[REVIEW]: APCtools: Descriptive and Model-based Age-Period-Cohort Analysis

whedon commented 2 years ago

Submitting author: !--author-handle-->@bauer-alex@Nikoleta-v3<!--end-editor-- Reviewers: @strengejacke, @jaybee84 Archive: 10.5281/zenodo.6514036

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@strengejacke & @fernandomayer, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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✨ 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 ✨

Review checklist for @strengejacke

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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.

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General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@bauer-alex) 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

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 and who the target audience is?
[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?

Review checklist for @fernandomayer

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
[ ] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[ ] Contribution and authorship: Has the submitting author (@bauer-alex) 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

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 and who the target audience is?
[ ] 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?

jaybee84 commented 2 years ago

@Nikoleta-v3 Re: Contribution and authorship: From the commit history of the package the contributions of 2 out of 3 authors is evident. From some of the references the contribution of the third author is implicit. Would it be ideal to include an author contribution section (similar to https://www.elsevier.com/authors/policies-and-guidelines/credit-author-statement) in the readme so that the contribution and attributions are more explicit?

Nikoleta-v3 commented 2 years ago

No worries at all :) thank you again for volunteering your time!

I am not against the suggestion but it’s something that is required for publication. JOSS has chosen a style where it doesn’t list the contributions per author. I am not sure why 🤷🏻 I am happy to drop a message to the rest of the editors and get back to you with more information 😄

bauer-alex commented 2 years ago

Thanks so much for the input @jaybee84. I have now added the explicit license text in the LICENSE file (see https://github.com/bauer-alex/APCtools/issues/7).

Also, I found that we made a minor mistake in the labels of the density matrix in the paper. I fixed it now and will re-generate the pdf with the next message. Nothing else has changed in the paper.

bauer-alex commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

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

bauer-alex commented 2 years ago

I just updated the paper regarding the points raised by @jaybee84 in https://github.com/bauer-alex/APCtools/issues/8. See the respective issue for details.

bauer-alex commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

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

bauer-alex commented 2 years ago

The final points of @jaybee84 were now addressed in https://github.com/bauer-alex/APCtools/issues/8. I'm newly generating the pdf with the latest additions. Thanks again for the input @jaybee84!

So I thing we resolved all issues, or am I missing something?

bauer-alex commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

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

jaybee84 commented 2 years ago

Thanks! looks great. I am happy to recommend accepting the article.

bauer-alex commented 2 years ago

@Nikoleta-v3 Are we ready for publication, or is something else missing from your side?

Nikoleta-v3 commented 2 years ago

Thank you @bauer-alex for your work! Apologies for the delay I was out of the office 🇬🇷

Some last minor comments from me:

Can you please fix the reference Apc: Age-period-cohort analysis. to be apc: Age-period-cohort analysis.
In your README file it is easy to miss the documentation (useful materials). Could you make Useful materials a section? and maybe rename it to documentation and useful material?

bauer-alex commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

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

Nikoleta-v3 commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago

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

OK DOIs

- 10.1002/sim.2764 is OK
- 10.1093/biostatistics/kxi028 is OK
- 10.1097/EDE.0000000000001236 is OK
- 10.1093/biomet/asn026 is OK
- 10.1158/1055-9965.EPI-14-0300 is OK
- 10.18637/jss.v021.i08 is OK
- 10.1177/1354816620987198 is OK
- 10.1201/9781315370279 is OK
- 10.1201/b13902 is OK

MISSING DOIs

- None

INVALID DOIs

- None

bauer-alex commented 2 years ago

@Nikoleta-v3 Thanks for the final input, especially regarding the reference! Both points are now resolved.

Nikoleta-v3 commented 2 years ago

Thank you! At this point could you:

[ ] Make a tagged release of your software, and list the version tag of the archived version here.
[ ] Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
[ ] Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
[ ] Please list the DOI of the archived version here.

I can then move forward with accepting the submission. Let me know if you need any help with any of the above 😄

bauer-alex commented 2 years ago

Alright. All aboves tasks are done. Here's the doi: 10.5281/zenodo.6514036

Nikoleta-v3 commented 2 years ago

Great thank you! The tagged release is v1.0.3 correct?

Also note that these tests: https://github.com/bauer-alex/APCtools/actions/runs/2262761820 are failing

bauer-alex commented 2 years ago

Yeah, v1.0.3 is correct.

And yeah, the Ubuntu devel test currently fails. This randomly happens to me every once in a while with some packages on GitHub, even when no error in the codebase is present (-> all other OS tests run without any error). I hope this is not a problem? Otherwise I'll just re-run it in the following days until it works again, and then I'll let you know again.

Nikoleta-v3 commented 2 years ago

It's okay :)

Nikoleta-v3 commented 2 years ago

@editorialbot set 10.5281/zenodo.6514036 as archive

editorialbot commented 2 years ago

Done! Archive is now 10.5281/zenodo.6514036

Nikoleta-v3 commented 2 years ago

@editorialbot set v1.0.3 as version

editorialbot commented 2 years ago

Done! version is now v1.0.3

Nikoleta-v3 commented 2 years ago

@editorialbot recommend-accept

editorialbot commented 2 years ago

Attempting dry run of processing paper acceptance...

editorialbot commented 2 years ago

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

OK DOIs

- 10.1002/sim.2764 is OK
- 10.1093/biostatistics/kxi028 is OK
- 10.1097/EDE.0000000000001236 is OK
- 10.1093/biomet/asn026 is OK
- 10.1158/1055-9965.EPI-14-0300 is OK
- 10.18637/jss.v021.i08 is OK
- 10.1177/1354816620987198 is OK
- 10.1201/9781315370279 is OK
- 10.1201/b13902 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 2 years ago

:wave: @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/3186

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/3186, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

kyleniemeyer commented 2 years ago

@editorialbot accept

editorialbot commented 2 years ago

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

editorialbot commented 2 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot commented 2 years ago

🚨🚨🚨 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 :point_right: https://github.com/openjournals/joss-papers/pull/3189
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04056
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kyleniemeyer commented 2 years ago

Congratulations @bauer-alex on your article's publication in JOSS!

Many thanks to @strengejacke and @jaybee84 for reviewing this, and @Nikoleta-v3 for editing.

editorialbot commented 2 years ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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