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[REVIEW]: HRnV-Calc: A Software for Heart Rate n-Variability and Heart Rate Variability Analysis #5391

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editorialbot opened this issue Apr 20, 2023 · 84 comments
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accepted Matlab published Papers published in JOSS recommend-accept Papers recommended for acceptance in JOSS. review TeX Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials

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editorialbot commented Apr 20, 2023

Submitting author: @charlienew (Chenglin Niu)
Repository: https://github.com/nliulab/HRnV-Calc
Branch with paper.md (empty if default branch):
Version: v1.0.0
Editor: @bmcfee
Reviewers: @smnnlt, @itismeghasyam
Archive: 10.5281/zenodo.7963493

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/046f485611387cd8f6d7ab5eab5514c4"><img src="https://joss.theoj.org/papers/046f485611387cd8f6d7ab5eab5514c4/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/046f485611387cd8f6d7ab5eab5514c4/status.svg)](https://joss.theoj.org/papers/046f485611387cd8f6d7ab5eab5514c4)

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

@smnnlt & @itismeghasyam, 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 @bmcfee 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 @smnnlt

📝 Checklist for @itismeghasyam

@editorialbot editorialbot added Matlab review TeX Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials labels Apr 20, 2023
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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

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Software report:

github.com/AlDanial/cloc v 1.88  T=0.04 s (514.2 files/s, 168485.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
MATLAB                          18            887           1909           3046
TeX                              1             34              0            918
Markdown                         2            108              0            284
YAML                             1              1              4             18
-------------------------------------------------------------------------------
SUM:                            22           1030           1913           4266
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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Wordcount for paper.md is 1583

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

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

OK DOIs

- 10.1007/s10439-014-0993-9 is OK
- 10.1016/j.amjsurg.2015.06.002 is OK
- 10.1103/PhysRevLett.89.068102 is OK
- 10.1152/ajpheart.2000.278.6.H2163 is OK
- 10.3390/s20030765 is OK
- 10.1016/j.canep.2013.04.016 is OK
- 10.3892/etm.2016.3104 is OK
- 10.3389/fpubh.2017.00240 is OK
- 10.1016/j.cmpb.2019.05.032 is OK
- 10.1088/0967-3334/36/8/1665 is OK
- 10.3389/fphys.2020.602027 is OK
- 10.3758/s13428-011-0107-7 is OK
- 10.1177/147323000603400308 is OK
- 10.3390/e20120952 is OK
- 10.1016/j.compbiomed.2012.11.005 is OK
- 10.1186/s12872-020-01455-8 is OK
- 10.1371/journal.pone.0249868 is OK
- 10.1016/j.cmpb.2019.105127 is OK
- 10.1109/jbhi.2013.2244902 is OK
- 10.1056/NEJMoa1901183 is OK
- 10.1007/s11517-006-0119-0 is OK
- 10.1093/ndt/gfm634 is OK
- 10.1093/europace/euv015 is OK
- 10.3389/fpubh.2017.00258 is OK
- 10.1016/j.smrv.2011.02.005 is OK
- 10.1016/j.cmpb.2013.07.024 is OK
- 10.1088/1361-6579/aae021 is OK

MISSING DOIs

- None

INVALID DOIs

- - is INVALID

@smnnlt
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smnnlt commented Apr 28, 2023

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

General checks

  • Repository: Is the source code for this software available at the https://github.com/nliulab/HRnV-Calc?
  • 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 (@charlienew) 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
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smnnlt commented Apr 28, 2023

Hi @charlienew , here are some additional comments to my review:

First of all thank you very much for providing this interesting piece of software. I think the GUI interface for HR(n)V analysis may be very helpful in practical settings and I look forward to future insights into the newly developed measurement parameters. In addition to the checklist above and the issues I opened in the repo I have some remarks regarding the software paper:

Authorship: From what I can see, three of the ten authors listed on the paper have contributed code to the software. While it is ultimately your choice who to add as an author, please double-check that all other people have made non-code contributions specifically to this software (e.g., software testing, conceptualization).

Summary: I appreciate your efforts in providing a well-referenced introduction to HR(n)V analysis in the introduction of your paper. Even for me as a sport scientist (though not working in the field of HRV research) it was indeed hard to follow the technical parts of this section. Please note, that the summary section of the paper should avoid jargon and be adressed to a non-specialist audience (https://joss.readthedocs.io/en/latest/submitting.html#what-should-my-paper-contain).

Basic Usage: I believe this section could be much shorter. The quite detailed API walkthrough is mostly already part of your well-written README and should not be part of the JOSS paper. However I think that showing some high-level functionality of the software may also be useful in the paper, so I suggest to keep Figure 1 with the general workflow and to shortly mention important other features without going much into detail. This could also help you to archieve the target word count for the paper (<1000). Additionally, there are some references in this section related to specific processing options that should rather be part of the software documentation (i.e., the README in your case).

@itismeghasyam
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itismeghasyam commented May 1, 2023

Review checklist for @itismeghasyam

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

General checks

  • Repository: Is the source code for this software available at the https://github.com/nliulab/HRnV-Calc?
  • 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 (@charlienew) 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?

