[REVIEW]: REDCapTidieR: Extracting complex REDCap databases into tidy tables

[editorialbot]

Submitting author: @rsh52 (Richard Hanna)
Repository: https://github.com/CHOP-CGTInformatics/REDCapTidieR
Branch with paper.md (empty if default branch):
Version: v1.0.0-joss
Editor: @mikemahoney218
Reviewers: @RhysPeploe, @spgarbet
Archive: 10.5281/zenodo.10658773

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/19002e0cdd99ac89e516c73c76c232bd/status.svg)](https://joss.theoj.org/papers/19002e0cdd99ac89e516c73c76c232bd)

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

@RhysPeploe & @spgarbet, 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 @mikemahoney218 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 @spgarbet

📝 Checklist for @RhysPeploe

[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=0.08 s (746.5 files/s, 160403.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               31           1245           1826           4724
Markdown                        14            261              0           2468
HTML                             1             84              5            605
YAML                             6             33              9            249
Rmd                              5            355            505            146
TeX                              1             15              0            128
JSON                             1              0              0             19
-------------------------------------------------------------------------------
SUM:                            59           1993           2345           8339
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1189

[editorialbot]

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

OK DOIs

- 10.1016/j.jbi.2019.103208 is OK
- 10.1016/j.jbi.2008.08.010 is OK
- 10.18637/jss.v059.i10 is OK
- 10.5281/zenodo.11826 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[mikemahoney218]

👋🏼 @rsh52 , @RhysPeploe , @spgarbet , this is the review thread for {REDCapTidieR}. Just about all of our communications will happen here from now on 😄 .

We might have one more reviewer join us, but I figured it made sense to get things started while I wait to hear back there 😄

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. For best results, don't include anything else in the comment!

This will create a checklist that walks through the JOSS submission 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 openjournals/joss-reviews#6277 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 you require some more time.

Please feel free to ping me (@mikemahoney218) if you have any questions/concerns.

Thank you so much for agreeing to review this submission!

[mikemahoney218]

@editorialbot remind @mikemahoney218 in 2 weeks

(Setting up an automated reminder for myself to make sure this doesn't fall through the cracks 😄 )

[editorialbot]

Reminder set for @mikemahoney218 in 2 weeks

[spgarbet]

Review checklist for @spgarbet

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/CHOP-CGTInformatics/REDCapTidieR?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@rsh52) 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?

[spgarbet]

How do I see the more recent edited version?

[mikemahoney218]

Seems like @rsh52 has been making changes in a branch here:
https://github.com/CHOP-CGTInformatics/REDCapTidieR/tree/joss-feedback-1

(I'm assuming the plan is to eventually merge this into main?)

[rsh52]

Yes! I want to run the changes by the team first (an odd codecov check is currently failing) and then I was going to tag @spgarbet once I get some approvals.

[spgarbet]

With those it completes the checklist. Looks great.

[mikemahoney218]

Thanks for the extremely speedy review @spgarbet 😄

[mikemahoney218]

👋 @rsh52 and @RhysPeploe , just wanted to share that I'm going to be OOO from February 2nd through the 9th (so, Friday through the end of next week). I'll be around somewhat but will be much more delayed in responding on this issue; apologies in advance!

And as always, feel free to reach out if you have any questions or concerns 😄

[RhysPeploe]

Review checklist for @RhysPeploe

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/CHOP-CGTInformatics/REDCapTidieR?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@rsh52) 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?

[rsh52]

Seems like @rsh52 has been making changes in a branch here: https://github.com/CHOP-CGTInformatics/REDCapTidieR/tree/joss-feedback-1

(I'm assuming the plan is to eventually merge this into main?)

Just merged to main! Should I re-generate with the bot?

[mikemahoney218]

@editorialbot generate pdf

can't hurt 😄

[editorialbot]

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

[editorialbot]

👋 @mikemahoney218, please take a look at the state of the submission (this is an automated reminder).

[mikemahoney218]

@editorialbot set version v1.0.0-joss

[editorialbot]

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

@editorialbot commands

[mikemahoney218]

@editorialbot set v1.0.0-joss as version

[editorialbot]

Done! version is now v1.0.0-joss

[mikemahoney218]

@editorialbot set 10.5281/zenodo.10658773 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.10658773

[mikemahoney218]

@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

- 10.1016/j.jbi.2019.103208 is OK
- 10.1016/j.jbi.2008.08.010 is OK
- 10.18637/jss.v059.i10 is OK
- 10.5281/zenodo.10564837 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#5016, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[mikemahoney218]

🎉 With everything looking good on my end, it's time for me to hand this back to the EiC for last steps. Thanks @rsh52 for the submission, and thank you so much to @spgarbet and @RhysPeploe for reviewing!

[rsh52]

Thank you everyone!

[RhysPeploe]

Pleasure, thanks a lot!

[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: Hanna
  given-names: Richard
  orcid: "https://orcid.org/0009-0005-6496-8154"
- family-names: Porter
  given-names: Ezra
  orcid: "https://orcid.org/0000-0002-4690-8343"
- family-names: Romero
  given-names: Stephany
- family-names: Wildenhain
  given-names: Paul
- family-names: Beasley
  given-names: William
  orcid: "https://orcid.org/0000-0002-5613-5006"
- family-names: Kadauke
  given-names: Stephan
  orcid: "https://orcid.org/0000-0003-2996-8034"
doi: 10.5281/zenodo.10658773
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Hanna
    given-names: Richard
    orcid: "https://orcid.org/0009-0005-6496-8154"
  - family-names: Porter
    given-names: Ezra
    orcid: "https://orcid.org/0000-0002-4690-8343"
  - family-names: Romero
    given-names: Stephany
  - family-names: Wildenhain
    given-names: Paul
  - family-names: Beasley
    given-names: William
    orcid: "https://orcid.org/0000-0002-5613-5006"
  - family-names: Kadauke
    given-names: Stephan
    orcid: "https://orcid.org/0000-0003-2996-8034"
  date-published: 2024-02-17
  doi: 10.21105/joss.06277
  issn: 2475-9066
  issue: 94
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6277
  title: "REDCapTidieR: Extracting complex REDCap databases into tidy
    tables"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06277"
  volume: 9
title: "REDCapTidieR: Extracting complex REDCap databases into tidy
  tables"

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.06277 joss-papers#5021
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06277
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]

@RhysPeploe, @spgarbet – many thanks for your reviews here and to @mikemahoney218 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 ✨

@rsh52 – your paper is now accepted and published in JOSS ⚡🚀💥

[editorialbot]

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

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</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06277/status.svg
   :target: https://doi.org/10.21105/joss.06277

This is how it will look in your documentation:

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[rsh52]

Thank you so much, what great news!