Joss-reviews: [REVIEW]: Sit2StandPy: An Open-Source Python Package for Detecting and Quantifying Sit-to-Stand Transitions Using an Accelerometer on the Lower Back'

[whedon]

Submitting author: @LukasAdamowicz (Lukas Adamowicz)
Repository: https://github.com/PfizerRD/sit2standpy
Version: v1.1.2
Editor: @galessiorob
Reviewer: @jsgalan, @gweissman
Archive: 10.5281/zenodo.3988351

:warning: JOSS reduced service mode :warning:

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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Markdown: [![status](https://joss.theoj.org/papers/4ddd6608da7632ecc588e27ef802fdf0/status.svg)](https://joss.theoj.org/papers/4ddd6608da7632ecc588e27ef802fdf0)

Reviewers and authors:

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Reviewer instructions & questions

@jsgalan & @gweissman, 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 @jsgalan

Conflict of interest

• [x] 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

• [x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• [x] Repository: Is the source code for this software available at the repository url?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Contribution and authorship: Has the submitting author (@LukasAdamowicz) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• [x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] 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

• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• [x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• [x] 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

• [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] 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 @gweissman

Conflict of interest

• [x] 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

• [x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• [x] Repository: Is the source code for this software available at the repository url?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Contribution and authorship: Has the submitting author (@LukasAdamowicz) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• [x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] 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

• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• [x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• [x] 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

• [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] 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. @jsgalan, @gweissman it looks like you're currently assigned to review this paper :tada:.

:warning: JOSS reduced service mode :warning:

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.

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[whedon]

Reference check summary:

OK DOIs

- 10.1088/0967-3334/33/11/1947 is OK
- 10.1016/j.jbiomech.2009.06.023 is OK
- 10.1186/s12984-015-0090-9 is OK
- 10.1016/j.gaitpost.2012.10.008 is OK
- 10.1186/s12984-017-0241-2 is OK
- 10.1186/s12984-015-0026-4 is OK
- 10.3389/fneur.2018.00652 is OK
- 10.1016/j.patrec.2018.03.020 is OK
- 10.1093/geronj/49.2.m85 is OK
- 10.1109/MCSE.2011.37 is OK
- 10.21105/joss.01237 is OK
- 10.5281/zenodo.3898987 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[LukasAdamowicz]

Hi all,
Thank you for the comments/work so far - DOIs were added and look like they are showing up, I'll look into making sure that the file is packed with the installation @jsgalan

[LukasAdamowicz]

@jsgalan you should be able to now re-install from pip (make sure you get version 1.1.1.post4), which should contain the files needed for the tests (also made changes so that all the tests that were supposed to run are found correctly)

[gweissman]

I was able to install the package easily without apparent errors. To assess functionality, I ran the accompanying tests using pytest and all passed. I did not import the library directly or try running any of my own code with it.

One scientific concern is that the validation of the algorithms implemented in this software package appear to have been reported in a paper that is currently under review. Therefore, the scientific validity of the algorithms can't be assessed here. If that is important for JOSS, then I would suggest pending this review until those results have passed through some peer review process.

One ethical concern is that the repo appears at the Pfizer site, and I did not see any statement of funding regarding the research or disclosure about the involvement of the funding source in the development, testing, or reporting of the software or associated manuscript.

[LukasAdamowicz]

Thank you for your comments, @gweissman.

Regarding your last point, I added the following statement to the paper, which has been on the other papers our group has published (GaitPy, SleepPy)

Acknowledgements

The Digital Medicine & Translational Imaging group at Pfizer, Inc supported the development of this package.

[galessiorob]

Thank you so much for your review @gweissman! ⚡ I am looking into policies regarding this comment, I'll update the issue with my findings.

@jsgalan checking in, I know you started the review back in the pre-review issue, feel free to copy over your comments and start checking off the list at the top assigned to you. I tried installing today and didn't run into any issues.

Let me know if I can help with anything and thanks again for your work.

[jsgalan]

Hi all, I proceed to clone the git

Then created a Venv

Then did an initial install try (Python 2.7)

Then installed pip

Then a second install with python 3.8

Then did a manual installation of the requierements

Then installed Pytest

then ran the tests

V1

V2

All passed without problems!

Then went and did ran the code in the repository for V2 usage and old usage (here called test2 and test3, respectively)

I try in my editor, just after a fresh pip install

and got the same errors:

Not sure what is going wrong of if I am missing a step somewhere.

Best

[LukasAdamowicz]

@jsgalan thank you for finding those issues. I've addressed both of them with the usage examples, which have been updated in the repository README. In summary, there was a typo in the V1 (old usage) example, which should be fixed now:

... with resources.path('sit2standpy.data', 'sample.csv') as file_path: ...

