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rcrossref.Rmd
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rcrossref.Rmd
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---
title: rcrossref introduction
author: Scott Chamberlain
date: "2021-08-19"
output: rmarkdown::html_vignette
vignette: >
%\VignetteIndexEntry{rcrossref introduction}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{UTF-8}
---
## Installation
Install stable version from CRAN
```r
install.packages("rcrossref")
```
Or development version from GitHub
```r
remotes::install_github("ropensci/rcrossref")
```
```r
library("rcrossref")
```
## Citation search
CrossRef's DOI Content Negotiation service, where you can citations back in various formats, including `apa`
```r
cr_cn(dois = "10.1371/journal.pone.0112608", format = "text", style = "apa")
#> [1] "Wang, Q., & Taylor, J. E. (2014). Quantifying Human Mobility Perturbation and Resilience in Hurricane Sandy. PLoS ONE, 9(11), e112608. doi:10.1371/journal.pone.0112608"
```
There are a lot more styles. We include a dataset as a character vector within the package, accessible via the `get_styles()` function, e.g.,
```r
get_styles()[1:5]
#> [1] "academy-of-management-review"
#> [2] "accident-analysis-and-prevention"
#> [3] "aci-materials-journal"
#> [4] "acm-sig-proceedings-long-author-list"
#> [5] "acm-sig-proceedings"
```
`bibtex`
```r
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`
```r
cr_cn(dois = "10.6084/m9.figshare.97218", format = "bibentry")
#> $doi
#> [1] "10.6084/M9.FIGSHARE.97218"
#>
#> $url
#> [1] "https://figshare.com/articles/thesis/Regime_shifts_in_ecology_and_evolution_(PhD_Dissertation)/97218"
#>
#> $author
#> [1] "Boettiger, Carl"
#>
#> $keywords
#> [1] "Evolutionary Biology, FOS: Biological sciences, FOS: Biological sciences, Ecology"
#>
#> $title
#> [1] "Regime shifts in ecology and evolution (PhD Dissertation)"
#>
#> $publisher
#> [1] "figshare"
#>
#> $year
#> [1] "2012"
#>
#> $copyright
#> [1] "Creative Commons Attribution 4.0 International"
#>
#> $key
#> [1] "https://doi.org/10.6084/m9.figshare.97218"
#>
#> $entry
#> [1] "article"
```
## Citation count
Citation count, using OpenURL
```r
cr_citation_count(doi="10.1371/journal.pone.0042793")
#> doi count
#> 1 10.1371/journal.pone.0042793 43
```
## Search Crossref metadata API
The following functions all use the CrossRef API.
### Look up funder information
```r
cr_funders(query="NSF")
#> $meta
#> total_results search_terms start_index items_per_page
#> 1 39 NSF 0 20
#>
#> $data
#> # A tibble: 20 × 6
#> id location name alt.names uri tokens
#> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 100000001 United States National Sc… "USA NSF, NSF,… http:/… national, s…
#> 2 100015388 United States Kansas NSF … "KNE, NSF EPSC… http:/… kansas, nsf…
#> 3 100016323 United States Arkansas NS… "Arkansas EPSC… http:/… arkansas, n…
#> 4 100003187 United States National Sl… "NSF" http:/… national, s…
#> 5 501100000930 Australia National St… "NSF" http:/… national, s…
#> 6 501100004190 Norway Norsk Sykep… "NSF, Norwegia… http:/… norsk, syke…
#> 7 501100020414 United Kingdom Neuroscienc… "The Neuroscie… http:/… neuroscienc…
#> 8 100000154 United States Division of… "IOS, NSF Divi… http:/… division, o…
#> 9 100017338 China Key Program… "" http:/… key, progra…
#> 10 100000084 United States Directorate… "NSF Directora… http:/… directorate…
#> 11 100016620 United States Nick Simons… "NSF, The Nick… http:/… nick, simon…
#> 12 100006445 United States Center for … "CHM, NSF, Uni… http:/… center, for…
#> 13 100017325 United States Engineering… "ERC, The NSF … http:/… engineering…
#> 14 100008367 Denmark Statens Nat… "Danish Nation… http:/… statens, na…
#> 15 100000179 United States Office of t… "NSF Office of… http:/… office, of,…
#> 16 501100019492 China National Na… "NSFC-General … http:/… national, n…
#> 17 501100011002 China National Na… "NSFC-Yunnan J… http:/… national, n…
#> 18 501100008982 Sri Lanka National Sc… "National Scie… http:/… national, s…
#> 19 501100001809 China National Na… "NNSF of China… http:/… national, n…
#> 20 501100014220 China National Na… "NSFC-Henan Jo… http:/… national, n…
#>
#> $facets
#> NULL
```
### Check the DOI minting agency
```r
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, books, etc.)
