Maëlle Salmon

Proper identification of individuals is crucial for acknowledging
andstudying their scientific work, be it journal articles or pieces
ofsoftware. In this tech note, one year after CRAN started
supportingORCIDs, we shall explain why and how to use unique author
identifiers inDESCRIPTION files.

## Why use ORCIDs on CRAN?

When analyzing the authorship of CRAN packages, one can look at
authors'names and email addresses. Names can be written with and without
quotes,email addresses change, which makes it all tricky as [noted by
DavidSmith when he looked for the most prolific
CRANauthors](https://blog.revolutionanalytics.com/2018/03/the-most-prolific-package-maintainers-on-cran.html)(notice
our very own Scott Chamberlain and Jeroen Ooms in thatscoreboard by the
way?). Besides, several people can have the same name!

So all in all, using an unique ID per author makes sense.
That'ssomething offered for the academic world and beyond
by[ORCID](https://www.crossref.org/community/orcid/), ORCID meaning
"OpenResearcher and Contributor ID". Anyone can set up an ORCID account
forfree and link it up to the rest of their online persona, as well as
totheir employment and works. When the authors of a scientific paper
givetheir ORCID ID to the publisher, [these can be included in the html
andPDF versions of
apaper](https://orcid.org/content/journal-article-display-guidelines).Note
that there's no, say, [Keybase verification
forORCIDs](https://github.com/keybase/proofs/issues/126), and often
theinput of an ORCID ID for a paper is declarative as well. Read more
aboutORCID [here](https://orcid.org/node/8).

About one year ago, CRAN added [support
forORCID](https://twitter.com/AchimZeileis/status/917319708713668608)
inDESCRIPTION files by [a minimally
invasivehack](https://twitter.com/AchimZeileis/status/917660536459939840).
Onecan add the ORCID ID of an author as a `comment` field in
`person()`,see e.g. [Carl Boettiger's ID in
`codemetar`DESCRIPTION](https://github.com/ropensci/codemetar/blob/387456e9d62fdb9be936a089d7173e8d21d783b8/DESCRIPTION#L10),and
one gets a nice little green bubble near their name on CRAN, seee.g.
[`codemetar`
CRANpage](https://cran.r-project.org/web/packages/codemetar/index.html).

![screenshot of](/img/blog-images/2018-10-08-orcid/codemetar-1.png)

The advantages of using ORCID IDs in DESCRIPTION are:

- **Unique identifiers for free!** Sure, there's no verification
  sosomeone could use your identity, but at least, it should
  helpassigning your own work to you.

- **Clickable name on CRAN pages, METACRAN pages and pkgdownwebsites!**
  E.g. when clicking on Carl's green bubble on `codemetar`CRAN page, one
  gets to [his ORCIDprofile](https://orcid.org/0000-0002-1642-628X)
  including a link tohis personal website. See also [`codemetar`
  METACRANpage](https://www.r-pkg.org/pkg/codemetar) and [`codemetar`
  pkgdownwebsite](https://docs.ropensci.org/codemetar/).

![screenshot of](/img/blog-images/2018-10-08-orcid/carl-1.png)

Even for non academics, making one's online persona more accessible
froma CRAN DESCRIPTION can't hurt.

## How to manipulate ORCIDs in DESCRIPTION?

So, how does one add add and interact with ORCID in DESCRIPTION?
Well,thankfully, the current dev version of the RStudio
[`desc`package](https://github.com/r-lib/desc) by
[GáborCsárdi](https://github.com/gaborcsardi) has some direct support
ofORCIDs! *Gábor too is well ranked in [the scoreboard
mentionedearlier](https://blog.revolutionanalytics.com/2018/03/the-most-prolific-package-maintainers-on-cran.html)!*

::: {.highlight}
``` {.chroma tabindex="0"}
remotes::install_github("r-lib/desc")
```
:::

### Search authors by ORCID

`desc` offers many functions for manipulating authors: adding ordeleting
them or their roles. Now you can perform these operations usingORCID to
identify authors to be modified. E.g. if you want to add a roleto an
existing author, say Carl who worked hard enough to earn the "aut"role,
you'd run

::: {.highlight}
``` {.chroma tabindex="0"}
desc::desc_add_role(role = "aut",                    orcid = "0000-0002-1642-628X")
```
:::

Obviously this very example above has probably little
real-lifeapplicability, but you could imagine manipulating DESCRIPTION
files *enmasse* using a table of ORCIDs and new roles.

