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[REVIEW]: bayestestR: Describing Effects and their Uncertainty, Existence and Significance within the Bayesian Framework #1541

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[REVIEW]: bayestestR: Describing Effects and their Uncertainty, Existence and Significance within the Bayesian Framework#1541
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@whedon
whedon
opened on Jul 2, 2019

Submitting author: @DominiqueMakowski (Dominique Makowski)
Repository: https://github.com/easystats/bayestestR
Version: 0.2.5
Editor: @cMadan
Reviewer: @paul-buerkner, @tjmahr
Archive: 10.5281/zenodo.3361605

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/1d180e6004a0dd1e6b235eb24fe66276"><img src="http://joss.theoj.org/papers/1d180e6004a0dd1e6b235eb24fe66276/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/1d180e6004a0dd1e6b235eb24fe66276/status.svg)](http://joss.theoj.org/papers/1d180e6004a0dd1e6b235eb24fe66276)

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

@paul-buerkner & @tjmahr, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

  1. Make sure you're logged in to your GitHub account
  2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @cMadan know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @paul-buerkner

Conflict of interest

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?
  • Version: 0.2.5
  • Authorship: Has the submitting author (@DominiqueMakowski) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 function 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

  • Authors: Does the paper.md file include a list of authors with their affiliations?
  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @tjmahr

Conflict of interest

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?
  • Version: 0.2.5
  • Authorship: Has the submitting author (@DominiqueMakowski) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 function 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

  • Authors: Does the paper.md file include a list of authors with their affiliations?
  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Activity

  1. whedon
    assigned
    cMadan
    on Jul 2, 2019
  2. whedon
    added
    review
    on Jul 2, 2019

  3. whedon commented on Jul 2, 2019

    @whedon
    whedon
    on Jul 2, 2019
    Author

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

    ⭐ 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:

    watching

    1. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

    notifications

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

    @whedon commands

  4. whedon commented on Jul 2, 2019

    @whedon
    whedon
    on Jul 2, 2019
    Author
    Attempting PDF compilation. Reticulating splines etc...

  5. whedon commented on Jul 2, 2019

    @whedon
    whedon
    on Jul 2, 2019
    Author

    👉 Check article proof 📄 👈

  6. whedon
    assigned
    paul-buerkner
    on Jul 3, 2019

  7. paul-buerkner commented on Jul 8, 2019

    @paul-buerkner
    paul-buerkner
    on Jul 8, 2019

    I have just finished my review and have very few minor comments.

    • All the citations in the software paper should list a DOI (if they have one) as per reviewer checklist above.
    • The definition of the maximum a-posteriori value as "the most probable value" is not entirely correct for continuous parameters. Instead it is the value with the highest density (which still have probability zero for continuous parameters).
    • you seem to use the abbreviation MAP both for the maximum a posteriori and the maximum a-priori value. This will likely confuse readers.

  8. cMadan commented on Jul 8, 2019

    @cMadan
    cMadan
    on Jul 8, 2019
    Member

    Thank you for the thorough review, @paul-buerkner!

  9. DominiqueMakowski commented on Jul 19, 2019

    @DominiqueMakowski
    DominiqueMakowski
    on Jul 19, 2019

    Dear @paul-buerkner, thanks a lot for your comments! We addressed them in this PR:

    Reviewer 1 (@paul-buerkner)

    • All the citations in the software paper should list a DOI (if they have one) as per reviewer checklist above.

    • Added DOIs for all refs but the following (none was found):

      • see package (here)
      • rstanarm package
      • BayesFactor package
      • Mill's "Objective Bayesian Precise Hypothesis Testing"
      • Multiple Comparisons with BayesFactor, Part 2 (Morey's blog, 2015)
      • Practical bayesian optimization of machine learning algorithms (Snoek's proceedings, 2012)
      • Jeffrey's Theory of Probability book

    • The definition of the maximum a-posteriori value as "the most probable value" is not entirely correct for continuous parameters. Instead it is the value with the highest density (which still have probability zero for continuous parameters).

    • We changed its definition to the following:

    "find the Highest Maximum A Posteriori (MAP) estimate of a posterior, i.e., the value associated with the highest probability density (the "peak" of the posterior distribution). In other words, it is an estimation of the mode for continuous parameters."

