Help for package rorcid

Title:

Interface to the 'Orcid.org' API

Description:

Client for the 'Orcid.org' API (https://orcid.org/). Functions included for searching for people, searching by 'DOI', and searching by 'Orcid' 'ID'.

Version:

0.7.0

License:

MIT + file LICENSE

URL:

https://github.com/ropensci/rorcid (devel), https://docs.ropensci.org/rorcid/ (docs)

BugReports:

https://github.com/ropensci/rorcid/issues

LazyLoad:

yes

LazyData:

true

Encoding:

UTF-8

Depends:

R (≥ 3.5.0)

Imports:

crul (≥ 0.7.4), httr, fauxpas (≥ 0.2.0), jsonlite (≥ 1.6), xml2 (≥ 1.2.0), tibble (≥ 2.1.3), data.table

Suggests:

testthat, knitr, rcrossref, handlr, httpuv, vcr

RoxygenNote:

7.1.1

X-schema.org-applicationCategory:

Literature

X-schema.org-keywords:

identifiers, literature, publications, citations, scholarly, people

X-schema.org-isPartOf:

https://ropensci.org

NeedsCompilation:

Packaged:

2021-01-20 19:44:41 UTC; sckott

Author:

Scott Chamberlain

[aut, cre], rOpenSci [fnd] (https://ropensci.org/)

Maintainer:

Scott Chamberlain <myrmecocystus@gmail.com>

Repository:

CRAN

Date/Publication:

2021-01-20 20:00:02 UTC

A programmatic R interface the Orcid.org API

Description

A R interface to the Orcid public API. rorcid is not a product developed or distributed by ORCID.

ORCID website: https://orcid.org/

Orcid API docs: http://members.orcid.org/api

Some key rorcid function:

as.orcid() - coerce various inputs to ORCID class
browse() - browse to a profile in your default browser
check_dois() - check that strings are likely to be DOIs
identifiers() - grab identifiers out of various objects
orcid() and orcid_search() - Search for ORCID id's
orcid_doi() - Search by DOI
orcid_id() - Search by ORCID id, and get either bio, profile, or works
works() - Parse out works from various objects

API routes not implemented

Not quite sure what these do so haven't messed with them.

⁠/{orcid}/notification-permission/{id}⁠
⁠/client/{client_id}⁠
⁠/group-id-record⁠
⁠/group-id-record/{putCode}⁠

Rate Limits

Definitions:

Request a second - Number of request that can be made a second. Value: 8 per second (24 with API v2rc+) - Haven't been able to find up to date values for API v3 (so assume they are the same I guess)
Burst - Number of request we will allow to be queued before rejecting. The request in the queue are slowed down at the request a second rate. Value: 40 (same with API v2rc+) - Haven't been able to find up to date values for API v3 (so assume they are the same I guess)

If you exceed the burst, you'll get a 503 responses. Developers should do their best to avoid approaching those limits.

Author(s)

Scott Chamberlain myrmecocystus@gmail.com

Convert an ORCID or something like an ORCID object

Description

Convert an ORCID or something like an ORCID object

Usage

as.orcid(x, ...)

Arguments

x

An ORCID id, passed to print

...

Further args passed on to orcid_id()

Value

an S3 object of class or_cid, which pretty prints for brevity

Examples

## Not run: 
as.orcid(x="0000-0002-1642-628X")
out <- orcid("text:English", rows = 20)
as.orcid(out$`orcid-identifier.path`[1])

# Passon further args to orcid_id()
as.orcid("0000-0002-1642-628X", verbose = TRUE)

# Browse to a profile
# browse(as.orcid("0000-0002-1642-628X"))

# many ORCIDs as a character vector
ids <- c("0000-0002-1642-628X", "0000-0002-9341-7985")
as.orcid(ids)

# many in a list via orcid_id()
(x <- lapply(ids, orcid_id))
as.orcid(x)

## End(Not run)

Navigate to an ORCID profile in your default browser

Description

Navigate to an ORCID profile in your default browser

Usage

browse(orcid)

Arguments

orcid

An or_cid class object

Examples

## Not run: 
browse(as.orcid("0000-0002-1642-628X"))

## End(Not run)

Verify DOI's are likely good

Description

Verify DOI's are likely good

Usage

check_dois(x)

Arguments

x

One or more DOIs

Value

A list of length two, one slot for good DOIs, one for bad

Examples

## Not run: 
check_dois("10.1087/20120404")

dois=c("10.1371/journal.pone.0025995","10.1371/journal.pone.0053712",
       "10.1371/journal.pone.0054608","10.1371/journal.pone.0055937")
check_dois(dois)

dois=c("10.1016/j.medpal.2008.12.005","10.1080/00933104.2000.10505926",
       "10.1037/a0024480", "10.1002/anie.196603172","2344","asdf","232",
       "asdf","23dd")
check_dois(dois)

## End(Not run)

Lookup table for search fields

Description

Lookup table for search fields

Get identifiers

Description

This function aims to pluck out just identifiers into a vector for easy use downstream (e.g., use DOIs to fetch article metadata). You can still manually fetch additional data from outputs of functions in this package.

Usage

identifiers(x, type = "doi", ...)

## S3 method for class 'works'
identifiers(x, type = "doi", ...)

## S3 method for class 'list'
identifiers(x, type = "doi", ...)

## S3 method for class 'orcid_id'
identifiers(x, type = "doi", ...)

## S3 method for class 'orcid'
identifiers(x, type = "doi", ...)

## S3 method for class 'orcid_doi'
identifiers(x, type = "doi", ...)

Arguments

x

An object of class works, orcid, orcid_id, orcid_doi, or a list that contains any number of the previous objects.

type

(character) One of doi (default), pmid, pmc, eid, other_id, orcid, scopus, researcherid. The orcid's here are for works, not individuals. This parameter is ignored for classes orcid and orcid_doi both of which would go down a rabbit hole of getting works for all ORCIDs which could take a while.

...

Ignored.

