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openalexR: an R package to interface with the OpenAlex API #560

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12 of 29 tasks
trangdata opened this issue Nov 8, 2022 · 49 comments
Closed
12 of 29 tasks

openalexR: an R package to interface with the OpenAlex API #560

trangdata opened this issue Nov 8, 2022 · 49 comments

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@trangdata
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trangdata commented Nov 8, 2022

Date accepted: 2023-02-23

Submitting Author Name: Trang Le
Submitting Author Github Handle: @trangdata
Other Package Authors Github handles: (comma separated, delete if none) @massimoaria
Repository: https://github.com/massimoaria/openalexR
Version submitted: 1.0.2
Submission type: Standard
Editor: @ldecicco-USGS
Reviewers: @BriannaLind, @pachadotdev

Due date for @BriannaLind: 2022-12-22

Due date for
Due date for @pachadotdev: 2023-01-24
Archive: TBD
Version accepted: TBD
Language: en

  • Paste the full DESCRIPTION file inside a code block below:
Type: Package
Package: openalexR
Title: Getting Bibliographic Records from 'OpenAlex' Database Using 'DSL'
    API
Version: 1.0.2
Authors@R: c(
    person(given = "Massimo",
           family = "Aria",
           role = c("aut", "cre", "cph"),
           email = "aria@unina.it",
           comment = c(ORCID = "0000-0002-8517-9411")),
    person(given = "Corrado",
           family = "Cuccurullo",
           role = c("ctb"),
           email = "cuccurullocorrado@gmail.com",
           comment = c(ORCID = "0000-0002-7401-8575")),       
    person(given = "Trang",
           family = "Le",
           role = "aut",
           email = "grixor@gmail.com",
           comment = c(ORCID = "0000-0003-3737-6565"))
    )
Description: A set of tools to extract bibliographic content from
    'OpenAlex' database using API <https://docs.openalex.org/api/>.
License: MIT + file LICENSE
URL: https://github.com/massimoaria/openalexR,
    https://massimoaria.github.io/openalexR/
BugReports: https://github.com/massimoaria/openalexR/issues
Imports: 
    curl,
    httr,
    jsonlite,
    progress,
    tibble
Suggests: 
    testthat (>= 3.0.0),
    dplyr,
    knitr,
    rmarkdown,
    tidyr,
    purrr,
    ggplot2,
    covr
VignetteBuilder: 
    knitr
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.2.1
Config/testthat/edition: 3
Depends: 
    R (>= 2.10)

Scope

  • Please indicate which category or categories from our package fit policies this package falls under: (Please check an appropriate box below. If you are unsure, we suggest you make a pre-submission inquiry.):

    • data retrieval
    • data extraction
    • data munging
    • data deposition
    • data validation and testing
    • workflow automation
    • version control
    • citation management and bibliometrics
    • scientific software wrappers
    • field and lab reproducibility tools
    • database software bindings
    • geospatial data
    • text analysis
  • Explain how and why the package falls under these categories (briefly, 1-2 sentences): The package interacts with the OpenAlex API. Similar packages in the same category are rcrossref and rotl.

  • Who is the target audience and what are scientific applications of this package?
    Anyone who wants to work in R to interact with the OpenAlex API to acquire information on publications, authors, etc., including researchers in the field of bibliometrics, text mining, etc. We include several example analyses in our README.

  • Are there other R packages that accomplish the same thing? If so, how does yours differ or meet our criteria for best-in-category?
    Please see the detailed answer here with a detailed table of comparison and examples of code differences.

  • (If applicable) Does your package comply with our guidance around Ethics, Data Privacy and Human Subjects Research?
    Yes.

  • If you made a pre-submission inquiry, please paste the link to the corresponding issue, forum post, or other discussion, or @tag the editor you contacted.
    Presubmission inquiry - openalexR: interacts with OpenAlex API #557

  • Explain reasons for any pkgcheck items which your package is unable to pass.
    N/A. Passed all checks.

