[REVIEW]: minorbsem: An R package for structural equation models that account for the influence of minor factors

[editorialbot]

Submitting author: @jamesuanhoro (James Ohisei Uanhoro)
Repository: https://github.com/jamesuanhoro/minorbsem
Branch with paper.md (empty if default branch): joss-paper
Version: v0.2.4
Editor: @samhforbes
Reviewers: @smasongarrison, @aaronpeikert
Archive: 10.5281/zenodo.8057759

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/c0cd5b1a2d66bbf21fb00d237f646180/status.svg)](https://joss.theoj.org/papers/c0cd5b1a2d66bbf21fb00d237f646180)

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

@smasongarrison & @aaronpeikert, 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 @samhforbes 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 @aaronpeikert

📝 Checklist for @smasongarrison

[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:

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

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.04 s (1034.0 files/s, 126605.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               26            236            721           2108
Markdown                         4            201              0            750
TeX                              1             16              0            178
C++                              2             15             11             91
YAML                             4              9              3             80
Rmd                              1             62            171              1
-------------------------------------------------------------------------------
SUM:                            38            539            906           3208
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 650

[editorialbot]

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

OK DOIs

- 10.1080/10705511.2022.2142128 is OK
- 10.1037/0033-2909.109.3.502 is OK
- 10.1007/s11336-015-9451-3 is OK
- 10.1016/j.jpsychores.2012.10.010 is OK
- 10.3389/fpsyg.2014.01521 is OK
- 10.4232/1.1840 is OK
- 10.18637/jss.v076.i01 is OK
- 10.18637/jss.v048.i02 is OK
- 10.18637/jss.v040.i08 is OK
- 10.1037/a0026802 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[samhforbes]

OK @smasongarrison, @aaronpeikert the thread is here when you are ready to begin your reviews in early April. Please flag any issues as issues in the software repository, and link back here. Your reviewer checklist can be generated using the commands in the first thread. I look forward to digging into this software in more detail, and hearing both your thoughts.

[aaronpeikert]

Review checklist for @aaronpeikert

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/jamesuanhoro/minorbsem?
• 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 (@jamesuanhoro) 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?

[aaronpeikert]

@editorialbot generate pdf

[editorialbot]

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

[samhforbes]

Hi @smasongarrison, @aaronpeikert hope all is well. Let me know if I can help at all, otherwise feel free to link any issues back to this thread, or highlight any issues here if you want to discuss them further.

[smasongarrison]

Thanks for the nudge! I had put reviewing the paper on my docket for this friday. (My semester ends on Wednesday)

…

Message ID: ***@***.***>

[smasongarrison]

Review checklist for @smasongarrison

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/jamesuanhoro/minorbsem?
• 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 (@jamesuanhoro) 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?

Additional Notes/Comments:

• I'd love to see this made available on CRAN.
• Paper Summary: I think that the summary and features should explicitly mention that this method is for fitting Bayesian SEM (as opposed to frequentist SEM).
• Documentation Summary: I did some minor copy-editing that I think will make it a little easier for the audience, including spelling out a few acronyms. (I've issued a pull request Minor copy edits jamesuanhoro/minorbsem#92 , as I found it easier to just make the changes instead of describing them. However, I defer to the author @jamesuanhoro).
• References are out-of-date on the joss branch. (They're current on the main branch jamesuanhoro/minorbsem@6fe387a). To be fair, the paper is currently in press, so I don't fault the author. (I've issued a pull request. Update REFERENCES.bib jamesuanhoro/minorbsem#91 )

[smasongarrison]

@editorialbot commands

[editorialbot]

Hello @smasongarrison, here are the things you can ask me to do:

# List all available commands
@editorialbot commands

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@editorialbot list editors

# Check the references of the paper for missing DOIs
@editorialbot check references

# Perform checks on the repository
@editorialbot check repository

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@editorialbot generate my checklist

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[smasongarrison]

Title: Review of the minorbsem R package paper

I have reviewed the submission: "minorbsem: An R package for structural equation models that account for the influence of minor factors" and found that everything is in order. I was able to run everything and the package performed as expected. I recommend acceptance of this paper. During my review, I issued two minor pull-requests. My acceptance does not hinge on those changes, but I believe they would improve the user experience.

Minor Notes:

• I would love to see this package made available on CRAN.

Paper Summary

In the paper summary and features, I suggest explicitly mentioning that this method is for fitting Bayesian SEM (as opposed to frequentist SEM).

Documentation Summary

I performed some minor copy-editing that I think will make the paper more accessible for the audience, including spelling out a few acronyms. I have issued a pull request (jamesuanhoro/minorbsem#92), as I found it easier to make the changes directly instead of describing them. However, I defer to the author, @jamesuanhoro.

References

The references are out-of-date on the JOSS branch. They are current on the main branch (jamesuanhoro/minorbsem@6fe387a). To be fair, the paper is currently in press, so I do not fault the author for this. I have issued a pull request (jamesuanhoro/minorbsem#91) to address this issue.