Value

(character) vector of identifiers, or NULL if none found

References

list of identifiers https://pub.qa.orcid.org/v2.0/identifiers?locale=en

Examples

## Not run: 
# Result of call to works()
x <- works(orcid_id("0000-0001-8607-8025"))
# doi by default
identifiers(x)
# orcids
identifiers(x, "orcid")
# pmid
identifiers(x, "pmid")
# pmc 
identifiers(x, "pmc") 
# other_id
identifiers(x, "other_id")

# Result of call to orcid_id()
x <- orcid_id(orcid = "0000-0002-9341-7985")
identifiers(x, "doi")
identifiers(x, "eid")

# Result of call to orcid()
x <- orcid(query="carl+boettiger")
identifiers(x)

# Result of call to orcid_doi()
x <- orcid_doi(dois="10.1087/20120404", fuzzy=TRUE)
identifiers(x)

## End(Not run)

Lookup vector for journal titles by ISSN

Description

named vector of journal titles. the values are journal titles and the names are ISSN's.

Details

length: 57,968

data collected on 2018-06-13 from Crossref

Search for ORCID ID's.

Description

Search for ORCID ID's.

Usage

orcid(
  query = NULL,
  start = NULL,
  rows = NULL,
  defType = NULL,
  q.alt = NULL,
  qf = NULL,
  mm = NULL,
  qs = NULL,
  pf = NULL,
  ps = NULL,
  pf2 = NULL,
  ps2 = NULL,
  pf3 = NULL,
  ps3 = NULL,
  tie = NULL,
  bq = NULL,
  bf = NULL,
  boost = NULL,
  uf = NULL,
  lowercaseOperators = NULL,
  fuzzy = FALSE,
  recursive = FALSE,
  ...
)

Arguments

query

Search terms. You can do quite complicated queries using the SOLR syntax. See examples below. For all possible fields to query, do data(fields)

start

Result number to start on. Keep in mind that pages start at 0. Default: 0

rows

Numer of results to return. Default: 10. Max: 200

defType

Query syntax. One of edismax or X. See Details for more.

q.alt

If specified, this query will be used (and parsed by default using standard query parsing syntax) when the main query string is not specified or blank. This comes in handy when you need something like a match-all-docs query (don't forget &rows=0 for that one!) in order to get collection-wise faceting counts.

qf

(Query Fields) List of fields and the "boosts" to associate with each of them when building DisjunctionMaxQueries from the user's query

mm

(Minimum 'Should' Match).

qs

(Query Phrase Slop) Amount of slop on phrase queries explicitly included in the user's query string (in qf fields; affects matching).

pf

(Phrase Fields) Once the list of matching documents has been identified using the "fq" and "qf" params, the "pf" param can be used to "boost" the score of documents in cases where all of the terms in the "q" param appear in close proximity

ps

(Phrase Slop) Default amount of slop on phrase queries built with "pf", "pf2" and/or "pf3" fields (affects boosting).

pf2

(Phrase bigram fields) As with 'pf' but chops the input into bi-grams, e.g. "the brown fox jumped" is queried as "the brown" "brown fox" "fox jumped"

ps2

(Phrase bigram slop) As with 'ps' but sets default slop factor for 'pf2'. If not specified, 'ps' will be used.

pf3

(Phrase trigram fields) As with 'pf' but chops the input into tri-grams, e.g. "the brown fox jumped" is queried as "the brown fox" "brown fox jumped"

ps3

(Phrase trigram slop) As with 'ps' but sets default slop factor for 'pf3'. If not specified, 'ps' will be used.

tie

(Tie breaker) Float value to use as tiebreaker in DisjunctionMaxQueries (should be something much less than 1)

bq

(Boost Query) A raw query string (in the SolrQuerySyntax) that will be included with the user's query to influence the score. See references

bf

(Boost Function, additive) Functions (with optional boosts) that will be included in the user's query to influence the score. Any function supported natively by Solr can be used, along with a boost value, e.g.: recip(rord(myfield),1,2,3)^1.5

boost

(Boost Function, multiplicative) As for 'bf' but multiplies the boost into the score

uf

(User Fields) Specifies which schema fields the end user shall be allowed to query for explicitly. This parameter supports wildcards.

lowercaseOperators

This param controls whether to try to interpret lowercase words as boolean operators such as "and", "not" and "or". Set &lowercaseOperators=true to allow this. Default is "false".

fuzzy

Use fuzzy matching on input DOIs. Defaults to FALSE. If FALSE, we stick "digital-object-ids" before the DOI so that the search sent to ORCID is for that exact DOI. If TRUE, we use some regex to find the DOI.

recursive

DEFUNCT

...

Curl options passed on to crul::HttpClient()

Details

All query syntaxes available in SOLR 3.6 ( https://lucene.apache.org/solr/guide/8_7/the-standard-query-parser.html) are supported, including Lucene with Solr extensions (default), DisMax, and Extended Dismax.

You can use any of the following within the query statement: given-names, family-name, credit-name, other-names, email, grant-number, patent-number, keyword, worktitle, digital-objectids, current-institution, affiliation-name, current-primary-institution, text, past-institution, peer-review-type, peer-review-role, peer-review-group-id, biography, external-id-type-and-value

For more complicated queries the ORCID API supports using ExtendedDisMax. See the documentation on the web here: https://lucene.apache.org/solr/guide/8_7/the-extended-dismax-query-parser.html

Note that when constructing queries, you don't need to use syntax like +, etc., crul, the http client we use internally, will do that for you. For example, instead of writing johnson+cardiology, just write ⁠johnson cardiology⁠, and instead of writing johnson+AND+cardiology, write ⁠johnson AND cardiology⁠. Though, you still need to use AND, OR, etc. to join term/queries together.

Value

a data.frame (tibble). You can access number of results found like attr(result, "found"). Note that with ORCID API v2 and greater, results here are only the identifiers. To get other metadata/data you can take the identifiers and use other functions in this package.