Technical checks

Confirm each of the following by checking the box.

This package:

Publication options

  • Do you intend for this package to go on CRAN?

  • Do you intend for this package to go on Bioconductor?

  • Do you wish to submit an Applications Article about your package to Methods in Ecology and Evolution? If so:

MEE Options
  • The package is novel and will be of interest to the broad readership of the journal.
  • The manuscript describing the package is no longer than 3000 words.
  • You intend to archive the code for the package in a long-term repository which meets the requirements of the journal (see MEE's Policy on Publishing Code)
  • (Scope: Do consider MEE's Aims and Scope for your manuscript. We make no guarantee that your manuscript will be within MEE scope.)
  • (Although not required, we strongly recommend having a full manuscript prepared when you submit here.)
  • (Please do not submit your package separately to Methods in Ecology and Evolution)

Code of conduct

@ropensci-review-bot
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Thanks for submitting to rOpenSci, our editors and @ropensci-review-bot will reply soon. Type @ropensci-review-bot help for help.

@ropensci-review-bot
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🚀

Editor check started

👋

@ropensci-review-bot
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Checks for openalexR (v1.0.2)

git hash: c0d32fea

  • ✔️ Package is already on CRAN.
  • ✔️ has a 'codemeta.json' file.
  • ✔️ has a 'contributing' file.
  • ✔️ uses 'roxygen2'.
  • ✔️ 'DESCRIPTION' has a URL field.
  • ✔️ 'DESCRIPTION' has a BugReports field.
  • ✔️ Package has at least one HTML vignette
  • ✔️ All functions have examples.
  • ✔️ Package has continuous integration checks.
  • ✔️ Package coverage is 92.4%.
  • ✔️ R CMD check found no errors.
  • ✔️ R CMD check found no warnings.

Package License: MIT + file LICENSE


1. Package Dependencies

Details of Package Dependency Usage (click to open)

The table below tallies all function calls to all packages ('ncalls'), both internal (r-base + recommended, along with the package itself), and external (imported and suggested packages). 'NA' values indicate packages to which no identified calls to R functions could be found. Note that these results are generated by an automated code-tagging system which may not be entirely accurate.

type package ncalls
internal base 227
internal openalexR 67
internal utils 16
internal stats 12
internal graphics 2
internal methods 2
imports httr 5
imports jsonlite 2
imports curl NA
imports progress NA
imports tibble NA
suggests testthat NA
suggests dplyr NA
suggests knitr NA
suggests rmarkdown NA
suggests tidyr NA
suggests purrr NA
suggests ggplot2 NA
suggests covr NA
linking_to NA NA

Click below for tallies of functions used in each package. Locations of each call within this package may be generated locally by running 's <- pkgstats::pkgstats(<path/to/repo>)', and examining the 'external_calls' table.

base

list (62), c (23), lapply (16), do.call (15), length (14), if (11), for (7), unlist (7), vector (6), mode (5), paste (5), is.null (4), lengths (4), names (3), rbind.data.frame (3), by (2), duplicated (2), max (2), min (2), nrow (2), rbind (2), rep (2), search (2), sort (2), switch (2), unique (2), url (2), which (2), as.character (1), ceiling (1), environment (1), format (1), grepl (1), intersect (1), is.na (1), logical (1), mapply (1), merge (1), paste0 (1), seq_along (1), seq.int (1), strsplit (1), tolower (1), vapply (1)

openalexR

oa_fetch (13), oa_progress (7), au_collapse (5), subs_na (5), empty_list (3), oa_request (3), SR (3), abstract_build (2), api_request (2), append_flt (2), cfg (2), oa_entities (2), simple_rapply (2), asl (1), authors2df (1), concepts2df (1), get_auth_position (1), id_type (1), institutions2df (1), isValidEmail (1), oa_email (1), oa_query (1), oa_random (1), oa_snowball (1), oa2bibliometrix (1), oa2df (1), prepend (1), shorten_oaid (1), shorten_orcid (1)

utils

data (16)

stats

filter (11), setNames (1)

httr

content (2), GET (1), modify_url (1), user_agent (1)

graphics

text (2)

jsonlite

fromJSON (2)

methods

as (2)

NOTE: Some imported packages appear to have no associated function calls; please ensure with author that these 'Imports' are listed appropriately.


