rorcid

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

Orcid API docs:

Public API docs: http://members.orcid.org/api
Swagger docs: https://pub.orcid.org/v2.1/#/Public_API_v2.1

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.

Authentication

There are two ways to authenticate with rorcid:

Use a token as a result of a OAuth authentication process. 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, or as an R option in your .Rprofile file. See ?Startup for more information. Either an environment variable or R option work. If we don't find either we do the next option.
Interactively login with OAuth. 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.

We recommend the former option. That is, get a token and store it as an environment variable.

If both options above fail, we proceed without using authentication. ORCID does not require authentication at this point, but may in the future - this prepares you for when that happens :)

See https://members.orcid.org/api/orcid-scopes for more about ORCID OAuth Scopes.

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).

Package API

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

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): http://www.carlboettiger.info
#>   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"))

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 JOUR… PUBLIC     /000… 0                  1362713629019
#> 2    5296065 JOUR… PUBLIC     /000… 0                  1362713629025
#> 3    5296066 JOUR… PUBLIC     /000… 0                  1362713629032
#> 4    9012984 JOUR… PUBLIC     /000… 0                  1369326854424
#> 5    9012985 JOUR… PUBLIC     /000… 0                  1369326854429
#> 6    9012986 JOUR… PUBLIC     /000… 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-identifier.p… `orcid-identifier.h…
#>  * <chr>                         <chr>                <chr>               
#>  1 https://orcid.org/0000-0002-… 0000-0002-1642-628X  orcid.org           
#>  2 https://orcid.org/0000-0002-… 0000-0002-3554-5196  orcid.org           
#>  3 https://orcid.org/0000-0002-… 0000-0002-5951-4503  orcid.org           
#>  4 https://orcid.org/0000-0002-… 0000-0002-7462-1956  orcid.org           
#>  5 https://orcid.org/0000-0003-… 0000-0003-1021-5374  orcid.org           
#>  6 https://orcid.org/0000-0002-… 0000-0002-7790-5102  orcid.org           
#>  7 https://orcid.org/0000-0002-… 0000-0002-8885-5438  orcid.org           
#>  8 https://orcid.org/0000-0002-… 0000-0002-4791-6222  orcid.org           
#>  9 https://orcid.org/0000-0003-… 0000-0003-0471-9533  orcid.org           
#> 10 https://orcid.org/0000-0003-… 0000-0003-3675-4042  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-identifier.p… `orcid-identifier.h…
#>  * <chr>                         <chr>                <chr>               
#>  1 https://orcid.org/0000-0002-… 0000-0002-0897-2301  orcid.org           
#>  2 https://orcid.org/0000-0002-… 0000-0002-5281-4466  orcid.org           
#>  3 https://orcid.org/0000-0001-… 0000-0001-6172-5804  orcid.org           
#>  4 https://orcid.org/0000-0001-… 0000-0001-8188-0078  orcid.org           
#>  5 https://orcid.org/0000-0002-… 0000-0002-4968-6272  orcid.org           
#>  6 https://orcid.org/0000-0002-… 0000-0002-1918-5792  orcid.org           
#>  7 https://orcid.org/0000-0001-… 0000-0001-9667-1615  orcid.org           
#>  8 https://orcid.org/0000-0003-… 0000-0003-0945-6138  orcid.org           
#>  9 https://orcid.org/0000-0002-… 0000-0002-9503-6836  orcid.org           
#> 10 https://orcid.org/0000-0001-… 0000-0001-5156-0356  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-identifier.p… `orcid-identifier.h…
#>  * <chr>                         <chr>                <chr>               
#>  1 https://orcid.org/0000-0002-… 0000-0002-0026-2516  orcid.org           
#>  2 https://orcid.org/0000-0001-… 0000-0001-6495-9892  orcid.org           
#>  3 https://orcid.org/0000-0002-… 0000-0002-7042-5739  orcid.org           
#>  4 https://orcid.org/0000-0003-… 0000-0003-0533-6833  orcid.org           
#>  5 https://orcid.org/0000-0002-… 0000-0002-3909-2294  orcid.org           
#>  6 https://orcid.org/0000-0003-… 0000-0003-4021-2473  orcid.org           
#>  7 https://orcid.org/0000-0002-… 0000-0002-7705-5670  orcid.org           
#>  8 https://orcid.org/0000-0001-… 0000-0001-5320-7003  orcid.org           
#>  9 https://orcid.org/0000-0002-… 0000-0002-4207-6746  orcid.org           
#> 10 https://orcid.org/0000-0002-… 0000-0002-7676-5347  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-identifier.p… `orcid-identifier.h…
#> * <chr>                          <chr>                <chr>               
#> 1 https://orcid.org/0000-0001-6… 0000-0001-6172-5804  orcid.org           
#> 2 https://orcid.org/0000-0001-8… 0000-0001-8188-0078  orcid.org           
#> 3 https://orcid.org/0000-0002-4… 0000-0002-4968-6272  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: 8 x 3
#>   `orcid-identifier.uri`         `orcid-identifier.p… `orcid-identifier.h…
#> * <chr>                          <chr>                <chr>               
#> 1 https://orcid.org/0000-0001-5… 0000-0001-5727-2427  orcid.org           
#> 2 https://orcid.org/0000-0001-7… 0000-0001-7343-9784  orcid.org           
#> 3 https://orcid.org/0000-0003-1… 0000-0003-1603-8743  orcid.org           
#> 4 https://orcid.org/0000-0002-2… 0000-0002-2123-6317  orcid.org           
#> 5 https://orcid.org/0000-0003-3… 0000-0003-3188-6273  orcid.org           
#> 6 https://orcid.org/0000-0002-5… 0000-0002-5993-8592  orcid.org           
#> 7 https://orcid.org/0000-0001-5… 0000-0001-5109-3700  orcid.org           
#> 8 https://orcid.org/0000-0003-1… 0000-0003-1419-2405  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-identifier.p… `orcid-identifier.h…
#> * <chr>                          <chr>                <chr>               
#> 1 https://orcid.org/0000-0001-6… 0000-0001-6971-1351  orcid.org           
#> 2 https://orcid.org/0000-0001-5… 0000-0001-5919-8670  orcid.org           
#> 3 https://orcid.org/0000-0001-6… 0000-0001-6081-0708  orcid.org           
#> 4 https://orcid.org/0000-0001-6… 0000-0001-6555-0837  orcid.org           
#> 5 https://orcid.org/0000-0002-5… 0000-0002-5360-2529  orcid.org           
#> 
#> attr(,"class")
#> [1] "orcid_doi"

msaby/rorcid