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243 changes: 225 additions & 18 deletions vignettes/rcrossref.Rmd
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
---
title: rcrossref introduction
author: Scott Chamberlain
date: "2021-08-02"
date: "2021-08-19"
output: rmarkdown::html_vignette
vignette: >
%\VignetteIndexEntry{rcrossref introduction}
Expand Down Expand Up @@ -39,7 +39,7 @@ CrossRef's DOI Content Negotiation service, where you can citations back in vari

```r
cr_cn(dois = "10.1371/journal.pone.0112608", format = "text", style = "apa")
#> Error in cr_GET(endpoint = sprintf("works/%s/agency", x), args = list(), : res$response_headers$`content-type` == "application/json;charset=UTF-8" ist nicht TRUE
#> [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.,
Expand All @@ -59,15 +59,55 @@ get_styles()[1:5]

```r
cat(cr_cn(dois = "10.1126/science.169.3946.635", format = "bibtex"))
#> Error in cr_GET(endpoint = sprintf("works/%s/agency", x), args = list(), : res$response_headers$`content-type` == "application/json;charset=UTF-8" ist nicht TRUE
#> @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")
#> Error in cr_GET(endpoint = sprintf("works/%s/agency", x), args = list(), : res$response_headers$`content-type` == "application/json;charset=UTF-8" ist nicht TRUE
#> $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
Expand All @@ -90,55 +130,192 @@ The following functions all use the CrossRef API.

```r
cr_funders(query="NSF")
#> Error in cr_GET(path, args, todf = FALSE, ...): res$response_headers$`content-type` == "application/json;charset=UTF-8" ist nicht TRUE
#> $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')
#> Error in cr_GET(endpoint = sprintf("works/%s/agency", x), args = list(), : res$response_headers$`content-type` == "application/json;charset=UTF-8" ist nicht TRUE
#> $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)
#> Error in cr_GET(endpoint = path, args, todf = FALSE, ...): res$response_headers$`content-type` == "application/json;charset=UTF-8" ist nicht TRUE
#> $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'))
#> Error in cr_GET(endpoint = path, args, todf = FALSE, parse = TRUE, ...): res$response_headers$`content-type` == "application/json;charset=UTF-8" ist nicht TRUE
#> $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')
#> Error in cr_GET("licenses", args, todf = FALSE, on_error = stop, parse = parse, : res$response_headers$`content-type` == "application/json;charset=UTF-8" ist nicht TRUE
#> $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'))
#> Error in cr_GET(path, args, todf = FALSE, ...): res$response_headers$`content-type` == "application/json;charset=UTF-8" ist nicht TRUE
#> $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)
#> Error in cr_GET(endpoint = path, args, FALSE, parse = TRUE, ...): res$response_headers$`content-type` == "application/json;charset=UTF-8" ist nicht TRUE
#> $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
Expand All @@ -148,15 +325,24 @@ cr_members(query='ecology', limit = 5)

```r
cr_r()
#> Error in cr_GET(endpoint = path, args, todf = FALSE, ...): res$response_headers$`content-type` == "application/json;charset=UTF-8" ist nicht TRUE
#> [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)
#> Error in cr_GET(endpoint = path, args, todf = FALSE, ...): res$response_headers$`content-type` == "application/json;charset=UTF-8" ist nicht TRUE
#> [1] "10.5194/gmd-2021-94-supplement" "10.1108/prt.2009.12938bad.009"
```

## Get full text
Expand All @@ -170,17 +356,38 @@ Get some DOIs for articles that provide full text, and that have `CC-BY 3.0` lic
out <-
cr_works(filter = list(has_full_text = TRUE,
license_url = "http://creativecommons.org/licenses/by/3.0/"))
#> Error in cr_GET(endpoint = path, args, todf = FALSE, ...): res$response_headers$`content-type` == "application/json;charset=UTF-8" ist nicht TRUE
(dois <- out$data$doi)
#> Error in eval(expr, envir, enclos): Objekt 'out' nicht gefunden
#> [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)
#> Error in do.call("rbind", out$data$link): Objekt 'out' nicht gefunden
#> # 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
Expand All @@ -200,9 +407,9 @@ if (!requireNamespace("crminer")) {

```r
library(crminer)
#> Error in library(crminer): es gibt kein Paket namens '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"): konnte Funktion "crm_links" nicht finden
#> Error in crm_links("10.1155/2014/128505"): could not find function "crm_links"
```

Then use those URLs to get full text
Expand Down

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