[REVIEW]: greta: simple and scalable statistical modelling in R

[whedon]

Submitting author: @goldingn (Nick Golding)
Repository: https://github.com/greta-dev/greta
Version: 0.3.1
Editor: @terrytangyuan
Reviewers: @lionel68, @joethorley, @lionel68
Archive: 10.5281/zenodo.819476

Status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/62e62338d8ba44ff9e5dc295cf631477"><img src="http://joss.theoj.org/papers/62e62338d8ba44ff9e5dc295cf631477/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/62e62338d8ba44ff9e5dc295cf631477/status.svg)](http://joss.theoj.org/papers/62e62338d8ba44ff9e5dc295cf631477)

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

@lionel68 @joethorley, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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

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

Review checklist for @joethorley

Conflict of interest

• As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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?
• Version: 0.3.1
• Authorship: Has the submitting author (@goldingn) 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 @lionel68

Conflict of interest

• As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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?
• Version: 0.3.1
• Authorship: Has the submitting author (@goldingn) 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)?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @lionel68 @joethorley 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:

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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]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[joethorley]

@goldingn greta is a fantastic piece of software. I just have three minor issues that need to be addressed

greta-dev/greta#295
greta-dev/greta#296
greta-dev/greta#297

[goldingn]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[goldingn]

Thanks @joethorley!

Resolved two of those issues now. The last formatting issue (#297) doesn't seem to be present in the article proof, but I may have misunderstood.

[terrytangyuan]

Nice job @goldingn and thanks @joethorley for the review!
👋 @lionel68 Have you got a chance to review this paper yet?

[lionel68]

On my agenda for this friday :) @terrytangyuan

[goldingn]

Thanks for the review @joethorley! There's one item (references) still unchecked in your review list. I think that's resolved now.

[lionel68]

@whedon @terrytangyuan I am starting the review but I can't seem to be able to update the review checklist above. Am I missing something?

[terrytangyuan]

It looks like you are not a collaborator of this repo, @kyleniemeyer could you help take a look?

[lionel68]

greta is a very promising software and is likely to become a very handy tool in the data scientist toolbox.

I opened three issues:

greta-dev/greta#299 (example R code not running on my laptop)
greta-dev/greta#300 (python warnings when running greta::model)
greta-dev/greta#301 (minor textual comments)

Looking forward to using the capacities of greta.

[kyleniemeyer]

@whedon add @lionel68 as reviewer

[goldingn]

This version of the software is now released on GitHub and on CRAN. Here's a figshare archive of this version of the software:
https://doi.org/10.6084/m9.figshare.9461447.v1
Title and authors are the same as this paper.

[terrytangyuan]

@whedon set 10.5281/zenodo.819476 as archive

[whedon]

OK. 10.5281/zenodo.819476 is the archive.

[terrytangyuan]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[terrytangyuan]

@whedon check references

[whedon]

Attempting to check references...

[whedon]

OK DOIs

- 10.1080/10618600.2016.1172487 is OK
- 10.18637/jss.v076.i01 is OK
- 10.7717/peerj-cs.55 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[terrytangyuan]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Check final proof 👉 openjournals/joss-papers#892

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#892, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[terrytangyuan]

The paper looks good to me. I am handing this over to our editors-in-chief now. @openjournals/joss-eics

[goldingn]

Thanks @terrytangyuan!

[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.01601 joss-papers#895
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01601
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]

@lionel68, @joethorley - many thanks for your reviews and to @terrytangyuan for editing this submission.

@goldingn - your paper is now accepted into JOSS ⚡🚀💥

[whedon]

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

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