References

https://members.orcid.org/api/tutorial/search-orcid-registry https://lucene.apache.org/solr/guide/8_7/the-extended-dismax-query-parser.html

Examples

## Not run: 
# Get a list of names and Orcid IDs matching a name query
orcid(query="carl+boettiger")
orcid(query="given-names:carl AND family-name:boettiger")

# by email
orcid(query="email:cboettig@berkeley.edu")

# You can string together many search terms
orcid(query="johnson cardiology houston")

# peer review group id
orcid("peer-review-group-id:1996-3068")

# And use boolean operators
orcid("johnson AND(caltech OR 'California Institute of Technology')")

# And you can use start and rows arguments to do pagination
orcid("johnson cardiology houston", start = 2, rows = 3)

# Use search terms, here family name
orcid("family-name:Sanchez", start = 4, rows = 6)

# Use search terms, here...
orcid(query="Raymond", start=0, rows=10, defType="edismax")

# Search using keywords
orcid(query="keyword:ecology")

# Search by DOI
orcid(query="10.1087/20120404")

# Note the difference between the first wrt the second and third
## See also orcid_doi() function for searching by DOIs
orcid("10.1087/20120404")
orcid('"10.1087/20120404"')
## doi
orcid('digital-object-ids:"10.1087/20120404"')
## doi prefix
orcid('digital-object-ids:"10.1087/*"')

# search by work titles
orcid('work-titles:Modern developments in holography and its materials')
orcid('pmc:PMC3901677')

## Using more complicated SOLR queries

# Use the qf parameter to "boost" query fields so they are ranked higher
# 	See how it is different than the second query without using "qf"
orcid(defType = "edismax", query = "Raymond",
   qf = "given-names^1.0 family-name^2.0", start = 0, rows = 10)
orcid(query = "Raymond", start = 0, rows = 10)

# Use other SOLR parameters as well, here mm. Using the "mm" param, 1 and
# 2 word queries require that all of the optional clauses match, but for
# queries with three or more clauses one missing clause is allowed...
# See for more: http://bit.ly/1uyMLDQ
orcid(defType = "edismax",
      query="keyword:ecology OR evolution OR conservation",
      mm = 2, rows = 20)

## End(Not run)

Get activities for a person

Description

Get activities for a person

Usage

orcid_activities(orcid, ...)

Arguments

orcid

(character) Orcid identifier(s), of the form XXXX-XXXX-XXXX-XXXX. required.

...

Curl options passed on to crul::HttpClient()

Details

This function is vectorized, so you can pass in many ORCID's, and there's an element returned for each ORCID you put in.

Value

A list of results for each Orcid ID passed in, with each element named by the Orcid ID

Examples

## Not run: 
res <- orcid_activities(orcid = "0000-0002-9341-7985")
res$`0000-0002-9341-7985`
names(res$`0000-0002-9341-7985`)
res$`0000-0002-9341-7985`$`last-modified`
res$`0000-0002-9341-7985`$`educations`
res$`0000-0002-9341-7985`$`fundings`
res$`0000-0002-9341-7985`$`peer-reviews`
res$`0000-0002-9341-7985`$`works`

## End(Not run)

Get address information for a person

Description

Get address information for a person

Usage

orcid_address(orcid, put_code = NULL, format = "application/json", ...)

Arguments

orcid

(character) Orcid identifier(s), of the form XXXX-XXXX-XXXX-XXXX. required.

put_code

(character/integer) one or more put codes. up to 50. optional

format

(character) Name of the content-type format. One of "application/vnd.orcid+xml; qs=5", "application/orcid+xml; qs=3", "application/xml", "application/vnd.orcid+json; qs=4", "application/orcid+json; qs=2", "application/json" "application/vnd.citationstyles.csl+json". optional

...

Curl options passed on to crul::HttpClient()

Details

This function is vectorized, so you can pass in many ORCID's, and there's an element returned for each ORCID you put in.

Value

A list of results for each Orcid ID passed in, with each element named by the Orcid ID

Examples

## Not run: 
# all addresses
res <- orcid_address(orcid = "0000-0002-1642-628X")
res$`0000-0002-1642-628X`
names(res$`0000-0002-1642-628X`)
res$`0000-0002-1642-628X`$`address`

# individual address
orcid_address(orcid = "0000-0002-1642-628X", 288064)

# format
orcid_address(orcid = "0000-0002-1642-628X", 288064, "application/xml")

## End(Not run)

ORCID authorization

Description

ORCID authorization

Usage

orcid_auth(
  scope = "/authenticate",
  reauth = FALSE,
  redirect_uri = getOption("rorcid.redirect_uri"),
  client_id = NULL,
  client_secret = NULL
)

Arguments

scope

(character) one or more scopes. default: "/authenticate". see "ORCID OAuth Scopes" section below for other scope options

reauth

(logical) Force re-authorization? default: FALSE

redirect_uri

(character) a redirect URI. optional. set by passing to this parameter or using the R option rorcid.redirect_uri

client_id

(character) a client id. optional

client_secret

(character) a client secret. optional

Details

There are three ways to authorise with rorcid:

Interactively login with OAuth. This doesn't require any input on your part. We use a client id and client secret key to ping ORCID.org; at which point you log in with your username/password; then we get back a token (same as the above option). We don't know your username or password, only the token that we get back. We cache that token locally in a hidden file in whatever working directory you're in. If you delete that file, or run the code from a new working directory, then we re-authorize.
Use a client_id and client_secret to do 2-legged OAuth. ORCID docs at https://members.orcid.org/api/oauth/2legged-oauth and https://members.orcid.org/api/post-oauthtoken-reading-public-data This requires you to register a "client application". See https://orcid.org/content/register-client-application-2 for instructions
Use a token as a result of either of the two above approaches. The token is a alphanumeric UUID, e.g. ⁠dc0a6b6b-b4d4-4276-bc89-78c1e9ede56e⁠. You can get this token by running orcid_auth(), then storing that key (the uuid alone, not the "Bearer " part) either as en environment variable in your .Renviron file in your home directory (with the name ORCID_TOKEN), or as an R option in your .Rprofile file (with the name orcid_token). See Startup for more information. Either an environment variable or R option work. If we don't find either we do the next option.

We recommend the 3rd option if possible, specifically, storing the token as an environment variable permanently.

If authentication fails, you can still use rorcid. ORCID does not require authentication at this point, but may in the future - this prepares you for when that happens :)

Value

a character string with the access token prefixed with "Bearer "

ORCID OAuth Scopes

https://info.orcid.org/faq/what-is-an-oauth-scope-and-which-scopes-does-orcid-support/

Computing environments without browsers

One pitfall is when you are using rorcid on a server, and you're ssh'ed in, so that there's no way to open a browser to do the OAuth browser flow. Similarly for any other situation in which a browser can not be opened. In this case, run orcid_auth() on another machine in which you do have the ability to open a browser, then collect the info that's ouptput from orcid_auth() and store it as an environment variable (see above).

