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

[editorialbot]

Submitting author: !--author-handle-->@gavinsimpson<!--end-author-handle-- (Gavin L. Simpson) Repository: https://github.com/gavinsimpson/gratia Branch with paper.md (empty if default branch): joss-paper Version: v0.9.2 Editor: !--editor-->@lrnv<!--end-editor-- Reviewers: @dill, @vankesteren, @njtierney Archive: Pending

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/8d2134cd22269bc7d268368d333f1a97"><img src="https://joss.theoj.org/papers/8d2134cd22269bc7d268368d333f1a97/status.svg"></a>
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

[editorialbot]

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:

@editorialbot commands

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

@editorialbot generate pdf

[editorialbot]

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]

Paper file info:

📄 Wordcount for paper.md is 2636

✅ The paper includes a Statement of need section

[editorialbot]

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]

License info:

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

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[lrnv]

@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 openjournals/joss-reviews#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]

@editorialbot add @njtierney as reviewer

[editorialbot]

@njtierney added to the reviewers list!

[lrnv]

@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]

Review checklist for @dill

Conflict of interest

• [x] 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

• [x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• [x] Repository: Is the source code for this software available at the https://github.com/gavinsimpson/gratia?
• [x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• [x] 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?
• [x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• [x] 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.
• [x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• [x] 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

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] 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

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

• [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [x] 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?
• [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] 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]

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]

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]

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

[dill]

Comments on the paper are given in https://github.com/gavinsimpson/gratia/issues/296.

[dill]

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]

Review checklist for @vankesteren

Conflict of interest

• [x] 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

• [x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• [x] Repository: Is the source code for this software available at the https://github.com/gavinsimpson/gratia?
• [x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• [x] 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?
• [x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• [x] 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.
• [x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• [x] 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

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] 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

• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• [x] 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

• [x] 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?
• [x] 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]

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]

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!

[lrnv]

@njtierney, did you have the time to take a look at the package yet?

@gavinsimpson, how is the review going so far? It looks like the discussions are extensive and interesting from here, but I wanted to ask your opinion!