[REVIEW]: lavaanExtra: Convenience Functions for Package *lavaan*

[editorialbot]

Submitting author: @rempsyc (Rémi Thériault)
Repository: https://github.com/rempsyc/lavaanExtra
Branch with paper.md (empty if default branch):
Version: v0.1.9
Editor: @arfon
Reviewers: @jamesuanhoro, @TDJorgensen
Archive: 10.5281/zenodo.8421873

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/cf99bdccfe86664e00468ebcfa132f68/status.svg)](https://joss.theoj.org/papers/cf99bdccfe86664e00468ebcfa132f68)

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

@jamesuanhoro & @TDJorgensen, 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 @arfon 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 @jamesuanhoro

📝 Checklist for @TDJorgensen

[editorialbot]

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.17 s (596.4 files/s, 178367.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                            28            975             87           8096
JavaScript                      10           2278           2217           8002
XML                              2              0            133           1871
R                               21            175            492           1168
Markdown                         7            208              0            830
Rmd                              7            354            751            698
CSS                              9            100             57            535
YAML                            12             75             27            390
TeX                              1              8              0             67
SVG                              1              0              1             11
JSON                             1              0              0              1
-------------------------------------------------------------------------------
SUM:                            99           4173           3765          21669
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 2148

[editorialbot]

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

OK DOIs

- 10.18637/jss.v048.i02 is OK

MISSING DOIs

- 10.21105/joss.05466 may be a valid DOI for title: rempsyc: Convenience Functions for Psychology

INVALID DOIs

- None

[editorialbot]

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

[arfon]

@jamesuanhoro, @TDJorgensen – This is the review thread for the paper. All of our communications will happen here from now on.

Please read the "Reviewer instructions & questions" in the first comment above. Please create your checklist typing:

@editorialbot generate my checklist

As you go over the submission, please check any items that you feel have been satisfied. There are also 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 https://github.com/openjournals/joss-reviews/issues/5701 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 the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

[arfon]

Friendly reminder to start your reviews soon @jamesuanhoro & @TDJorgensen. Thank you!

[jamesuanhoro]

Friendly reminder to start your reviews soon @jamesuanhoro & @TDJorgensen. Thank you!

Thank you for the reminder. Will try to complete my review before the start of next week.

[jamesuanhoro]

Review checklist for @jamesuanhoro

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/rempsyc/lavaanExtra?
• 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 (@rempsyc) 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?

[arfon]

👋 @TDJorgensen – friendly bump again on getting going on your review.

[arfon]

@jamesuanhoro – thanks for completing your review. Could you link here any issues you opened on the software repository (https://github.com/rempsyc/lavaanExtra) and write a short summary statement for your review? Thank you!

[arfon]

Update: I just emailed @TDJorgensen to ask when they might be able to get to this review.

[rempsyc]

In the eventuality that all reviewers are satisfied with the changes and that this paper gets accepted for publication before October 11, I will be able to include it in my postdoctoral fellowship application :) No worry if we cannot make this deadline.

[jamesuanhoro]

Thanks @rempsyc for linking the issues here. My review is complete.

lavaanExtra functions are described and provides desirable end-user functionalities. @rempsyc and I had some discussions about which indices to report, given the different possibilities. My modifications to the repo were limited in scope:

• slight modifications for safer code.
• slight changes to reported fit indices.
• minor changes to the paper.

[TDJorgensen]

Review checklist for @TDJorgensen

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/rempsyc/lavaanExtra?
• 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 (@rempsyc) 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?

[TDJorgensen]

@editorialbot commands

[editorialbot]

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

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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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[TDJorgensen]

@editorialbot check repository

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.25 s (408.3 files/s, 118290.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                            28            975             87           8096
JavaScript                      10           2278           2217           8002
XML                              2              0            133           1871
R                               24            186            557           1271
Markdown                         8            217              0            874
Rmd                              7            354            751            698
CSS                              9            100             57            535
YAML                            12             75             27            390
TeX                              1              8              0             67
SVG                              1              0              1             11
JSON                             1              0              0              1
-------------------------------------------------------------------------------
SUM:                           103           4193           3830          21816
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[arfon]

@rempsyc – given @TDJorgensen's most recent comment and @jamesuanhoro's review too – I think we're ready to move forward here.

Please give your own paper a final read to check for any potential typos etc.

After that, could you make a new release of this software that includes the changes that have resulted from this review. Then, please make an archive of the software in Zenodo/figshare/other service and update this thread with the DOI of the archive? For the Zenodo/figshare archive, please make sure that:

• The title of the archive is the same as the JOSS paper title
• That the authors of the archive are the same as the JOSS paper authors
• I can then move forward with accepting the submission.

[rempsyc]

Great, thank you!

Here is the release (version 0.1.9): https://github.com/rempsyc/lavaanExtra/releases/tag/v0.1.9

Here is the Zenodo archive and doi: https://doi.org/10.5281/zenodo.8421873

[arfon]

@editorialbot set v0.1.9 as version

[editorialbot]

Done! version is now v0.1.9

[arfon]

@editorialbot set 10.5281/zenodo.8421873 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.8421873

[arfon]

@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

- 10.18637/jss.v048.i02 is OK

MISSING DOIs

- 10.21105/joss.05466 may be a valid DOI for title: rempsyc: Convenience Functions for Psychology

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/dsais-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#4670, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[arfon]

@rempsyc – please take a look at this final draft PDF. I note there's a fair number of things that look like {lavaanExtra} in the text which I'm assuming is a formatting mistake?

[rempsyc]

Originally, I used code formatting for packages, like lavaanExtra, but my colleagues from easystats have suggested that it is better for JOSS to actually use brackets {lavaanExtra} when referring to packages (a recently published example). So, what is the official preference? I can change it based on that.

Note: I have added to doi for rempsyc since it has now been published in JOSS as well.

[arfon]

So, what is the official preference? I can change it based on that.

I don't think we have one. I personally prefer lavaanExtra (hence my comment) but I'll leave it up to you!

[rempsyc]

Ok, I changed it back as suggested! The new version should be good to go :)

[arfon]

@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

- 10.18637/jss.v048.i02 is OK
- 10.21105/joss.05466 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/dsais-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#4683, 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]

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: Thériault
  given-names: Rémi
  orcid: "https://orcid.org/0000-0003-4315-6788"
doi: 10.5281/zenodo.8421873
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Thériault
    given-names: Rémi
    orcid: "https://orcid.org/0000-0003-4315-6788"
  date-published: 2023-10-11
  doi: 10.21105/joss.05701
  issn: 2475-9066
  issue: 90
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5701
  title: "lavaanExtra: Convenience Functions for Package lavaan"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05701"
  volume: 8
title: "lavaanExtra: Convenience Functions for Package *lavaan*"

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.05701 joss-papers#4684
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05701
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...

[rempsyc]

Wonderful! I boosted the toot. For now, the doi shared in the toot leads to the message

404: File not found

But I suppose it will solve automatically soon.

[arfon]

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

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

[editorialbot]

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

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