[REVIEW]: PRDA: An R pakcage for Prospective and Retrospective Design Analysis

[whedon]

Submitting author: @ClaudioZandonella (Claudio Zandonella Callegher)
Repository: https://github.com/ClaudioZandonella/PRDA
Version: v1.0.0
Editor: @cMadan
Reviewer: @DominiqueMakowski, @mmrabe
Archive: 10.5281/zenodo.4533739

⚠️ JOSS reduced service mode ⚠️

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Reviewers and authors:

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@DominiqueMakowski & @mmrabe, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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Review checklist for @DominiqueMakowski

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 (@ClaudioZandonella) 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: Do the authors clearly state 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 @mmrabe

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 (@ClaudioZandonella) 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: Do the authors clearly state 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. @DominiqueMakowski, @mmrabe 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.

⭐ Important ⭐

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:

1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

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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]

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

OK DOIs

- 10.3389/fpsyg.2019.02893 is OK
- 10.31234/osf.io/q9f86 is OK
- 10.1177/1745691614551642 is OK
- 10.7326/0003-4819-121-3-199408010-00008 is OK
- 10.2527/jas.2006-449 is OK
- 10.1111/bmsp.12132 is OK
- 10.1136/bmj.325.7375.1304 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

[DominiqueMakowski]

PRDA is an R package aiming at facilitating the implementation of design analysis, a recent framework extending traditional power analysis.

The package is very well documented, with a thorough yet accessible introduction to the conceptual framework.

Regarding its API, it is also very accessible, well-documented with good examples and clear (helped by the low number of functions).
The paper is well-written, clear and to the point.
Overall, it's a really good and useful piece of software that will improve the accessibility of design analysis.

I only have some minor comments that I made directly on the software's repo (see above ☝️) ☺️

[mmrabe]

The submitted paper describes the R package PRDA, which can be used for retrospective and prospective design analysis. It has significant advantages over prior R packages, such as an option for prospective design analysis and using standardized effect sizes, which are more common than unstandardized effect sizes in some scientific disciplines.

The paper, documentation, and examples are thoughtfully crafted and very straightforward. As a whole, they could possibly make the rather complex issue of power/design analysis more graspable and easy to address for researchers without advanced skills in statistical programming.

@DominiqueMakowski has already thoroughly evaluated the paper/package with an exemplary speed 😲 and made a number of suggestions, all of which I support. I made three additional minor suggestions (see above 👆). Once these have been addressed, I can fully recommend the paper for publication in JOSS.

[ClaudioZandonella]

@DominiqueMakowski and @mmrabe thanks for your very rapid reviews and thanks for your encouraging opinions!

I had a quick look at the issues and all your suggestions are very useful. Most of them will require small changes so at the weekend I will have the time to fix everything. Thanks!

[cMadan]

@DominiqueMakowski @mmrabe, thanks for the prompt and thorough reviews. I really appreciate the time and effort you are putting in to review this submission!

[cMadan]

@ClaudioZandonella, how are the revisions coming along?

[ClaudioZandonella]

Dear @cMadan I have integrated all the useful suggestions and comments by @mmrabe and @DominiqueMakowski.

The only missing issue is ClaudioZandonella/PRDA#2 regarding the upload of the package to CRAN. I have re-submitted the package to CRAN after they required a few changes to abide by their policy. In a few days, everything should be ok and I will be able to ultimate the revision.

[ClaudioZandonella]

Dear @cMadan, I have reviewed all the issues and updated the paper/paper.md file.

Thanks, @mmrabe and @DominiqueMakowski I really appreciate your comments and suggestions. They helped me to improve the overall quality of the package.

[mmrabe]

@whedon generate pdf

[whedon]

PDF failed to compile for issue #2810 with the following error:

Error producing PDF.
! Use of \author doesn't match its definition.
\new@ifnextchar ...served@d = #1\def \reserved@a {
#2}\def \reserved@b {#3}\f...
l.327 ...nolinkurl{claudiozandonella@gmail.com}}}}

Looks like we failed to compile the PDF

[ClaudioZandonella]

I have removed the note with the email fo the corresponding author that caused the error.

@whedon generate pdf

[cMadan]

@ClaudioZandonella, apologies for the delay. It's been a busy time for me with exam marking/other responsibilities, but I'll try and get this wrapped up over the next few days.

[ClaudioZandonella]

@cMadan perfect thanks! I was just worried there might be some problems. Absolutely no rush, I know that unfortunately, these are difficult and busy times and indeed, thanks for the time you have already dedicated to our work.

[cMadan]

@whedon check references

[whedon]

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

OK DOIs

- 10.3389/fpsyg.2019.02893 is OK
- 10.31234/osf.io/q9f86 is OK
- 10.1177/1745691614551642 is OK
- 10.7326/0003-4819-121-3-199408010-00008 is OK
- 10.2527/jas.2006-449 is OK
- 10.1111/bmsp.12132 is OK
- 10.1136/bmj.325.7375.1304 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[cMadan]

@whedon generate pdf

[whedon]

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

[cMadan]

@ClaudioZandonella, everything looks good to me!

To move forward with accepting your submission, there are a few last things to take care of:

• Make a tagged release of your software, and list the version tag of the archived version here.
• Archive the reviewed software in Zenodo
• Check the Zenodo deposit has the correct metadata, this includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it); you may also add the authors' ORCID.
• List the Zenodo DOI of the archived version here.

[ClaudioZandonella]

Dear @cMadan, thanks for your work.

Here the last required information:

• tag version v1.0.0 https://github.com/ClaudioZandonella/PRDA/releases/tag/v1.0.0
• Zenodo DOI http://doi.org/10.5281/zenodo.4533739

Let me know if there is something else I can do.
Thanks!

[arfon]

@whedon set v1.0.0 as version

[whedon]

OK. v1.0.0 is the version.

[arfon]

@whedon set 10.5281/zenodo.4533739 as archive

[whedon]

OK. 10.5281/zenodo.4533739 is the archive.

[arfon]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.3389/fpsyg.2019.02893 is OK
- 10.31234/osf.io/q9f86 is OK
- 10.1177/1745691614551642 is OK
- 10.7326/0003-4819-121-3-199408010-00008 is OK
- 10.2527/jas.2006-449 is OK
- 10.1111/bmsp.12132 is OK
- 10.1136/bmj.325.7375.1304 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#2101

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2101, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[arfon]

@cMadan - I'm currently trying to move a bunch of submissions that are very close to finished through the last steps. I believe this is one of these so will proceed the accept and publish now.

[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.02810 joss-papers#2103
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02810
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]

@DominiqueMakowski, @mmrabe - many thanks for your reviews here and to @cMadan for editing this submission. JOSS relies upon the volunteer efforts of people like you, and we simply wouldn't be able to do it without you! ✨

@ClaudioZandonella - your paper is now accepted and published in JOSS ⚡🚀💥

[whedon]

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

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