[REVIEW]: The stantargets R package: a workflow framework for efficient reproducible Stan-powered Bayesian data analysis pipelines

[whedon]

Submitting author: @wlandau (William Landau)
Repository: /~https://github.com/ropensci/stantargets
Version: 0.0.0.9003
Editor: @kyleniemeyer
Reviewer: @kyleniemeyer
Archive: 10.5281/zenodo.4706113

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Review checklist for @kyleniemeyer

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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 (@wlandau) 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

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Documentation

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• 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)?
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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?
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• 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. @kyleniemeyer 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.

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

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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=0.24 s (327.2 files/s, 53720.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               54             90           1434           8226
SVG                              2              0              0            810
Rmd                              3            126            210            520
Markdown                        10             92              0            353
JSON                             1              0              0            307
YAML                             5             41             64            255
TeX                              2             11              0            104
-------------------------------------------------------------------------------
SUM:                            77            360           1708          10575
-------------------------------------------------------------------------------


Statistical information for the repository 'a0b9e3e7311d217955e2ca1b' was
gathered on 2021/04/19.
No commited files with the specified extensions were found.

[whedon]

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

[whedon]

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

OK DOIs

- 10.21105/joss.02959 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[kyleniemeyer]

For reference: this submission was already reviewed and accepted by rOpenSci ropensci/software-review#430

[kyleniemeyer]

Hi @wlandau, I just noticed a few minor issues with some references, it looks like some need additional information or different formatting. In particular, the Cndstanr and Stantargets citations should both include a URL or DOI (if one exists), and both should have years (e.g., for the latest version, if you aren't citing a particular version).

[wlandau]

Thanks @kyleniemeyer, should be fixed in ropensci/stantargets@1f9b58f.

[kyleniemeyer]

@whedon generate pdf

[whedon]

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

[kyleniemeyer]

@wlandau looks good! Please now archive the software repository (e.g., on Zenodo) and report the DOI here, and then I will accept this.

[wlandau]

I created a release with DOI https://doi.org/10.5281/zenodo.4706113. Looks to be still pending.

[kyleniemeyer]

@whedon set 10.5281/zenodo.4706113 as archive

@wlandau works now! Before I publish, can you just clean up the author list of that? It looks to have you listed twice.

[whedon]

OK. 10.5281/zenodo.4706113 is the archive.

[wlandau]

Thanks, I removed the duplicate author entry.

[kyleniemeyer]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.21105/joss.02959 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#2251

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2251, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[kyleniemeyer]

@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.03193 joss-papers#2252
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03193
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...

[kyleniemeyer]

Congratulations @wlandau on your article's publication in JOSS!

[whedon]

🎉🎉🎉 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.03193/status.svg)](https://doi.org/10.21105/joss.03193)

HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.03193/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03193/status.svg
   :target: https://doi.org/10.21105/joss.03193

This is how it will look in your documentation:

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[wlandau]

Thanks so much, @kyleniemeyer!