102

rorcid

Interface to the 'Orcid.org' API

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

Build Status Build status codecov.io rstudio mirror downloads cran version

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

Orcid API docs:

The package now works with the v2.1 ORCID API now. It's too complicated to allow users to work with different versions of the API, so it's hard-coded to v2.1.

  • orcid_educations
  • orcid_ping
  • orcid_bio
  • orcid_address
  • orcid_email
  • browse
  • orcid_employments
  • orcid_works
  • check_dois
  • orcid_researcher_urls
  • orcid_peer_reviews
  • orcid_external_identifiers
  • orcid_doi
  • orcid
  • orcid_activities
  • identifiers
  • orcid_auth
  • as.orcid
  • orcid_fundings
  • orcid_person
  • works
  • orcid_id
  • orcid_other_names
  • orcid_keywords

Installation

Stable version

install.packages("rorcid")

Development version

install.packages("devtools")
devtools::install_github("ropensci/rorcid")
library('rorcid')

as.orcid

There's a function as.orcid() in this package to help coerce an Orcid ID to an object that holds details for that Orcid ID, prints a nice summary, and you can browse easily to that profile. E.g.

as.orcid(x = "0000-0002-1642-628X")
#> <ORCID> 0000-0002-1642-628X
#>   Name: Boettiger, Carl
#>   URL (first): 
#>   Country: US
#>   Keywords: Ecology, Evolution, Regime Shifts, Stochastic Dynamics

Or you can pass in many IDs

as.orcid(c("0000-0003-1620-1408", "0000-0002-9341-7985"))
#> [[1]]
#> <ORCID> 0000-0003-1620-1408
#>   Name: Johnson, Thomas
#>   URL (first): 
#>   Country: US
#>   Keywords: 
#> 
#> [[2]]
#> <ORCID> 0000-0002-9341-7985
#>   Name: Binfield, Peter
#>   URL (first): 
#>   Country: US
#>   Keywords:

The browse() function lets you browser to a profile easily with a single function call

browse(as.orcid("0000-0002-1642-628X"))

profile

Get works

The works() function helps get works data from an orcid data object. The output of works() is a data.frame

(out <- works(orcid_id("0000-0002-0233-1757")))
#> # A tibble: 6 x 27
#>   `put-code` type    visibility path      `display-index` `created-date.v…
#> *      <int> <chr>   <chr>      <chr>     <chr>                      <dbl>
#> 1    5296064 JOURNA… PUBLIC     /0000-00… 0                  1362713629019
#> 2    5296065 JOURNA… PUBLIC     /0000-00… 0                  1362713629025
#> 3    5296066 JOURNA… PUBLIC     /0000-00… 0                  1362713629032
#> 4    9012984 JOURNA… PUBLIC     /0000-00… 0                  1369326854424
#> 5    9012985 JOURNA… PUBLIC     /0000-00… 0                  1369326854429
#> 6    9012986 JOURNA… PUBLIC     /0000-00… 0                  1369326854433
#> # ... with 21 more variables: `last-modified-date.value` <dbl>,
#> #   `source.source-client-id` <lgl>, `source.source-orcid.uri` <chr>,
#> #   `source.source-orcid.path` <chr>, `source.source-orcid.host` <chr>,
#> #   `source.source-name.value` <chr>, title.subtitle <lgl>,
#> #   `title.translated-title` <lgl>, title.title.value <chr>,
#> #   `external-ids.external-id` <list>,
#> #   `publication-date.media-type` <lgl>,
#> #   `publication-date.year.value` <chr>,
#> #   `publication-date.month.value` <chr>,
#> #   `publication-date.day.value` <chr>, `publication-date.day` <lgl>,
#> #   `external-ids` <lgl>, `publication-date` <lgl>,
#> #   `source.source-orcid` <lgl>, `source.source-client-id.uri` <chr>,
#> #   `source.source-client-id.path` <chr>,
#> #   `source.source-client-id.host` <chr>

