[REVIEW]: gratia: An R package for exploring generalized additive models #6962

editorialbot · 2024-07-04T16:42:00Z

Submitting author: @gavinsimpson (Gavin L. Simpson)
Repository: https://github.com/gavinsimpson/gratia
Branch with paper.md (empty if default branch): joss-paper
Version: v0.10.0
Editor: @lrnv
Reviewers: @dill, @vankesteren
Archive: 10.5281/zenodo.14531826

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/8d2134cd22269bc7d268368d333f1a97/status.svg)](https://joss.theoj.org/papers/8d2134cd22269bc7d268368d333f1a97)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@dill & @vankesteren, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @lrnv know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @dill

📝 Checklist for @njtierney

📝 Checklist for @vankesteren

The text was updated successfully, but these errors were encountered:

editorialbot · 2024-07-04T16:42:03Z

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

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For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

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editorialbot · 2024-07-04T16:42:30Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.31 s (1312.0 files/s, 352583.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                            251              0              0          72564
R                              100           2827           7316          18046
Markdown                        31            587              0           4019
Rmd                              6            251            619            562
XML                              2              0              3            456
TeX                              2             27              0            369
YAML                             7             46             19            226
make                             1             20              1             72
CSS                              1              0              0              4
Sass                             1              0              0              1
-------------------------------------------------------------------------------
SUM:                           402           3758           7958          96319
-------------------------------------------------------------------------------

Commit count by author:

  2270	Gavin Simpson
   150	Gavin L. Simpson
    25	runner
    24	gavinsimpson
     5	Henrik Singmann
     3	Lars Dalby
     1	David Lawrence Miller
     1	DavisVaughan
     1	John Muschelli

editorialbot · 2024-07-04T16:42:34Z

Paper file info:

📄 Wordcount for paper.md is 2636

✅ The paper includes a Statement of need section

editorialbot · 2024-07-04T16:42:35Z

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1016/j.csda.2012.01.026 is OK
- 10.1111/j.1467-9868.2010.00749.x is OK
- 10.1080/01621459.2016.1180986 is OK
- 10.1007/s11222-019-09864-2 is OK
- 10.18637/jss.v080.i01 is OK
- 10.7717/peerj.6876 is OK
- 10.3389/fevo.2018.00149 is OK
- 10.18637/jss.v059.i10 is OK
- 10.1007/978-3-319-24277-4 is OK
- 10.1007/BFb0086566 is OK
- 10.32614/rj-2018-009 is OK
- 10.1201/9780429459016 is OK
- 10.1109/TVCG.2023.3327195 is OK
- 10.5281/ZENODO.10782896 is OK
- 10.1111/1467-9868.00374 is OK
- 10.1111/j.2517-6161.1983.tb01239.x is OK
- 10.1214/AOS/1176349743 is OK

MISSING DOIs

- No DOI given, and none found for title: Generalized Additive Models: An Introduction with ...
- 10.1201/9780203753781-6 may be a valid DOI for title: Generalized Additive Models
- No DOI given, and none found for title: Bayesian views of generalized additive modelling
- No DOI given, and none found for title: A practical guide to splines
- 10.32614/cran.package.gjrm may be a valid DOI for title: GJRM: Generalised Joint Regression Modelling
- No DOI given, and none found for title: R: A Language and Environment for Statistical Comp...
- No DOI given, and none found for title: R for data science: Import, tidy, transform, visua...
- 10.1214/aoms/1177697089 may be a valid DOI for title: A Correspondence Between Bayesian Estimation on St...
- 10.1111/j.2517-6161.1985.tb01327.x may be a valid DOI for title: Some Aspects of the Spline Smoothing Approach to N...

INVALID DOIs

- None

editorialbot · 2024-07-04T16:42:37Z

License info:

🟡 License found: Other (Check here for OSI approval)

editorialbot · 2024-07-04T16:43:33Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

lrnv · 2024-07-04T16:44:03Z

@dill, @vankesteren, @gavinsimpson this is the review thread for the paper. All of our communications will happen here (and on issues/prs on the submitted repository) from now on.

