[REVIEW]: respdetect: A Matlab tool for detecting breath events from whale biologger data

[editorialbot]

Submitting author: @ashleyblawas (Ashley Blawas)
Repository: https://github.com/ashleyblawas/respdetect
Branch with paper.md (empty if default branch):
Version: v1.0.0
Editor: @kthyng
Reviewers: @sfregosi, @smnnlt
Archive: Pending

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/a23ed8e527ddeac304d76252a39d8b57/status.svg)](https://joss.theoj.org/papers/a23ed8e527ddeac304d76252a39d8b57)

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

@sfregosi & @smnnlt, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

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

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @sfregosi

📝 Checklist for @smnnlt

[editorialbot]

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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

@editorialbot commands

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

@editorialbot generate pdf

[editorialbot]

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

✅ OK DOIs

- 10.1111/j.1748-7692.2008.00255.x is OK
- 10.1242/jeb.243872 is OK
- 10.1093/icb/45.2.305 is OK
- 10.1016/j.dsr2.2007.01.001 is OK
- 10.1016/j.dsr2.2006.11.009 is OK
- 10.1126/science.aao2740 is OK
- 10.1242/jeb.023366 is OK
- 10.1242/jeb.137513 is OK
- 10.1016/j.jembe.2014.05.014 is OK
- 10.1073/pnas.1914273116 is OK
- 10.1139/Z10-080 is OK
- 10.1139/z83-086 is OK
- 10.1111/j.1748-1716.1995.tb09834.x is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.98  T=0.02 s (999.0 files/s, 99695.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
MATLAB                          17            368            464           1262
TeX                              1             13              0            167
Markdown                         2             27              0             60
YAML                             1              1              4             19
Text                             3              2              0              8
-------------------------------------------------------------------------------
SUM:                            24            411            468           1516
-------------------------------------------------------------------------------

Commit count by author:

   212	Ashley Blawas

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 695

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🟡 License found: GNU General Public License v3.0 (Check here for OSI approval)

[kthyng]

Let me know if you have any questions!

👋🏼 @ashleyblawas @sfregosi, @smnnlt this is the review thread for the paper. All of our communications will happen here from now on.

As a reviewer, the first step is to create a checklist for your review by entering

@editorialbot generate my checklist

as the top of a new comment in this thread.

These checklists contain the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. The first comment in this thread also contains links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#7858 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

Please feel free to ping me (@kthyng) if you have any questions/concerns.

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[sfregosi]

Review checklist for @sfregosi

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 https://github.com/ashleyblawas/respdetect?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@ashleyblawas) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
• 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?

[smnnlt]

Review checklist for @smnnlt

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 https://github.com/ashleyblawas/respdetect?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@ashleyblawas) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
• 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?

[smnnlt]

Hi @ashleyblawas, thank you very much for creating this software and giving me the opportunity to review it.

I have finished my first round of review, see the issues opened in the repo and my review checklist. I tested the software on Windows 11 with Matlab 2024b installed.

As a short disclaimer, I have no experience in marine biology, so I am not qualified to make judgements about the correctness of the methods applied. But I have written research software and work in the field of human exercise physiology, so I feel that I am able to comment on some aspects.

I believe there are some major modifications that should be undertaken to improve this project in terms of usability and functionality. At the moment, the project feels more like a well-documented analysis script rather than research software. This is not a bad thing per se and totally fine for individual research projects. But if you want to make this work accessible to a wider user base there are several consideration you should make, see the issues I opened. And I definitely think it is worth going these extra miles, given the relevance of your software and the work you have already put into it.

Feel free to ask me any questions regarding my comments in this thread or the respective issues.

[kthyng]

@sfregosi Will you be able to work on your review soon?

[sfregosi]

@kthyng I will be able to complete my review by the end of next week!

[kthyng]

@sfregosi Thank you!

[sfregosi]

@kthyng I am working on my review and was going to start creating individual issues but can see that some of my concerns are already addressed by issues created by @smnnlt. Should I create a somewhat duplicated issue or just add a comment supporting that issue or adding any additional context?

[kthyng]

@sfregosi I would comment on the existing issues where it makes sense.

[sfregosi]

@ashleyblawas,

I've completed my initial review of respdetect. Overall, I think this is a useful toolset that complements existing dtagtools nicely and is an important contribution to the cetacean biologging field. I appreciate your work to share this with the community in an open and reproducible way. While I was able to get it mostly working as it stands, I agree with @smnnlt that it would be greatly improved if it is 'functionized.' I also identified some small bugs and areas the documentation could be improved to better guide a new user. I have provided comments as either new issues on the respdetect repository or as comments on existing issues. I am happy to provide clarity on or discuss any of these issues and would be happy to test a revised version in the future.

Best,
Selene