Note

This function is used within rorcid to get/do authentication.

Examples

## Not run: 
x <- orcid_auth()
orcid_auth(reauth = TRUE)
# orcid_auth(scope = "/read-public", reauth = TRUE)

# supply client_id AND client_secret to avoid 3 legged, interactive OAuth
# orcid_auth(client_id = "---", client_secret = "---")

## End(Not run)

Get biography data for a person

Description

Get biography data for a person

Usage

orcid_bio(orcid, format = "application/json", ...)

Arguments

orcid

(character) Orcid identifier(s), of the form XXXX-XXXX-XXXX-XXXX. required.

format

...

Curl options passed on to crul::HttpClient()

Details

This function is vectorized, so you can pass in many ORCID's, and there's an element returned for each ORCID you put in.

Value

A list of results for each Orcid ID passed in, with each element named by the Orcid ID

Examples

## Not run: 
res <- orcid_bio(orcid = "0000-0002-1642-628X")
res$`0000-0002-1642-628X`
res$`0000-0002-1642-628X`$`created-date`
res$`0000-0002-1642-628X`$`last-modified-date`
res$`0000-0002-1642-628X`$`content`
res$`0000-0002-1642-628X`$`visibility`
res$`0000-0002-1642-628X`$path

## End(Not run)

Get citations

Description

Get citations

Usage

orcid_citations(
  orcid,
  put_code = NULL,
  cr_format = "bibtex",
  cr_style = "apa",
  cr_locale = "en-US",
  ...
)

Arguments

orcid

(character) Orcid identifier(s) of the form XXXX-XXXX-XXXX-XXXX. required.

put_code

(character/integer) one or more put codes. up to 50. optional

cr_format

Used in Crossref queries only. 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. passed to rcrossref::cr_cn. The special "citeproc2bibtex" value asks for citeproc-json from Crossref, then converts it into bibtex format using handlr::HandlrClient

cr_style

Used in Crossref queries only. A CSL style (for text format only). See 'get_styles()' for options. Default: apa. passed to rcrossref::cr_cn

cr_locale

Used in Crossref queries only. Language locale. See Sys.getlocale, passed to rcrossref::cr_cn

...

Curl options passed on to crul::HttpClient

Details

This function is vectorized, so you can pass in many ORCID's, and there's an element returned for each ORCID you put in.

This function is focused on getting citations only. You can get all citations for an ORCID, or for certain works using a PUT code, or for many PUT codes.

We attempt to get citations via Crossref using rcrossref whenever possible as they are the most flexible and don't have as many mistakes in the text. If there is no DOI, we fetch the citation from ORCID.

Right now we get JSON citations back. We'd like to support bibtex format. DOI.org supports this but not ORCID.

Value

A list of results for each Orcid ID passed in, with each element named by the Orcid ID

data.frame, with the columns:

put: ORCID PUT code, identifying the work identifier in ORCID's records
id: the external identifier
id_type: the type of external identifier
format: the citation format retrieved
citation: the citation as JSON

Examples

## Not run: 
(res <- orcid_citations(orcid = "0000-0002-9341-7985"))
(res2 <- orcid_citations(orcid = "0000-0002-1642-628X"))
(res2 <- orcid_citations(orcid = c("0000-0002-9341-7985", "0000-0002-1642-628X")))

# get individual works
## a single put code
(a <- orcid_citations(orcid = "0000-0002-9341-7985", put_code = 5011717))
## many put codes
(b <- orcid_citations(orcid = "0000-0002-9341-7985",
   put_code = c(5011717, 15536016)))

# request other formats, Crossref only
orcid_citations(orcid = "0000-0002-9341-7985", cr_format = "turtle")

# parse citation data if you wish
# for parsing bibtex can use bibtex package or others
(res <- orcid_citations(orcid = "0000-0002-9341-7985"))
lapply(res[res$format == "csl-json", "citation"][[1]], jsonlite::fromJSON)

# lots of citations
orcid_citations(orcid = "0000-0001-8642-6325")

# example with no external identifier, returns NA's
orcid_citations(orcid = "0000-0001-8642-6325", 26222265)

## End(Not run)

Get distinction for a person

Description

Get distinction for a person

Usage

orcid_distinctions(
  orcid,
  put_code = NULL,
  format = "application/json",
  summary = FALSE,
  ...
)

Arguments

orcid

(character) Orcid identifier(s), of the form XXXX-XXXX-XXXX-XXXX. required.

put_code

(character/integer) one or more put codes. up to 50. optional

format

summary

(logical) get education summary for a put code. Default: FALSE

...

Curl options passed on to crul::HttpClient()

Details

This function is vectorized, so you can pass in many ORCID's, and there's an element returned for each ORCID you put in.

Value

A list of results for each Orcid ID passed in, with each element named by the Orcid ID

Examples

## Not run: 
res <- orcid_distinctions(orcid = "0000-0002-1642-628X")
res$`0000-0002-1642-628X`
res$`0000-0002-1642-628X`$`created-date`
res$`0000-0002-1642-628X`$`affiliation-group`
res$`0000-0002-1642-628X`$path

## End(Not run)

Search for ORCID ID's using DOIs

Description

Search for ORCID ID's using DOIs

Usage

orcid_doi(dois = NULL, start = NULL, rows = NULL, fuzzy = FALSE, ...)

Arguments

dois

(character) Digital object identifier (DOI), a vector fo DOIs.

start

(integer) Result number to start on. Keep in mind that pages start at 0.

rows

(integer) Numer of results to return.

fuzzy

(logical) Use fuzzy matching on input DOIs. Defaults to FALSE. If FALSE, we stick "digital-object-ids" before the DOI so that the search sent to ORCID is for that exact DOI. If TRUE, we use some regex to find the DOI.

...