2. Statistical Properties

This package features some noteworthy statistical properties which may need to be clarified by a handling editor prior to progressing.

Details of statistical properties (click to open)

The package has:

  • code in R (100% in 8 files) and
  • 2 authors
  • 4 vignettes
  • 2 internal data files
  • 5 imported packages
  • 16 exported functions (median 36 lines of code)
  • 54 non-exported functions in R (median 8 lines of code)

Statistical properties of package structure as distributional percentiles in relation to all current CRAN packages
The following terminology is used:

  • loc = "Lines of Code"
  • fn = "function"
  • exp/not_exp = exported / not exported

All parameters are explained as tooltips in the locally-rendered HTML version of this report generated by the checks_to_markdown() function

The final measure (fn_call_network_size) is the total number of calls between functions (in R), or more abstract relationships between code objects in other languages. Values are flagged as "noteworthy" when they lie in the upper or lower 5th percentile.

measure value percentile noteworthy
files_R 8 50.7
files_vignettes 4 95.3
files_tests 8 88.2
loc_R 858 63.8
loc_vignettes 583 81.6
loc_tests 363 68.2
num_vignettes 4 96.6 TRUE
data_size_total 4058 66.2
data_size_median 2029 68.7
n_fns_r 70 66.8
n_fns_r_exported 16 60.6
n_fns_r_not_exported 54 69.6
n_fns_per_file_r 6 73.8
num_params_per_fn 2 11.9
loc_per_fn_r 14 42.4
loc_per_fn_r_exp 36 70.0
loc_per_fn_r_not_exp 8 26.4
rel_whitespace_R 23 70.2
rel_whitespace_vignettes 28 79.4
rel_whitespace_tests 16 59.8
doclines_per_fn_exp 46 58.1
doclines_per_fn_not_exp 0 0.0 TRUE
fn_call_network_size 63 70.9

2a. Network visualisation

Click to see the interactive network visualisation of calls between objects in package


3. goodpractice and other checks

Details of goodpractice checks (click to open)

3a. Continuous Integration Badges

R-CMD-check.yaml

GitHub Workflow Results

id name conclusion sha run_number date
3420154650 pages build and deployment success 3a012b 38 2022-11-08
3420037823 pkgcheck success c0d32f 2 2022-11-08
3420182325 pkgdown NA c4e6ce 88 2022-11-08
3420182323 R-CMD-check NA c4e6ce 73 2022-11-08
3420182324 test-coverage NA c4e6ce 30 2022-11-08

3b. goodpractice results

R CMD check with rcmdcheck

rcmdcheck found no errors, warnings, or notes

Test coverage with covr

Package coverage: 92.42

Cyclocomplexity with cyclocomp

The following functions have cyclocomplexity >= 15:

function cyclocomplexity
oa_request 19
works2df 16

Static code analyses with lintr

lintr found the following 74 potential issues:

message number of times
Avoid library() and require() calls in packages 9
Lines should not be more than 80 characters. 65


Package Versions

package version
pkgstats 0.1.1.66
pkgcheck 0.1.0.32


Editor-in-Chief Instructions:

This package is in top shape and may be passed on to a handling editor

@annakrystalli
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Thanks for submitting @trangdata! 🎉

I'm in the process of assigning a handling editor.

In the meantime, it appears there's a minor discrepancy in the version stated in the submission and pasted DESCRIPTION (1.0.1) and the actual current package version (1.0.2). Would you mind correcting and double-checking the pasted DESCRIPTION is up to date?

