[REVIEW]: Automated Sleep Stage Scoring Using k-Nearest Neighbors Classifier #2377

whedon · 2020-06-22T13:38:47Z

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

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Status

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Markdown: [![status](https://joss.theoj.org/papers/5726bdd4b144467c8093e90df0169c25/status.svg)](https://joss.theoj.org/papers/5726bdd4b144467c8093e90df0169c25)

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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.

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General checks

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Functionality

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Documentation

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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?

The text was updated successfully, but these errors were encountered:

whedon · 2020-06-22T13:38:51Z

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:

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

@whedon generate pdf

whedon · 2020-06-22T13:40:20Z

👉 Check article proof 📄 👈

oliviaguest · 2020-06-22T13:41:39Z

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 · 2020-06-24T21:00:01Z

@whedon add @trisbek as reviewer

whedon · 2020-06-24T21:00:08Z

OK, @trisbek is now a reviewer

sbuergers · 2020-06-25T01:12:57Z

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 · 2020-06-25T11:14:36Z

@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 · 2020-06-26T08:16:33Z

@whedon generate pdf

whedon · 2020-06-26T08:17:45Z

👉 Check article proof 📄 👈

teamPSG · 2020-06-26T08:39:35Z

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 · 2020-06-26T13:11:25Z

Hi @teamPSG,

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

Best,
Steffen.

oliviaguest · 2020-06-29T12:39:14Z

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 · 2020-07-06T08:42:00Z

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!

whedon · 2020-09-03T20:08:49Z

OK. 10.5281/zenodo.4009178 is the archive.

oliviaguest · 2020-09-04T08:02:08Z

@whedon check references

whedon · 2020-09-04T08:04:05Z

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 · 2020-09-04T08:04:34Z

@teamPSG can you fix these DOIs above, please?

teamPSG · 2020-09-04T08:49:15Z

@whedon check references

whedon · 2020-09-04T08:50:13Z

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 · 2020-09-04T08:50:35Z

@whedon generate pdf

whedon · 2020-09-04T08:52:56Z

👉 Check article proof 📄 👈

teamPSG · 2020-09-04T08:55:45Z

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

oliviaguest · 2020-09-04T10:54:15Z

@whedon accept

whedon · 2020-09-04T10:54:22Z

Attempting dry run of processing paper acceptance...

whedon · 2020-09-04T10:56:21Z

👋 @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 · 2020-09-04T15:40:42Z

Thanks @oliviaguest, both files look good to me.

oliviaguest · 2020-09-04T15:52:05Z

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

teamPSG · 2020-09-04T15:56:04Z

Great! Thanks for the adventure 🌋

kthyng · 2020-09-04T16:37:26Z

@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 · 2020-09-04T16:42:21Z

@teamPSG Your paper looks great!

teamPSG · 2020-09-04T17:54:25Z

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 · 2020-09-04T18:32:02Z

Ok, looks good.

kthyng · 2020-09-04T18:32:06Z

@whedon accept deposit=true

whedon · 2020-09-04T18:32:09Z

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

whedon · 2020-09-04T18:34:39Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon · 2020-09-04T18:34:40Z

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

Any issues? Notify your editorial technical team...

kthyng · 2020-09-04T18:36:24Z

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 · 2020-09-04T18:57:42Z

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

whedon · 2020-09-04T19:19:54Z

🎉🎉🎉 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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whedon added the review label Jun 22, 2020

whedon assigned oliviaguest Jun 22, 2020

whedon mentioned this issue Jun 22, 2020

[PRE REVIEW]: Automated Sleep Stage Scoring Using k-Nearest Neighbors Classifier #2201

Closed

whedon assigned Emma-k-ward and sbuergers Jun 23, 2020

whedon assigned Emma-k-ward, oliviaguest and sbuergers and unassigned oliviaguest, sbuergers and Emma-k-ward Jun 24, 2020

oliviaguest unassigned oliviaguest, sbuergers and Emma-k-ward Jun 25, 2020

whedon assigned Emma-k-ward, oliviaguest and sbuergers Jun 26, 2020

whedon added the recommend-accept Papers recommended for acceptance in JOSS. label Sep 4, 2020

whedon added accepted published Papers published in JOSS labels Sep 4, 2020

kthyng closed this as completed Sep 4, 2020

[REVIEW]: Automated Sleep Stage Scoring Using k-Nearest Neighbors Classifier #2377

[REVIEW]: Automated Sleep Stage Scoring Using k-Nearest Neighbors Classifier #2377

Comments

whedon commented Jun 22, 2020 • edited Loading

Status

Reviewer instructions & questions

Review checklist for @Emma-k-ward

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @sbuergers

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @trisbek

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @samikakumar

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented Jun 22, 2020

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oliviaguest commented Jun 22, 2020 • edited Loading

oliviaguest commented Jun 24, 2020

whedon commented Jun 24, 2020

sbuergers commented Jun 25, 2020

oliviaguest commented Jun 25, 2020

teamPSG commented Jun 26, 2020

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oliviaguest commented Jun 29, 2020

teamPSG commented Jul 6, 2020

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whedon commented Jun 22, 2020 •

edited

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oliviaguest commented Jun 22, 2020 •

edited

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