Regarding V2 usage, data_transform_function was intended to be the users own function for achieving the required format. The comments around this have been updated, and I added a link to a gist as well, that provides a simple data loader function

data loader GIST

[jsgalan]

Hi @LukasAdamowicz,

V1 works fine

V2 using the loader as suggested give me an error

After an small inspection I realized there was an error is 'Unix Time' instead of 'Unix Timestamps' (I know it is kind off-topic since is just an example)

After that correction I get to this error, not sure why?

Best

[LukasAdamowicz]

@jsgalan thank you, apologies for these difficulties. I've gone an updated the README with the v2 usage (tested on my end) - basically what was missing was the library prefix for the WindowDays (and following calls) that got added to the Sequence, so it becomes

...
sequence.add(s2s.v2.WindowDays(hours=[8, 20]))
sequence.add(s2s.v2.AccelerationFilter())
sequence.add(s2s.v2.Detector(stillness_constraint=True)) 
...

Also please note that path_to_csv_output is undefined, and would need to be defined as well to get the code working fully

I also fixed the gist as well to correctly use the correct key names

[jsgalan]

Hi @LukasAdamowicz

It worked!

[jsgalan]

HI about the written articles, I am not sure I am seeing the last version. Since I am not seeing the acknowledgment you mentioned earlier.

Thank you for your comments, @gweissman.

Regarding your last point, I added the following statement to the paper, which has been on the other papers our group has published (GaitPy, SleepPy)

Acknowledgements

The Digital Medicine & Translational Imaging group at Pfizer, Inc supported the development of this package.

Also I think this can be easily solved, just adding a line to the code.

As @gweissman has made me notice in his review, I think the authors should give a few more details on other (open souse) software implementations, or state that is a novel implementation, to be able to answer this _State of the field: Do the authors describe how this software compares to other commonly-used packages?_

[LukasAdamowicz]

The paper is updated with the acknowledgements, just no new pdf preview yet.

[LukasAdamowicz]

@whedon generate pdf

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[jsgalan]

Hi Lukas, Please check the Availability Section seems to have the same error I noted earlier.

[LukasAdamowicz]

Fixed. I also added a statement regarding existing implementations/software of sit-to-stand algorithms

[LukasAdamowicz]

@whedon generate pdf

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[jsgalan]

Hi all, I just checked the last version of the article and am satisfied with the results.

I am happy to accept the submission.

Best,

[LukasAdamowicz]

Thank you so much for your review @gweissman! ⚡ I am looking into policies regarding this comment, I'll update the issue with my findings.

@jsgalan checking in, I know you started the review back in the pre-review issue, feel free to copy over your comments and start checking off the list at the top assigned to you. I tried installing today and didn't run into any issues.

Let me know if I can help with anything and thanks again for your work.

Hi, is there any update on this @galessiorob @gweissman?

Thanks!

[galessiorob]

Hey @LukasAdamowicz

I talked to other editors and the consensus was that it's okay to publish the paper despite it citing an algorithm that is still not published as long as:

1. You can confirm that the other publication for which you are also an author (_Assessment of sit to stand during daily life using an accelerometer on the lower back. IEEE Journal of Biomedical and Health Informatics_) is (at least partly) focused on determining the validity/applicability of the algorithm for this area of research.
2. You can confirm this other paper is not simply about the software as well, as this might constitute self-plagiarism.
3. Finally, adding some complementary documentation around the algorithm itself:
   
   
   
   • State what the algorithm is in the documentation.
   
   
   • Demonstrate that their implementation is verifiable through tests.
   
   
   • Discuss the role the other manuscript plays in vetting the application of the algorithm.
   
   

Let me know if you have any questions!

[galessiorob]

Hey @LukasAdamowicz wanted to check in, do you have any questions, is there anything I can do to help get your paper across the finish line?

[LukasAdamowicz]

Only some clarification for now - for the third point - is that documentation in the paper, or as part of the package documentation?

[galessiorob]

@LukasAdamowicz on the paper, thanks for asking!

[galessiorob]

@gweissman I noticed that you haven't checked off the State of the field item from your list, the paper states that "_to the author's knowledge there are no commonly used open-source, and easy to use and configure, implementations of sit-to-stand algorithms available_", do you think this needs to be expanded?

[gweissman]

@gweissman I noticed that you haven't checked off the State of the field item from your list, the paper states that "_to the author's knowledge there are no commonly used open-source, and easy to use and configure, implementations of sit-to-stand algorithms available_", do you think this needs to be expanded?

