rcrossref
Client for Various 'CrossRef' 'APIs'
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.
R interface to various CrossRef APIs
- Crossref API: https://github.com/CrossRef/rest-api-doc/blob/master/rest_api.md
- Crossref metadata search API (http://search.labs.crossref.org/)
- CrossRef DOI Content Negotiation
- Text and Data Mining TDM
Installation
Stable version from CRAN
install.packages("rcrossref")Or development version from GitHub
install.packages("devtools")devtools::install_github("ropensci/rcrossref")Load rcrossref
library('rcrossref')Register for the Polite Pool
If you are intending to access Crossref regularly you will want to send your email address with your queries. This has the advantage that queries are placed in the polite pool of servers. Including your email address is good practice as described in the Crossref documentation under Good manners. The second advantage is that Crossref can contact you if there is a problem with a query.
Details on how to register your email in a call can be found at ?rcrossref-package. To pass your email address to Crossref, simply store it as an 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
To stop sharing your email when using rcrossref simply delete it from your .Renviron file.
Citation search
Use CrossRef's DOI Content Negotiation service, where you can citations back in various formats, including apa
cr_cn(dois = "10.1126/science.169.3946.635", format = "text", style = "apa")#> [1] "Frank, H. S. (1970). The Structure of Ordinary Water: New data and interpretations are yielding new insights into this fascinating substance. Science, 169(3946), 635–641. doi:10.1126/science.169.3946.635"bibtex
cat(cr_cn(dois = "10.1126/science.169.3946.635", format = "bibtex"))#> @article{Frank_1970,#> doi = {10.1126/science.169.3946.635},#> url = {https://doi.org/10.1126%2Fscience.169.3946.635},#> year = 1970,#> month = {aug},#> publisher = {American Association for the Advancement of Science ({AAAS})},#> volume = {169},#> number = {3946},#> pages = {635--641},#> author = {H. S. Frank},#> title = {The Structure of Ordinary Water: New data and interpretations are yielding new insights into this fascinating substance},#> journal = {Science}#> }bibentry
cr_cn(dois = "10.6084/m9.figshare.97218", format = "bibentry")#> $doi#> [1] "10.6084/m9.figshare.97218"#> #> $url#> [1] "https://figshare.com/articles/Regime_shifts_in_ecology_and_evolution_(PhD_Dissertation)/97218"#> #> $author#> [1] "Boettiger, Carl"#> #> $keywords#> [1] "Evolutionary Biology, Ecology"#> #> $title#> [1] "Regime shifts in ecology and evolution (PhD Dissertation)"#> #> $publisher#> [1] "Figshare"#> #> $year#> [1] "2012"#> #> $key#> [1] "https://doi.org/10.6084/m9.figshare.97218"#> #> $entry#> [1] "article"Citation count
Citation count, using OpenURL
cr_citation_count(doi = "10.1371/journal.pone.0042793")#> doi count#> 1 10.1371/journal.pone.0042793 25Search Crossref metadata API
The following functions all use the CrossRef API.
