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")

Citation count

Citation count, using OpenURL

cr_citation_count(doi = "10.1371/journal.pone.0042793")
#>                            doi count
#> 1 10.1371/journal.pone.0042793    25

Search 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     name          alt.names         uri       tokens         location
#>    <chr>  <chr>         <chr>             <chr>     <chr>          <chr>   
#>  1 50110… Norsk Sykepl… NSF, Norwegian N… http://d… norsk, sykepl… <NA>    
#>  2 10000… Center for H… CHM, NSF, Univer… http://d… center, for, … United …
#>  3 10000… National Sle… NSF               http://d… national, sle… United …
#>  4 50110… National Str… NSF               http://d… national, str… <NA>    
#>  5 10000… Statens Natu… Danish National … http://d… statens, natu… Denmark 
#>  6 10000… Office of th… NSF Office of th… http://d… office, of, t… United …
#>  7 50110… National Sci… National Science… http://d… national, sci… <NA>    
#>  8 10000… National Sci… NSF               http://d… national, sci… United …
#>  9 50110… National Nat… NSFC-Yunnan Join… http://d… national, nat… China   
#> 10 50110… National Nat… Natural Science … http://d… national, nat… China   
#> 
#> $facets
#> NULL

Check 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       2452441           NA           0              1
#> 
#> $data
#> # A tibble: 1 x 25
#>   container.title created deposited published.online doi   indexed issn 
#>   <chr>           <chr>   <chr>     <chr>            <chr> <chr>   <chr>
#> 1 The Cryosphere  2013-0… 2018-07-… 2013-02-11       10.5… 2019-0… 1994…
#> # … with 18 more variables: issue <chr>, issued <chr>, member <chr>,
#> #   page <chr>, prefix <chr>, publisher <chr>, reference.count <chr>,
#> #   score <chr>, source <chr>, title <chr>, type <chr>, url <chr>,
#> #   volume <chr>, abstract <chr>, author <list>, link <list>,
#> #   license <list>, reference <list>
#> 
#> $facets
#> NULL

Search 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… 2019-03-24       TRUE             FALSE           
#> 2 Jour… American… 2326… 2019-03-24       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
#> NULL

Search license information

cr_licenses(query = 'elsevier')
#> $meta
#>   total_results search_terms start_index items_per_page
#> 1            34     elsevier           0             20
#> 
#> $data
#> # A tibble: 34 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/2.0                        1
#>  7 http://creativecommons.org/licenses/by/3.0/                       1
#>  8 http://creativecommons.org/licenses/by/4.0                        3
#>  9 http://creativecommons.org/licenses/by/4.0/                       6
#> 10 http://doi.wiley.com/10.1002/tdm_license_1                      155
#> # … with 24 more rows

Search 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… 2019-04-16       1220       145         
#> 2  1950 Journal of … Suite 8… 2019-04-16       27         0           
#> 3  2080 The Japan S… 5-3 Yon… 2019-04-16       691        21          
#> 4  2151 Ecology and… 5-3 Yon… 2019-04-16       404        60          
#> 5  2169 Italian Soc… Diparti… 2019-04-16       1286       302         
#> # … 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
#> NULL

Get N random DOIs

cr_r() uses the function cr_works() internally.

cr_r()
#>  [1] "10.1097/00005110-199711000-00007"  
#>  [2] "10.4079/vol1iss1pp65-66"           
#>  [3] "10.4172/2161-038x.s5-003"          
#>  [4] "10.1111/j.1540-6261.1967.tb02994.x"
#>  [5] "10.1080/095740401750534484"        
#>  [6] "10.4236/jssm.2017.103026"          
#>  [7] "10.1159/000448755"                 
#>  [8] "10.1021/ja01175a045"               
#>  [9] "10.1149/05810.0087ecst"            
#> [10] "10.1016/0378-1135(90)90004-f"

You can pass in the number of DOIs you want back (default is 10)

cr_r(2)
#> [1] "10.1016/j.bbcan.2012.03.004"       
#> [2] "10.1111/j.1476-5381.1950.tb00568.x"

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] "10.1016/j.celrep.2013.01.013"     "10.1016/j.biortech.2013.01.084"  
#>  [3] "10.1016/j.epsl.2013.01.005"       "10.1016/j.neuropharm.2013.01.024"
#>  [5] "10.1016/j.ebcr.2012.12.001"       "10.1155/2013/121692"             
#>  [7] "10.1155/2013/158969"              "10.1155/2013/721606"             
#>  [9] "10.1155/2013/150397"              "10.1155/2013/178138"             
#> [11] "10.1155/2013/710579"              "10.1155/2013/528279"             
#> [13] "10.1155/2013/634670"              "10.1155/2013/729162"             
#> [15] "10.1155/2013/127497"              "10.1155/2013/635086"             
#> [17] "10.1155/2013/263285"              "10.1155/2013/248159"             
#> [19] "10.1155/2013/748687"              "10.1155/2013/673601"