Curl options passed on to crul::HttpClient()

Examples

## Not run: 
orcid_doi(dois="10.1087/20120404", fuzzy=TRUE)

# fuzzy is FALSE by default
orcid_doi(dois="10.1087/20120404", fuzzy=FALSE)

# This DOI is not a real one, but a partial DOI, then we can fuzzy search
# get more than defualt 10 records (or rows)
orcid_doi(dois="10.1087/2", fuzzy=TRUE, rows=20) 

# If you don't input proper DOIs, the function will get mad
dois <- c("10.1371/journal.pone.0025995","10.1371/journal.pone.0053712",
       "10.1371/journal.pone.0054608","10.1371/journal.pone.0055937")
orcid_doi(dois=dois)

# dois <- c("10.1016/j.medpal.2008.12.005","10.1080/00933104.2000.10505926",
#          "10.1037/a0024480", "10.1002/anie.196603172","2344","asdf","232",
#          "asdf","23dd")
# orcid_doi(dois=dois)

orcid_doi(dois="10.1087/20120404", fuzzy=FALSE) 
orcid_doi(dois="10.1371/journal.pone.0025995", fuzzy=FALSE)

## End(Not run)

Get education information for a person

Description

Get education information for a person

Usage

orcid_educations(
  orcid,
  put_code = NULL,
  format = "application/json",
  summary = FALSE,
  ...
)

Arguments

orcid

(character) Orcid identifier(s), of the form XXXX-XXXX-XXXX-XXXX. required.

put_code

(character/integer) one or more put codes. up to 50. optional

format

summary

(logical) get education summary for a put code. Default: FALSE

...

Curl options passed on to crul::HttpClient()

Details

This function is vectorized, so you can pass in many ORCID's, and there's an element returned for each ORCID you put in.

Value

A list of results for each Orcid ID passed in, with each element named by the Orcid ID

Examples

## Not run: 
# all education data
res <- orcid_educations(orcid = "0000-0002-1642-628X")
res$`0000-0002-1642-628X`
names(res$`0000-0002-1642-628X`)
res$`0000-0002-1642-628X`$`education-summary`

# individual education records
orcid_educations(orcid = "0000-0002-1642-628X", 148494)

# education summary information
orcid_educations(orcid = "0000-0002-1642-628X", 148494, summary = TRUE)

## End(Not run)

Get education information for a person

Description

Get education information for a person

Usage

orcid_email(orcid, ...)

Arguments

orcid

(character) Orcid identifier(s), of the form XXXX-XXXX-XXXX-XXXX. required.

...

Curl options passed on to crul::HttpClient()

Details

This function is vectorized, so you can pass in many ORCID's, and there's an element returned for each ORCID you put in.

Value

A list of results for each Orcid ID passed in, with each element named by the Orcid ID

Examples

## Not run: 
res <- orcid_email(orcid = "0000-0002-1642-628X")
res$`0000-0002-1642-628X`
names(res$`0000-0002-1642-628X`)
res$`0000-0002-1642-628X`$`email`

## End(Not run)

Get employment information for a person

Description

Get employment information for a person

Usage

orcid_employments(
  orcid,
  put_code = NULL,
  format = "application/json",
  summary = FALSE,
  ...
)

Arguments

orcid

(character) Orcid identifier(s), of the form XXXX-XXXX-XXXX-XXXX. required.

put_code

(character/integer) one or more put codes. up to 50. optional

format

summary

(logical) get employment summary for a put code. Default: FALSE

...

Curl options passed on to crul::HttpClient()

Details

This function is vectorized, so you can pass in many ORCID's, and there's an element returned for each ORCID you put in.

Value

A list of results for each Orcid ID passed in, with each element named by the Orcid ID

Examples

## Not run: 
# all employment data
res <- orcid_employments(orcid = "0000-0002-1642-628X")
res$`0000-0002-1642-628X`
names(res$`0000-0002-1642-628X`)
res$`0000-0002-1642-628X`$`employment-summary`

# individual employment records
orcid_employments(orcid = "0000-0002-1642-628X", 1115445)
orcid_employments(orcid = "0000-0002-1642-628X", 148496)

# employment summary information
orcid_employments(orcid = "0000-0002-1642-628X", 1115445, summary = TRUE)

## End(Not run)

Get external identifiers for a person

Description

Get external identifiers for a person

Usage

orcid_external_identifiers(
  orcid,
  put_code = NULL,
  format = "application/json",
  ...
)

Arguments

orcid

(character) Orcid identifier(s), of the form XXXX-XXXX-XXXX-XXXX. required.

put_code

(character/integer) one or more put codes. up to 50. optional

format

...

Curl options passed on to crul::HttpClient()

Details

This function is vectorized, so you can pass in many ORCID's, and there's an element returned for each ORCID you put in.

Value

A list of results for each Orcid ID passed in, with each element named by the Orcid ID

Examples

## Not run: 
# all data
res <- orcid_external_identifiers(orcid = "0000-0002-1642-628X")
res$`0000-0002-1642-628X`
names(res$`0000-0002-1642-628X`)
res$`0000-0002-1642-628X`$`external-identifier`

# individual records
orcid_external_identifiers(orcid = "0000-0002-1642-628X", 141736)

## End(Not run)

Get funding information for a person

Description

Get funding information for a person

Usage

orcid_fundings(
  orcid,
  put_code = NULL,
  format = "application/json",
  summary = FALSE,
  ...
)

Arguments

orcid

(character) Orcid identifier(s), of the form XXXX-XXXX-XXXX-XXXX. required.

put_code

(character/integer) one or more put codes. up to 50. optional

format

summary

(logical) get funding summary for a put code. Default: FALSE

...

Curl options passed on to crul::HttpClient()

Details

This function is vectorized, so you can pass in many ORCID's, and there's an element returned for each ORCID you put in.

Value

A list of results for each Orcid ID passed in, with each element named by the Orcid ID

Examples

## Not run: 
# all funding data
res <- orcid_fundings(orcid = "0000-0002-1642-628X")
res$`0000-0002-1642-628X`
names(res$`0000-0002-1642-628X`)
res$`0000-0002-1642-628X`$`group`

# individual funding records
orcid_fundings(orcid = "0000-0002-1642-628X", 385627)

# funding summary information
orcid_fundings(orcid = "0000-0002-1642-628X", 385627, summary = TRUE)

## End(Not run)

Get data for particular ORCID's

Description

Get data for particular ORCID's

Usage

orcid_id(orcid, ...)