Look up funder information
cr_funders(query = "NSF")#> $meta#> total_results search_terms start_index items_per_page#> 1 10 NSF 0 20#> #> $data#> # A tibble: 10 x 6#> id location name alt.names uri tokens #> <chr> <chr> <chr> <chr> <chr> <chr> #> 1 50110… Norway Norsk Sykepl… NSF, Norwegian … http://d… norsk, sykepl…#> 2 10000… United S… Center for H… CHM, NSF, Unive… http://d… center, for, …#> 3 10000… United S… National Sle… NSF http://d… national, sle…#> 4 50110… Sri Lanka National Sci… National Scienc… http://d… national, sci…#> 5 10000… Denmark Statens Natu… Danish National… http://d… statens, natu…#> 6 10000… United S… Office of th… NSF Office of t… http://d… office, of, t…#> 7 50110… Australia National Str… NSF http://d… national, str…#> 8 10000… United S… National Sci… NSF http://d… national, sci…#> 9 50110… China National Nat… NSFC-Yunnan Joi… http://d… national, nat…#> 10 50110… China National Nat… Natural Science… http://d… national, nat…#> #> $facets#> NULLCheck the DOI minting agency
cr_agency(dois = '10.13039/100000001')#> $DOI#> [1] "10.13039/100000001"#> #> $agency#> $agency$id#> [1] "crossref"#> #> $agency$label#> [1] "Crossref"Search works (i.e., articles)
cr_works(filter = c(has_orcid = TRUE, from_pub_date = '2004-04-04'), limit = 1)#> $meta#> total_results search_terms start_index items_per_page#> 1 2085016 NA 0 1#> #> $data#> # A tibble: 1 x 27#> alternative.id container.title created deposited published.print#> <chr> <chr> <chr> <chr> <chr> #> 1 BFgim2014129 Genetics in Me… 2014-0… 2017-12-… 2015-06 #> # … with 22 more variables: published.online <chr>, doi <chr>,#> # indexed <chr>, issn <chr>, issue <chr>, issued <chr>, member <chr>,#> # page <chr>, prefix <chr>, publisher <chr>, reference.count <chr>,#> # score <chr>, source <chr>, title <chr>, type <chr>,#> # update.policy <chr>, url <chr>, volume <chr>, author <list>,#> # link <list>, license <list>, reference <list>#> #> $facets#> NULLSearch journals
cr_journals(issn = c('1803-2427','2326-4225'))#> $data#> # A tibble: 2 x 53#> title publisher issn last_status_che… deposits_abstra… deposits_orcids…#> <chr> <chr> <chr> <date> <lgl> <lgl> #> 1 Jour… "De Gruy… 1805… 2019-01-14 TRUE FALSE #> 2 Jour… American… 2326… 2019-01-14 FALSE FALSE #> # … with 47 more variables: deposits <lgl>,#> # deposits_affiliations_backfile <lgl>,#> # deposits_update_policies_backfile <lgl>,#> # deposits_similarity_checking_backfile <lgl>,#> # deposits_award_numbers_current <lgl>,#> # deposits_resource_links_current <lgl>, deposits_articles <lgl>,#> # deposits_affiliations_current <lgl>, deposits_funders_current <lgl>,#> # deposits_references_backfile <lgl>, deposits_abstracts_backfile <lgl>,#> # deposits_licenses_backfile <lgl>,#> # deposits_award_numbers_backfile <lgl>,#> # deposits_open_references_backfile <lgl>,#> # deposits_open_references_current <lgl>,#> # deposits_references_current <lgl>,#> # deposits_resource_links_backfile <lgl>,#> # deposits_orcids_backfile <lgl>, deposits_funders_backfile <lgl>,#> # deposits_update_policies_current <lgl>,#> # deposits_similarity_checking_current <lgl>,#> # deposits_licenses_current <lgl>, affiliations_current <dbl>,#> # similarity_checking_current <dbl>, funders_backfile <dbl>,#> # licenses_backfile <dbl>, funders_current <dbl>,#> # affiliations_backfile <dbl>, resource_links_backfile <dbl>,#> # orcids_backfile <dbl>, update_policies_current <dbl>,#> # open_references_backfile <dbl>, orcids_current <dbl>,#> # similarity_checking_backfile <dbl>, references_backfile <dbl>,#> # award_numbers_backfile <dbl>, update_policies_backfile <dbl>,#> # licenses_current <dbl>, award_numbers_current <dbl>,#> # abstracts_backfile <dbl>, resource_links_current <dbl>,#> # abstracts_current <dbl>, open_references_current <dbl>,#> # references_current <dbl>, total_dois <int>, current_dois <int>,#> # backfile_dois <int>#> #> $facets#> NULLSearch license information
