Download and wrangle publication data for Monash EBS academic staff • spiderorchid

Download and wrangle publication data for Monash EBS academic staff

Overview

The spiderorchid R package provides tools to retrieve research publications from Google Scholar and ORCID, or from DOIs, along with CRAN package download statistics. It is tailored for academic researchers in the EBS department who wish to consolidate and analyze their research outputs, while also monitoring their contributions to CRAN.

The main functions included are:

fetch_scholar: Retrieves publication details from Google Scholar given IDs.
fetch_orcid: Retrieves publication details from ORCID given IDs.
fetch_doi: Retrieves publication details given DOIS.
fetch_pure: Retrieves publication details from PURE for specific years.
fetch_cran: Searches for CRAN packages by an author’s name and returns relevant package information such as the number of downloads and last update date.

The package caches results within each R session. So if you fetch the same data multiple times, it will only download it once.

Installation

# Install the packages needed
pak::pak(c("robjhyndman/pkgmeta", "numbats/spiderorchid"))

library(spiderorchid)
library(dplyr)
#> 
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag
#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union

Datasets

staff_ids.csv

This dataset contains mappings between researchers’ names and their respective ORCID and Google Scholar IDs. It is useful for linking and identifying academic profiles across different platforms.

staff_ids
#> # A tibble: 57 × 4
#>    first_name last_name orcid_id            scholar_id  
#>    <chr>      <chr>     <chr>               <chr>       
#>  1 Akanksha   Negi      0000-0003-2531-9408 Gcz8Ng0AAAAJ
#>  2 Alan       Powell    <NA>                <NA>        
#>  3 Andrew     Matthews  <NA>                <NA>        
#>  4 Ann        Maharaj   0000-0002-5513-962X BZ07eocAAAAJ
#>  5 Athanasios Pantelous 0000-0001-5738-1471 ZMaiiQwAAAAJ
#>  6 Benjamin   Wong      0000-0002-1665-6165 Nneg6GAAAAAJ
#>  7 Bin        Peng      0000-0003-4231-4713 5d3ZOm4AAAAJ
#>  8 Bonsoo     Koo       0000-0002-7247-9773 OmK08lAAAAAJ
#>  9 Brett      Inder     <NA>                Wx6eeWgAAAAJ
#> 10 Catherine  Forbes    0000-0003-3830-5865 jm73LccAAAAJ
#> # ℹ 47 more rows

ebs_pure

This dataset contains publication data from the PURE system for EBS staff. It includes information such as titles, authors, publication years, and DOIs. The data includes publications from January 2018 to May 2025.

ebs_pure
#> # A tibble: 613 × 8
#>    pure_id    year authors                     title journal subtype bib   doi  
#>    <chr>     <int> <chr>                       <chr> <chr>   <chr>   <chr> <chr>
#>  1 580119537  2024 Negi, A & Wooldridge, JM    Doub… Econom… Article Negi… 10.1…
#>  2 578896645  2024 Negi, A                     Doub… Journa… Article Negi… 10.1…
#>  3 577211348  2024 Nibbering, D                A hi… Journa… Article Nibb… 10.1…
#>  4 576146015  2024 Rostami-Tabar, B & Hyndman… Hier… Journa… Article Rost… 10.1…
#>  5 574756920  2024 Fang, X, Zhou, J, Pantelou… A ma… Expert… Article Fang… 10.1…
#>  6 574375066  2023 Pullin, JM, Gurrin, LC & V… Stat… The R … Article Pull… 10.3…
#>  7 571851299  2024 Kim, HY & McLaren, KR       Inte… Resear… Article Kim,… 10.1…
#>  8 571257919  2024 Gao, J, Peng, B, Wu, WB & … Time… Journa… Article Gao,… 10.1…
#>  9 571257838  2024 Yan, Y, Gao, J & Peng, B    Asym… Econom… Article Yan,… 10.1…
#> 10 567405205  2023 Zhou, J, Jiang, G, Pantelo… Onli… IEEE T… Article Zhou… 10.1…
#> # ℹ 603 more rows