@trangdata
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Thanks so much @annakrystalli! 🌻

it appears there's a minor discrepancy in the version stated in the submission and pasted DESCRIPTION (1.0.1) and the actual current package version (1.0.2).

Ah my bad. I forgot to update the version. Edited now.

@annakrystalli
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@ropensci-review-bot assign @ldecicco-USGS as editor

@ropensci-review-bot
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Assigned! @ldecicco-USGS is now the editor

@ldecicco-USGS
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ldecicco-USGS commented Nov 14, 2022

Editor checks:

  • Documentation: The package has sufficient documentation available online (README, pkgdown docs) to allow for an assessment of functionality and scope without installing the package. In particular,
    • Is the case for the package well made?
    • Is the reference index page clear (grouped by topic if necessary)?
    • Are vignettes readable, sufficiently detailed and not just perfunctory?
  • Fit: The package meets criteria for fit and overlap.
  • Installation instructions: Are installation instructions clear enough for human users?
  • Tests: If the package has some interactivity / HTTP / plot production etc. are the tests using state-of-the-art tooling?
  • Contributing information: Is the documentation for contribution clear enough e.g. tokens for tests, playgrounds?
  • License: The package has a CRAN or OSI accepted license.
  • Project management: Are the issue and PR trackers in a good shape, e.g. are there outstanding bugs, is it clear when feature requests are meant to be tackled?

Editor comments


@ldecicco-USGS
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Hi @trangdata ! The package looks great! I'll try to find some editors as soon as possible

@trangdata
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Thank you so much @ldecicco-USGS. 🪴 And you mean reviewers right? 😅

@ldecicco-USGS
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😆Yup!

@ldecicco-USGS
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@ropensci-review-bot assign @BriannaLind as reviewer

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@BriannaLind added to the reviewers list. Review due date is 2022-12-22. Thanks @BriannaLind for accepting to review! Please refer to our reviewer guide.

rOpenSci’s community is our best asset. We aim for reviews to be open, non-adversarial, and focused on improving software quality. Be respectful and kind! See our reviewers guide and code of conduct for more.

@ropensci-review-bot
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@BriannaLind: If you haven't done so, please fill this form for us to update our reviewers records.

@BriannaLind
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Sorry for the delay team - I am diving into the review, will get back asap

@ropensci ropensci deleted a comment from ropensci-review-bot Dec 29, 2022
@ropensci ropensci deleted a comment from ropensci-review-bot Dec 29, 2022
@ldecicco-USGS
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It turns out I had assigned the review to a fake account that was impersonating the actual reviewer. I'm verifying he's still interested in reviewing. Sorry for the delay @trangdata !

@ldecicco-USGS
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@ropensci-review-bot assign @pachadotdev as reviewer

@ropensci-review-bot
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@pachadotdev added to the reviewers list. Review due date is 2023-01-24. Thanks @pachadotdev for accepting to review! Please refer to our reviewer guide.

rOpenSci’s community is our best asset. We aim for reviews to be open, non-adversarial, and focused on improving software quality. Be respectful and kind! See our reviewers guide and code of conduct for more.

@ldecicco-USGS
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Hi @pachadotdev and @BriannaLind , checking in to see if you could update us on an approximate timeline for when you'll be able to do the review.

@trangdata
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I think its totally fine for users to install extra packages separately - I mostly was thinking of a 'new R user' who is going to want to really work through your examples and copy and paste the script ---that it would be nice to have library(XXX) above the code snippet to reduce frustration.

@BriannaLind ah gotcha! That makes sense. I'll keep this in mind when updating the readme.

ll try to have my review done by Thu

@pachadotdev Thank you!!! I'm excited to hear your feedback! 🙌🏽

@maurolepore
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Dear all,

My EiC rotation just started and I'm checking the status of open issues. I don't mean to intrude but to save you time. So while I'm here I note the second review might be ready soon.

@pachadotdev, any updates?

@pachadotdev
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Dear all,

My EiC rotation just started and I'm checking the status of open issues. I don't mean to intrude but to save you time. So while I'm here I note the second review might be ready soon.