@charlienew
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Thank you @smnnlt and @itismeghasyam for reviewing our software and the constructive comments.

To respond to the comments from @smnnlt, first of all, thank you for pointing out the concern for authorship. We know that the list might be longer than most papers on JOSS. However, we can confirm that all other authors listed have contributed to our software either in conceptualization or in testing. Although the code was only written by three people, the design and the workflow of HRnV-Calc are the results of wide collaboration between clinicians and HRV researchers.

We understand that the introduction of our paper might be somewhat lengthy and exhaustive. However, we do think a bit of technical details is necessary since the HRnV method is quite new, and not many people are familiar with its background and the motives for its introduction. We believe most of the potential users of HRnV-Calc to be in the field of HRV and related research, in particular, clinicians dealing with cardiac-related conditions. Therefore, some in-depth descriptions and discussions of HRnV would help them to decide whether to try our software. However, we will work on the writing of this section to make it more appealing to a broader audience.

The comments on the basic usage section are absolutely right. We will remove all the figures except Figure 1 and shorten the descriptions for each GUI.

We will also address the issues raised in our HRnV-Calc repo and respond directly in the corresponding issue threads. Once all necessary changes are done, we will update our code and paper in the repo. Thanks again for your feedback and suggestions!

@itismeghasyam
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@charlienew Thanks for your comments, and for confirming @smnnlt's comment on authorship - it clarified my doubts too.

Can you please include a section in the README/documentation about how to contribute to the repository, and/or how issues are reported and handled?

@charlienew
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charlienew commented May 4, 2023

Hi @itismeghasyam, thanks for your suggestions. Yes, we will include a section in our README about contributing guidelines and a code of conduct, which should be completed by the end of this week or early next week along with some other issues raised by @smnnlt.

@charlienew
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Hi @smnnlt and @itismeghasyam,

Thanks again for reviewing our software and paper. We have updated our code and GitHub page to address the valuable feedback and suggestions. For the issues raised on our GitHub page, we have addressed them individually in the issue thread and made necessary changes to our code to fix the issues.

We have also revised our paper to shorten the ‘Basic Usage’ section, which now only includes Figure 1 and some brief descriptions of each GUI.

Thank you.

@bmcfee
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bmcfee commented May 15, 2023

Thanks @itismeghasyam and @smnnlt for the reviews so far, and @charlienew for the updates.

Reviewers: when you can, please look over the changes made in response to your reviews, and update your checklists as warranted.

@smnnlt
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smnnlt commented May 15, 2023

@editorialbot generate pdf

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

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smnnlt commented May 15, 2023

Hi @charlienew, thank you for answering the issues raised and for revising the paper.

@bmcfee If the level of technical details in the summary section of the paper is fine from an editorial perspective, I am happy to endorse publishing the software paper. I have completed my review and have therefore updated my checklist.

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bmcfee commented May 15, 2023

@smnnlt yes, I think the level of technical detail here is in keeping with the expectations outlined in the submission guidelines: https://joss.readthedocs.io/en/latest/submitting.html#what-should-my-paper-contain

@itismeghasyam
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@charlienew Thanks for the revisions, they look good to me :)

@bmcfee I competed my review checklist and am happy with this paper getting published.

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bmcfee commented May 19, 2023

@editorialbot generate pdf

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bmcfee commented May 19, 2023

@editorialbot check references

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

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#4266, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

@editorialbot editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label May 25, 2023
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@editorialbot generate post review checklist

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I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

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Kevin-Mattheus-Moerman commented May 30, 2023

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

  • Double check authors and affiliations (including ORCIDs)
  • Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
  • Archive the release on Zenodo/figshare/etc and post the DOI here.
  • Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
  • Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

  • Read the text of the paper and offer comments/corrections (as either a list or a PR)
  • Check the references in the paper for corrections (e.g. capitalization)
  • Check that the archive title, author list, version tag, and the license are correct
  • Set archive DOI with @editorialbot set <DOI here> as archive
  • Set version with @editorialbot set <version here> as version
  • Double check rendering of paper with @editorialbot generate pdf
  • Specifically check the references with @editorialbot check references and ask author(s) to update as needed
  • Recommend acceptance with @editorialbot recommend-accept

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@bmcfee thanks for editing here. I recommend the new functionality @editorialbot generate post review checklist, as you can see it generates a list of final check. In this case the title of the archive doesn't match yet so we'll ask the authors to fix that.

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bmcfee commented May 30, 2023

Thanks @Kevin-Mattheus-Moerman - I knew that feature was coming, but somehow missed that it was now active.

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Kevin-Mattheus-Moerman commented May 30, 2023

@charlienew can you check the above list of tick mark points? ☝️ In particular the archive title should match the paper title, and the license listed on your repository should match the archive listed license (currently says Other(Open) ).