cr_licenses(query = 'elsevier')#> $meta#> total_results search_terms start_index items_per_page#> 1 31 elsevier 0 20#> #> $data#> # A tibble: 31 x 2#> URL work.count#> <chr> <int>#> 1 http://aspb.org/publications/aspb-journals/open-articles 1#> 2 http://creativecommons.org/licenses/by-nc-nd/3.0/ 13#> 3 http://creativecommons.org/licenses/by-nc-nd/4.0/ 7#> 4 http://creativecommons.org/licenses/by-nc/4.0 1#> 5 http://creativecommons.org/licenses/by-nc/4.0/ 2#> 6 http://creativecommons.org/licenses/by/3.0/ 1#> 7 http://creativecommons.org/licenses/by/4.0 2#> 8 http://creativecommons.org/licenses/by/4.0/ 4#> 9 http://doi.wiley.com/10.1002/tdm_license_1 155#> 10 http://doi.wiley.com/10.1002/tdm_license_1.1 2207#> # … with 21 more rowsSearch based on DOI prefixes
cr_prefixes(prefixes = c('10.1016','10.1371','10.1023','10.4176','10.1093'))#> $meta#> NULL#> #> $data#> member name#> 1 http://id.crossref.org/member/78 Elsevier BV#> 2 http://id.crossref.org/member/340 Public Library of Science (PLoS)#> 3 http://id.crossref.org/member/297 Springer Nature#> 4 http://id.crossref.org/member/1989 Co-Action Publishing#> 5 http://id.crossref.org/member/286 Oxford University Press (OUP)#> prefix#> 1 http://id.crossref.org/prefix/10.1016#> 2 http://id.crossref.org/prefix/10.1371#> 3 http://id.crossref.org/prefix/10.1023#> 4 http://id.crossref.org/prefix/10.4176#> 5 http://id.crossref.org/prefix/10.1093#> #> $facets#> list()Search CrossRef members
cr_members(query = 'ecology', limit = 5)#> $meta#> total_results search_terms start_index items_per_page#> 1 19 ecology 0 5#> #> $data#> # A tibble: 5 x 56#> id primary_name location last_status_che… total.dois current.dois#> <int> <chr> <chr> <date> <chr> <chr> #> 1 336 Japanese So… 5-3 Yon… 2019-01-14 1202 127 #> 2 1950 Journal of … Suite 8… 2019-01-14 27 0 #> 3 2080 The Japan S… 5-3 Yon… 2019-01-14 688 18 #> 4 2151 Ecology and… 5-3 Yon… 2019-01-14 394 50 #> 5 2169 Italian Soc… Diparti… 2019-01-14 1261 277 #> # … with 50 more variables: backfile.dois <chr>, prefixes <chr>,#> # coverge.affiliations.current <chr>,#> # coverge.similarity.checking.current <chr>,#> # coverge.funders.backfile <chr>, coverge.licenses.backfile <chr>,#> # coverge.funders.current <chr>, coverge.affiliations.backfile <chr>,#> # coverge.resource.links.backfile <chr>, coverge.orcids.backfile <chr>,#> # coverge.update.policies.current <chr>,#> # coverge.open.references.backfile <chr>, coverge.orcids.current <chr>,#> # coverge.similarity.checking.backfile <chr>,#> # coverge.references.backfile <chr>,#> # coverge.award.numbers.backfile <chr>,#> # coverge.update.policies.backfile <chr>,#> # coverge.licenses.current <chr>, coverge.award.numbers.current <chr>,#> # coverge.abstracts.backfile <chr>,#> # coverge.resource.links.current <chr>, coverge.abstracts.current <chr>,#> # coverge.open.references.current <chr>,#> # coverge.references.current <chr>,#> # flags.deposits.abstracts.current <chr>,#> # flags.deposits.orcids.current <chr>, flags.deposits <chr>,#> # flags.deposits.affiliations.backfile <chr>,#> # flags.deposits.update.policies.backfile <chr>,#> # flags.deposits.similarity.checking.backfile <chr>,#> # flags.deposits.award.numbers.current <chr>,#> # flags.deposits.resource.links.current <chr>,#> # flags.deposits.articles <chr>,#> # flags.deposits.affiliations.current <chr>,#> # flags.deposits.funders.current <chr>,#> # flags.deposits.references.backfile <chr>,#> # flags.deposits.abstracts.backfile <chr>,#> # flags.deposits.licenses.backfile <chr>,#> # flags.deposits.award.numbers.backfile <chr>,#> # flags.deposits.open.references.backfile <chr>,#> # flags.deposits.open.references.current <chr>,#> # flags.deposits.references.current <chr>,#> # flags.deposits.resource.links.backfile <chr>,#> # flags.deposits.orcids.backfile <chr>,#> # flags.deposits.funders.backfile <chr>,#> # flags.deposits.update.policies.current <chr>,#> # flags.deposits.similarity.checking.current <chr>,#> # flags.deposits.licenses.current <chr>, names <chr>, tokens <chr>#> #> $facets#> NULLGet N random DOIs
cr_r() uses the function cr_works() internally.