Google scholar publications

staff_ids |>
  filter(last_name %in% c("Negi", "Lydeamore")) |>
  pull(scholar_id) |>
  fetch_scholar()
#> # A tibble: 51 × 6
#>    scholar_id   authors                title publication_year journal_name DOI  
#>    <chr>        <chr>                  <chr>            <int> <chr>        <chr>
#>  1 Gcz8Ng0AAAAJ A Negi, D Roy          The …             2015 IFPRI Discu… <NA> 
#>  2 Gcz8Ng0AAAAJ R Chandra, PK Joshi, … Dyna…             2017 IFPRI book … <NA> 
#>  3 Gcz8Ng0AAAAJ P Birthal, A Negi, PK… Unde…             2019 Journal of … <NA> 
#>  4 Gcz8Ng0AAAAJ A Negi                 Robu…             2020 Michigan St… <NA> 
#>  5 Gcz8Ng0AAAAJ A Negi, JM Wooldridge  Revi…             2021 Econometric… <NA> 
#>  6 Gcz8Ng0AAAAJ C Cox, A Negi, D Negi  Risk…             2023 Available a… <NA> 
#>  7 Gcz8Ng0AAAAJ G Rathnayake, A Negi,… Diff…             2024 arXiv prepr… <NA> 
#>  8 Gcz8Ng0AAAAJ A Negi, W Jeffrey M    Doub…             2024 Econometric… <NA> 
#>  9 Gcz8Ng0AAAAJ A Negi                 Doub…             2024 Journal of … <NA> 
#> 10 Gcz8Ng0AAAAJ A Negi                 Jour…             2024 de Gruyter   <NA> 
#> # ℹ 41 more rows

ORCID publications

The fetch_orcid() function requires authentication on ORCID. If you have not previously authenticated, it will prompt you to do so when first run. If you just follow the prompts, you will be authenticated, but only for downloading your own papers. If you want to download papers from other ORCID IDs, you will need to authenticate with a 2-legged OAuth. Follow the instructions at https://info.orcid.org/register-a-client-application-production-member-api/. To avoid having to do this in each session, store the token obtained from orcid_auth() in your .Renviron file by running usethis::edit_r_environ(). It should be of the form ORCID_TOKEN=<your token>.

staff_ids |>
  filter(last_name %in% c("Negi", "Lydeamore")) |>
  pull(orcid_id) |>
  fetch_orcid()
#> # A tibble: 15 × 9
#>    orcid_id authors publication_year title journal_name volume issue doi   page 
#>    <chr>    <chr>              <int> <chr> <chr>        <chr>  <chr> <chr> <chr>
#>  1 0000-00… "Micha…             2016 Choi… Bulletin of… 78     2     10.1… 293-…
#>  2 0000-00… "Thiri…             2017 Indi… PeerJ        5      <NA>  10.7… e3958
#>  3 0000-00… "M. J.…             2018 Calc… Epidemiolog… 146    9     10.1… 1194…
#>  4 0000-00… "M.J. …             2019 A bi… Mathematica… 309    <NA>  10.1… 163-…
#>  5 0000-00… "Will …             2019 High… Australian … 43     2     10.1… 149-…
#>  6 0000-00… "MICHA…             2019 MECH… Bulletin of… 101    1     10.1… 174-…
#>  7 0000-00… "James…             2020 Brin… Journal of … 76     3     10.1… 547-…
#>  8 0000-00… "Micha…             2020 Esti… PLOS Comput… 16     10    10.1… e100…
#>  9 0000-00… "  "                2021 Popu… The Lancet … 17     <NA>  10.1… 1002…
#> 10 0000-00… "Camer…             2021 Risk… Journal of … 18     174   10.1… 2020…
#> 11 0000-00… "James…             2021 Unde… Nature Comm… 12     1     10.1… <NA> 
#> 12 0000-00… "M. J.…             2022 Burd… Antimicrobi… 11     1     10.1… <NA> 
#> 13 0000-00… "Camer…             2022 COVI… Science Adv… 8      14    10.1… <NA> 
#> 14 0000-00… "Prata…             2019 Unde… Journal of … 9      3     10.1… 255-…
#> 15 0000-00… "Akank…             2020 Revi… Econometric… 40     5     10.1… 504-…