Arguments

orcid

(character) A single Orcid identifier, of the form XXXX-XXXX-XXXX-XXXX

...

Curl options passed on to crul::HttpClient()

Value

A named list of results - from a call to orcid_person()

Examples

## Not run: 
res <- orcid_id(orcid = "0000-0002-9341-7985")
res$`0000-0002-9341-7985`
res$`0000-0002-9341-7985`$`name`
res$`0000-0002-9341-7985`$`other-names`
res$`0000-0002-9341-7985`$`biography`
res$`0000-0002-9341-7985`$`researcher-urls`
res$`0000-0002-9341-7985`$`emails`
res$`0000-0002-9341-7985`$`addresses`
res$`0000-0002-9341-7985`$`keywords`
res$`0000-0002-9341-7985`$`external-identifiers`
res$`0000-0002-9341-7985`$`emails`

ids <- c("0000-0003-1620-1408", "0000-0002-9341-7985")
res <- lapply(ids, orcid_id)
vapply(res, function(x) x[[1]]$name$`family-name`$value, "")

## End(Not run)

Get invited positions for a person

Description

Get invited positions for a person

Usage

orcid_invited_positions(
  orcid,
  put_code = NULL,
  format = "application/json",
  summary = FALSE,
  ...
)

Arguments

orcid

(character) Orcid identifier(s), of the form XXXX-XXXX-XXXX-XXXX. required.

put_code

(character/integer) one or more put codes. up to 50. optional

format

summary

(logical) get education summary for a put code. Default: FALSE

...

Curl options passed on to crul::HttpClient()

Details

This function is vectorized, so you can pass in many ORCID's, and there's an element returned for each ORCID you put in.

Value

A list of results for each Orcid ID passed in, with each element named by the Orcid ID

Examples

## Not run: 
res <- orcid_invited_positions(orcid = "0000-0002-1642-628X")
res$`0000-0002-1642-628X`
res$`0000-0002-1642-628X`$`created-date`
res$`0000-0002-1642-628X`$`affiliation-group`
res$`0000-0002-1642-628X`$path

## End(Not run)

Get education information for a person

Description

Get education information for a person

Usage

orcid_keywords(orcid, put_code = NULL, format = "application/json", ...)

Arguments

orcid

(character) Orcid identifier(s), of the form XXXX-XXXX-XXXX-XXXX. required.

put_code

(character/integer) one or more put codes. up to 50. optional

format

...

Curl options passed on to crul::HttpClient()

Details

This function is vectorized, so you can pass in many ORCID's, and there's an element returned for each ORCID you put in.

Value

A list of results for each Orcid ID passed in, with each element named by the Orcid ID

Examples

## Not run: 
# all data
res <- orcid_keywords(orcid = "0000-0002-1642-628X")
res$`0000-0002-1642-628X`
names(res$`0000-0002-1642-628X`)
res$`0000-0002-1642-628X`$`keyword`

# individual ones
orcid_keywords("0000-0002-1642-628X", 31202)

## End(Not run)

Get memberships for a person

Description

Get memberships for a person

Usage

orcid_memberships(
  orcid,
  put_code = NULL,
  format = "application/json",
  summary = FALSE,
  ...
)

Arguments

orcid

(character) Orcid identifier(s), of the form XXXX-XXXX-XXXX-XXXX. required.

put_code

(character/integer) one or more put codes. up to 50. optional

format

summary

(logical) get education summary for a put code. Default: FALSE

...

Curl options passed on to crul::HttpClient()

Details

This function is vectorized, so you can pass in many ORCID's, and there's an element returned for each ORCID you put in.

Value

A list of results for each Orcid ID passed in, with each element named by the Orcid ID

Examples

## Not run: 
res <- orcid_memberships(orcid = "0000-0002-1642-628X")
res$`0000-0002-1642-628X`
res$`0000-0002-1642-628X`$`created-date`
res$`0000-0002-1642-628X`$`affiliation-group`
res$`0000-0002-1642-628X`$memberships

## End(Not run)

Get education information for a person

Description

Get education information for a person

Usage

orcid_other_names(orcid, put_code = NULL, format = "application/json", ...)

Arguments

orcid

(character) Orcid identifier(s), of the form XXXX-XXXX-XXXX-XXXX. required.

put_code

(character/integer) one or more put codes. up to 50. optional

format

...

Curl options passed on to crul::HttpClient()

Details

This function is vectorized, so you can pass in many ORCID's, and there's an element returned for each ORCID you put in.

Value

A list of results for each Orcid ID passed in, with each element named by the Orcid ID

Examples

## Not run: 
# all data
res <- orcid_other_names(orcid = "0000-0001-7893-4389")
res$`0000-0001-7893-4389`
names(res$`0000-0001-7893-4389`)
res$`0000-0001-7893-4389`$`other-name`

# individual ones
orcid_other_names("0000-0001-7893-4389", 239534)

# formats
orcid_other_names("0000-0001-7893-4389", format = "application/xml")

## End(Not run)

Get peer review information for a person

Description

Get peer review information for a person

Usage

orcid_peer_reviews(
  orcid,
  put_code = NULL,
  format = "application/json",
  summary = FALSE,
  ...
)

Arguments

orcid

(character) Orcid identifier(s), of the form XXXX-XXXX-XXXX-XXXX. required.

put_code

(character/integer) one or more put codes. up to 50. optional

format

summary

(logical) get peer review summary for a put code. Default: FALSE

...

Curl options passed on to crul::HttpClient()

Details

This function is vectorized, so you can pass in many ORCID's, and there's an element returned for each ORCID you put in.

Value

A list of results for each Orcid ID passed in, with each element named by the Orcid ID

Examples

## Not run: 
# all peer review data
res <- orcid_peer_reviews(orcid = "0000-0001-7678-8656")
res$`0000-0001-7678-8656`
names(res$`0000-0001-7678-8656`)
res$`0000-0001-7678-8656`$`group`

# get individual works
orcid_peer_reviews("0000-0003-1444-9135", 75565)

# summary
orcid_peer_reviews("0000-0003-1444-9135", 75565, summary = TRUE)

# get Journal titles via ISSN's provided in results, using the 
# provided issn_title dataset
x <- orcid_peer_reviews("0000-0001-7678-8656", put_code = "220419")
issn <- strsplit(x[[1]]$`review-group-id`, ":")[[1]][[2]]
issn_title[[issn]]

## End(Not run)

Get personal data for a person

Description

Get personal data for a person

Usage

orcid_person(orcid, details = FALSE, ...)

