[REVIEW]: mcboost: Multi-Calibration Boosting for R

[whedon]

Submitting author: @pfistfl (Florian Pfisterer)
Repository: https://github.com/mlr-org/mcboost
Version: v.0.3.3
Editor: @osorensen
Reviewer: @mwt, @OwenWard
Archive: 10.5281/zenodo.5156518

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HTML: <a href="https://joss.theoj.org/papers/19899bbe517d82bb1d5c7dbb2e8c539f"><img src="https://joss.theoj.org/papers/19899bbe517d82bb1d5c7dbb2e8c539f/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/19899bbe517d82bb1d5c7dbb2e8c539f/status.svg)](https://joss.theoj.org/papers/19899bbe517d82bb1d5c7dbb2e8c539f)

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Review checklist for @mwt

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 (@pfistfl) 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 @OwenWard

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 (@pfistfl) 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. @mwt, @OwenWard 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:

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

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]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.03 s (1368.2 files/s, 134688.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               22            180            687           1125
Markdown                         6            141              0            458
JSON                             1              0              0            367
Rmd                              3            245            406            354
YAML                             2             25             28             99
TeX                              1             23              2             85
SVG                              8              0              0              8
-------------------------------------------------------------------------------
SUM:                            43            614           1123           2496
-------------------------------------------------------------------------------


Statistical information for the repository '9e953606421e4ed3702ebec1' was
gathered on 2021/07/04.
No commited files with the specified extensions were found.

[whedon]

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

OK DOIs

- 10.1038/s41467-020-18297-9 is OK
- 10.1093/jamia/ocaa283 is OK
- 10.1109/FOCS.2019.00016 is OK
- 10.1145/3306618.3314287 is OK
- 10.21105/joss.01903 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

[whedon]

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

[whedon]

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

[mwt]

@osorensen @pfistfl it looks all clear to me. There are automated tests which all pass and there are vignettes which compile and seem to be doing what they're supposed to.

[osorensen]

Thanks for conducting the review, @mwt!

[pfistfl]

@mwt @osorensen Thank you so much for the review! If there are any questions/ issues please let me know!

[osorensen]

@OwenWard, could you please update us on how it is going with your review?

[OwenWard]

@osorensen I'm nearly done, hoping to finish this week!

[OwenWard]

@whedon generate pdf

[whedon]

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

[OwenWard]

@pfistfl I opened a pull request for two very small typos I spotted, one in an error message and one in the paper. Also the figure doesn't currently appear in the pdf of the article proof, but that should be an easy fix.
@osorensen otherwise everything looks good to me.

[pfistfl]

@whedon generate pdf

[whedon]

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

[pfistfl]

Thanks a lot for the PR, I think I have addressed everything.

[osorensen]

Thanks for completing the review, @OwenWard!

[osorensen]

@pfistfl, I have one final comment to the article proof. On page 2, lines 52-54, I believe the last part of the sentence is not grammatically correct, particularly the word "helps".

We hope that with mcboost, Multi-Calibration Boosting can be utilized by a wide community
53 of developers and data scientists to audit and post-process prediction models and helps to
54 promote fairness in machine learning and statistical estimation applications.

Here is a suggested rewrite, put feel free to phrase it differently:

We hope that mcboost lets Multi-Calibration Boosting be utilized by a wide community
53 of developers and data scientists to audit and post-process prediction models, and helps to
54 promote fairness in machine learning and statistical estimation applications.

[chkern]

@whedon generate pdf

[whedon]

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

[chkern]

Thanks @osorensen, we followed your suggestion.

[osorensen]

@whedon check references

[whedon]

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

OK DOIs

- 10.1038/s41467-020-18297-9 is OK
- 10.1093/jamia/ocaa283 is OK
- 10.1109/FOCS.2019.00016 is OK
- 10.1145/3306618.3314287 is OK
- 10.21105/joss.01903 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[osorensen]

@pfistfl, before we proceed, could you please do the following?

• Make a tagged release of the software.
• Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
• Check the archival deposit (e.g., in Zenodo) 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.
• Please list the DOI of the archived version here.

[pfistfl]

@osorensen, thanks so much for the quick & smooth progress

• tagged release: v.0.3.3
• DOI: 10.5281/zenodo.5156518

[osorensen]

@whedon set 10.5281/zenodo.5156518 as archive

[whedon]

OK. 10.5281/zenodo.5156518 is the archive.

[osorensen]

@whedon set <v0.3.3> as version

[whedon]

OK. <v0.3.3> is the version.

[osorensen]

@whedon set v.0.3.3 as version

[whedon]

OK. v.0.3.3 is the version.

[osorensen]

@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

- 10.1038/s41467-020-18297-9 is OK
- 10.1093/jamia/ocaa283 is OK
- 10.1109/FOCS.2019.00016 is OK
- 10.1145/3306618.3314287 is OK
- 10.21105/joss.01903 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#2492

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2492, 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]

@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.03453 joss-papers#2500
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03453
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]

@mwt, @OwenWard – many thanks for your reviews here and to @osorensen 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 ✨

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

Also, congratulations to @osorensen for editing his first JOSS paper ✨!

[whedon]

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

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