[R-pkg-devel] ORCID ID finder via tools::CRAN_package_db() ?
Thierry Onkelinx
th|erry@onke||nx @end|ng |rom |nbo@be
Tue Aug 20 16:25:25 CEST 2024
Dear Ben,
This is as simple as setting mandatory given and family fields.
checklist::check_description() ensures that given and family are set unless
the role is "cph" or "fnd". Allowing for organisations to be listed with
only the given field.
The 0.4.1 branch of checklist
<https://github.com/inbo/checklist/tree/0.4.1> now
exports the author2df() function which now can handle objects of call
person, list, logical (NA) and NULL. Feedback is welcome.
library(checklist)
df <- tools::CRAN_package_db()
vapply(
df$`Authors using R`[df$Package %in% c("git2rdata", "A3", "digest", "abe")],
function(x) {
parse(text = x) |>
eval() |>
list()
},
vector(mode = "list", 1)
) |>
unname() |>
author2df()
Best regards,
ir. Thierry Onkelinx
Statisticus / Statistician
Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND
FOREST
Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
thierry.onkelinx using inbo.be
Havenlaan 88 bus 73, 1000 Brussel
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<https://www.inbo.be>
Op di 20 aug 2024 om 15:59 schreef Ben Bolker <bbolker using gmail.com>:
> Looking into one particular example,
>
> https://github.com/seabbs/idmodelr/blob/master/DESCRIPTION
>
> this appears to be the authors' fault:
>
> Authors using R: c(
> person(given = "Sam Abbott",
> role = c("aut", "cre"),
> email = "contact using samabbott.co.uk",
> comment = c(ORCID = "0000-0001-8057-8037")),
> person(given = "Akira Endo",
> role = c("aut"),
> email = "akira.endo using lshtm.ac.uk",
> comment = c(ORCID = "0000-0001-6377-7296")))
>
> Maybe CRAN should start checking for missing 'family' fields in
> Authors using R ... ???
>
> cheers
> Ben Bolker
>
> On 2024-08-20 9:47 a.m., Kurt Hornik wrote:
> >>>>>> Kurt Hornik writes:
> >
> > The variant attaches drops the URL and does unique.
> >
> > Hmm, the ones in
> >
> > head(with(a, sort_by(a, ~ family + given)), 100)
> >
> > without a family look suspicious ...
> >
> > Best
> > -k
> >
> >
> >
> >
> >>>>>> Dirk Eddelbuettel writes:
> >>> On 20 August 2024 at 07:57, Dirk Eddelbuettel wrote:
> >>> |
> >>> | Hi Kurt,
> >>> |
> >>> | On 20 August 2024 at 14:29, Kurt Hornik wrote:
> >>> | | I think for now you could use something like what I attach below.
> >>> | |
> >>> | | Not ideal: I had not too long ago starting adding orcidtools.R to
> tools,
> >>> | | which e.g. has .persons_from_metadata(), but that works on the
> unpacked
> >>> | | sources and not the CRAN package db. Need to think about that ...
> >>> |
> >>> | We need something like that too as I fat-fingered the string
> 'ORCID'. See
> >>> | fortune::fortunes("Dirk can type").
> >>> |
> >>> | Will the function below later. Many thanks for sending it along.
> >
> >>> Very nice. Resisted my common impulse to make it a data.table for easy
> >>> sorting via keys etc. After running your code the line
> >
> >>> head(with(a, sort_by(a, ~ family + given)), 100)
> >
> >>> shows that we need a bit more QA as person entries are not properly
> split
> >>> between 'family' and 'given', use the URL and that we have repeats.
> >>> Excluding those is next.
> >
> >> Right. One should canonicalize the ORCID (having the URLs is from being
> >> nice) and then do unique() ...
> >
> >> Best
> >> -k
> >
> >
> >
> >>> Dirk
> >
> >>> | Dirk
> >>> |
> >>> | |
> >>> | | Best
> >>> | | -k
> >>> | |
> >>> | |
> ********************************************************************
> >>> | | x <- tools::CRAN_package_db()
> >>> | | a <- lapply(x[["Authors using R"]],
> >>> | | function(a) {
> >>> | | if(!is.na(a)) {
> >>> | | a <-
> tryCatch(utils:::.read_authors_at_R_field(a),
> >>> | | error = identity)
> >>> | | if (inherits(a, "person"))
> >>> | | return(a)
> >>> | | }
> >>> | | NULL
> >>> | | })
> >>> | | a <- do.call(c, a)
> >>> | | a <- lapply(a,
> >>> | | function(e) {
> >>> | | if(is.null(o <- e$comment["ORCID"]) || is.na(o))
> >>> | | return(NULL)
> >>> | | cbind(given = paste(e$given, collapse = " "),
> >>> | | family = paste(e$family, collapse = " "),
> >>> | | oid = unname(o))
> >>> | | })
> >>> | | a <- as.data.frame(do.call(rbind, a))
> >>> | |
> ********************************************************************
> >>> | |
> >>> | | > Salut Thierry,
> >>> | |
> >>> | | > On 20 August 2024 at 13:43, Thierry Onkelinx wrote:
> >>> | | > | Happy to help. I'm working on a new version of the checklist
> package. I could
> >>> | | > | export the function if that makes it easier for you.
> >>> | |
> >>> | | > Would be happy to help / iterate. Can you take a stab at making
> the
> >>> | | > per-column split more robust so that we can bulk-process all
> non-NA entries
> >>> | | > of the returned db?
> >>> | |
> >>> | | > Best, Dirk
> >>> | |
> >>> | | > --
> >>> | | > dirk.eddelbuettel.com | @eddelbuettel | edd using debian.org
> >>> |
> >>> | --
> >>> | dirk.eddelbuettel.com | @eddelbuettel | edd using debian.org
> >
> >>> --
> >>> dirk.eddelbuettel.com | @eddelbuettel | edd using debian.org
> >>>
> >>> ______________________________________________
> >>> R-package-devel using r-project.org mailing list
> >>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
> --
> Dr. Benjamin Bolker
> Professor, Mathematics & Statistics and Biology, McMaster University
> Director, School of Computational Science and Engineering
> > E-mail is sent at my convenience; I don't expect replies outside of
> working hours.
>
> ______________________________________________
> R-package-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
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