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[REVIEW]: Analysing 24-hour behaviour sequence data with an Rshiny application #2282

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whedon opened this issue Jun 1, 2020 · 20 comments
Open

[REVIEW]: Analysing 24-hour behaviour sequence data with an Rshiny application #2282

whedon opened this issue Jun 1, 2020 · 20 comments
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@danielskatz @mikerspencer @aj2duncan
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@whedon
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@whedon whedon commented Jun 1, 2020 •
edited by aj2duncan

Submitting author: @jcolomb (Colomb, J.)
Repository: https://github.com/jcolomb/HCS_analysis
Version: v0.1.3
Editor: @danielskatz
Reviewer: @mikerspencer, @aj2duncan
Archive: Pending

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/ecdda22f808463b29e7808b114c1fd01"><img src="https://joss.theoj.org/papers/ecdda22f808463b29e7808b114c1fd01/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/ecdda22f808463b29e7808b114c1fd01/status.svg)](https://joss.theoj.org/papers/ecdda22f808463b29e7808b114c1fd01)

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

@mikerspencer & @aj2duncan, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

  1. Make sure you're logged in to your GitHub account
  2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

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

✨ Please try and complete your review in the next six weeks ✨

Review checklist for @mikerspencer

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

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 (@jcolomb) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state 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?

Review checklist for @aj2duncan

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

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 (@jcolomb) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state 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?
@whedon whedon added the review label Jun 1, 2020
@whedon whedon mentioned this issue Jun 1, 2020
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@whedon
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@whedon whedon commented Jun 1, 2020

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @mikerspencer, @aj2duncan it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

  1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

watching

  1. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

notifications

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

@whedon commands

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

@whedon generate pdf
@whedon
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@whedon whedon commented Jun 1, 2020

👉 Check article proof 📄 👈

@danielskatz
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@danielskatz danielskatz commented Jun 1, 2020

👋 @mikerspencer & @aj2duncan - thanks again for agreeing to review this submission. Please be sure to read the comments above, and let me know if you have any questions. Basically, your job is to check the article proof and repository and check items off your checklist above.

If you see small problems that need to be discussed, feel free to discuss them here. But if you can, create a new issue in the target repository and link to this review thread in that issue to create corresponding breadcrumb trail here.

I look forward to seeing how this review goes!
@mikerspencer
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@mikerspencer mikerspencer commented Jun 8, 2020

@danielskatz to be clear - @aj2duncan and I work together a little. Reviewers working together isn't specifically mentioned in the conflict of interest, but I feel it's best to be transparent.
@danielskatz
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@danielskatz danielskatz commented Jun 8, 2020

Thanks for letting me know. This isn't 100% ideal, but given that you both likely have different backgrounds and experiences, and we're focusing on a checklist-driven process, it should be ok. Let's see how it goes.
@aj2duncan
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@aj2duncan aj2duncan commented Jun 9, 2020

Thanks @mikerspencer and apologies @danielskatz, I should have raised this too. I'm happy to provide more detail on this if needed and I'm pretty sure @mikerspencer would be too.
@mikerspencer mikerspencer mentioned this issue Jun 12, 2020
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@danielskatz
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@danielskatz danielskatz commented Jun 16, 2020

👋 @jcolomb - it looks like there's an issue blocking @mikerspencer ..

@aj2duncan & @mikerspencer - how are your reviews coming along otherwise?
@aj2duncan
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@aj2duncan aj2duncan commented Jun 18, 2020

@danielskatz now @jcolomb has confirmed a particular part of the installation isn't necessary I will push on with the review.
@danielskatz
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@danielskatz danielskatz commented Jun 18, 2020

Thanks - please make sure the documentation matches what you learn
@aj2duncan aj2duncan mentioned this issue Jun 19, 2020
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@danielskatz
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@danielskatz danielskatz commented Jun 26, 2020

👋 @aj2duncan & @mikerspencer - how are your reviews doing?
@aj2duncan
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@aj2duncan aj2duncan commented Jul 1, 2020

@jcolomb quick query - In the shiny app and article you make reference to the 18 Berlin categories. Should this have a reference?
@aj2duncan aj2duncan mentioned this issue Jul 1, 2020
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@jcolomb
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@jcolomb jcolomb commented Jul 2, 2020

no, this is a "in-house" categorisation that was (so far) not published.
@aj2duncan
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@aj2duncan aj2duncan commented Jul 2, 2020

no, this is a "in-house" categorisation that was (so far) not published.

Thanks for the clarification.
@danielskatz
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@danielskatz danielskatz commented Jul 5, 2020

👋 @aj2duncan & @mikerspencer - I'm just checking on your reviews and their progress again...
@aj2duncan
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@aj2duncan aj2duncan commented Jul 8, 2020

@danielskatz everything seems to be moving along ok for me.
@mikerspencer
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@mikerspencer mikerspencer commented Jul 17, 2020

@danielskatz can I check the scope of the review? How involved should we be as reviewers? I think testing should be done prior to review, but realise that's a grey area on problems picked up in the review.
@danielskatz
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@danielskatz danielskatz commented Jul 17, 2020

@mikerspencer - I don't think I understand what you are asking. You should do as much as possible to verify the criteria in the checklist, subject to reasonable effort, and then report what problems you come across so that the submitter can respond. I'm confused when you say "I think testing should be done prior to review" There should be some tests provided by the submitter (either manual or via some script or something else), and part of your job is to verify that they work and that you think they are reasonable, given the software, and the JOSS documentation about testing

Let me know if this helps, and if not, please ask me again.
@mikerspencer
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@mikerspencer mikerspencer commented Jul 20, 2020

Thanks @danielskatz your comment on verification is helpful. I think working on this issue (jcolomb/HCS_analysis#18) is becoming more like co-creation. Keen to have your experienced view!
@danielskatz
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@danielskatz danielskatz commented Jul 20, 2020

Well, ideally everything should work for the reviewer when they first try it, but if that was guaranteed, we wouldn't need any reviews :)

So, yes, sometimes the reviewers will work with the author to test things and this can be somewhat iterative. If it's too much work, you can ask the author to go off and test with colleagues and come back when they are fairly sure the tests will pass for the reviewers, but sometimes, there is something tricky that does need to be worked out between reviewers and authors too.

Thanks for your help in doing this, and getting this far.
@mikerspencer
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@mikerspencer mikerspencer commented Jul 20, 2020

No problem, thanks for clarifying - I appreciate it's a fine line!

@aj2duncan has done most of the work so far I think.
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