### Add ORCID to authors of a package

The new `add_orcid()` method and `desc_add_orcid()` functions make
itpossible to add ORCID IDs to authors directly instead of via
the`comment` argument. So you could write some script

::: {.highlight}
``` {.chroma tabindex="0"}
desc::desc_add_orcid("0000-0002-2815-0399",                     given = "Maëlle",                     family = "Salmon")
```
:::

and run it inside all your local package folders to add your ORCID.
Itwill add this ORCID ID to the author whose given name is "Maëlle"
andwhose family name is "Salmon". If you only write

::: {.highlight}
``` {.chroma tabindex="0"}
desc::desc_add_orcid("0000-0002-2815-0399",                     given = "Maëlle")
```
:::

and there are two Maëlle's, the function will error and you'll need
torun it with more specific arguments.

### Add all of *your* identity at once!

The coolest feature of `desc` ORCID support might be
that`desc::desc_add_me()` will now use the ORCID of the environment
variable`ORCID_ID` if you created it. Hence, once per machine it'd now
berecommended to

- install the `whoami` package necessary for `desc::desc_add_me()`
  towork. `install.packages("whoami")`.

- create an environment variable `ORCID_ID`, editing `.Renviron`
  bycalling e.g. `usethis::edit_r_environ()`. Here's how
  thecorresponding `.Renviron` line looks for me:

::: {.highlight}
``` {.chroma tabindex="0"}
ORCID_ID="0000-0002-2815-0399"
```
:::

`desc::desc_add_me()` looks for your name and email addresses in
yourexisting configuration (git configuration, GitHub profile), see
[the`whoami` package docs](https://github.com/r-lib/whoami). So say
you'vejust been told to add yourself as contributor of a package
you'veimproved: inside the package directory, you'd just need to
run`desc::desc_add_me()` and voilà ! No risk to wrongly copy-paste
yourORCID.

As a conclusion of this section, not only are ORCIDs useful, but
they'regetting citizen status in the world of as-automatic-as-possible
packagedevelopment. Now, we shall see how one could use ORCIDs inside R
togather information about package authors.

## How to study CRAN authors via their ORCID

As mentioned earlier, rOpenSci's Scott Chamberlain is the [most
prolificCRAN
packagemaintainer](https://blog.revolutionanalytics.com/2018/03/the-most-prolific-package-maintainers-on-cran.html),so
perhaps unsurprisingly, he maintains a package interacting withORCID's
API, [`rorcid`](https://github.com/ropensci/rorcid)!

The API requires authentication so the first step after installing
thepackage is to run:

::: {.highlight}
``` {.chroma tabindex="0"}
rorcid::orcid_auth()
```
:::

and to save the resulting token as an `ORCID_TOKEN` environment
variablein `.Renviron` (again, `usethis::edit_r_environ()` can help with
that).Authentication warrants your having an ORCID account, so if you
haven'tone yet, [register via this link](https://orcid.org/register).

Then, we'll query all `comment`'s of `Authors@R` of CRAN packages.
SomeCRAN packages use the `Author` field instead, which is not
recommendedand doesn't allow using `comment`.

*Side-note, in general, how would one analyze stuff over the whole
CRANcollection?*

- *Some information can be found in `tools::CRAN_package_db()` as seenin
  [this recent technote](/technotes/2018/09/10/github-badges/).*

- *There's [an official read-only mirror of each all CRAN packages
  onGitHub](https://github.com/cran) thanks to METACRAN.*

- *METACRAN serves a [CRAN
  packagedatabase](https://r-pkg.org/services#crandb), wrapped by an
  Rpackage of course.*

- *One could try setting up a local CRAN mirror.*

Thanks to Gábor, who maintains METACRAN, for patiently answering
myquestions about meta-CRAN things. If we were after the comments
sectionof just a few packages, we could query METACRAN database like so:

::: {.highlight}
``` {.chroma tabindex="0"}
url <- "https://crandb.r-pkg.org/-/latest?keys=[%22desc%22,%22codemetar%22]"obj  <- jsonlite::fromJSON(url, simplifyVector = FALSE)lapply(obj, function(x) eval(parse(text = x$`Authors@R`))$comment)
```
:::

but in our case, when wanting to get all the current CRAN authors,
it'seasier to use `tools::CRAN_package_db()`. As a side-note, if you
find abetter solution than the functions defined below `parse_authors()`
and`parse_author()` (some `purrr` magic?) to coerce all authors
informationto a `data.frame`, feel free to comment under the post!

