[REVIEW]: Automated Sleep Stage Scoring Using k-Nearest Neighbors Classifier

[whedon]

Submitting author: @teamPSG (Tamas Kiss)
Repository: https://github.com/teamPSG/kNN_Sleep_Scorer_kNNSS
Version: v1.0.0
Editor: @oliviaguest
Reviewers: @Emma-k-ward, @sbuergers, @trisbek, @samikakumar
Archive: 10.5281/zenodo.4009178

⚠️ 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

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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

@Emma-k-ward & @sbuergers, 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 try and complete your review in the next six weeks ✨

Review checklist for @Emma-k-ward

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 (@teamPSG) 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 @sbuergers

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 (@teamPSG) 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 @trisbek

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 (@teamPSG) 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 @samikakumar

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 (@teamPSG) 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]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @Emma-k-ward, @sbuergers 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:

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

👉 Check article proof 📄 👈

[oliviaguest]

Hey @Emma-k-ward, @sbuergers, and @trisbek this is where the main review occurs, if you need to open something very technical as an issue please do so as an issue at the original repo but all other comments — so most, if not all, of the review — should be here. Hope this is all clear but please ask me any questions you may have! ☺️

[oliviaguest]

@whedon add @trisbek as reviewer

[whedon]

OK, @trisbek is now a reviewer

[sbuergers]

Hey @teamPSG,

This is a nicely written and well documented toolbox, well done! I used Matlab 2019b for testing and the SoftwareVerification ran without problems.

From what I could gather there are only a few points to consider:

Contribution and authorship: From the commit history it is unclear who, apart from Tamás Kiss, contributed to the software. Can you include a statement of contributions for the other authors?

References: The references in the main text do not render properly (e.g. [@STEPHENSON2009263,@BASTIANINI2014277...]). It might be that this can simply be fixed by putting a semicolon instead of a comma in-between authors, see this guide.

Community guidelines: I did not see clear guidelines for third-parties wishing to: i.) Contribute to the software, ii.) Report issues or problems with the software (other than contacting the author, but it would be useful to have some pointers for how to use github for this). There are plenty of examples here on github that do this well, for instance here.

@oliviaguest, thanks for setting us up! I take it these comments should not go in the issues of the project?

Cheers,
Steffen.

[oliviaguest]

@sbuergers thank you for your feedback so far! These seem to be appropriate to stay here — although feel free to talk to @teamPSG on how to organise these, of course!

[teamPSG]

@whedon generate pdf

[whedon]

👉 Check article proof 📄 👈

[teamPSG]

Hi @sbuergers,

Thanks for your feedback and really fast action! Glad you like the toolbox and thanks for the suggestions.

Contributions and authorship: I included a section on who did what at the end of the manuscript.

References: thanks for the hint, it worked, references are now rendered properly (during writing I checked the ms offline using the local compiler and it looked good there -- some components of the compilation workflow might have changed in the course of development...)

Community guidelines: good point, I missed this one. I added a CONTRIBUTING.md to the repo.

I guess the comments are fine right here. Thanks for the review!

Best,
Tamás

[sbuergers]

Hi @teamPSG,

thanks for implementing the feedback! This looks good to me now.

Best,
Steffen.

[oliviaguest]

Hey @Emma-k-ward and @trisbek can you give me a rough ETA for your reviews? I ask not to hurry you but just to be organised. Thank you. ☺️

[teamPSG]

Hi @oliviaguest, have you received feedback on ETA from @Emma-k-ward and/or @trisbek? (The text editor doesn't auto-complete the mention for_trisbek_ for me -- does it mean anything?) Thanks!

[oliviaguest]

@whedon check references

[whedon]

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

OK DOIs

- 10.5664/jcsm.6576 is OK
- 10.1371/journal.pcbi.1006968 is OK

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1016/S0165-0270(99)00027-8 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1053/smrv.1999.0087 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.cmpb.2016.12.004 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.jneumeth.2009.08.014 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.jneumeth.2014.07.018 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.3389/fnins.2019.00207 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.jneumeth.2020.108668 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1111/jsr.12991 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1007/s11325-019-02008-w is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.smrv.2019.07.007 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.cmpb.2019.04.032 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.3389/fphar.2018.00035 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1371/journal.pone.0224642 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.biopsych.2012.05.014 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.3109/0954898x.2013.880003 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.neuropharm.2013.06.020 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.cmpb.2020.105448 is INVALID because of 'https://doi.org/' prefix

[oliviaguest]

@teamPSG can you fix these DOIs above, please?

[teamPSG]

@whedon check references

[whedon]

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

OK DOIs

- 10.5664/jcsm.6576 is OK
- 10.1016/S0165-0270(99)00027-8 is OK
- 10.1053/smrv.1999.0087 is OK
- 10.1016/j.cmpb.2016.12.004 is OK
- 10.1371/journal.pcbi.1006968 is OK
- 10.1016/j.jneumeth.2009.08.014 is OK
- 10.1016/j.jneumeth.2014.07.018 is OK
- 10.3389/fnins.2019.00207 is OK
- 10.1016/j.jneumeth.2020.108668 is OK
- 10.1111/jsr.12991 is OK
- 10.1007/s11325-019-02008-w is OK
- 10.1016/j.smrv.2019.07.007 is OK
- 10.1016/j.cmpb.2019.04.032 is OK
- 10.3389/fphar.2018.00035 is OK
- 10.1371/journal.pone.0224642 is OK
- 10.1016/j.biopsych.2012.05.014 is OK
- 10.3109/0954898x.2013.880003 is OK
- 10.1016/j.neuropharm.2013.06.020 is OK
- 10.1016/j.cmpb.2020.105448 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[teamPSG]

@whedon generate pdf

[whedon]

👉 Check article proof 📄 👈

[teamPSG]

@oliviaguest: DOIs fixed, proof looks good to me. Thanks.

[oliviaguest]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

Check final proof 👉 openjournals/joss-papers#1706

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1706, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[teamPSG]

Thanks @oliviaguest, both files look good to me.

[oliviaguest]

Cool! Somebody from @openjournals/joss-eics will take over this final step — so just sit tight. 😊

[teamPSG]

Great! Thanks for the adventure 🌋

[kthyng]

@teamPSG Hi! I will take over from here. Can you verify the version number for your software? I also encourage you to tag a release to mark this occasion if you want.

[kthyng]

@teamPSG Your paper looks great!

[teamPSG]

Hello @kthyng! Thanks for guiding us through the last steps 🗺️

Version number is v1.0 and I created a release with this tag here: https://github.com/teamPSG/kNN_Sleep_Scorer_kNNSS/releases/tag/v1.0

[kthyng]

Ok, looks good.

[kthyng]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.02377 joss-papers#1709
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02377
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[kthyng]

Congrats on your new publication @teamPSG! Thanks to editor @oliviaguest and reviewers @Emma-k-ward, @sbuergers, @trisbek, and @samikakumar. This process couldn't happen without your time and hard work.

(will leave issue open until the doi resolves)

[teamPSG]

Thanks everybody for your contribution in the work! (The DOI now resolves alright).

[whedon]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.02377/status.svg)](https://doi.org/10.21105/joss.02377)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02377">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02377/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02377/status.svg
   :target: https://doi.org/10.21105/joss.02377

This is how it will look in your documentation:

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