cr_r()#> [1] "10.1104/pp.105.059972" #> [2] "10.21192/scll.62..201002.003" #> [3] "10.1227/neu.0b013e31821551c5" #> [4] "10.1002/1097-0142(197609)38:3<1259::aid-cncr2820380328>3.0.co;2-m"#> [5] "10.1063/1.1696818" #> [6] "10.1353/dar.2007.0023" #> [7] "10.1177/2048872613475891" #> [8] "10.1037/e615052007-001" #> [9] "10.1088/0026-1394/42/6/s11" #> [10] "10.1038/s41566-017-0014-2"You can pass in the number of DOIs you want back (default is 10)
cr_r(2)#> [1] "10.1016/0031-9384(74)90186-3" "10.1371/journal.pone.0107259.g002"Get full text
Publishers can optionally provide links in the metadata they provide to Crossref for full text of the work, but that data is often missing. Find out more about it at http://tdmsupport.crossref.org/.
Get some DOIs for articles that provide full text, and that have CC-BY 3.0 licenses (i.e., more likely to actually be open)
out <- cr_works(filter = list(has_full_text = TRUE, license_url = "http://creativecommons.org/licenses/by/3.0/"))(dois <- out$data$doi)#> [1] "10.5194/acpd-14-24183-2014" "10.5194/bgd-11-13343-2014" #> [3] "10.5194/bgd-11-13455-2014" "10.1155/2014/128505" #> [5] "10.1155/2014/124592" "10.1155/2014/154204" #> [7] "10.1155/2014/718415" "10.1155/2014/727135" #> [9] "10.1155/2014/264217" "10.1155/2014/484656" #> [11] "10.1155/2014/490386" "10.1155/2014/528696" #> [13] "10.1155/2014/934510" "10.1155/2014/907584" #> [15] "10.5194/amtd-7-9453-2014" "10.1088/1742-6596/536/1/012003"#> [17] "10.1088/1742-6596/536/1/012001" "10.1088/1742-6596/536/1/012016"#> [19] "10.5194/sed-6-2779-2014" "10.5194/amtd-7-9537-2014"From the output of cr_works we can get full text links if we know where to look:
do.call("rbind", out$data$link)#> # A tibble: 54 x 4#> URL content.type content.version intended.applica…#> <chr> <chr> <chr> <chr> #> 1 http://www.atmos-chem-ph… unspecified vor similarity-check…#> 2 http://www.biogeoscience… unspecified vor similarity-check…#> 3 http://www.biogeoscience… unspecified vor similarity-check…#> 4 http://downloads.hindawi… application… vor text-mining #> 5 http://downloads.hindawi… application… vor text-mining #> 6 http://downloads.hindawi… unspecified vor similarity-check…#> 7 http://downloads.hindawi… application… vor text-mining #> 8 http://downloads.hindawi… application… vor text-mining #> 9 http://downloads.hindawi… unspecified vor similarity-check…#> 10 http://downloads.hindawi… application… vor text-mining #> # … with 44 more rowsFrom there, you can grab your full text, but because most links require
authentication, enter another package: crminer.
You'll need package crminer for the rest of the work.
Onc we have DOIs, get URLs to full text content
if (!requireNamespace("crminer")) { install.packages("crminer")}library(crminer)(links <- crm_links("10.1155/2014/128505"))#> $pdf#> <url> http://downloads.hindawi.com/archive/2014/128505.pdf#> #> $xml#> <url> http://downloads.hindawi.com/archive/2014/128505.xml#> #> $unspecified#> <url> http://downloads.hindawi.com/archive/2014/128505.pdfThen use those URLs to get full text
crm_pdf(links)#> <document>/Users/sckott/Library/Caches/R/crminer/128505.pdf#> Pages: 1#> No. characters: 1565#> Created: 2014-09-15See also fulltext for getting scholarly text for text mining.
Meta
- Please report any issues or bugs.
- License: MIT
- Get citation information for
rcrossrefin R doingcitation(package = 'rcrossref') - Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.
This package is part of a richer suite called fulltext, along with several other packages, that provides the ability to search for and retrieve full text of open access scholarly articles.