```r
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 6556799 NA 0 1
#>
#> $data
#> # A tibble: 1 × 26
#> container.title created deposited published.online doi indexed issn issue
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 Belügyi Szemle 2021-04… 2021-04-26 2021-04-26 10.3… 2021-0… 2677… 4
#> # … with 18 more variables: issued <chr>, member <chr>, page <chr>,
#> # prefix <chr>, publisher <chr>, score <chr>, source <chr>,
#> # reference.count <chr>, references.count <chr>,
#> # is.referenced.by.count <chr>, title <chr>, type <chr>, url <chr>,
#> # volume <chr>, abstract <chr>, short.container.title <chr>, author <list>,
#> # link <list>
#>
#> $facets
#> NULL
```
### Search journals
```r
cr_journals(issn=c('1803-2427','2326-4225'))
#> $data
#> # A tibble: 2 × 53
#> title publisher issn last_status_che… deposits_abstra… deposits_orcids…
#> <chr> <chr> <chr> <date> <lgl> <lgl>
#> 1 Journal… De Gruyter… 1803-… 2021-08-18 TRUE TRUE
#> 2 Journal… American S… 2326-… 2021-08-18 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>, …
#>
#> $facets
#> NULL
```
### Search license information
```r
cr_licenses(query = 'elsevier')
#> $meta
#> total_results search_terms start_index items_per_page
#> 1 52 NA NA NA
#>
#> $data
#> # A tibble: 20 × 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 3
#> 3 http://creativecommons.org/licenses/by-nc-nd/3.0/ 11
#> 4 http://creativecommons.org/licenses/by-nc-nd/4.0/ 21
#> 5 http://creativecommons.org/licenses/by-nc/4.0/ 6
#> 6 http://creativecommons.org/licenses/by-sa/4.0 1
#> 7 http://creativecommons.org/licenses/by/2.0 2
#> 8 http://creativecommons.org/licenses/by/3.0 2
#> 9 http://creativecommons.org/licenses/by/3.0/ 2
#> 10 http://creativecommons.org/licenses/by/3.0/igo/ 1
#> 11 http://creativecommons.org/licenses/by/4.0 11
#> 12 http://creativecommons.org/licenses/by/4.0/ 22
#> 13 http://doi.wiley.com/10.1002/tdm_license_1 136
#> 14 http://doi.wiley.com/10.1002/tdm_license_1.1 2255
#> 15 http://iopscience.iop.org/info/page/text-and-data-mining 2
#> 16 http://iopscience.iop.org/page/copyright 2
#> 17 http://journals.iucr.org/services/copyrightpolicy.html 11
#> 18 http://journals.iucr.org/services/copyrightpolicy.html#TDM 11
#> 19 http://journals.sagepub.com/page/policies/text-and-data-mining-license 365
#> 20 http://onlinelibrary.wiley.com/termsAndConditions 63
```
### Search based on DOI prefixes
```r
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 Science and Business Media LLC
#> 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
```r
cr_members(query='ecology', limit = 5)
#> $meta
#> total_results search_terms start_index items_per_page
#> 1 24 ecology 0 5
#>
#> $data
#> # A tibble: 5 × 56
#> id primary_name location last_status_che… current.dois backfile.dois
#> <int> <chr> <chr> <date> <chr> <chr>
#> 1 4302 Immediate Scie… Toronto, ON… 2021-08-18 0 6
#> 2 6933 Knowledge Ecol… Washington,… 2021-08-18 0 1
#> 3 1950 Journal of Vec… United Stat… 2021-08-18 0 0
#> 4 2899 Association fo… Eugene, OR,… 2021-08-18 0 0
#> 5 7745 Institute of A… Makhachkala… 2021-08-18 172 678
#> # … with 50 more variables: total.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>, …
#>
#> $facets
#> NULL
```
### Get N random DOIs
`cr_r()` uses the function `cr_works()` internally.