I will check it off. I think that is sufficient although I am not knowledgeable in this field to know how true that statement is. A quick web search seems to confirm that while numerous algorithms have been published, the software does not seem to be readily available.

[LukasAdamowicz]

@whedon generate pdf

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[LukasAdamowicz]

Hi @galessiorob,
After a discussion with my co-author, we decided instead to remove the citation to the pending paper.

Let me know if there is anything else to do now, at this point.

[LukasAdamowicz]

@whedon generate pdf

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[galessiorob]

@whedon check references

[whedon]

Reference check summary:

OK DOIs

- 10.1088/0967-3334/33/11/1947 is OK
- 10.1016/j.jbiomech.2009.06.023 is OK
- 10.1186/s12984-015-0090-9 is OK
- 10.1016/j.gaitpost.2012.10.008 is OK
- 10.1186/s12984-017-0241-2 is OK
- 10.1186/s12984-015-0026-4 is OK
- 10.3389/fneur.2018.00652 is OK
- 10.1016/j.patrec.2018.03.020 is OK
- 10.1093/geronj/49.2.m85 is OK
- 10.1109/MCSE.2011.37 is OK
- 10.21105/joss.01237 is OK
- 10.5281/zenodo.3898987 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[galessiorob]

@LukasAdamowicz I think leaving the pending paper citation out is fine, at this point the next thing we need from you is to deposit your software in Zenodo and post the DOI here. After that, we can set the final version, generate a final proof and have an Editor in Chief do the publishing.

[LukasAdamowicz]

https://zenodo.org/record/3988351

DOI: 10.5281/zenodo.3988351

[galessiorob]

@whedon set v1.1.2 as version

[whedon]

OK. v1.1.2 is the version.

[galessiorob]

@whedon set 10.5281/zenodo.3988351 as archive

[whedon]

OK. 10.5281/zenodo.3988351 is the archive.

[galessiorob]

@whedon generate pdf

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[galessiorob]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Reference check summary:

OK DOIs

- 10.1088/0967-3334/33/11/1947 is OK
- 10.1016/j.jbiomech.2009.06.023 is OK
- 10.1186/s12984-015-0090-9 is OK
- 10.1016/j.gaitpost.2012.10.008 is OK
- 10.1186/s12984-017-0241-2 is OK
- 10.1186/s12984-015-0026-4 is OK
- 10.3389/fneur.2018.00652 is OK
- 10.1016/j.patrec.2018.03.020 is OK
- 10.1093/geronj/49.2.m85 is OK
- 10.1109/MCSE.2011.37 is OK
- 10.21105/joss.01237 is OK
- 10.5281/zenodo.3898987 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1648

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1648, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

[galessiorob]

@LukasAdamowicz could you please give this last version a final proofread? An editor in chief will take it from here and get it published now ✨

[LukasAdamowicz]

@galessiorob Paper looks good in proofread. Thanks for your time!

[kyleniemeyer]

Hello @LukasAdamowicz, everything looks good, except for one minor set of changes needed in the paper: can you please add commas after "e.g." throughout? Thanks!

[LukasAdamowicz]

@kyleniemeyer Done!

[arfon]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Reference check summary:

OK DOIs

- 10.1088/0967-3334/33/11/1947 is OK
- 10.1016/j.jbiomech.2009.06.023 is OK
- 10.1186/s12984-015-0090-9 is OK
- 10.1016/j.gaitpost.2012.10.008 is OK
- 10.1186/s12984-017-0241-2 is OK
- 10.1186/s12984-015-0026-4 is OK
- 10.3389/fneur.2018.00652 is OK
- 10.1016/j.patrec.2018.03.020 is OK
- 10.1093/geronj/49.2.m85 is OK
- 10.1109/MCSE.2011.37 is OK
- 10.21105/joss.01237 is OK
- 10.5281/zenodo.3898987 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1655

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1655, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

[arfon]

@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:

1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/1656
2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02449
3. If everything looks good, then close this review issue.

4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

   Any issues? Notify your editorial technical team...

[arfon]

@jsgalan, @gweissman - many thanks for your reviews here and to @galessiorob for editing this submission ✨

@LukasAdamowicz - your paper is now published in JOSS :zap::rocket::boom:

One last thing, it seems like Crossref is having issues yet and so the DOI for the paper isn't yet resolving (https://doi.org/10.21105/joss.02449). I'll leave this issue open until this is fixed.

[whedon]

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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.02449/status.svg)](https://doi.org/10.21105/joss.02449)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02449">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02449/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02449/status.svg
   :target: https://doi.org/10.21105/joss.02449

This is how it will look in your documentation:

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