[jamesuanhoro]

Hi @samhforbes, both reviewers have completed their checklists. What should I do next? Thank you.

[aaronpeikert]

Hi @samhforbes, both reviewers have completed their checklists. What should I do next? Thank you.

Sorry, haven't finished yet sorry!

[samhforbes]

No worries @aaronpeikert - if there's anything you needs further discussion beyond an issue for the authors to address, please feel free to place it here.

[jamesuanhoro]

Hi @samhforbes, both reviewers have completed their checklists. What should I do next? Thank you.

Sorry, haven't finished yet sorry!

Oh sorry, I wrongly assumed you were done. I'm not in a hurry with this btw.

[aaronpeikert]

@jamesuanhoro I defend my thesis beginning next week, so I hope it is ok if I finish my review after that. Feel free to remind me in case I forget.

[jamesuanhoro]

@jamesuanhoro I defend my thesis beginning next week, so I hope it is ok if I finish my review after that. Feel free to remind me in case I forget.

No problem at all. Best of luck with your defence :).

[samhforbes]

Best of luck @aaronpeikert!

[smasongarrison]

Good luck!!!

…

On Thu, May 18, 2023, 8:54 AM Sam Forbes ***@***.***> wrote: Best of luck @aaronpeikert <https://github.com/aaronpeikert>! — Reply to this email directly, view it on GitHub <#5292 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNZHSE3EXOM4ZVX263V5JDXGYL2DANCNFSM6AAAAAAWDXOB3E> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[jamesuanhoro]

Ah yeah I realised that just after I messaged, sorry!

One thing I have noticed though is we ask authors to ensure the title on the archive matches the paper title, so if you wouldn't mind fixing that, that would be great

No problem. And I updated the archive title.

[samhforbes]

Well I think this is a great package that makes a contribution, and the reviewers are satisfied, so I'm going to recommend accept and pass over to the EiCs. Well done @jamesuanhoro, and thank you both @smasongarrison & @aaronpeikert

[samhforbes]

@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

- 10.1177/00131644231165306 is OK
- 10.1080/10705511.2022.2142128 is OK
- 10.1037/0033-2909.109.3.502 is OK
- 10.1007/s11336-015-9451-3 is OK
- 10.1016/j.jpsychores.2012.10.010 is OK
- 10.3389/fpsyg.2014.01521 is OK
- 10.4232/1.1840 is OK
- 10.18637/jss.v076.i01 is OK
- 10.18637/jss.v048.i02 is OK
- 10.18637/jss.v040.i08 is OK
- 10.1037/a0026802 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

⚠️ Error preparing paper acceptance. The generated XML metadata file is invalid.

Element isbn: [facet 'minLength'] The value has a length of '9'; this underruns the allowed minimum length of '10'.

[samhforbes]

@jamesuanhoro I think if I've understood this correctly, the issue is that the ISBN for Muthen 2012 contains the ISSN. Perhaps that field needs to be removed?

[jamesuanhoro]

@samhforbes I see, fixed it now. Thank you.

[samhforbes]

@editorialbot generate pdf

[editorialbot]

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

[samhforbes]

@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

- 10.1177/00131644231165306 is OK
- 10.1080/10705511.2022.2142128 is OK
- 10.1037/0033-2909.109.3.502 is OK
- 10.1007/s11336-015-9451-3 is OK
- 10.1016/j.jpsychores.2012.10.010 is OK
- 10.3389/fpsyg.2014.01521 is OK
- 10.4232/1.1840 is OK
- 10.18637/jss.v076.i01 is OK
- 10.18637/jss.v048.i02 is OK
- 10.18637/jss.v040.i08 is OK
- 10.1037/a0026802 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/sbcs-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#4330, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[arfon]

@editorialbot accept

[editorialbot]

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

[editorialbot]

⚠️ Couldn't acccept/publish paper. An error happened.

[arfon]

@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: Uanhoro
  given-names: James Ohisei
  orcid: "https://orcid.org/0000-0002-4843-927X"
doi: 10.5281/zenodo.8057759
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Uanhoro
    given-names: James Ohisei
    orcid: "https://orcid.org/0000-0002-4843-927X"
  date-published: 2023-06-21
  doi: 10.21105/joss.05292
  issn: 2475-9066
  issue: 86
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5292
  title: "minorbsem: An R package for structural equation models that
    account for the influence of minor factors"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05292"
  volume: 8
title: "minorbsem: An R package for structural equation models that
  account for the influence of minor factors"

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]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[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.05292 joss-papers#4331
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05292
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...

[arfon]

@smasongarrison, @aaronpeikert – many thanks for your reviews here and to @samhforbes for editing this submission! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@jamesuanhoro – your paper is now accepted and published in JOSS ⚡🚀💥

[editorialbot]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

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HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.05292/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05292/status.svg
   :target: https://doi.org/10.21105/joss.05292

This is how it will look in your documentation:

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