@pachadotdev, any updates?

hi!
I can send it by tonight

@pachadotdev
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ready
how do I upload this?

@ldecicco-USGS
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Hi @pachadotdev - copy and paste the text in the comments. If there are any formatting issues I can take a look and see how to fix it up.

@pachadotdev
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Package Review (1)

Please check off boxes as applicable, and elaborate in comments below. Your review is not limited to these topics, as described in the reviewer guide

  • Briefly describe any working relationship you have (had) with the package authors.

  • As the reviewer I confirm that there are no conflicts of interest for me to review this work (if you are unsure whether you are in conflict, please speak to your editor before starting your review).

Documentation

The package includes all the following forms of documentation:

  • A statement of need: clearly stating problems the software is designed to solve and its target audience in README

  • Installation instructions: for the development version of package and any non-standard dependencies in README

  • Vignette(s): demonstrating major functionality that runs successfully locally

  • Function Documentation: for all exported functions

  • Examples: (that run successfully locally) for all exported functions

  • Community guidelines: including contribution guidelines in the README or CONTRIBUTING, and DESCRIPTION with URL, BugReports and Maintainer (which may be autogenerated via Authors@R).

Functionality

  • Installation: Installation succeeds as documented.

  • Functionality: Any functional claims of the software been confirmed.

  • Performance: Any performance claims of the software been confirmed.

  • Automated tests: Unit tests cover essential functions of the package and a reasonable range of inputs and conditions. All tests pass on the local machine.

  • Packaging guidelines: The package conforms to the rOpenSci packaging guidelines.

Estimated hours spent reviewing: 3.5

  • Should the author(s) deem it appropriate, I agree to be acknowledged as a package reviewer ("rev" role) in the package DESCRIPTION file.

Review Comments

Sorry for the delay! The outputs look strange on Windows, but it works perfect on Ubuntu. After checking, it is because I had older pkgs on Windows.

@pachadotdev
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Package Review

Please check off boxes as applicable, and elaborate in comments below. Your review is not limited to these topics, as described in the reviewer guide

  • Briefly describe any working relationship you have (had) with the package authors.

  • As the reviewer I confirm that there are no conflicts of interest for me to review this work (if you are unsure whether you are in conflict, please speak to your editor before starting your review).

Documentation

The package includes all the following forms of documentation:

  • A statement of need: clearly stating problems the software is designed to solve and its target audience in README

  • Installation instructions: for the development version of package and any non-standard dependencies in README

  • Vignette(s): demonstrating major functionality that runs successfully locally

  • Function Documentation: for all exported functions

  • Examples: (that run successfully locally) for all exported functions

  • Community guidelines: including contribution guidelines in the README or CONTRIBUTING, and DESCRIPTION with URL, BugReports and Maintainer (which may be autogenerated via Authors@R).

Functionality

  • Installation: Installation succeeds as documented.

  • Functionality: Any functional claims of the software been confirmed.

  • Performance: Any performance claims of the software been confirmed.

  • Automated tests: Unit tests cover essential functions of the package and a reasonable range of inputs and conditions. All tests pass on the local machine.

  • Packaging guidelines: The package conforms to the rOpenSci packaging guidelines.

Estimated hours spent reviewing: 3.5

  • Should the author(s) deem it appropriate, I agree to be acknowledged as a package reviewer ("rev" role) in the package DESCRIPTION file.

Review Comments

Sorry for the delay! The outputs look strange on Windows, but it works perfect on Ubuntu. After checking, it is because I had older pkgs on Windows.

@ldecicco-USGS
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@ropensci-review-bot submit review #560 (comment) time 3.5

@ropensci-review-bot
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Couldn't find entry for pachadotdev in the reviews log

@ldecicco-USGS
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@ropensci-review-bot submit review #560 (comment) time 6

@ropensci-review-bot
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Logged review for BriannaLind (hours: 6)

@ldecicco-USGS
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Thanks @pachadotdev and @BriannaLind for the reviews!

