[PRE 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 Managing EiC: Chris Vernon

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[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]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.31 s (1286.5 files/s, 345732.8 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:

  2268  Gavin Simpson
   150  Gavin L. Simpson
    25  runner
    23  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 2623

✅ The paper includes a Statement of need section

[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:

[editorialbot]

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⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

[gavinsimpson]

Suggestions for reviewers from list:

• vankesteren
• njtierney
• epiben

Suggestions for reviewers

• Andreas Bender (adibender) - maintainer of pammtools an R package for fitting and visualizing event history models fitted as GAMs
• Nick Golding (goldingn) would be suitable too

Depending on the statute of limitations on CoIs from having coauthored a paper 5-ish years ago, obvious reviewers would be

• Dave Miller (dill)
• Noam Ross (noamross)

But they might decline anyway. Paper we published: https://doi.org/10.7717/peerj.6876

[gavinsimpson]

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

The package is licensed MIT: https://github.com/gavinsimpson/gratia/blob/main/LICENSE.md. That this isn't clearer in the repo is because of the requirements for conveying license info in R packages that are on CRAN.

[crvernon]

@editorialbot invite @lrnv as editor

:wave: @lrnv - are you able to take this one on?

[editorialbot]

Invitation to edit this submission sent!

[lrnv]

Yes I can of course !

[lrnv]

@editorialbot assign me as editor

[editorialbot]

Assigned! @lrnv is now the editor

[lrnv]

@vankesteren, @njtierney, @epiben, @adibender, @goldingn, @dill, @noamross, would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

[epiben]

Would have loved to, but I have one week left before the summer holiday and a lot on my plate, so I think it's best if I sit this one over. Hopefully, the others are available as this seem a solid package.

[dill]

@lrnv happy to do so, provided I don't have too strict a time limit. I can probably get it done within the next 3-4 weeks if that works for you.

[lrnv]

@epiben okay then.

@dill we usually aim for a 6 to 8 weeks review time, so your constraint seem to fit, great !

We aim for 2/3 reviewers so let us wait for others to answer and then we'll start the review.

[goldingn]

Sorry @lrnv, I haven't done a JOSS review in ages so would love to, but I will be slammed for at least the next couple of months :(

[vankesteren]

I can do it in August! Will be on holiday in the second half of July. I'll set a reminder to myself to do it asap after.

[lrnv]

Ok that is great ! Let us wait a bit more to see if we get a third reviewer and we'll launch the review.

[noamross]

I'm afraid I can't do it this month.

[adibender]

Unfortunately, I won't be able to do it.

[lrnv]

@njtierney would you be available to take up this review ?

[lrnv]

@editorialbot add @dill as reviewer

[editorialbot]

@dill added to the reviewers list!

[lrnv]

@editorialbot add @vankesteren as reviewer

[editorialbot]

@vankesteren added to the reviewers list!

[lrnv]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/6962.

[njtierney]

Hi there! Sorry I missed the opportunity to review this package! It's a great piece of work, sounds like you are all sorted for reviewers, @gavinsimpson and @crvernon but let me know if I can help

[lrnv]

@njtierney If you want to review it, we accept extra reviewers as the more the btter for the quantity -- and hence often quality -- of feedback to the authors. I could still add you to the reviewer list if you want ?

[njtierney]

@njtierney If you want to review it, we accept extra reviewers as the more the btter for the quantity -- and hence often quality -- of feedback to the authors. I could still add you to the reviewer list if you want ?

Sounds good! I'd be happy to review

[lrnv]

Okay then I'll add you up :)