News
rcrossref 0.9.0
NEW FEATURES
- big Crossref Addin update (#171) all work by @haozhu233
- Async HTTP introduced for
cr_works(),cr_works_(), andcr_citation_count(). See the new parameterasync(logical) in those functions. Forcr_citation_count(), it now accepts more than 1 DOI, and the output has changed from a numeric value to a data.frame (columns:doiandcount). Withasync=TRUEforcr_works()you get a list of data.frame's; while forcr_works_()you get a list of JSON's (#121) (#160) (#182)
MINOR IMPROVEMENTS
- package tests now using
vcrfor HTTP request/response caching (#178) (#179) - in
worksdata, now returningpublished-printandpublished-onlinefields (#181) - add new filters for
/worksroutes (whenworks = TRUE):isbn,reference_visibility,has_content_domain, andhas_domain_restriction(#176) (#177) - add new return element in
/worksroutes (whenworks = TRUE):$referencegives the references cited in the article (these are not the articles citing the target article, sorry) (#176) - improve documentation on the "polite pool". If you supply an email address Crossref will put you in the polite pool (#173) (#175) thanks @poldham
- added example to
cr_abstract()of handling many DOIs while allowing for failures without stopping progress (#174) thanks @zackbatist
BUG FIXES
- fix internal parsing of funder data in
cr_works()(#180) thanks @nicholasmfraser for the bug report - fix for
cr_citation_count(): when given a bad/invalid/malformed DOI, throw warning and give back anNA(#164) thanks for the report @chreman - Fix for instances in the package where we incorrectly were doing logical comparison's; detected via R_CHECK_LENGTH_1_LOGIC2
rcrossref 0.8.4
NEW FEATURES
- The RStudio Addin now includes ability to search by article metadata, e.g., title (#148) (#152)
- you can now set a different base url for
cr_cn()(#168)
MINOR IMPROVEMENTS
- better behavior for
cr_cn()when bibentry not valid, that is not parseable. before the package we use to parsebibtexwould stop on invalid bibentry data, but now we get around the invalid bits and give back the bibentry (#147) - updated and improved documentation for filters (#161)
- improved description of the
doisparameter (#162) thanks @ms609 - Much improved error behavior for
cr_*functions. We now give errors like404 (client error): /works/blblbl - Resource not found., which includes HTTP status code, major class of error (success, redirect, client, server), the route requested, and the error message (#163)
BUG FIXES
- fixed bug in
cr_works()in which field queries should have been possible for title and affiliation, but were not. Fixed now. (#149) cr_journals()was not correctly parsing data when more than 1 ISSN given andworksset toTRUE, fixed now (#156)cr_journals()was not correctly parsing data when no ISSN found andworksset toTRUE, fixed now (#150)cr_journals()was not correctly handling queries with multiple ISSN's andworksset toFALSE, fixed now (#151)- fixed bug in
cr_works(), and any othercr_*function that setworks=TRUE. thelicenseslot can have more than 1 result, and we were only giving the first back. fixed the parsing on this to give back all license results (#170)
rcrossref 0.8.0
NEW FEATURES
- Include documentation and internals to support passing a user supplied email to Crossref to get put into higher rate limit pool (#145) thanks @njahn82
- Functions that operate on the
/worksroute gain aselectparameter to select certain fields to return (#146)
MINOR IMPROVEMENTS
- Updated docs for additional options for the
sortparameter (#142) - Updated docs for additional options for doing field queries (the
flqparameter) (#143) - Filters: New filters added to the package, and some removed
(e.g,
publisher-name). You can see the filters with the functionsfilter_details/filter_names. Beware, some filters error sometimes with the Crossref API - they may not work, but they may, let me know at https://github.com/ropensci/rcrossref/issues or let Crossref know at https://github.com/CrossRef/rest-api-doc/issues (#136) (#139) (#141)
rcrossref 0.7.0
NEW FEATURES
- All text mining functionality moved into a new package:
crminerhttps://github.com/ropensci/crminer . Functions that did text mining stuff now defunct, see?rcrossref-defunct(#122) - All Crossref API requests now using
httpsinstead ofhttp(#133)
