[REVIEW]: chessboard: An R package for creating network connections based on chess moves

[editorialbot]

Submitting author: @ahasverus (Nicolas Casajus)
Repository: https://github.com/FRBCesab/chessboard
Branch with paper.md (empty if default branch): main
Version: v0.1.0
Editor: @Nikoleta-v3
Reviewers: @Pentaonia, @gsapijaszko
Archive: 10.5281/zenodo.8424609

Status

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Markdown: [![status](https://joss.theoj.org/papers/f709edaff050ed0cb1ffb8dd4ad2a1bb/status.svg)](https://joss.theoj.org/papers/f709edaff050ed0cb1ffb8dd4ad2a1bb)

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

@Pentaonia & @gsapijaszko, 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 @Nikoleta-v3 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 @gsapijaszko

📝 Checklist for @Pentaonia

[editorialbot]

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

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.04 s (2461.1 files/s, 303565.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               84           2375           1917           5148
Markdown                         6            206              0            710
Rmd                              4            531            719            588
YAML                             7             42             24            235
TeX                              1              8              0             78
-------------------------------------------------------------------------------
SUM:                           102           3162           2660           6759
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1199

[editorialbot]

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

OK DOIs

- 10.1007/s11749-018-0599-x is OK
- 10.1016/j.ecolmodel.2006.02.015 is OK
- 10.32614/RJ-2018-009 is OK
- 10.1038/s41559-017-0101 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[Nikoleta-v3]

@ahasverus @Pentaonia, @gsapijaszko 👋🏼 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 #5753 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.

We aim for reviews to be completed within about 2-4 weeks. Please let me know if any of you require some more time. We can also use EditorialBot (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@Nikoleta-v3) if you have any questions/concerns. 😄 🙋🏻

[editorialbot]

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

[gsapijaszko]

Review checklist for @gsapijaszko

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/FRBCesab/chessboard?

• 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 (@ahasverus) 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?

[Pentaonia]

Review checklist for @Pentaonia

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/FRBCesab/chessboard?
• 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 (@ahasverus) 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?

[Pentaonia]

Hi all,

As far as I can see, I am mostly done with my review. The last three points can be ticked off when the issues are closed. But these were all just minor issues. 😁

[ahasverus]

Hi @gsapijaszko and @Pentaonia 👋
Thank you for agreeing to review our works!

@Pentaonia: Thanks for your review. I have answered your questions in the issue FRBCesab/chessboard#2.

[Nikoleta-v3]

Hey @gsapijaszko and @Pentaonia 👋 😄 any update regarding your reviews? Thank you 🙏🏻

[Pentaonia]

Hey @Nikoleta-v3 im almost done with the review, my checklist has been ticked off. Im just waiting for an answer to the comment FRBCesab/chessboard#2 (comment). After that, I think there is nothing to stop it being published.

[Nikoleta-v3]

Thank you @Pentaonia! My apologises I missed your latest reply on the issue 😄

[gsapijaszko]

Hi @Nikoleta-v3, @ahasverus,

my review is done as well. If I may, I would recommend to publish the paper.

Regards,
Grzegorz

[ahasverus]

Hi @gsapijaszko,
Thanks for your contribution.

[ahasverus]

Hi @Nikoleta-v3, @Pentaonia & @gsapijaszko
Thanks for this review. I think I have answered to all comments and suggestions.
All the best,
Nicolas

[Pentaonia]

Hey @Nikoleta-v3 @ahasverus,

I just checked the changes and closed the issue (FRBCesab/chessboard#2 (comment)). From my point of view it looks great. I have nothing more to comment on.

All the best
Louis

[Nikoleta-v3]

Thank you both for your time and your reviews 🙏🏻 @ahasverus I will have a final look at the submission in the next few days. I will leave my comments (if any) here 😄

[Nikoleta-v3]

Hello @ahasverus and thank you for your patience! I can confirm that I now have had the time to review the manuscript, documentation, and go over the source code. The package is well-developed, tested, and documented. I am very happy to move forward with acceptance. I just have some minor comments.

Regarding the paper, in lines 19-20 where you describe the connectivity matrix, use a math environment. So, $n \times n$, and in line 20, simply use $n$.

You state: "chessboard implements the following rules to detect neighbors and to create edges:

• Degree
• Orientation
• Direction

In Figure 1, you give an example of the neighbors; however, these concepts are not clearly captured in the figure. In my understanding the argument degree is for the degree, reverse and directed are for the direction, and orientation is for values like "Pawn," "Fool," etc. Could you update the figure to better reflect this?

Also, for the direction parameter, there are two input arguments,reverse and directed. Both of these arguments can be set to True at the same time, and then the package just uses reverse. Is this behavior documented somewhere in the function? Do you want to include a warning message if a user sets both as True?

Regarding the contributing file, thank you very much for adding one and thanks to our reviewers. The "Contributing code" section needs a bit more information and examples. For instance, including a command for the "Fork this repository" would be helpful. Additionally, running the test suite is not trivial for someone new to software development and open source, but just reading the contributing file 😄 Please assume that someone new to this might want to contribute to the package and provide a bite more guidance.

[ahasverus]

Hello @ahasverus and thank you for your patience! I can confirm that I now have had the time to review the manuscript, documentation, and go over the source code. The package is well-developed, tested, and documented. I am very happy to move forward with acceptance. I just have some minor comments.

Hi @Nikoleta-v3! Thank you for your positive feedbacks.

