[REVIEW]: mhealthtools: A Modular R Package for Extracting Features from Mobile and Wearable Sensor Data

[whedon]

Submitting author: @philerooski (Phillip Snyder)
Repository: https://github.com/Sage-Bionetworks/mhealthtools
Version: 0.2.0
Editor: @trallard
Reviewer: @Ebedthan, @AKuederle
Archive: 10.5281/zenodo.3731707

Status

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Markdown: [![status](https://joss.theoj.org/papers/31e0a47b0019df423be2360652ba60b3/status.svg)](https://joss.theoj.org/papers/31e0a47b0019df423be2360652ba60b3)

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

@Ebedthan & @AKuederle, 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 @trallard know.

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

Review checklist for @Ebedthan

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 (@philerooski) 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 @AKuederle

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 (@philerooski) 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. @Ebedthan, @AKuederle it looks like you're currently assigned to review this paper 🎉.

⭐ 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]

Reference check summary:

OK DOIs

- 10.1038/s41746-019-0090-4 is OK
- 10.21105/joss.01778 is OK
- 10.18637/jss.v059.i10 is OK
- 10.1038/s41746-019-0078-0 is OK
- 10.1038/s41746-019-0084-2 is OK
- 10.1146/annurev-bioeng-062117-121036 is OK
- 10.1145/3341162.3346277 is OK
- 10.5281/zenodo.3563546 is OK

MISSING DOIs

- https://doi.org/10.1038/s41746-019-0178-x may be missing for title: Detecting the impact of subject characteristics on machine learning-based diagnostic applications
- https://doi.org/10.1145/3267305.3267612 may be missing for title: Remote Assessment, in Real-World Setting, of Tremor Severity in Parkinson’s Disease Patients Using Smartphone Inertial Sensors

INVALID DOIs

- None

[whedon]

👉 Check article proof 📄 👈

[Ebedthan]

Hello @philerooski,
Just opened an issue on the mhealthtools repository for adding details for support seekers as of community guidelines.

Regards.

[Ebedthan]

Hi @philerooski,
I have added another issue related to references.

[philerooski]

Thanks Anicet! I am working on them.

[AKuederle]

I added a review issue for the package repo Sage-Bionetworks/mhealthtools#209 and the paper Sage-Bionetworks/mhealthtools#210

[Ebedthan]

My review is complete. Recommend accept it with changes provided by authors. This package will ease stuff on extracting features from sensor.

[trallard]

Thanks for completing your review @Ebedthan

@AKuederle do you have any updates on this? It seems like there is only one item on your checklist missing?

[AKuederle]

I am waiting for a response on Sage-Bionetworks/mhealthtools#210

[arfon]

Dear authors and reviewers

We wanted to notify you that in light of the current COVID-19 pandemic, JOSS has decided to suspend submission of new manuscripts and to handle existing manuscripts (such as this one) on a "best efforts basis". We understand that you may need to attend to more pressing issues than completing a review or updating a repository in response to a review. If this is the case, a quick note indicating that you need to put a "pause" on your involvement with a review would be appreciated but is not required.

Thanks in advance for your understanding.

Arfon Smith, Editor in Chief, on behalf of the JOSS editorial team.

[AKuederle]

My final comments to the paper are addressed. If the open pull request are merged, the paper can be accepted from my side!

[philerooski]

Great! Thank you again @AKuederle and @Ebedthan ! The last open PR has been merged into master.

[philerooski]

Hi @trallard I believe things have wrapped up here.

I've made a tagged v0.2.0 release on the main repository and uploaded to Zenodo.

Zenodo: https://zenodo.org/record/3731707
Zenodo DOI: 10.5281/zenodo.3731707

There is one review check box left unchecked ("Performance") which I think should be checked. I did not make any performance claims in the paper.

[arfon]

@whedon check references

[whedon]

Reference check summary:

OK DOIs

- 10.1038/sdata.2016.11 is OK
- 10.1038/s41746-019-0090-4 is OK
- 10.21105/joss.01778 is OK
- 10.18637/jss.v059.i10 is OK
- 10.1038/s41746-019-0078-0 is OK
- 10.1038/s41746-019-0084-2 is OK
- 10.1016/j.amepre.2013.03.017 is OK
- 10.3390/s19092164 is OK
- 10.1146/annurev-bioeng-062117-121036 is OK
- 10.1038/s41746-019-0178-x is OK
- 10.1145/3267305.3267612 is OK
- 10.1145/3341162.3346277 is OK
- 10.5281/zenodo.3563546 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[arfon]

@whedon generate pdf

[whedon]

👉 Check article proof 📄 👈

[arfon]

@trallard - I'm not sure of your availability currently so if we don't hear back from you by early next week, one of the EiCs will move ahead with accepting and publishing this paper.

[arfon]

@whedon set 10.5281/zenodo.3731707 as archive

[whedon]

OK. 10.5281/zenodo.3731707 is the archive.

[arfon]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Reference check summary:

OK DOIs

- 10.1038/sdata.2016.11 is OK
- 10.1038/s41746-019-0090-4 is OK
- 10.21105/joss.01778 is OK
- 10.18637/jss.v059.i10 is OK
- 10.1038/s41746-019-0078-0 is OK
- 10.1038/s41746-019-0084-2 is OK
- 10.1016/j.amepre.2013.03.017 is OK
- 10.3390/s19092164 is OK
- 10.1146/annurev-bioeng-062117-121036 is OK
- 10.1038/s41746-019-0178-x is OK
- 10.1145/3267305.3267612 is OK
- 10.1145/3341162.3346277 is OK
- 10.5281/zenodo.3563546 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

Check final proof 👉 openjournals/joss-papers#1392

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1392, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[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.02106 joss-papers#1394
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02106
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]

Congratulations to @philerooski on your new publication! Thanks to editor @trallard and reviewers @Ebedthan and @AKuederle — we couldn't do this process without your time and expertise!

[whedon]

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

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