MINOR IMPROVEMENTS
- replace
xml2::xml_find_onewithxml2::xml_find_first(#128) thanks @njahn82 - replaced
httrwithcrulfor HTTP requests (#132) - Now using markdown for documentation (#135)
- Added more documentation to
cr_journalsandcr_worksabout what the returned data fieldsbackfile_doisandcurrent_doisreally mean (#105) thanks @SteveViss
BUG FIXES
- Fix to
cr_prefixesto not fail when no results found (#130) thanks @globbestael - Fixed
cr_worksto allow queries likefacet = license:*to be passed tofacetparameter (was always allowed by Crossref, but we neglected to allow it - previously only allowed a boolean) (#129) - Fixed
cr_fundersandcr_journalsto give back facet data along with other data (#134) - Fix to
cr_*functions to check for a missing content-type headers and instead of failing, we continue anyway and try to parse data as sometimes Crossref doesn't give back a content type header at all (#127)
rcrossref 0.6.0
NEW FEATURES
- Added support for field queries (see
https://github.com/CrossRef/rest-api-doc/blob/master/rest_api.md#field-queries
for information on them). Means that you can query on specific fields rather
than using
queryparameter which queries across all fields (#111) - Now using
rappdirsfor local storage and caching forcr_ft_text(#106)
MINOR IMPROVEMENTS
- Added to man files where appropriate new 10K max value for the
offsetparameter (#126) - Added to pkg level man file new rate limit headers included,
and how users can get to those, via
config=verbose()call (#124) - Better failure modes on input parameters, still more work to do surely (#101)
- sleeping now between tests to avoid making crossref rate limit gate keepers mad (#125)
cr_searchandcr_search_freeare now defunct. They were marked deprecated in previous version, and warned of defunct, and now they are defunct. Similar functionality can be done with e.g.,cr_works()(#102)crossciteis now defunct. The functionality of this function can be achieved withcr_cn()(#82)cr_fundrefis now defunct. Crossref changed their namefundreftofunders, so we've changed our function, seecr_funders()(#83)- parameter
samplemaximum value is now 100, was previously 1000. documentation updated. (#118) - New filters
has-clinical-trial-numberandhas-abstractadded to the package, see?filtersfor help (#120)
rcrossref 0.5.8
NEW FEATURES
- Added an RStudio Addin for searching for citations. See
?rcrossreffor more. Addin authored by Hao Zhu @haozhu233 (#114) - New function
cr_abstract()that tries to get an abstract via XML provided by Crossref - NOTE: an abstract is rarely available though (#116)
BUG FIXES
- Fixed bug in
cr_cn()where DOIs with no minting agency found were failing because we were previously stopping when no agency found. Now, we just assume Crossref and move on from there. (#117) thanks @dfalster ! - Fix to
cr_r()when number requested > 100. Actual fix is incr_works(). Max for sample used to be 1000, asked this on the Crossref API forum, see https://github.com/CrossRef/rest-api-doc/issues/146 (#115) - Fix to
cr_journals()in internal parsing, was failing in cases whereISSNarray was of length zero
rcrossref 0.5.4
MINOR IMPROVEMENTS
- Improved documentation for
cr_citation_count()to remove PLOS reference as the function isn't only for PLOS works (#108) - Changed use of
dplyr::rbind_all()todplyr::bind_rows()(#113)
rcrossref 0.5.2
NEW FEATURES
- User-agent string is passed with every request to Crossref with
names and versions of this package, and its HTTP dependency packages:
httrandcurl(whichhttrdepends on). Will potentially be useful to Crossref to know how many requests come from this R client (#100)
DEPRECATED
cr_search()andcr_search_free()use old Crossref web services, so are now marked deprecated, and will throw a deprecation message, but can still be used. They will both be defunct inv0.6of this package (#99)
MINOR IMPROVEMENTS
XMLreplaced withxml2(#98)httr::content()calls: all parse to text then parse content manually. in addition, encoding explicitly set toUTF-8onhttr::content()calls (#98)
BUG FIXES
- Bug fix to
cr_journals()- fix to parse correctly on some failed requests (#97) thanks @nkorf - Bug fix to
cr_fundref()/cr_funders()- parsing wasn't working correctly in all cases
rcrossref 0.5.0
Skipped v0.4 to v0.5 because of many changes - as described below.
