[REVIEW]: POSSA: Power simulation for sequential analyses and multiple hypotheses

[editorialbot]

Submitting author: @gasparl (Gáspár Lukács)
Repository: https://github.com/gasparl/possa/
Branch with paper.md (empty if default branch):
Version: v0.6.1
Editor: @fboehm
Reviewers: @mingzehuang, @mmrabe
Archive: 10.5281/zenodo.7027767

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/3018b5213b07c69049bec226949b29f7/status.svg)](https://joss.theoj.org/papers/3018b5213b07c69049bec226949b29f7)

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

@mingzehuang & @mmrabe, 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 @fboehm 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 @mmrabe

📝 Checklist for @mingzehuang

[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:

@editorialbot commands

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

@editorialbot generate pdf

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.06 s (444.5 files/s, 151670.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
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HTML                             4            144              8           3424
R                               11            115            664           1929
Rmd                              4            356           1369            245
TeX                              1             11              0            105
Markdown                         3             31              0             61
YAML                             2             11              6             52
-------------------------------------------------------------------------------
SUM:                            25            668           2047           5816
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 339

[editorialbot]

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

OK DOIs

- 10.1002/ejsp.2023 is OK
- 10.1177/0146167220913363 is OK
- 10.5334/irsp.181 is OK
- 10.5964/meth.2811 is OK
- 10.1111/2041-210X.12504 is OK
- 10.1177/2515245920951503 is OK

MISSING DOIs

- 10.1016/c2013-0-10517-x may be a valid DOI for title: Statistical power analysis for the behavioral sciences

INVALID DOIs

- None

[editorialbot]

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

[mmrabe]

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 https://github.com/gasparl/possa/?
• 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 (@gasparl) 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, 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?

[mingzehuang]

Review checklist for @mingzehuang

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/gasparl/possa/?
• 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 (@gasparl) 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, 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?

[fboehm]

@mmrabe and @mingzehuang - how are the reviews going? Please feel free to discuss here any revisions that the authors must make before publication. Thanks again!

[mmrabe]

Hi @fboehm ! I expect to finish the review by Tuesday. I hope that still works. Sorry for the delay.

[mingzehuang]

Hi, @gasparl, your package looks nice:) I see you have "contribution" section in your README file. I would suggest you also include code of conduct like many other open source packages:)

[mingzehuang]

Hi, @fboehm, I'm reviewing! Hopefully I can get it done by this weekend:)

[mingzehuang]

Hi, @gasparl, you have numerous great example with the link in your README:) Would you mind picking one simple example as an illustration of functionality and putting it in your JOSS paper like many other papers on JOSS?

[fboehm]

Thanks so much, @mmrabe and @mingzehuang ! Please feel free to ask me questions - here, in the comments - if you're unsure about anything. Thanks again!

[gasparl]

Sure.

• I added Code of Conduct together with more details on how contribution works.
• I added a short example to the paper.

[gasparl]

@editorialbot generate pdf

[editorialbot]

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

[mingzehuang]

Hi, @gasparl, there is a requirement about automatic test in checklist. Would you mind using codecov and embedding the badge of coverage rate into your README.md?

[gasparl]

Hi, @gasparl, there is a requirement about automatic test in checklist. Would you mind using codecov and embedding the badge of coverage rate into your README.md?

Sure, I added it. (The relatively low percentage [52%] is because I included lots of warning messages for making the functions more foolproof, but these don't really need to be tested.)

[gasparl]

@editorialbot generate pdf

[editorialbot]

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

[mmrabe]

The author @gasparl has written a very useful and flexible tool for simulation-based power analysis. The documentation and vignettes exceed the expected extent by far and provide many helpful examples. The submitted paper has become a lot stronger after adding a simple example, as @mingzehuang suggested.

Before I can check off all items on my checklist and recommend this software paper for publication, please attend to the following:

1. I can not yet check off the license checkbox because the repo contains two license files. Please make sure they match. Issue: JOSS: Conflicting (?) LICENSE files gasparl/possa#9
2. In the example in the paper, I recommend that you add a citation for Pocock's correction. Issue: JOSS paper: Add reference gasparl/possa#10

I would also like to make a minor suggestion, which may make the package more straightforward to use for the average R user and possibly increase the audience:

1. Provide a wrapper function for common test objects that assists the user to extract the p-value. Issue: Suggestion: Extract p-value from common test objects? gasparl/possa#11

[mmrabe]

@gasparl already worked on the issues I posted to the repo as I was writing the lines above. So I can check off the remaining two boxes from my checklist right away. Thanks!

[editorialbot]

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

[gasparl]

• Thank you for noticing @fboehm, I corrected to {R}, as well as a few other lettercasing issues among the references (R package names to correspond to their original paper/CRAN titles).
• The auto-suggested doi is not the right one (wrong edition), but I found the right one and added it.

[fboehm]

Excellent, @gasparl! thanks for making those additions.

[fboehm]

@editorialbot generate pdf

[editorialbot]

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

[fboehm]

The references all look good now. For the next steps, @gasparl, we need you to make a new release of the package and archive it, for example, with zenodo.org. Once you complete those tasks, please report here the version number and doi. Please ensure that the archive's author names and title match exactly those of the paper.pdf.

[gasparl]

Sure @fboehm, here it is:
Version number: v0.6.1
DOI: https://doi.org/10.5281/zenodo.7027767

(The Zenodo badge with permanent DOI is also displayed on the GitHub repo.)

[fboehm]

@editorialbot set 10.5281/zenodo.7027767 as doi

[editorialbot]

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

@editorialbot commands

[fboehm]

@editorialbot set 10.5281/zenodo.7027767 as archive

[editorialbot]

Done! Archive is now 10.5281/zenodo.7027767

[fboehm]

@editorialbot set v0.6.1 as version

[editorialbot]

Done! version is now v0.6.1

[fboehm]

@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

- 10.1002/ejsp.2023 is OK
- 10.1093/biomet/64.2.191 is OK
- 10.1177/0146167220913363 is OK
- 10.4324/9780203771587 is OK
- 10.5334/irsp.181 is OK
- 10.5964/meth.2811 is OK
- 10.1111/2041-210X.12504 is OK
- 10.1177/2515245920951503 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/joss-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#3483, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[fboehm]

@gasparl - an editor-in-chief will soon review the submission before accepting it for publication. Monitor this thread to see their comments.

[arfon]

@editorialbot accept

[editorialbot]

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

[editorialbot]

🐦🐦🐦 👉 Tweet 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.04643 joss-papers#3485
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04643
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]

@mingzehuang, @mmrabe – many thanks for your reviews here and to @fboehm 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 ✨

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

[editorialbot]

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

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reStructuredText:
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[gasparl]

Thanks very much @arfon, and once again to @fboehm as well. Always a pleasure to publish with JOSS.