It seems like you both gave the package a test drive and things are looking pretty good. I don't see any major suggestions that were put forth yet to fix. Is that right? When I first looked at the package via the editor review, I also thought it was in pretty good shape!

If that's correct, @pachadotdev and @BriannaLind , could you use the Approval template and verify:
https://devguide.ropensci.org/approval2template.html

@BriannaLind
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BriannaLind commented Feb 10, 2023

Reviewer Response

Final approval (post-review)

  • The author has responded to my review and made changes to my satisfaction. I recommend approving this package.

Estimated hours spent reviewing: 6

@pachadotdev
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pachadotdev commented Feb 11, 2023

Reviewer Response

Final approval (post-review)

  • The author has responded to my review and made changes to my satisfaction. I recommend approving this package.

Estimated hours spent reviewing: 3.5

@ldecicco-USGS
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@ropensci-review-bot approve openalexR

@ropensci-review-bot
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Approved! Thanks @trangdata for submitting and @BriannaLind, @pachadotdev for your reviews! 😁

To-dos:

  • Transfer the repo to rOpenSci's "ropensci" GitHub organization under "Settings" in your repo. I have invited you to a team that should allow you to do so. You will need to enable two-factor authentication for your GitHub account.
    This invitation will expire after one week. If it happens write a comment @ropensci-review-bot invite me to ropensci/<package-name> which will re-send an invitation.
  • After transfer write a comment @ropensci-review-bot finalize transfer of <package-name> where <package-name> is the repo/package name. This will give you admin access back.
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Should you want to acknowledge your reviewers in your package DESCRIPTION, you can do so by making them "rev"-type contributors in the Authors@R field (with their consent).

Welcome aboard! We'd love to host a post about your package - either a short introduction to it with an example for a technical audience or a longer post with some narrative about its development or something you learned, and an example of its use for a broader readership. If you are interested, consult the blog guide, and tag @ropensci/blog-editors in your reply. They will get in touch about timing and can answer any questions.

We maintain an online book with our best practice and tips, this chapter starts the 3d section that's about guidance for after onboarding (with advice on releases, package marketing, GitHub grooming); the guide also feature CRAN gotchas. Please tell us what could be improved.

Last but not least, you can volunteer as a reviewer via filling a short form.

@ldecicco-USGS
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@trangdata Congratulations on the great package. Sorry the timing went a little longer than usual. The "bot" automatically closes this issue when the package gets approved, but we can still use the issue to communicate (or feel free to re-open it if you have any questions).

Let me know if you have any questions on the instructions above.

Once again, thanks for submitting to rOpenSci and great work! 🎉

@trangdata
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trangdata commented Feb 23, 2023

@ldecicco-USGS Thank you so much! ❤️ And huge thank you to the reviewers @pachadotdev and @BriannaLind for your valuable feedback! 🌈 Would you both be okay with us listing you as reviewers in our DESCRIPTION file?

On the first TODO: @ldecicco-USGS Could you please add (or ask the bot to add) @massimoaria to ropensci so he could transfer "ownership" of the repository, please? The package currently lives at https://github.com/massimoaria/openalexR. Thank you!

@maelle
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maelle commented Feb 24, 2023

I sent an invitation to the organization to @massimoaria. Please ping me when the repo is transferred so that I might give @massimoaria admin access back.

Sorry for the clunkiness, it's only the second time in a short time we encounter this case ropensci-org/buffy#98

@massimoaria
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massimoaria commented Feb 24, 2023 via email

@maelle
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maelle commented Feb 24, 2023

Awesome, thanks! I've given you admin rights and write access to @trangdata but now that you have admin rights you can increase @trangdata's as needed.

@trangdata
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@massimoaria Any chance you could give me admin access so it's easier for me to make changes such as change the repo description url. Thank you! 🌱

@massimoaria
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Done!

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