```r
cr_r()
#> [1] "10.1111/biot.1990.4.issue-2"
#> [2] "10.7717/peerj.5714/table-5"
#> [3] "10.1061/(asce)0733-947x(2008)134:1(34)"
#> [4] "10.1016/j.clml.2015.04.108"
#> [5] "10.1371/journal.pntd.0009063.s016"
#> [6] "10.31616/asj.2020.0425"
#> [7] "10.15446/revfacmed.v65n3.61313"
#> [8] "10.1586/ecp.09.36"
#> [9] "10.1007/978-3-8348-9174-7_1"
#> [10] "10.1080/09511920601160171"
```
You can pass in the number of DOIs you want back (default is 10)
```r
cr_r(2)
#> [1] "10.5194/gmd-2021-94-supplement" "10.1108/prt.2009.12938bad.009"
```
## Get full text
Publishers can optionally provide links in the metadata they provide to Crossref for full text of the work, but that data is often missing. Find out more about it at https://support.crossref.org/hc/en-us/articles/215750183-Crossref-Text-and-Data-Mining-Services
Get some DOIs for articles that provide full text, and that have `CC-BY 3.0` licenses (i.e., more likely to actually be open)
```r
out <-
cr_works(filter = list(has_full_text = TRUE,
license_url = "http://creativecommons.org/licenses/by/3.0/"))
(dois <- out$data$doi)
#> [1] "10.1155/jamsa/2006/42542" "10.1016/s0370-2693(02)01651-9"
#> [3] "10.1016/s0370-2693(02)01624-6" "10.1155/ijmms/2006/89545"
#> [5] "10.1016/s0370-2693(01)01058-9" "10.1016/s0370-2693(01)01257-6"
#> [7] "10.1016/s0370-2693(01)01287-4" "10.1016/s0370-2693(01)01385-5"
#> [9] "10.1002/cfg.80" "10.1002/cfg.118"
#> [11] "10.1002/cfg.166" "10.1002/cfg.59"
#> [13] "10.1002/cfg.108" "10.1088/1742-6596/1147/1/012044"
#> [15] "10.1088/1742-6596/1147/1/012077" "10.1088/1742-6596/578/1/012006"
#> [17] "10.1088/1755-1315/222/1/012020" "10.1002/ecs2.2575"
#> [19] "10.1088/1755-1315/214/1/012004" "10.1088/1755-1315/214/1/012021"
```
From the output of `cr_works` we can get full text links if we know where to look:
```r
do.call("rbind", out$data$link)
#> # A tibble: 55 × 4
#> URL content.type content.version intended.applica…
#> <chr> <chr> <chr> <chr>
#> 1 http://downloads.hindawi.com… application/… vor text-mining
#> 2 http://downloads.hindawi.com… unspecified vor similarity-check…
#> 3 https://api.elsevier.com/con… text/xml vor text-mining
#> 4 https://api.elsevier.com/con… text/plain vor text-mining
#> 5 https://api.elsevier.com/con… text/xml vor text-mining
#> 6 https://api.elsevier.com/con… text/plain vor text-mining
#> 7 http://downloads.hindawi.com… application/… vor text-mining
#> 8 http://downloads.hindawi.com… unspecified vor similarity-check…
#> 9 https://api.elsevier.com/con… text/xml vor text-mining
#> 10 https://api.elsevier.com/con… 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
```r
if (!requireNamespace("crminer")) {
install.packages("crminer")
}
```
```r
library(crminer)
#> Error in library(crminer): there is no package called 'crminer'
(links <- crm_links("10.1155/2014/128505"))
#> Error in crm_links("10.1155/2014/128505"): could not find function "crm_links"
```
Then use those URLs to get full text
```r
crm_pdf(links)
#> <document>/Users/sckott/Library/Caches/R/crminer/128505.pdf
#> Pages: 1
#> No. characters: 1565
#> Created: 2014-09-15
```
See also fulltext (https://github.com/ropensci/fulltext) for getting scholarly text
for text mining.