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[REVIEW]: APCtools: Descriptive and Model-based Age-Period-Cohort Analysis #4056

Closed whedon closed 2 years ago

whedon commented 2 years ago

Submitting author: !--author-handle-->@bauer-alex<!--end-author-handle-- (Alexander Bauer) Repository: https://github.com/bauer-alex/APCtools Branch with paper.md (empty if default branch): Version: v1.0.3 Editor: !--editor-->@Nikoleta-v3<!--end-editor-- Reviewers: @strengejacke, @jaybee84 Archive: 10.5281/zenodo.6514036

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Conflict of interest

Code of Conduct

General checks

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whedon commented 2 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @strengejacke , @fernandomayer it looks like you're currently assigned to review this paper :tada:.

:warning: JOSS reduced service mode :warning:

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whedon commented 2 years ago

Wordcount for paper.md is 991

whedon commented 2 years ago 
Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.04 s (1044.8 files/s, 145674.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               25            650           1199           1927
SVG                              2              1              1            697
YAML                             7             50             13            214
Markdown                         3             45              0            190
TeX                              1             11              0             98
Rmd                              2            107            278             96
-------------------------------------------------------------------------------
SUM:                            40            864           1491           3222
-------------------------------------------------------------------------------

Statistical information for the repository '91f3f69d15904ad483789651' was
gathered on 2022/01/12.
No commited files with the specified extensions were found.
whedon 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
whedon 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

👋🏼 @bauer-alex @strengejacke @fernandomayer this is the review thread for the paper. All of our communications will happen here from now on.

Both reviewers have checklists at the top of this thread with the JOSS requirements 🔝 As you go over the submission, please check any items that you feel have been satisfied. There are also 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 #4056 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 Whedon (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 (@Nikoleta-v3 ) if you have any questions/concerns 👍🏻

whedon commented 2 years ago

:wave: @strengejacke , please update us on how your review is going (this is an automated reminder).

whedon commented 2 years ago

:wave: @fernandomayer, please update us on how your review is going (this is an automated reminder).

Nikoleta-v3 commented 2 years ago

👋 @strengejacke & @fernandomayer - I hope you are well. Any updates regarding your reviews? 😄

strengejacke commented 2 years ago

Sorry for the delay. Will go on with my reviews the next days. :-)

Nikoleta-v3 commented 2 years ago

Great! Thank you for your reply 😄

fernandomayer commented 2 years ago

Hi, I will be able to start my review in the next week.

strengejacke commented 2 years ago

I have finished my review. Three points have not yet been addressed satisfactory, so some minor revisions needed for acceptance.

bauer-alex commented 2 years ago

@strengejacke Thanks so much for the review and the helpful comments in our issues. We now changed the readme and the paper itself to try to resolve all issues (see issue 1, issue 2 and issue 3).

Regarding the last of the above issues (the missing high-level summary) we were a bit unsure of what you think is missing in the paper, since we already had a short, high-level introduction. Either way, we now extended this high-level introduction a bit and restructured the initial part of the paper, s.t. it hopefully fits the need. What do you think?

bauer-alex commented 2 years ago

@whedon generate pdf

whedon 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:

strengejacke commented 2 years ago

Yes, that looks better, thanks! I'm following the guidelines (see e.g. https://joss.readthedocs.io/en/latest/submitting.html#what-should-my-paper-contain) that require the paper to have a short summary, followed by statement-of-need section. I'm not sure how @Nikoleta-v3 likes to handle this, if preferred as two separate sections or integrated in one (as you have it now), so I would leave this decision to the editors. In general, your additions would meet the needs for a short summary, you could just make two sections from your currently one statement-of-need section in the paper. Else, all remaining issues have been addressed.

Nikoleta-v3 commented 2 years ago

Thank you for your review @strengejacke!

I agree with the reviewer that the paper should include both a summary and a statement-of-need. The summary describes what the package is whereas the statement of need describes why the package is important. I find summaries very useful. You can just include 2-3 sentences describing APCtools. Here is an example: https://joss.theoj.org/papers/10.21105/joss.03465.

One comment regarding https://github.com/bauer-alex/APCtools/issues/5. I can see that your package includes tests.