Arguments

orcid

(character) Orcid identifier(s), of the form XXXX-XXXX-XXXX-XXXX. required.

details

(logical). also get details. Default: FALSE

...

Curl options passed on to crul::HttpClient()

Details

This function is vectorized, so you can pass in many ORCID's, and there's an element returned for each ORCID you put in.

Value

A list of results for each Orcid ID passed in, with each element named by the Orcid ID

Examples

## Not run: 
res <- orcid_person(orcid = "0000-0002-9341-7985")
res$`0000-0002-9341-7985`
names(res$`0000-0002-9341-7985`)
res$`0000-0002-9341-7985`$`last-modified`
res$`0000-0002-9341-7985`$`keywords`
res$`0000-0002-9341-7985`$`biography`

## End(Not run)

Check if ORCID API is up and running

Description

Check if ORCID API is up and running

Usage

orcid_ping(...)

Arguments

...

Curl options passed on to crul::HttpClient()

Value

a text string

Examples

## Not run: 
orcid_ping()

## End(Not run)

Get qualifications for a person

Description

Get qualifications for a person

Usage

orcid_qualifications(
  orcid,
  put_code = NULL,
  format = "application/json",
  summary = FALSE,
  ...
)

Arguments

orcid

(character) Orcid identifier(s), of the form XXXX-XXXX-XXXX-XXXX. required.

put_code

(character/integer) one or more put codes. up to 50. optional

format

summary

(logical) get peer review summary for a put code. Default: FALSE

...

Curl options passed on to crul::HttpClient()

Details

This function is vectorized, so you can pass in many ORCID's, and there's an element returned for each ORCID you put in.

Value

A list of results for each Orcid ID passed in, with each element named by the Orcid ID

Get research resources for a person

Description

Get research resources for a person

Usage

orcid_research_resources(
  orcid,
  put_code = NULL,
  format = "application/json",
  summary = FALSE,
  ...
)

Arguments

orcid

(character) Orcid identifier(s), of the form XXXX-XXXX-XXXX-XXXX. required.

put_code

(character/integer) one or more put codes. up to 50. optional

format

summary

(logical) get education summary for a put code. Default: FALSE

...

Curl options passed on to crul::HttpClient()

Details

This function is vectorized, so you can pass in many ORCID's, and there's an element returned for each ORCID you put in.

Value

A list of results for each Orcid ID passed in, with each element named by the Orcid ID

Examples

## Not run: 
res <- orcid_research_resources(orcid = "0000-0002-1642-628X")
res$`0000-0002-1642-628X`
res$`0000-0002-1642-628X`$`last-modified-date`
res$`0000-0002-1642-628X`$`group`
res$`0000-0002-1642-628X`$path

## End(Not run)

Get researcher urls for a person

Description

Get researcher urls for a person

Usage

orcid_researcher_urls(orcid, put_code = NULL, format = "application/json", ...)

Arguments

orcid

(character) Orcid identifier(s), of the form XXXX-XXXX-XXXX-XXXX. required.

put_code

(character/integer) one or more put codes. up to 50. optional

format

...

Curl options passed on to crul::HttpClient()

Details

This function is vectorized, so you can pass in many ORCID's, and there's an element returned for each ORCID you put in.

Value

A list of results for each Orcid ID passed in, with each element named by the Orcid ID

Examples

## Not run: 
# all data
res <- orcid_researcher_urls(orcid = "0000-0003-1444-9135")
res$`0000-0003-1444-9135`
names(res$`0000-0003-1444-9135`)
res$`0000-0003-1444-9135`$`researcher-url`

# individual ones
orcid_researcher_urls("0000-0003-1444-9135", 304093)
orcid_researcher_urls("0000-0003-1444-9135", c(332241, 304093))

# formats
orcid_researcher_urls("0000-0003-1444-9135", 304093, 
  format = "application/xml")

## End(Not run)

Orcid search - more user friendly than `orcid()`

Description

Orcid search - more user friendly than orcid()

Usage

orcid_search(
  given_name = NULL,
  family_name = NULL,
  past_inst = NULL,
  current_inst = NULL,
  affiliation_org = NULL,
  ringgold_org_id = NULL,
  grid_org_id = NULL,
  credit_name = NULL,
  other_name = NULL,
  email = NULL,
  digital_object_ids = NULL,
  work_title = NULL,
  grant_number = NULL,
  keywords = NULL,
  text = NULL,
  rows = 10,
  start = NULL,
  ...
)

Arguments

given_name

(character) given name

family_name

(character) family name

past_inst

(character) past institution

current_inst

(character) current institution

affiliation_org

(character) affiliation organization name

ringgold_org_id

(character) ringgold organization id

grid_org_id

(character) grid organization id

credit_name

(character) credit name

other_name

(character) other name

email

(character) email

digital_object_ids

(character) digital object ids

work_title

(character) work title

grant_number

(character) grant number

keywords

(character) keywords to search. character vector, one or more keywords

text

(character) text to search

rows

(integer) number of records to return

start

(integer) record number to start at

...

curl options passed on to crul::HttpClient

Details

The goal of this function is to make a human friendly way to search ORCID.

Thus, internally we map the parameters given to this function to the actual parameters that ORCID wants that are not so human friendly.

We don't include all possible fields you could search against here - for that use orcid()

Importantly, we return the first 10 results, following the default setting for the rows parameter in orcid(). You can set the rows parameter in this function to a max of 200. The maximum is an upper bound set by the ORCID API. You can get the number of results found programatically by fetching the found attribute on the ouput of this function, e.g., attr(x, "found").