Search Orcid

Get a list of names and Orcid IDs matching a name query

orcid(query = "carl boettiger")
#> # A tibble: 100 x 3
#>    `orcid-identifier.uri`                `orcid-identifi… `orcid-identifi…
#>  * <chr>                                 <chr>            <chr>           
#>  1 https://orcid.org/0000-0002-1642-628X 0000-0002-1642-… orcid.org       
#>  2 https://orcid.org/0000-0002-3554-5196 0000-0002-3554-… orcid.org       
#>  3 https://orcid.org/0000-0002-5951-4503 0000-0002-5951-… orcid.org       
#>  4 https://orcid.org/0000-0002-7462-1956 0000-0002-7462-… orcid.org       
#>  5 https://orcid.org/0000-0003-1021-5374 0000-0003-1021-… orcid.org       
#>  6 https://orcid.org/0000-0002-8885-5438 0000-0002-8885-… orcid.org       
#>  7 https://orcid.org/0000-0002-4791-6222 0000-0002-4791-… orcid.org       
#>  8 https://orcid.org/0000-0002-2171-9124 0000-0002-2171-… orcid.org       
#>  9 https://orcid.org/0000-0002-2683-5888 0000-0002-2683-… orcid.org       
#> 10 https://orcid.org/0000-0002-3141-3057 0000-0002-3141-… orcid.org       
#> # ... with 90 more rows

You can string together many search terms

orcid(query = "johnson cardiology houston")
#> # A tibble: 100 x 3
#>    `orcid-identifier.uri`                `orcid-identifi… `orcid-identifi…
#>  * <chr>                                 <chr>            <chr>           
#>  1 https://orcid.org/0000-0002-0897-2301 0000-0002-0897-… orcid.org       
#>  2 https://orcid.org/0000-0002-4968-6272 0000-0002-4968-… orcid.org       
#>  3 https://orcid.org/0000-0001-9667-1615 0000-0001-9667-… orcid.org       
#>  4 https://orcid.org/0000-0003-0945-6138 0000-0003-0945-… orcid.org       
#>  5 https://orcid.org/0000-0002-9503-6836 0000-0002-9503-… orcid.org       
#>  6 https://orcid.org/0000-0003-2447-553X 0000-0003-2447-… orcid.org       
#>  7 https://orcid.org/0000-0001-7724-5784 0000-0001-7724-… orcid.org       
#>  8 https://orcid.org/0000-0002-5164-6296 0000-0002-5164-… orcid.org       
#>  9 https://orcid.org/0000-0002-5078-9551 0000-0002-5078-… orcid.org       
#> 10 https://orcid.org/0000-0002-9701-0568 0000-0002-9701-… orcid.org       
#> # ... with 90 more rows

And use boolean operators

orcid("johnson AND(caltech OR 'California Institute of Technology')")
#> # A tibble: 100 x 3
#>    `orcid-identifier.uri`                `orcid-identifi… `orcid-identifi…
#>  * <chr>                                 <chr>            <chr>           
#>  1 https://orcid.org/0000-0002-0026-2516 0000-0002-0026-… orcid.org       
#>  2 https://orcid.org/0000-0001-6495-9892 0000-0001-6495-… orcid.org       
#>  3 https://orcid.org/0000-0001-5320-7003 0000-0001-5320-… orcid.org       
#>  4 https://orcid.org/0000-0003-0533-6833 0000-0003-0533-… orcid.org       
#>  5 https://orcid.org/0000-0003-0692-4178 0000-0003-0692-… orcid.org       
#>  6 https://orcid.org/0000-0001-9837-9773 0000-0001-9837-… orcid.org       
#>  7 https://orcid.org/0000-0002-1875-7007 0000-0002-1875-… orcid.org       
#>  8 https://orcid.org/0000-0002-4207-6746 0000-0002-4207-… orcid.org       
#>  9 https://orcid.org/0000-0002-7676-5347 0000-0002-7676-… orcid.org       
#> 10 https://orcid.org/0000-0001-9761-1059 0000-0001-9761-… orcid.org       
#> # ... with 90 more rows