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: 55 x 4
#>    URL                       content.type content.version intended.applica…
#>    <chr>                     <chr>        <chr>           <chr>            
#>  1 https://api.elsevier.com… text/xml     vor             text-mining      
#>  2 https://api.elsevier.com… text/plain   vor             text-mining      
#>  3 https://api.elsevier.com… text/xml     vor             text-mining      
#>  4 https://api.elsevier.com… text/plain   vor             text-mining      
#>  5 https://api.elsevier.com… text/xml     vor             text-mining      
#>  6 https://api.elsevier.com… text/plain   vor             text-mining      
#>  7 https://api.elsevier.com… text/xml     vor             text-mining      
#>  8 https://api.elsevier.com… text/plain   vor             text-mining      
#>  9 https://api.elsevier.com… text/xml     vor             text-mining      
#> 10 https://api.elsevier.com… text/plain   vor             text-mining      
#> # … with 45 more rows

From 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.pdf

Then 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: 2014-09-15

See also fulltext for getting scholarly text for text mining.

News

rcrossref 0.9.2

NEW FEATURES

cr_funders(), cr_journals(), cr_licenses(), cr_members(), cr_prefixes(), cr_types(), cr_works() gain ability to show a progress bar when using deep pagination when using works=TRUE (#186) (#188)

MINOR IMPROVEMENTS

fix a test fixture that had non-ascii characters (#187)
cr_works() returned a tibble in the $data slot in each case except for when a single DOI was passed to the doi parameter. now fixed (#184) thanks @martinjhnhadley

rcrossref 0.9.0

NEW FEATURES

big Crossref Addin update (#171) all work by @haozhu233
Async HTTP introduced for cr_works(), cr_works_(), and cr_citation_count(). See the new parameter async (logical) in those functions. For cr_citation_count(), it now accepts more than 1 DOI, and the output has changed from a numeric value to a data.frame (columns: doi and count). With async=TRUE for cr_works() you get a list of data.frame's; while for cr_works_() you get a list of JSON's (#121) (#160) (#182)

MINOR IMPROVEMENTS

package tests now using vcr for HTTP request/response caching (#178) (#179)
in works data, now returning published-print and published-online fields (#181)
add new filters for /works routes (when works = TRUE): isbn, reference_visibility, has_content_domain, and has_domain_restriction (#176) (#177)
add new return element in /works routes (when works = TRUE): $reference gives 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 an NA (#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 parse bibtex would 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 dois parameter (#162) thanks @ms609
Much improved error behavior for cr_* functions. We now give errors like 404 (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 and works set to TRUE, fixed now (#156)
cr_journals() was not correctly parsing data when no ISSN found and works set to TRUE, fixed now (#150)
cr_journals() was not correctly handling queries with multiple ISSN's and works set to FALSE, fixed now (#151)
fixed bug in cr_works(), and any other cr_* function that set works=TRUE. the license slot 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 /works route gain a select parameter to select certain fields to return (#146)

MINOR IMPROVEMENTS

Updated docs for additional options for the sort parameter (#142)
Updated docs for additional options for doing field queries (the flq parameter) (#143)
Filters: New filters added to the package, and some removed (e.g, publisher-name). You can see the filters with the functions filter_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: crminer https://github.com/ropensci/crminer . Functions that did text mining stuff now defunct, see ?rcrossref-defunct (#122)
All Crossref API requests now using https instead of http (#133)

MINOR IMPROVEMENTS

replace xml2::xml_find_one with xml2::xml_find_first (#128) thanks @njahn82
replaced httr with crul for HTTP requests (#132)
Now using markdown for documentation (#135)
Added more documentation to cr_journals and cr_works about what the returned data fields backfile_dois and current_dois really mean (#105) thanks @SteveViss

BUG FIXES

Fix to cr_prefixes to not fail when no results found (#130) thanks @globbestael
Fixed cr_works to allow queries like facet = license:* to be passed to facet parameter (was always allowed by Crossref, but we neglected to allow it - previously only allowed a boolean) (#129)
Fixed cr_funders and cr_journals to 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 query parameter which queries across all fields (#111)
Now using rappdirs for local storage and caching for cr_ft_text (#106)

