[REVIEW]: mcbette: model comparison using babette

[whedon]

Submitting author: @richelbilderbeek (Richel Bilderbeek)
Repository: https://github.com/ropensci/mcbette
Version: v1.8.3
Editor: @kthyng
Reviewer: @kthyng
Archive: 10.5281/zenodo.4076183

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Status

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Markdown: [![status](https://joss.theoj.org/papers/6bde4138f86795a27ab4a30914f4e553/status.svg)](https://joss.theoj.org/papers/6bde4138f86795a27ab4a30914f4e553)

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Review checklist for @kthyng

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.

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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 (@richelbilderbeek) 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. @kthyng it looks like you're currently assigned to review this paper 🎉.

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[whedon]

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

OK DOIs

- 10.1111/2041-210X.13032 is OK
- 10.1371/journal.pcbi.1006650 is OK
- 10.1093/molbev/msi103 is OK
- 10.1098/rstb.1994.0068 is OK
- 10.1093/sysbio/syy050 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

[kthyng]

This submission was reviewed in rOpenSci.

[kthyng]

I have some edits for your paper:

• caption should probably end with a period
• "allows to select that" --> "allows for selecting the"
• "underlied" --> "led to"? or "consistent with"? I don't think underlied is a word but I'm not sure what the correct replacement is in this technical sentence.
• "mcbette can be both be" --> remove a "be"
• "is aimed to be used" --> "is aimed at being used"
• "consist out of" --> "consist of"

Also, the capitalization in your references is off. For example, the first reference has "r" in it instead of "R". You can add {} around words to preserve capitalization. Please carefully check all of your references and let me know if you have questions.

[kthyng]

I see your Zenodo archive at 10.5281/zenodo.4076183. Can you check the author list and metadata to exactly match your JOSS paper?

[whedon]

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

[richelbilderbeek]

@whedon generate pdf

[whedon]

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

[richelbilderbeek]

I see your Zenodo archive at 10.5281/zenodo.4076183. Can you check the author list and metadata to exactly match your JOSS paper?

Done.

@kthyng: AFAICS I have processed your feedback. Thanks for checking up on me! If I missed something, please let me know 👍

[kthyng]

Is there a new DOI? I checked the same one (10.5281/zenodo.4076184) and it looks the same. I am looking for the title to be "mcbette: model comparison using babette".

[kthyng]

(other things look good!)

[richelbilderbeek]

@kthyng: sorry, my bad! I've fixed it, thanks 👍!

[kthyng]

Ok! Looks good now! We can wrap this up.

[kthyng]

@whedon set 10.5281/zenodo.4076183 as archive

[whedon]

OK. 10.5281/zenodo.4076183 is the archive.

[kthyng]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1111/2041-210X.13032 is OK
- 10.1371/journal.pcbi.1006650 is OK
- 10.1093/molbev/msi103 is OK
- 10.1098/rstb.1994.0068 is OK
- 10.1093/sysbio/syy050 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#1861

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1861, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[kthyng]

@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.02762 joss-papers#1862
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02762
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...

[kthyng]

Congrats on your JOSS submission @richelbilderbeek!

[whedon]

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

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