@dill, @vankesteren, as reviewers, the first step for each of you is to create a checklist for your review by entering

@editorialbot generate my checklist

as the top of a new comment in this thread. These checklists contain the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. The first comment in this thread also contains links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention #6962 so that a link is created to this thread (and I can keep an eye on what is happening !). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within about 2-4 weeks. Please let me know if any of you require some more time. We can also use EditorialBot (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@lrnv) if you have any questions/concerns.

lrnv · 2024-07-12T07:52:22Z

@editorialbot add @njtierney as reviewer

editorialbot · 2024-07-12T07:52:25Z

@njtierney added to the reviewers list!

lrnv · 2024-07-12T07:53:24Z

@njtierney there you go ! Look at the instructions that i wrote for other reviewers in this thread (which is now the review thread, the other one should stay closed up), nice to have you onboard too !

dill · 2024-07-14T07:39:44Z

Review checklist for @dill

Conflict of interest

I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the https://github.com/gavinsimpson/gratia?
License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@gavinsimpson) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed?
Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
State of the field: Do the authors describe how this software compares to other commonly-used packages?
Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

njtierney · 2024-07-15T03:37:37Z

Review checklist for @njtierney

Conflict of interest

I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the https://github.com/gavinsimpson/gratia?
License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@gavinsimpson) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed?
Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
State of the field: Do the authors describe how this software compares to other commonly-used packages?
Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

dill · 2024-07-15T06:34:30Z

In terms of conflict of interest: I've worked with @gavinsimpson several times, having written a paper together and taught two courses. I've also made a contribution to gratia. I don't feel like this will have a material impact on my ability to review the paper -- I'm invested in the package being the best it can be, this requires constructive criticism.

lrnv · 2024-07-15T07:22:58Z

@dill, Yes, I think we discussed this already in the pre-review, and decided it was fine.

dill · 2024-07-15T07:24:49Z

Comments on the paper are given in gavinsimpson/gratia#296.

dill · 2024-07-15T07:26:52Z

Great! Just wanted to make sure everything was above board here :)On 15 Jul 2024, at 08:23, Oskar Laverny ***@***.***> wrote: @dill, Yes, I think we discussed this already in the pre-review, and decided it was fine. —Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you were mentioned.Message ID: ***@***.***>

vankesteren · 2024-07-29T08:49:53Z

Review checklist for @vankesteren

Conflict of interest

I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the https://github.com/gavinsimpson/gratia?
License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@gavinsimpson) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed?
Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
State of the field: Do the authors describe how this software compares to other commonly-used packages?
Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

vankesteren · 2024-08-05T10:41:34Z

I have finished my review and added my comment in the two issues mentioned above. I will update my checklist as the comments are resolved.

dill · 2024-08-12T09:56:27Z

Sorry for the late reply here, I concluded my review with comments listed above in the gratia repo. Once those are resolved, I'm happy with the package!

editorialbot · 2024-12-20T10:02:10Z

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

lrnv · 2024-12-20T10:02:24Z

@editorialbot recommend-accept

editorialbot · 2024-12-20T10:02:27Z

Attempting dry run of processing paper acceptance...

editorialbot · 2024-12-20T10:02:57Z

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- 10.1016/j.csda.2012.01.026 is OK
- 10.1201/9781315370279 is OK
- 10.1201/9780203753781-6 is OK
- 10.1111/j.1467-9868.2010.00749.x is OK
- 10.1080/01621459.2016.1180986 is OK
- 10.1007/s11222-019-09864-2 is OK
- 10.48550/arXiv.1902.01330 is OK
- 10.18637/jss.v080.i01 is OK
- 10.32614/CRAN.package.GJRM is OK
- 10.7717/peerj.6876 is OK
- 10.3389/fevo.2018.00149 is OK
- 10.18637/jss.v059.i10 is OK
- 10.1007/978-3-319-24277-4 is OK
- 10.1007/BFb0086566 is OK
- 10.32614/rj-2018-009 is OK
- 10.1201/9780429459016 is OK
- 10.1109/TVCG.2023.3327195 is OK
- 10.5281/ZENODO.10782896 is OK
- 10.1111/1467-9868.00374 is OK
- 10.1214/AOMS/1177697089 is OK
- 10.1111/j.2517-6161.1983.tb01239.x is OK
- 10.1111/j.2517-6161.1985.tb01327.x is OK
- 10.1214/AOS/1176349743 is OK
- 10.32614/CRAN.package.itsadug is OK
- 10.32614/CRAN.package.tidygam is OK
- 10.32614/CRAN.package.tidymv is OK
- 10.1080/10618600.2019.1629942 is OK
- 10.1080/01621459.2020.1725521 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: A practical guide to splines
- No DOI given, and none found for title: R: A Language and Environment for Statistical Comp...
- No DOI given, and none found for title: R for data science: Import, tidy, transform, visua...
- No DOI given, and none found for title: How to Interpret Statistical Models Using marginal...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

editorialbot · 2024-12-20T10:04:33Z

👋 @openjournals/dsais-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#6275, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

gavinsimpson · 2024-12-20T10:06:27Z

@lrnv Just noticed a minor typo in my affiliation. Is there time to fix this?

lrnv · 2024-12-20T10:11:17Z

@gavinsimpson Yep you can continue to fix anything you njeed to before the final publication

gavinsimpson · 2024-12-20T11:18:20Z

@editorialbot generate pdf

editorialbot · 2024-12-20T11:20:01Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

gavinsimpson · 2024-12-20T11:22:51Z

@lrnv I have fixed the two typos I found after a final read through of the proofs and am now finished editing.