Value

a data.frame with three columns:

first: given name
last: family name
orcid: ORCID identifier

If no results are found, an empty (0 rows) data.frame is returned

How parameters are combined

We combine multiple parameters with AND, such that e.g., given_name="Jane" and family_name="Doe" gets passed to ORCID as ⁠given-names:Jane AND family-name:Doe⁠

Note

current_prim_inst and patent_number parameters have been removed as ORCID has removed them

References

https://members.orcid.org/api/tutorial/search-orcid-registry

Examples

## Not run: 
orcid_search(given_name = "carl", family_name = "boettiger")
orcid_search(given_name = "carl")
orcid_search(given_name = "carl", rows = 2)
orcid_search(keywords = c("birds", "turtles"))
orcid_search(affiliation_org = '("Boston University" OR BU)')
orcid_search(ringgold_org_id = '1438')
orcid_search(grid_org_id = 'grid.5509.9')
orcid_search(email = '*@orcid.org')
orcid_search(given_name = "carl", verbose = TRUE)
# get number of results found
x <- orcid_search(ringgold_org_id = '1438')
attr(x, "found")

## End(Not run)

Get services

Description

Get services

Usage

orcid_services(
  orcid,
  put_code = NULL,
  format = "application/json",
  summary = FALSE,
  ...
)

Arguments

orcid

(character) Orcid identifier(s), of the form XXXX-XXXX-XXXX-XXXX. required.

put_code

(character/integer) one or more put codes. up to 50. optional

format

summary

(logical) get education summary for a put code. Default: FALSE

...

Curl options passed on to crul::HttpClient()

Details

This function is vectorized, so you can pass in many ORCID's, and there's an element returned for each ORCID you put in.

Value

A list of results for each Orcid ID passed in, with each element named by the Orcid ID

Examples

## Not run: 
res <- orcid_services(orcid = "0000-0002-1642-628X")
res$`0000-0002-1642-628X`
res$`0000-0002-1642-628X`$`last-modified-date`
res$`0000-0002-1642-628X`$`affiliation-group`
res$`0000-0002-1642-628X`$path

## End(Not run)

Get works for a person

Description

Get works for a person

Usage

orcid_works(orcid, put_code = NULL, format = "application/json", ...)

Arguments

orcid

(character) Orcid identifier(s), of the form XXXX-XXXX-XXXX-XXXX. required.

put_code

(character/integer) one or more put codes. up to 50. optional

format

...

Curl options passed on to crul::HttpClient()

Details

This function is vectorized, so you can pass in many ORCID's, and there's an element returned for each ORCID you put in.

Value

A list of results for each Orcid ID passed in, with each element named by the Orcid ID

Examples

## Not run: 
# get all works
res <- orcid_works(orcid = "0000-0002-9341-7985")
res$`0000-0002-9341-7985`
res$`0000-0002-9341-7985`$works
res$`0000-0002-9341-7985`$works$type
str(res$`0000-0002-9341-7985`)

# get individual works
a <- orcid_works(orcid = "0000-0002-9341-7985", put_code = 5011717)
a$`0000-0002-9341-7985`
a$`0000-0002-9341-7985`$works
b <- orcid_works(orcid = "0000-0002-9341-7985", 
   put_code = c(5011717, 15536016))
b$`0000-0002-9341-7985`

# change formats
orcid_works("0000-0002-9341-7985", 5011717, "application/json")
orcid_works("0000-0002-9341-7985", 5011717, "application/xml")
orcid_works("0000-0002-9341-7985", 5011717, 
  "application/vnd.orcid+xml; qs=5")
orcid_works("0000-0002-9341-7985", 5011717, 
  "application/vnd.citationstyles.csl+json")

# get citations
id <- "0000-0001-7678-8656"
x <- orcid_works(id)
wks <- orcid_works(id, put_code = x[[1]]$works$`put-code`)
wks[[1]]$works$`work.citation.citation-value`

## or send many put codes at once, will be split into chunks of 50 each
id <- "0000-0001-6758-5101"
z <- orcid_works(id)
pcodes <- z[[1]]$works$`put-code`
length(pcodes)
res <- orcid_works(orcid = id, put_code = pcodes)
head(res$`0000-0001-6758-5101`$works)

## End(Not run)

Defunct functions in rorcid

Description

summary.or_cid(): Function is gone. Deemed not really that useful, and hard to maintain given other changes in the package.

This function is defunct.

Description

This function is defunct.

Usage

## S3 method for class 'or_cid'
summary(object, ...)

Get works data

Description

Get works data

Usage

works(x)

Arguments

x

Anything that can be coerced via as.orcid(), see as.orcid() for help

Details

This function gets works using the function orcid_works and packages up the data in a data.frame for easier processing

Value

A tibble (data.frame)

Examples

## Not run: 
out <- works(orcid_id("0000-0002-9341-7985"))
out
out$type
out$path

works( orcid_id("0000-0002-1642-628X") )
works( orcid_id("0000-0003-1444-9135") )
works( orcid_id("0000-0003-1419-2405") )

out <- orcid(query="keyword:ecology")
works(orcid_id(out$`orcid-identifier.path`[7]))
works(orcid_id(out$`orcid-identifier.path`[8]))
works(orcid_id(out$`orcid-identifier.path`[9]))
works(orcid_id(out$`orcid-identifier.path`[10]))

## End(Not run)

A programmatic R interface the Orcid.org API

Description

API routes not implemented

Rate Limits

Author(s)

See Also

Convert an ORCID or something like an ORCID object

Description

Usage

Arguments

Value

Examples

Navigate to an ORCID profile in your default browser

Description

Usage

Arguments

Examples

Verify DOI's are likely good

Description

Usage

Arguments

Value

Examples

Lookup table for search fields

Description

Get identifiers

Description

Usage

Arguments

Value

References

Examples

Lookup vector for journal titles by ISSN

Description

Details

Search for ORCID ID's.

Description

Usage

Arguments

Details

Value

References

See Also

Examples

Get activities for a person

Description

Usage

Arguments

Details

Value

Examples

Get address information for a person

Description

Usage

Arguments

Details

Value

Examples

ORCID authorization

Description

Usage

Arguments

Details

Value

ORCID OAuth Scopes

Computing environments without browsers

Note

Examples

Get biography data for a person

Description

Usage

Arguments

Details

Value

Examples

Get citations

Description

Usage

Arguments

Details