And you can use start and rows arguments to do pagination

orcid("johnson cardiology houston", start = 2, rows = 3)
#> # A tibble: 3 x 3
#>   `orcid-identifier.uri`                `orcid-identifie… `orcid-identifi…
#> * <chr>                                 <chr>             <chr>           
#> 1 https://orcid.org/0000-0001-9667-1615 0000-0001-9667-1… orcid.org       
#> 2 https://orcid.org/0000-0003-0945-6138 0000-0003-0945-6… orcid.org       
#> 3 https://orcid.org/0000-0002-9503-6836 0000-0002-9503-6… orcid.org

Search by Orcid ID

out <- orcid_id(orcid = "0000-0002-9341-7985")
out$`0000-0002-9341-7985`$name
#> $`created-date`
#> $`created-date`$value
#> [1] 1.460762e+12
#> 
#> 
#> $`last-modified-date`
#> $`last-modified-date`$value
#> [1] 1.460762e+12
#> 
#> 
#> $`given-names`
#> $`given-names`$value
#> [1] "Peter"
#> 
#> 
#> $`family-name`
#> $`family-name`$value
#> [1] "Binfield"
#> 
#> 
#> $`credit-name`
#> NULL
#> 
#> $source
#> NULL
#> 
#> $visibility
#> [1] "PUBLIC"
#> 
#> $path
#> [1] "0000-0002-9341-7985"

Search by DOIs

There is a helper function check_dois() that uses a regex checker to see if your DOIs are likely good or likely bad:

All good DOIs

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)
#> $good
#> [1] "10.1371/journal.pone.0025995" "10.1371/journal.pone.0053712"
#> [3] "10.1371/journal.pone.0054608" "10.1371/journal.pone.0055937"
#> 
#> $bad
#> NULL

Some good, some bad

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)
#> $good
#> [1] "10.1016/j.medpal.2008.12.005"   "10.1080/00933104.2000.10505926"
#> [3] "10.1037/a0024480"               "10.1002/anie.196603172"        
#> 
#> $bad
#> [1] "2344" "asdf" "232"  "asdf" "23dd"

Basic search

orcid_doi(dois = "10.1087/20120404")
#> [[1]]
#> # A tibble: 6 x 3
#>   `orcid-identifier.uri`                `orcid-identifie… `orcid-identifi…
#> * <chr>                                 <chr>             <chr>           
#> 1 https://orcid.org/0000-0003-1603-8743 0000-0003-1603-8… orcid.org       
#> 2 https://orcid.org/0000-0002-2123-6317 0000-0002-2123-6… orcid.org       
#> 3 https://orcid.org/0000-0002-5993-8592 0000-0002-5993-8… orcid.org       
#> 4 https://orcid.org/0000-0003-3188-6273 0000-0003-3188-6… orcid.org       
#> 5 https://orcid.org/0000-0001-5109-3700 0000-0001-5109-3… orcid.org       
#> 6 https://orcid.org/0000-0003-1419-2405 0000-0003-1419-2… orcid.org       
#> 
#> attr(,"class")
#> [1] "orcid_doi"

This DOI is not a real one, but a partial DOI, then we can fuzzy search

orcid_doi(dois = "10.1087/2", fuzzy = TRUE, rows = 5)
#> [[1]]
#> # A tibble: 5 x 3
#>   `orcid-identifier.uri`                `orcid-identifie… `orcid-identifi…
#> * <chr>                                 <chr>             <chr>           
#> 1 https://orcid.org/0000-0001-6081-0708 0000-0001-6081-0… orcid.org       
#> 2 https://orcid.org/0000-0001-6971-1351 0000-0001-6971-1… orcid.org       
#> 3 https://orcid.org/0000-0002-5528-4704 0000-0002-5528-4… orcid.org       
#> 4 https://orcid.org/0000-0002-6298-6771 0000-0002-6298-6… orcid.org       
#> 5 https://orcid.org/0000-0002-5360-2529 0000-0002-5360-2… orcid.org       
#> 
#> attr(,"class")
#> [1] "orcid_doi"

