[PRE 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: Pending
Reviewers: Pending
Managing EiC: Kristen Thyng

Status

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Software report:

github.com/AlDanial/cloc v 1.90  T=0.02 s (934.9 files/s, 105773.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
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MATLAB                          17            368            464           1262
TeX                              1             13              0            167
Markdown                         2             22              0             56
YAML                             1              1              4             19
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SUM:                            21            404            468           1504
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Commit count by author:

   177	Ashley Blawas

[editorialbot]

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

✅ OK DOIs

- 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

- 10.1242/jeb.243872 may be a valid DOI for title: An accelerometer-derived ballistocardiogram method...

❌ INVALID DOIs

- https://doi.org/10.1111/j.1748-7692.2008.00255.x is INVALID because of 'https://doi.org/' prefix

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 696

✅ The paper includes a Statement of need section

[editorialbot]

License info:

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

[editorialbot]

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

[editorialbot]

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[kthyng]

Hi @ashleyblawas and thanks for your submission! I am looking for some specific items to make sure your submission fits our requirements at a high level (not at the more detailed review level) before moving on to finding an editor or putting this on our waitlist if no relevant editors are available. I'll comment over time as I have a chance to go through them:

• OSI-approved license
• Installation instructions
• Documentation exists at all
• Tests of some sort
• Check paper (make sure compiles, read through, check for length 250-1000 words)
• Substantial scholarly effort
• Clear research application

In the meantime, please take a look at the comments above ⬆️ from the editorialbot to address any DOI, license, or paper issues if you're able (there may not be any), or suggest reviewers. For reviewers, please suggest 5 reviewers from the database listed above or your own (non-conflicted) extended network. Their github handles are most useful to receive but please don't use "@" to reference them since it will prematurely ping them.

[ashleyblawas]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

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[ashleyblawas]

Potential Reviewers: smnnlt, peterakirk, abhishektha, platipodium,bastienqueste

[kthyng]

@ashleyblawas

• any plans to make a matlab package for more seamless installation?
• maybe make it more obvious there is a wiki with a link in your readme
• The "plotting" in the wiki didn't have a plot?
• test directory just seems to have .mat files — no test code?

[ashleyblawas]

• This toolbox can be installed directly by downloading the repository and adding its path to Matlab so it does not save the user significant effort to instead install through a Matlab package
• I added a more obvious link to the Wiki in the Usage section of the readme
• This can been updated to add the plots that were missing!
• These test files are intended to be manually run through the series of processing steps. There is a built-in function within main.m to automatically compare the outputs of the two manual tests to the validation files also included in the test folder

[kthyng]

These test files are intended to be manually run through the series of processing steps. There is a built-in function within main.m to automatically compare the outputs of the two manual tests to the validation files also included in the test folder

Is this meant to be described in step 7 in the wiki? If so, are the subsequent steps 7a and 7b missing, which would walk the user through the testing to see if the code is working correctly?

[kthyng]

@ashleyblawas

• can you also check those DOIs listed above
• also there are some inline reference issues in your paper (check example paper for help https://joss.readthedocs.io/en/latest/example_paper.html#example-paper)

[kthyng]

@ashleyblawas I have a few questions then we can move to finding an editor.

[kthyng]

@ashleyblawas Checking in here.

[ashleyblawas]

Not sure if this is regarding the initial DOI issues on Sept. 25th but those are all corrected now. The inline reference issues have also been corrected.

[ashleyblawas]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

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⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

[ashleyblawas]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

Five most similar historical JOSS papers:

mmrefpoints: Projecting long-term marine mammal abundance with bycatch
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Similarity score: 0.6426

biopeaks: a graphical user interface for feature extraction from heart- and breathing biosignals
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Reviewers: @TomDonoghue, @sappelhoff, @jamesheathers
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A MATLAB toolbox to detect and analyze marine heatwaves
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Handling editor: @kthyng (Active)
Reviewers: @mvdh7
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ocean_data_tools: A MATLAB toolbox for interacting with bulk freely-available oceanographic data
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⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

[ashleyblawas]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

Five most similar historical JOSS papers:

biopeaks: a graphical user interface for feature extraction from heart- and breathing biosignals
Submitting author: @JanCBrammer
Handling editor: @oliviaguest (Active)
Reviewers: @TomDonoghue, @sappelhoff, @jamesheathers
Similarity score: 0.6388

mmrefpoints: Projecting long-term marine mammal abundance with bycatch
Submitting author: @mcsiple
Handling editor: @fboehm (Active)
Reviewers: @ha0ye, @tbrown122387
Similarity score: 0.6266

A MATLAB toolbox to detect and analyze marine heatwaves
Submitting author: @ZijieZhaoMMHW
Handling editor: @kthyng (Active)
Reviewers: @mvdh7
Similarity score: 0.6250

spiro: An R package for analyzing data from cardiopulmonary exercise testing
Submitting author: @smnnlt
Handling editor: @Kevin-Mattheus-Moerman (Active)
Reviewers: @Kevin-Mattheus-Moerman
Similarity score: 0.6194

ocean_data_tools: A MATLAB toolbox for interacting with bulk freely-available oceanographic data
Submitting author: @lnferris
Handling editor: @kthyng (Active)
Reviewers: @kakearney, @castelao
Similarity score: 0.6129

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

[ashleyblawas]

These test files are intended to be manually run through the series of processing steps. There is a built-in function within main.m to automatically compare the outputs of the two manual tests to the validation files also included in the test folder

Is this meant to be described in step 7 in the wiki? If so, are the subsequent steps 7a and 7b missing, which would walk the user through the testing to see if the code is working correctly?

This has been addressed to make it more clear how the user should use Step 7 for testing, including a more thorough description of Steps 7a & 7b.

[kthyng]

Please check that your inline vs. parenthetical references are correct. You can compare with the example paper here: https://joss.readthedocs.io/en/latest/example_paper.html — line 32.

This has been addressed to make it more clear how the user should use Step 7 for testing, including a more thorough description of Steps 7a & 7b.

I see there is some description. Jumping there and reading it, I wouldn't know how to do the testing, but I'll let the reviewers comment on it if they choose to do so.

We have a backlog of submissions so I will add this to our waitlist. Thanks for your patience.

[ashleyblawas]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

Five most similar historical JOSS papers:

biopeaks: a graphical user interface for feature extraction from heart- and breathing biosignals
Submitting author: @JanCBrammer
Handling editor: @oliviaguest (Active)
Reviewers: @TomDonoghue, @sappelhoff, @jamesheathers
Similarity score: 0.6360

mmrefpoints: Projecting long-term marine mammal abundance with bycatch
Submitting author: @mcsiple
Handling editor: @fboehm (Active)
Reviewers: @ha0ye, @tbrown122387
Similarity score: 0.6225

A MATLAB toolbox to detect and analyze marine heatwaves
Submitting author: @ZijieZhaoMMHW
Handling editor: @kthyng (Active)
Reviewers: @mvdh7
Similarity score: 0.6200

spiro: An R package for analyzing data from cardiopulmonary exercise testing
Submitting author: @smnnlt
Handling editor: @Kevin-Mattheus-Moerman (Active)
Reviewers: @Kevin-Mattheus-Moerman
Similarity score: 0.6165

MorphoMetriX: a photogrammetric measurement GUI for morphometric analysis of megafauna
Submitting author: @wingtorres
Handling editor: @Kevin-Mattheus-Moerman (Active)
Reviewers: @isaacvandor, @bw4sz
Similarity score: 0.6097

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.