NEW FEATURES
- Support added for 'deep paging' with the newer Crossref search API. Two new params added to each function:
cursor, which accepts a cursor alphanumeric string or the special*, which indicates that you want to initiate deep paging;cursor_max, which is not in the Crossref API, but just used here in this package to indicate where to stop - otherwise, you'd get all results, even if there was 70 million, for example. A new internalR6class used to make cursor requests easy (#77) - New function
id_converter()to get a PMID from a DOI and vice versa (#49) - Added a Code of Conduct.
- New function
cr_types(), along with its low level equivalentcr_types_()for when you just want a list or json back (#92) - New suite of functions composing a low-level API for the Crossref search API. These functions only do data request, and return json or a list, and do not attempt to parse to a data.frame. The new functions:
cr_funders_(),cr_journals_(),cr_licenses_(),cr_members_(),cr_prefixes_(),cr_types_(),cr_works_(). These functions are a bit faster, and aren't subject to parsing errors in the event of a change in the Crossref API. (#93) - Added new
filter_names()andfilter_details()functions to get information on what filters are available, the expected values, and what they mean.
MINOR IMPROVEMENTS
- Added documentation for new filter types, and added them to list of filters for
filter_names()andfilter_details()(#73) cr_funders()alias added tocr_fundref()(#74)- Made note in docs that funders without IDs don't show up on the
/fundersroute,s incr_funders()(#79) - Made note in docs that
sampleparameter ignored unlessworks=TRUE(#81) - Added note to docs that only what is returned in the API is what is searched when you search the Crossref API - that is, abstracts and full text aren't searched (#91)
cr_cn()now checks that the user supplied content-type is supported for the DOI minting agency associated with the DOI (#88) (thanks @njahn82)- Removed
.progressparameter use internally where it wasn't applicable. sampleparameter dropped fromcr_licenses().cr_works()parsing changed. We now don't attempt to flatten nested arrays, but instead give them back as data.frame's nested within the main data.frame. For example,authoroften has many entries, so we return that as a single column, but indexing to that column gives back a data.frame with a row for each author, and N number of columns. Hopefully this doesn't break too much code downstream :)- Additional text added to the package level man file (
?rcrossref) to explain: what you're actually searching when you search; deprecated and defunct functions; and explanation of high vs. low level API.
BUG FIXES
- Fix to
cr_members()to warn on error instead of stop during parsing (#68) - Fix to internal parser for
cr_works()to output links data, for full text links (#70) - Minor fix in
cr_cn()example that didn't work (#80) - Fixed parsing of
affiliationdata insideauthorobject in Crossref search API returned data (#84) - Fixed parsing of funder
awardslot in Crossref search API returned data (#90)
DEPRECATED
crosscite()deprecated, will be removed in a future version of this package (#78)cr_fundref()now has a deprecated message, and will be removed in the next version (#74)
rcrossref 0.3.4
NEW FEATURES
- Added new function
crosscite()to work with the Citeproc service (http://crosscite.org/citeproc/) (#60)
BUG FIXES
- Fixed problems related to
httrv1(#65) - Import all non-base R functions (#64)
- The agency route was down used by the
cr_agency()function, back up and fixed now (#63)
rcrossref 0.3.0
NEW FEATURES
- New function
extract_pdf()to extract text from pdfs - New function
cr_ft_links()to get links for full text content of an article (#10) - New function
cr_ft_text()to get links for full text content of an article. In addition,cr_ft_pdf(),cr_ft_plain(), andcr_ft_xml()are convenience functions that will get the format pdf, plain text, or xml, respectively. You can of course specify format in thecr_ft_text()function with thetypeparameter (#10) (#42)
MINOR IMPROVEMENTS
- Filled out more tests (#45)
BUG FIXES
- No longer assign queried doi to the
data.frameincr_works(), which caused failure if a non-Crossref DOI included (#52) pmid2doi()anddoi2pmid()functions removed temporarily as the web service is down temporarily, but will be online again soon from Crossref (#48)
rcrossref 0.2.1
MINOR IMPROVEMENTS
- Fixes for man file examples. (#35)
cr_citation()is deprecated (stil useable, but will be removed in a future version of the package). usecr_cn()instead. (#34)
rcrossref 0.2.0
NEW FEATURES
- released to CRAN