Meta

  • Please report any issues or bugs
  • License: MIT
  • Get citation information for rorcid in R doing citation(package = 'rorcid')
  • Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.

ropensci_footer

News

rorcid 0.4.0

Most changes in this version are to update the package to work with the new ORCID API (v2.1). (#37) (#40)

NEW FEATURES

  • rorcid now support OAuth authentication. We still recommend to not use OAuth, but to get a token and store that as an environment variable. See ?orcid_auth for help (#26)
  • To work with the new ORCID API, we've introduced new functions: orcid_activities(), orcid_address(), orcid_auth(), orcid_bio(), orcid_educations(), orcid_email(), orcid_employments(), orcid_external_identifiers(), orcid_fundings(), orcid_keywords(), orcid_other_names(), orcid_peer_reviews(), orcid_person(), orcid_ping(), orcid_researcher_urls(), orcid_works()
  • we've introduced a new packcage import data.table for binding lists together into a data.frame

MINOR IMPROVEMENTS

  • Fixes to identifiers() for new API. Includes better failure behavior on classes it doesn't support (#34) (#39)
  • No changes here other than adding some examples, but ORCID API now allows ot search on some works metadata (e.g., titles) (#33)
  • Examples added for searching on specific fields (#36)
  • orcid_id() changed internally; now wraps the new function orcid_person() (#41)
  • using Markdown docs now (#35)
  • replaced httr with crul for HTTP requests. we have retained httr only to do OAuth (#32)
  • orcid_id() loses its profile parameter due to the ORCID API change. it does pass on parameters to orcid_person(), so see that man file
  • works() now returns a tibble/data.frame instead of a list of items
  • A much updated package level man file with lots of docs

rorcid 0.3.0

NEW FEATURES

  • Added a vignette (#20)
  • orcid_id() function gains output for employment and funding (#24) (#29)

MINOR IMPROVEMENTS

  • change all is() calls to inherits() (#30)
  • using tibble package now for compact data.frame outputs instead of internal code. an associated change in the output of both orcid() and orcid_doi() is that we now return a tibble (data.frame) instead of a data.frame as a slot in a list. we add how many results are returned from your search as an attribute on the data.frame. Access it like attr(out, "found") (#25)
  • base ORCID API URL changed from http to https scheme
  • genereal improvements to documentation throughout package

DEPRECATED AND DEFUNCT

  • summary.or_id() is now defunct. see ?rorcid-defunct

rorcid 0.2.2

NEW FEATURES

  • Require httr >= v1.1.0 (#23)

MINOR IMPROVEMENTS

  • Updated dplyr tidy data.frame internal code (#21)
  • Changes to internal use of httr::content() to parse to text, then read JSON manually using jsonlite & to always set encoding explicitly in the same calls (#22)

BUG FIXES

  • Fix to as.orcid() and presumably other function calls by requiring httr >= v1.1.0 because older versions cause a problem when parsing responses (#23) thanks @ericwatt

rorcid 0.2.0

NEW FEATURES

  • released to CRAN

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.
install.packages("rorcid")

0.7.0 by Scott Chamberlain, 3 months ago

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

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

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

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

Documentation:   PDF Manual  

Task views: Web Technologies and Services

MIT + file LICENSE license

Imports crul, httr, fauxpas, jsonlite, xml2, tibble, data.table

Suggests testthat, knitr, rcrossref, handlr, httpuv, vcr

Suggested by vitae.

See at CRAN

R links

R homepage

Download R

Mailing lists

R documentation

R manuals

R FAQs

The R Journal

CRAN links

CRAN homepage

CRAN repository policy

Submit a package

METACRAN stuff

About METACRAN

At github

Report a bug