MINOR IMPROVEMENTS

Added to man files where appropriate new 10K max value for the offset parameter (#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_search and cr_search_free are 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)
crosscite is now defunct. The functionality of this function can be achieved with cr_cn() (#82)
cr_fundref is now defunct. Crossref changed their name fundref to funders, so we've changed our function, see cr_funders() (#83)
parameter sample maximum value is now 100, was previously 1000. documentation updated. (#118)
New filters has-clinical-trial-number and has-abstract added to the package, see ?filters for help (#120)

rcrossref 0.5.8

NEW FEATURES

Added an RStudio Addin for searching for citations. See ?rcrossref for 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 in cr_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 where ISSN array 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() to dplyr::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: httr and curl (which httr depends on). Will potentially be useful to Crossref to know how many requests come from this R client (#100)

DEPRECATED

cr_search() and cr_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 in v0.6 of this package (#99)

MINOR IMPROVEMENTS

XML replaced with xml2 (#98)
httr::content() calls: all parse to text then parse content manually. in addition, encoding explicitly set to UTF-8 on httr::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 internal R6 class 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 equivalent cr_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() and filter_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() and filter_details() (#73)
cr_funders() alias added to cr_fundref() (#74)
Made note in docs that funders without IDs don't show up on the /funders route,s in cr_funders() (#79)
Made note in docs that sample parameter ignored unless works=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 .progress parameter use internally where it wasn't applicable.
sample parameter dropped from cr_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, author often 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 affiliation data inside author object in Crossref search API returned data (#84)
Fixed parsing of funder award slot 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 httr v1 (#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(), and cr_ft_xml() are convenience functions that will get the format pdf, plain text, or xml, respectively. You can of course specify format in the cr_ft_text() function with the type parameter (#10) (#42)

MINOR IMPROVEMENTS

Filled out more tests (#45)

BUG FIXES

No longer assign queried doi to the data.frame in cr_works(), which caused failure if a non-Crossref DOI included (#52)
pmid2doi() and doi2pmid() 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). use cr_cn() instead. (#34)

rcrossref 0.2.0

NEW FEATURES

released to CRAN

Reference manual

install.packages("rcrossref")

0.9.2 by Scott Chamberlain, 9 months ago

https://github.com/ropensci/rcrossref

Report a bug at https://github.com/ropensci/rcrossref/issues

Browse source code at https://github.com/cran/rcrossref

Authors: Scott Chamberlain [aut, cre] , Hao Zhu [aut] , Najko Jahn [aut] , Carl Boettiger [aut] , Karthik Ram [aut]

Documentation: PDF Manual

Task views: Web Technologies and Services

MIT + file LICENSE license

Imports methods, utils, jsonlite, crul, xml2, plyr, bibtex, dplyr, R6, shiny, miniUI, stringr, DT, stats

Suggests roxygen2, testthat, knitr, vcr

Imported by fulltext, pubchunks, suppdata.

Suggested by crminer, rcoreoa, ref.ICAR, roadoi, rorcid.

See at CRAN

rcrossref

Client for Various 'CrossRef' 'APIs'

R interface to various CrossRef APIs

Installation

Register for the Polite Pool

Citation search

Citation count

Search Crossref metadata API

Look up funder information

Check the DOI minting agency

Search works (i.e., articles)

Search journals

Search license information

Search based on DOI prefixes

Search CrossRef members

Get N random DOIs

Get full text

Meta

News

rcrossref 0.9.2

NEW FEATURES

MINOR IMPROVEMENTS

rcrossref 0.9.0

NEW FEATURES

MINOR IMPROVEMENTS

BUG FIXES

rcrossref 0.8.4

NEW FEATURES

MINOR IMPROVEMENTS

BUG FIXES

rcrossref 0.8.0

NEW FEATURES

MINOR IMPROVEMENTS

rcrossref 0.7.0

NEW FEATURES

MINOR IMPROVEMENTS

BUG FIXES

rcrossref 0.6.0

NEW FEATURES

MINOR IMPROVEMENTS

rcrossref 0.5.8

NEW FEATURES

BUG FIXES

rcrossref 0.5.4

MINOR IMPROVEMENTS

rcrossref 0.5.2

NEW FEATURES

DEPRECATED

MINOR IMPROVEMENTS

BUG FIXES

rcrossref 0.5.0

NEW FEATURES

MINOR IMPROVEMENTS

BUG FIXES

DEPRECATED

rcrossref 0.3.4

NEW FEATURES

BUG FIXES

rcrossref 0.3.0

NEW FEATURES

MINOR IMPROVEMENTS

BUG FIXES

rcrossref 0.2.1

MINOR IMPROVEMENTS

rcrossref 0.2.0

NEW FEATURES

Reference manual

R links

R homepage

Download R

Mailing lists

R documentation

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