Thank you for handling my submission to JOSS

crvernon · 2024-12-20T16:37:56Z

editorialbot · 2024-12-20T16:39:58Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

crvernon · 2024-12-20T23:35:25Z

@editorialbot remove @njtierney from reviewers

editorialbot · 2024-12-20T23:35:27Z

@njtierney is not in the reviewers list

crvernon · 2024-12-20T23:58:23Z

👋 @gavinsimpson - I just need you to address the following before I move to accept this for publication:

Please remove the "forthcoming" citation from the paper and bibliography.
LINE 220: The "b" in "bayesian" should be capitalized. You can achieve this by placing curly brackets around characters you wish to maintain formatting of in your bib file. Please also check all other references for correct capitalization as well.

After you have made these changes, let me know. Thanks!

gavinsimpson · 2024-12-21T00:57:52Z

@crvernon

Please remove the "forthcoming" citation from the paper and bibliography.
This paper was just published so I have updated the reference in the paper with the new metadata.
LINE 220: The "b" in "bayesian" should be capitalized. You can achieve this by placing curly brackets around characters you wish to maintain formatting of in your bib file. Please also check all other references for correct capitalization as well.
Fixed this plus another. All other references have been checked.

Thanks

crvernon · 2024-12-21T14:18:14Z

@editorialbot generate pdf

editorialbot · 2024-12-21T14:19:49Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

crvernon · 2024-12-21T14:21:26Z

@editorialbot accept

editorialbot · 2024-12-21T14:21:28Z

Doing it live! Attempting automated processing of paper acceptance...

editorialbot · 2024-12-21T14:28:31Z

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Simpson
  given-names: Gavin L.
  orcid: "https://orcid.org/0000-0002-9084-8413"
doi: 10.5281/zenodo.14531826
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Simpson
    given-names: Gavin L.
    orcid: "https://orcid.org/0000-0002-9084-8413"
  date-published: 2024-12-21
  doi: 10.21105/joss.06962
  issn: 2475-9066
  issue: 104
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6962
  title: "gratia: An R package for exploring generalized additive
    models"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06962"
  volume: 9
title: "gratia: An R package for exploring generalized additive models"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

editorialbot · 2024-12-21T14:28:35Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2024-12-21T14:28:36Z

🦋🦋🦋 👉 Bluesky post for this paper 👈 🦋🦋🦋

editorialbot · 2024-12-21T14:28:37Z

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.06962 joss-papers#6280
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06962
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

crvernon · 2024-12-21T14:47:34Z

🥳 Congratulations on your new publication @gavinsimpson! Many thanks to @lrnv for editing and @dill and @vankesteren for your time, hard work, and expertise!! JOSS wouldn't be able to function nor succeed without your efforts.

Please consider becoming a reviewer for JOSS if you are not already: https://reviewers.joss.theoj.org/join

editorialbot · 2024-12-21T14:47:36Z

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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</a>

reStructuredText:
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This is how it will look in your documentation:

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editorialbot added Makefile R review TeX Track: 5 (DSAIS) Data Science, Artificial Intelligence, and Machine Learning labels Jul 4, 2024

editorialbot assigned lrnv Jul 4, 2024

editorialbot mentioned this issue Jul 4, 2024

[PRE REVIEW]: gratia: An R package for exploring generalized additive models #6935

Closed

dill mentioned this issue Jul 15, 2024

Comments on JOSS paper gavinsimpson/gratia#296

Closed

dill mentioned this issue Jul 29, 2024

JOSS review: Community guidelines gavinsimpson/gratia#302

Closed

This was referenced Aug 5, 2024

JOSS review: paper comments gavinsimpson/gratia#304

Closed

JOSS review: code points gavinsimpson/gratia#305

Closed

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Dec 20, 2024

editorialbot added accepted published Papers published in JOSS labels Dec 21, 2024

crvernon closed this as completed Dec 21, 2024

[REVIEW]: gratia: An R package for exploring generalized additive models #6962

[REVIEW]: gratia: An R package for exploring generalized additive models #6962

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