[REVIEW]: cofad: An R package and shiny app for contrast analysis

[whedon]

Submitting author: @johannes-titz (Johannes Titz)
Repository: https://github.com/johannes-titz/cofad
Version: v0.2.0
Editor: @chartgerink
Reviewer: @tianxzhu, @svmiller
Archive: 10.5281/zenodo.5702779

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Markdown: [![status](https://joss.theoj.org/papers/b86ad7d9c7500604c0c66df652475406/status.svg)](https://joss.theoj.org/papers/b86ad7d9c7500604c0c66df652475406)

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Review checklist for @tianxzhu

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
• 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 (@johannes-titz) 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

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 and who the target audience is?
• 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?

Review checklist for @svmiller

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
• 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 (@johannes-titz) 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

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 and who the target audience is?
• 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?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @tianxzhu, @svmiller it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

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For a list of things I can do to help you, just type:

@whedon commands

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

@whedon generate pdf

[whedon]

Wordcount for paper.md is 555

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.06 s (469.9 files/s, 63286.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               15             91            498           1298
XML                              1              0             14            761
Markdown                         5            146              0            603
TeX                              2             12              0            116
Rmd                              2            117            173             92
Bourne Shell                     1              2              9             60
YAML                             2              1              4             21
INI                              1              4              0             10
HTML                             1              3              0              5
-------------------------------------------------------------------------------
SUM:                            30            376            698           2966
-------------------------------------------------------------------------------


Statistical information for the repository 'ca72b9ece9263960d61ab75a' was
gathered on 2021/10/13.
No commited files with the specified extensions were found.

[whedon]

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

OK DOIs

- 10.1207/s15328031us0301_1 is OK
- 10.1017/CBO9780511804403 is OK
- 10/gdz7q2 is OK
- 10/b5f2gc is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

[whedon]

👋 @svmiller, please update us on how your review is going (this is an automated reminder).

[svmiller]

Should have just completed my review now.

[chartgerink]

@whedon generate pdf

[whedon]

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

[chartgerink]

@whedon check references

[whedon]

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

OK DOIs

- 10.1207/s15328031us0301_1 is OK
- 10.1017/CBO9780511804403 is OK
- 10/gdz7q2 is OK
- 10/b5f2gc is OK

MISSING DOIs

- None

INVALID DOIs

- None

[chartgerink]

@svmiller and @tianxzhu - could you provide a small summary of your review? I see you checked off everything, and it would help me understand your evaluation. Many thanks 😊

[chartgerink]

@johannes-titz could you please update the short DOIs to full length DOIs? Specifically these two

- 10/gdz7q2 is OK
- 10/b5f2gc is OK

[johannes-titz]

@chartgerink Thanks for the update! I changed the short DOIs to full length DOIs. Is this OK?

[danielskatz]

@whedon check references

[whedon]

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

OK DOIs

- 10.1207/s15328031us0301_1 is OK
- 10.1017/CBO9780511804403 is OK
- 10.18637/jss.v069.i01 is OK
- 10.1002/bimj.200810425 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[chartgerink]

many thanks @johannes-titz!

I am only awaiting a short summary from the reviewers - after that I can move forward with the editorial process based on their assessment.

[svmiller]

I think what Titz and Burkhardt offer here merits publication in the Journal of Open Source Software. The authors advocate for greater use of a contrast analysis for testing hypotheses about means in a factorial design. The authors note that alternatives to the contrast analysis exist, though with important limitations. To better advocate its use, the authors offer a Shiny app that allows users to upload their own data to do their own contrast analyses.

I think the authors have provided an important contribution to researchers working in psychology and the social sciences (who would assuredly benefit from these methods). I was able to upload a pilot data set and calculate my own contrast analyses, so the software behaves as it should. I'm also a big proponent of rewarding those who make software to make all our lives easier. I recommend JOSS proceed with publication here.

[chartgerink]

I haven't heard back from @tianxzhu, but given the positive review from @svmiller and no negative comments from @tianxzhu - I will move forward and am happy to accept this for publication, @johannes-titz 😊

@johannes-titz could you please deposit the software in Zenodo/FigShare and share the DOI with me? See also here

I will initiate some of whedon's checks in the meantime.

[chartgerink]

@whedon generate pdf

[whedon]

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

[chartgerink]

@whedon check references

[whedon]

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

OK DOIs

- 10.1207/s15328031us0301_1 is OK
- 10.1017/CBO9780511804403 is OK
- 10.18637/jss.v069.i01 is OK
- 10.1002/bimj.200810425 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[johannes-titz]

@chartgerink Thank you very much! I just made a final commit for the release and released version 0.2.1 on github (tag v0.2.1), which is also linked at zenodo (https://zenodo.org/record/5702779) with the following doi: 10.5281/zenodo.5702779

Do you need anything else?

@svmiller Thank you for such a positive feedback! I hope the software will be as useful as your review suggests :).

@tianxzhu Thank you very much for your time and effort to review the submission!

[chartgerink]

@whedon set 10.5281/zenodo.5702779 as archive

[whedon]

OK. 10.5281/zenodo.5702779 is the archive.

[chartgerink]

@whedon recommend-accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1207/s15328031us0301_1 is OK
- 10.1017/CBO9780511804403 is OK
- 10.18637/jss.v069.i01 is OK
- 10.1002/bimj.200810425 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

Check final proof 👉 openjournals/joss-papers#2751

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2751, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[chartgerink]

@johannes-titz the editor in chief that's on rotation will do a final pass and may come back with a final bit here and there. Otherwise, we're good and thank you for your patience as we worked through this :)

[arfon]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 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.03822 joss-papers#2754
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03822
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]

@tianxzhu, @svmiller – many thanks for your reviews here and to @chartgerink 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 ✨

@johannes-titz – your paper is now accepted and published in JOSS ⚡🚀💥

[whedon]

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

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[johannes-titz]

@arfon Thank you for being so quick with the final steps! @chartgerink Thanks for the professional editing process! @svmiller @tianxzhu Thanks again for taking the time to review this submission.

[chartgerink]

Congratulations @johannes-titz 💯 Thanks for considering JOSS and see you around on the interwebs 😊 It was lovely to be a part of your paper!