DOI publications

fetch_doi(c("10.1016/j.ijforecast.2023.10.003", "10.1080/10618600.2020.1807353"))
#> # A tibble: 2 × 8
#>   doi             authors publication_year title journal_name volume issue page 
#>   <chr>           <chr>              <int> <chr> <chr>        <chr>  <chr> <chr>
#> 1 10.1016/j.ijfo… Daniel…             2024 Cros… Internation… 40     3     1134…
#> 2 10.1080/106186… Sevvan…             2020 Dime… Journal of … 30     1     204-…

PURE publications

The fetch_pure() function requires an API key to access the PURE system. The API key is stored in the environment variable PURE_API_KEY. This function is restricted to Monash IP addresses; so either use it on campus or invoke the VPN before using it off campus. It will return publications in the specified years, coauthored by members of the Department of Econometrics & Business Statistics, Monash University.

fetch_pure(2024)

#> # A tibble: 83 × 8
#>    pure_id    year authors                     title journal subtype bib   doi  
#>    <chr>     <int> <chr>                       <chr> <chr>   <chr>   <chr> <chr>
#>  1 580119537  2024 Negi, A & Wooldridge, JM    Doub… Econom… Article Negi… 10.1…
#>  2 578896645  2024 Negi, A                     Doub… Journa… Article Negi… 10.1…
#>  3 577211348  2024 Nibbering, D                A hi… Journa… Article Nibb… 10.1…
#>  4 576146015  2024 Rostami-Tabar, B & Hyndman… Hier… Journa… Article Rost… 10.1…
#>  5 574756920  2024 Fang, X, Zhou, J, Pantelou… A ma… Expert… Article Fang… 10.1…
#>  6 571851299  2024 Kim, HY & McLaren, KR       Inte… Resear… Article Kim,… 10.1…
#>  7 571257919  2024 Gao, J, Peng, B, Wu, WB & … Time… Journa… Article Gao,… 10.1…
#>  8 571257838  2024 Yan, Y, Gao, J & Peng, B    Asym… Econom… Article Yan,… 10.1…
#>  9 565992428  2024 Athanasopoulos, G, Hyndman… Fore… Intern… Article Atha… 10.1…
#> 10 564353599  2024 Wang, G, Zhou, J, Pantelou… A de… Comput… Article Wang… 10.1…
#> # ℹ 73 more rows

CRAN packages

This function retrieves information about CRAN packages authored by a specified individual. It returns a data frame containing the package name, number of downloads, the authors, and the last update date.

fetch_cran(c(
  "Michael Lydeamore",
  "Di Cook",
  "Dianne Cook"
))
#> # A tibble: 40 × 11
#>    package         date       title   description version authors url   cran_url
#>    <chr>           <date>     <chr>   <chr>       <chr>   <chr>   <chr> <chr>   
#>  1 cardinalR       2024-04-16 "Colle… "A collect… 0.1.1   "Jayan… http… https:/…
#>  2 condensr        2023-08-30 "Acade… "Helps aut… 1.0.0   "Micha… http… https:/…
#>  3 HospitalNetwork 2024-12-22 "Build… "Set of to… 0.9.4   "Pasca… http… https:/…
#>  4 quollr          2024-03-05 "Visua… "To constr… 0.1.1   "Jayan… http… https:/…
#>  5 brolgar         2024-05-10 "Brows… "Provides … 1.0.1   "Nicho… http… https:/…
#>  6 eechidna        2021-02-25 "Explo… "Data from… 1.4.1   "Jerem… http… https:/…
#>  7 fabletools      2024-09-17 "Core … "Provides … 0.5.0   "Mitch… http… https:/…
#>  8 feasts          2024-09-25 "Featu… "Provides … 0.4.1   "Mitch… http… https:/…
#>  9 geozoo          2016-05-07 "Zoo o… "Geometric… 0.5.1   "Barre… http… https:/…
#> 10 GGally          2024-02-13 "Exten… "\nThe R p… 2.2.1   "Barre… http… https:/…
#> # ℹ 30 more rows
#> # ℹ 3 more variables: github_url <chr>, first_download <date>, downloads <dbl>