Regarding the paper, in lines 19-20 where you describe the connectivity matrix, use a math environment. So, n×n, and in line 20, simply use n.

This has been done in #4963b92

You state: "chessboard implements the following rules to detect neighbors and to create edges:

• Degree
• Orientation
• Direction

In Figure 1, you give an example of the neighbors; however, these concepts are not clearly captured in the figure. In my understanding the argument degree is for the degree, reverse and directed are for the direction, and orientation is for values like "Pawn," "Fool," etc. Could you update the figure to better reflect this?

I have made some modifications to Fig.1 in #60b5ac4. What do you think?

Also, for the direction parameter, there are two input arguments,reverse and directed. Both of these arguments can be set to True at the same time, and then the package just uses reverse. Is this behavior documented somewhere in the function? Do you want to include a warning message if a user sets both as True?

Indeed. Both directed and reverse arguments control the direction of the network. The argument reverse can be used to change the default direction of the network. But if the argument directed is set to FALSE the argument reverse is ignored as it is mentioned in the documentation. For instance here.

Regarding the contributing file, thank you very much for adding one and thanks to our reviewers. The "Contributing code" section needs a bit more information and examples. For instance, including a command for the "Fork this repository" would be helpful. Additionally, running the test suite is not trivial for someone new to software development and open source, but just reading the contributing file 😄 Please assume that someone new to this might want to contribute to the package and provide a bite more guidance.

Thanks for this suggestion: I have improved the section Contribute Code of the Contributing Guidelines in #0e8081a

[editorialbot]

Done! archive is now 10.5281/zenodo.8424609

[Nikoleta-v3]

@editorialbot set v0.1.0 as version

[editorialbot]

Done! version is now v0.1.0

[Nikoleta-v3]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1007/s11749-018-0599-x is OK
- 10.1016/j.ecolmodel.2006.02.015 is OK
- 10.32614/RJ-2018-009 is OK
- 10.1038/s41559-017-0101 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[Nikoleta-v3]

@Pentaonia and @gsapijaszko thank you very much for your time and your help with this submission 🙏🏻

[editorialbot]

👋 @openjournals/csism-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#4678, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[ahasverus]

Thank you very much @Nikoleta-v3, @gsapijaszko, @Pentaonia for your great contribution to this paper!
Nicolas

[danielskatz]

@ahasverus - sorry for the delay in getting to this - I'm the editor for this track, and I'll now proofread the paper and let you know what next steps are needed.

[ahasverus]

Hi @danielskatz. No worries. Thanks for dealing with the next steps.

[danielskatz]

I've suggested some minor changes in FRBCesab/chessboard#14 - please merge this, or let me know what you disagree with, then we can proceed.

[ahasverus]

Thanks! I have merged your PR.

[danielskatz]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1007/s11749-018-0599-x is OK
- 10.1016/j.ecolmodel.2006.02.015 is OK
- 10.32614/RJ-2018-009 is OK
- 10.1038/s41559-017-0101 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/csism-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#4689, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[danielskatz]

@editorialbot accept

[editorialbot]

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

[editorialbot]

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: Casajus
  given-names: Nicolas
  orcid: "https://orcid.org/0000-0002-5537-5294"
- family-names: Borges
  given-names: Érica Rievrs
  orcid: "https://orcid.org/0000-0001-7751-6265"
- family-names: Tabacchi
  given-names: Éric
  orcid: "https://orcid.org/0000-0001-7729-4439"
- family-names: Fried
  given-names: Guillaume
  orcid: "https://orcid.org/0000-0002-3653-195X"
- family-names: Mouquet
  given-names: Nicolas
  orcid: "https://orcid.org/0000-0003-1840-6984"
contact:
- family-names: Casajus
  given-names: Nicolas
  orcid: "https://orcid.org/0000-0002-5537-5294"
doi: 10.5281/zenodo.8424609
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Casajus
    given-names: Nicolas
    orcid: "https://orcid.org/0000-0002-5537-5294"
  - family-names: Borges
    given-names: Érica Rievrs
    orcid: "https://orcid.org/0000-0001-7751-6265"
  - family-names: Tabacchi
    given-names: Éric
    orcid: "https://orcid.org/0000-0001-7729-4439"
  - family-names: Fried
    given-names: Guillaume
    orcid: "https://orcid.org/0000-0002-3653-195X"
  - family-names: Mouquet
    given-names: Nicolas
    orcid: "https://orcid.org/0000-0003-1840-6984"
  date-published: 2023-10-13
  doi: 10.21105/joss.05753
  issn: 2475-9066
  issue: 90
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5753
  title: "chessboard: An R package for creating network connections
    based on chess moves"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05753"
  volume: 8
title: "chessboard: An R package for creating network connections based
  on chess moves"

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.

[editorialbot]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

🚨🚨🚨 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.05753 joss-papers#4690
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05753
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...

[ahasverus]

Thanks a lot @danielskatz, @Nikoleta-v3, @gsapijaszko, and @Pentaonia for contributing to this paper and for accepting it for publication.
I really enjoy the review process via GitHub.
Nicolas

[danielskatz]

Congratulations to @ahasverus (Nicolas Casajus) and co-authors on your publication!!

And thanks to @Pentaonia and @gsapijaszko for reviewing, and to @Nikoleta-v3 for editing!
JOSS depends on volunteers and wouldn't be successful without you

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[Pentaonia]

With great pleasure! Thanks @ahasverus for letting me participate, and get my first experience!

Congrats from me as well!