Please include in your documentation guidelines on running these tests (apologies if they already exist and I missed them). That way if someone wants to contribute to the package they will know how to run your test suite.

bauer-alex commented 2 years ago

Alright, thanks for the input @strengejacke and @Nikoleta-v3.

We now

  1. added a note on running the unit tests in the readme.
  2. splitted our introduction in the paper into a Summary section (serving as a really short abstract for the paper) and a Statement of Need section.

Hope this fits your expectations?

bauer-alex commented 2 years ago

@whedon generate pdf

whedon 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'll render the pdf once again, after another minor update to enlarge one figure in the rendered version.

bauer-alex commented 2 years ago

@whedon generate pdf

whedon 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:

strengejacke commented 2 years ago

Thanks, looks good to me! I recommend accept.

Nikoleta-v3 commented 2 years ago

Thank you both for your work 😃

Nikoleta-v3 commented 2 years ago

@bauer-alex once @fernandomayer has completed their review and you have addressed their comments - I will also have a final look at the paper, and then it should be good to go 👍🏻

bauer-alex commented 2 years ago

@fernandomayer Do you know when you will be able to review the paper? Thing is that the paper is part of my PhD thesis which I want to submit in about 10 days. If possible, it would be great if you could do the revision next week? I absolutely do not want to push you, as I know that this is just additional work on the side for you. I just wanted to note that, if possible, it would be nice-to-have to start the revision in the following week. :) If not possible, it's also no big deal for me to use the in submission version of the paper for the thesis.

fernandomayer commented 2 years ago

Hi @bauer-alex, I will do my best to submit my review up to this Thursday.

bauer-alex commented 2 years ago

@fernandomayer Any update on the revision process? If you don't find time we could maybe also find another reviewer (which would of course be up to @Nikoleta-v3 to decide)?

Nikoleta-v3 commented 2 years ago

I would like to give @fernandomayer first some more time to complete their review 😄

bauer-alex commented 2 years ago

Alright. Sorry if my question came a few weeks too early!

Nikoleta-v3 commented 2 years ago

No worries 😄 Let's wait for the reviewer to get back to us.

fernandomayer commented 2 years ago

Hi @bauer-alex and @Nikoleta-v3, I regret to inform you that I will not be able to complete my review in the next few days. So, feel free to invite other reviewers. Sorry for the inconvenience.

Nikoleta-v3 commented 2 years ago

That's absolutely fine @fernandomayer! Thank you for letting us know 😄

Nikoleta-v3 commented 2 years ago

@editorialbot remove @fernandomayer from reviewers

editorialbot commented 2 years ago

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

@editorialbot commands

Nikoleta-v3 commented 2 years ago

@editorialbot commands

editorialbot commented 2 years ago

Hello @Nikoleta-v3, here are the things you can ask me to do:


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Nikoleta-v3 commented 2 years ago

@editorialbot remove @fernandomayer from reviewers

editorialbot commented 2 years ago

@fernandomayer removed from the reviewers list!

Nikoleta-v3 commented 2 years ago

@bauer-alex I've already reached out to someone else asking them to review this.

Nikoleta-v3 commented 2 years ago

@editorialbot add @jaybee84 as reviewers

editorialbot commented 2 years ago

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

@editorialbot commands

Nikoleta-v3 commented 2 years ago

@editorialbot add @jaybee84 as reviewer

editorialbot commented 2 years ago

@jaybee84 added to the reviewers list!

Nikoleta-v3 commented 2 years ago

👋🏼 @jaybee84 thank you again for agreeing to review this submission!

Can you please comment:

@editorialbot generate my checklist

on this issue.

This will generate a checklist. As you go over the submission, please check any items that you feel have been satisfied.

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 https://github.com/openjournals/joss-reviews/issues/4056 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.

Please feel free to ping me (@Nikoleta-v3 ) if you have any questions/concerns 👍🏻

jaybee84 commented 2 years ago

Review checklist for @jaybee84

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Nikoleta-v3 commented 2 years ago

👋 @jaybee84 - I hope you are well. Any updates regarding your review? 😄

jaybee84 commented 2 years ago

@Nikoleta-v3 .. I had started the process but got behind on my own schedule.. I will try to finish it by early this week. Sorry for the delay..