::: {.highlight}
``` {.chroma tabindex="0"}
library("magrittr")all_info <- tools::CRAN_package_db()all_info <- all_info[!is.na(all_info$`Authors@R`),]all_info <- all_info[, c("Package", "Authors@R")]names(all_info)[2] <- "authors_at_r"null_to_na <- function(x){  if(is.null(x)){    NA  }else{    x  }}parse_author <- function(author){  author <- as.person(author)  tibble::tibble(given = null_to_na(author$given),                 family = null_to_na(author$family),                 email = null_to_na(author$email),                 comment = as.character(null_to_na(author$comment)),                 orcid = as.character(null_to_na(author$comment["ORCID"])))}parse_authors <- function(authors_at_r){  authors <- try(eval(parse(text = authors_at_r)),                silent = TRUE)  if(inherits(authors, "try-error")){    return(list(NA))  }    else{    list(purrr::map_dfr(authors, parse_author))  }  }cran_authors <- all_info %>%  as.data.frame() %>%  dplyr::select(Package, authors_at_r) %>%   dplyr::rowwise() %>%  dplyr::mutate(authors = parse_authors(authors_at_r)) %>%  tidyr::unnest(authors)
```
:::

This is how the resulting table looks like. Out of 13147 packages onCRAN
we are looking at 5421, i.e. packages using the `Authors@R` field.There
is one line per author in a package.

::: {.highlight}
``` {.chroma tabindex="0"}
str(cran_authors)
```
:::

    ## Classes 'tbl_df', 'tbl' and 'data.frame':    16272 obs. of  7 variables:##  $ Package     : chr  "abbyyR" "abc" "abc" "abc" ...##  $ authors_at_r: chr  "person(\"Gaurav\", \"Sood\", email = \"gsood07@gmail.com\", role = c(\"aut\", \"cre\"))" "c( \n    person(\"Csillery\", \"Katalin\", role = \"aut\", email=\"kati.csillery@gmail.com\"),\n    person(\"Le"| __truncated__ "c( \n    person(\"Csillery\", \"Katalin\", role = \"aut\", email=\"kati.csillery@gmail.com\"),\n    person(\"Le"| __truncated__ "c( \n    person(\"Csillery\", \"Katalin\", role = \"aut\", email=\"kati.csillery@gmail.com\"),\n    person(\"Le"| __truncated__ ...##  $ given       : chr  "Gaurav" "Csillery" "Lemaire" "Francois" ...##  $ family      : chr  "Sood" "Katalin" "Louisiane" "Olivier" ...##  $ email       : chr  "gsood07@gmail.com" "kati.csillery@gmail.com" NA NA ...##  $ comment     : chr  NA NA NA NA ...##  $ orcid       : chr  NA NA NA NA ...

We can count the number of occurrences of ORCIDs.

::: {.highlight}
``` {.chroma tabindex="0"}
(cran_authors %>%  dplyr::filter(!is.na(orcid)) %>%  dplyr::pull(Package) %>%  unique() %>%  length() -> orcid_pkg_no)
```
:::

    ## [1] 613

Only 613 packages have at least an ORCID ID out of 13147 CRAN
packages(you can't have an ORCID ID without using the `Authors@R`
field).

There are 512 unique ORCID IDs. Let's look at the most prolific
authorswith an ORCID ID.

::: {.highlight}
``` {.chroma tabindex="0"}
cran_authors %>%  dplyr::filter(!is.na(orcid)) %>%  dplyr::count(orcid, sort = TRUE) %>%  head(n = 10) -> most_prolific
```
:::

::: {.highlight}
``` {.chroma tabindex="0"}
knitr::kable(most_prolific)
```
:::

| orcid               |   n |
|:--------------------|----:|
| 0000-0003-1444-9135 |  29 |
| 0000-0002-4035-0289 |  21 |
| 0000-0003-0918-3766 |  21 |
| 0000-0003-4198-9911 |  19 |
| 0000-0003-4097-6326 |  16 |
| 0000-0001-8301-0471 |  13 |
| 0000-0003-0645-5666 |  12 |
| 0000-0001-5243-233X |  11 |
| 0000-0001-5670-2640 |  11 |
| 0000-0002-8584-459X |  10 |

Then we can use `rorcid` to get a glimpse of their profile.

::: {.highlight}
``` {.chroma tabindex="0"}
rorcid::as.orcid(most_prolific$orcid)
```
:::