    • you seem to use the abbreviation MAP both for the maximum a posteriori and the maximum a-priori value. This will likely confuse readers.
    • This was likely an error and was addressed by replacing instances of the latter by the former (the maximum a posteriori).

    Please note that there are still some references for which we did not find a DOI: we continue our search in the meantime. We hope you will find the revised version satisfying ☺️

  10. paul-buerkner commented on Jul 19, 2019

    @paul-buerkner
    paul-buerkner
    on Jul 19, 2019

    Looks good to me.

  11. cMadan commented on Jul 21, 2019

    @cMadan
    cMadan
    on Jul 21, 2019
    Member

    @tjmahr, are you still able to review this submission?

    @paul-buerkner, thanks again!!

  12. tjmahr commented on Jul 22, 2019

    @tjmahr
    tjmahr
    on Jul 22, 2019

    I would like to review it but won't be able to look at it until next week.

  13. whedon
    assigned
    tjmahr
    on Jul 23, 2019

  14. cMadan commented on Jul 24, 2019

    @cMadan
    cMadan
    on Jul 24, 2019
    Member

    @tjmahr, no problem, thanks for following up!

  15. strengejacke commented on Jul 25, 2019

    @strengejacke
    strengejacke
    on Jul 25, 2019

    @whedon generate pdf

  16. 37 remaining items

  17. danielskatz commented on Aug 13, 2019

    @danielskatz
    danielskatz
    on Aug 13, 2019

    @whedon accept

  18. whedon commented on Aug 13, 2019

    @whedon
    whedon
    on Aug 13, 2019
    Author
    Attempting dry run of processing paper acceptance...

  19. whedon commented on Aug 13, 2019

    @whedon
    whedon
    on Aug 13, 2019
    Author

    Check final proof 👉 openjournals/joss-papers#901

    If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#901, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

    @whedon accept deposit=true

  20. danielskatz commented on Aug 13, 2019

    @danielskatz
    danielskatz
    on Aug 13, 2019

    @whedon accept deposit=true

  21. whedon commented on Aug 13, 2019

    @whedon
    whedon
    on Aug 13, 2019
    Author
    Doing it live! Attempting automated processing of paper acceptance...
  22. whedon
    added
    accepted
    on Aug 13, 2019

  23. whedon commented on Aug 13, 2019

    @whedon
    whedon
    on Aug 13, 2019
    Author

    🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

  24. whedon commented on Aug 13, 2019

    @whedon
    whedon
    on Aug 13, 2019
    Author

    🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

    Here's what you must now do:

    1. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.01541 joss-papers#902
    2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01541
    3. If everything looks good, then close this review issue.
    4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

    Any issues? notify your editorial technical team...

  25. danielskatz
    closed this as completedon Aug 13, 2019

  26. whedon commented on Aug 13, 2019

    @whedon
    whedon
    on Aug 13, 2019
    Author

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

    If you would like to include a link to your paper from your README use the following code snippets:

    Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.01541/status.svg)](https://doi.org/10.21105/joss.01541)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01541">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01541/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01541/status.svg
   :target: https://doi.org/10.21105/joss.01541

    This is how it will look in your documentation:

    DOI

    We need your help!

    Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

  27. DominiqueMakowski commented on Aug 13, 2019

    @DominiqueMakowski
    DominiqueMakowski
    on Aug 13, 2019

    @cMadan @danielskatz @paul-buerkner @tjmahr Thanks a lot again for your time and contributions! 😍

  28. whedon
    added
    publishedPapers published in JOSS
    recommend-acceptPapers recommended for acceptance in JOSS.
    on Mar 2, 2020

  29. ajstewartlang commented on Oct 14, 2023

    @ajstewartlang
    ajstewartlang
    on Oct 14, 2023

    👋 @paul-buerkner Might you have the bandwidth to review the following submission? [PRE REVIEW]: jointVIP: Prioritizing variables in observational study design with joint variable importance plot in R

  30. paul-buerkner commented on Oct 14, 2023

    @paul-buerkner
    paul-buerkner
    on Oct 14, 2023

    Hey! I am currently swamped with reviews that I still have to complete so I cannot accept new ones right now unfortunately.

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