr_ft_text()
: This function and other text mining
functions are incorporated in a new package crminer
.
cr_ft_xml()
: This function and other text mining
functions are incorporated in a new package crminer
.
as.tdmurl()
: This function and other text mining
functions are incorporated in a new package crminer
.
extract_xpdf()
: This function and other text mining
functions are incorporated in a new package crminer
.