    ## [[1]]## <ORCID> 0000-0003-1444-9135##   Name: Chamberlain, Scott##   URL (first): /##   Country: US##   Keywords: ecology, open access, bioinformatics, evolution, R## ## [[2]]## <ORCID> 0000-0002-4035-0289##   Name: Ooms, Jeroen##   URL (first): https://github.com/jeroen##   Country: NL##   Country: US##   Keywords: ## ## [[3]]## <ORCID> 0000-0003-0918-3766##   Name: Zeileis, Achim##   URL (first): https://eeecon.uibk.ac.at/~zeileis/##   Country: AT##   Keywords: ## ## [[4]]## <ORCID> 0000-0003-4198-9911##   Name: Hornik, Kurt##   URL (first): ##   Country: ##   Keywords: ## ## [[5]]## <ORCID> 0000-0003-4097-6326##   Name: Leeper, Thomas##   URL (first): http://www.lse.ac.uk/government/whosWho/Academic%20profiles/ThomasLeeper.aspx##   Country: GB##   Keywords: Public Opinion, Survey Experiments, Political Behaviour, R, Research Design## ## [[6]]## <ORCID> 0000-0001-8301-0471##   Name: Hothorn, Torsten##   URL (first): ##   Country: ##   Keywords: ## ## [[7]]## <ORCID> 0000-0003-0645-5666##   Name: Xie, Yihui##   URL (first): https://yihui.name##   Country: ##   Keywords: ## ## [[8]]## <ORCID> 0000-0001-5243-233X##   Name: Tang, Yuan##   URL (first): https://terrytangyuan.github.io/about/##   Country: US##   Keywords: Machine Learning, Data Visualization, Open Source, Software Engineering## ## [[9]]## <ORCID> 0000-0001-5670-2640##   Name: Rudis, Bob##   URL (first): http://rud.is/b##   Country: US##   Keywords: cybersecurity, r, data visualization, web crawling/scraping## ## [[10]]## <ORCID> 0000-0002-8584-459X##   Name: You, Kisung##   URL (first): https://kisungyou.github.io/##   Country: KR##   Keywords:

Interestingly we recognize some names from the most prolific
CRANmaintainers (Scott and Jeroen, again!) but not only. Note that
anotherdifference with [David
Smith'spost](https://blog.revolutionanalytics.com/2018/03/the-most-prolific-package-maintainers-on-cran.html)is
that the list above includes authors no matter their role.

Over all authors with an ORCID, using `rorcid` one could extract
theirlocation and much more, but this is beyond the scope of this tech
note.

Inversely, if one wanted to find CRAN packages by ORCID ID, instead
ofORCID IDs by CRAN package, one could make the most of METACRAN. There
isno search by ORCID, but since everything in DESCRIPTION is indexed
byMETACRAN, one can use the ORCID ID as search term. Say you want to
findall packages by Scott Chamberlain:

- You can use this
  URL<https://r-pkg.org/search.html?q=0000-0003-1444-9135>

- Or this to get an API (and further parse the JSON in
  R?)<http://seer.r-pkg.org:9200/cran-devel/package/_search?q=%220000-0003-1444-9135%22>

- Other methods to search CRAN by ORCID ID might include [using
  the`seer` package (not
  possibleyet)](https://github.com/metacran/seer/issues/11).

## Conclusion

In this tech note we made the case for using ORCID IDs as identifiersfor
the authors of CRAN packages, for academics and non-academics aswell. We
described the current [`desc`](https://github.com/r-lib/desc)support for
ORCID. We also gave a small insight into the wealth ofinformation one
can get via[`rorcid`](https://github.com/ropensci/rorcid).

For academics, another aspect of making their software
contributionsvaluable is getting the software they write as work inside
their ORCIDprofile. One can do that by hand, but one can also

- get a legit DOI for each package release by
  activating[Zenodo](https://zenodo.org/) for the repository,

- write a software paper, e.g. via
  [JOSS](https://joss.theoj.org/),that'd have its own DOI.

But this is probably a topic for another time, such as would be thetopic
of CRAN potentially adopting other IDs like GitHub username,ideally via
Keybase. By the way if you'd like to see a Keybaseintegration of ORCID
happen, please "+1" [this issue by
StephLocke](https://github.com/keybase/proofs/issues/126). In the
meantime,let's hope ORCID IDs will be more adopted by academics and
non-academicsalike for:

- Making CRAN package authors easier to identify and their onlinepersona
  easier to find.

- Making academic CRAN package authors' scientific contributionseasier
  to access when studying packages.

Have *you* started `desc::add_orcid()`-ing? Don't hesitate to
commentbelow!

*Many thanks
to[0000-0002-1642-628X](https://orcid.org/0000-0002-1642-628X)
and[0000-0003-1419-2405](https://orcid.org/0000-0003-1419-2405) for
theirfeedback on this note.*


Proper identification of individuals is crucial for acknowledging andstudying their scientific work, be it journal articles or pieces ofsoftware. In this tech note, one year after CRAN started supportingORCIDs, we shall explain why and how to use unique author identifiers inDESCRIPTION files. Why use ORCIDs on CRAN? When analyzing the authorship of CRAN packages, one can look at authors’names and email addresses.

Messaggi di Rogue Scholar

Distinguish yourself in CRAN person() with ORCID