  • In addition, can you update your bib file references so that they do not use all caps letters for journal names (e.g. AMERICAN JOURNAL OF SURGERY, and CANCER EPIDEMIOLOGY)

@charlienew
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Hi @Kevin-Mattheus-Moerman, thanks for your feedback. I have updated the bib file accordingly.

The release we created was V1.0.0 on our GitHub repo, and the DOI for our Zenodo archive is 10.5281/zenodo.7963494. The title and the license for our archive have also been updated. Thanks.

Additional Author Tasks After Review is Complete

  • Double-check authors and affiliations (including ORCIDs)
  • Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
  • Archive the release on Zenodo/figshare/etc and post the DOI here.
  • Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
  • Make sure that the license listed for the archive is the same as the software license.

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@editorialbot set 10.5281/zenodo.7963493 as archive

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Done! archive is now 10.5281/zenodo.7963493

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@editorialbot check references

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

OK DOIs

- 10.1016/j.amjsurg.2015.06.002 is OK
- 10.1103/PhysRevLett.89.068102 is OK
- 10.1152/ajpheart.2000.278.6.H2163 is OK
- 10.1016/j.canep.2013.04.016 is OK
- 10.3892/etm.2016.3104 is OK
- 10.3389/fpubh.2017.00240 is OK
- 10.1016/j.cmpb.2019.05.032 is OK
- 10.3389/fphys.2020.602027 is OK
- 10.3758/s13428-011-0107-7 is OK
- 10.1177/147323000603400308 is OK
- 10.3390/e20120952 is OK
- 10.1016/j.compbiomed.2012.11.005 is OK
- 10.1186/s12872-020-01455-8 is OK
- 10.1371/journal.pone.0249868 is OK
- 10.1016/j.cmpb.2019.105127 is OK
- 10.1109/jbhi.2013.2244902 is OK
- 10.1056/NEJMoa1901183 is OK
- 10.1007/s11517-006-0119-0 is OK
- 10.1093/ndt/gfm634 is OK
- 10.1093/europace/euv015 is OK
- 10.3389/fpubh.2017.00258 is OK
- 10.1016/j.smrv.2011.02.005 is OK
- 10.1016/j.cmpb.2013.07.024 is OK
- 10.1088/1361-6579/aae021 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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@editorialbot generate pdf

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

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@charlienew thanks that all looks good now. We are good to proceed.

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@editorialbot accept

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

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Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Niu
  given-names: Chenglin
  orcid: "https://orcid.org/0000-0001-6677-7910"
- family-names: Guo
  given-names: Dagang
- family-names: Ong
  given-names: Marcus Eng Hock
- family-names: Koh
  given-names: Zhi Xiong
- family-names: Marie-Alix
  given-names: Guerry Alexiane Laure
- family-names: Ho
  given-names: Andrew Fu Wah
- family-names: Lin
  given-names: Zhiping
- family-names: Liu
  given-names: Chengyu
- family-names: Clifford
  given-names: Gari D.
- family-names: Liu
  given-names: Nan
  orcid: "https://orcid.org/0000-0003-3610-4883"
contact:
- family-names: Liu
  given-names: Nan
  orcid: "https://orcid.org/0000-0003-3610-4883"
doi: 10.5281/zenodo.7963493
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Niu
    given-names: Chenglin
    orcid: "https://orcid.org/0000-0001-6677-7910"
  - family-names: Guo
    given-names: Dagang
  - family-names: Ong
    given-names: Marcus Eng Hock
  - family-names: Koh
    given-names: Zhi Xiong
  - family-names: Marie-Alix
    given-names: Guerry Alexiane Laure
  - family-names: Ho
    given-names: Andrew Fu Wah
  - family-names: Lin
    given-names: Zhiping
  - family-names: Liu
    given-names: Chengyu
  - family-names: Clifford
    given-names: Gari D.
  - family-names: Liu
    given-names: Nan
    orcid: "https://orcid.org/0000-0003-3610-4883"
  date-published: 2023-05-31
  doi: 10.21105/joss.05391
  issn: 2475-9066
  issue: 85
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5391
  title: "HRnV-Calc: A Software for Heart Rate n-Variability and Heart
    Rate Variability Analysis"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05391"
  volume: 8
title: "HRnV-Calc: A Software for Heart Rate n-Variability and Heart
  Rate Variability Analysis"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

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🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

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🚨🚨🚨 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 👉 Creating pull request for 10.21105.joss.05391 joss-papers#4276
  2. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05391
  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...

@editorialbot editorialbot added accepted published Papers published in JOSS labels May 31, 2023
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@charlienew et al. congratulations on this publication in JOSS! 🎉

Thanks for editing @bmcfee!

And a special thanks to the reviewers: @smnnlt, @itismeghasyam !

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🎉🎉🎉 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.05391/status.svg)](https://doi.org/10.21105/joss.05391)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05391">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05391/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05391/status.svg
   :target: https://doi.org/10.21105/joss.05391

This is how it will look in your documentation:

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Hi @Kevin-Mattheus-Moerman, thanks for your help!

Thanks again to @bmcfee for your editing feedback, and thank you @smnnlt and @itismeghasyam for reviewing our paper!

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