[REVIEW]: infer: An R package for tidyverse-friendly statistical inference #3661

whedon · 2021-08-25T19:45:24Z

Submitting author: @simonpcouch (Simon Couch)
Repository: https://github.com/tidymodels/infer
Version: v1.0.1
Editor: @csoneson
Reviewer: @prdm0, @kellieotto
Archive: 10.5281/zenodo.5504495

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Review checklist for @prdm0

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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 (@simonpcouch) 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 @kellieotto

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 (@simonpcouch) 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?

The text was updated successfully, but these errors were encountered:

whedon · 2021-08-25T19:45:27Z

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @prdm0, @kellieotto 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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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:

Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

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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 · 2021-08-25T19:45:38Z

Wordcount for paper.md is 1089

whedon · 2021-08-25T19:45:39Z

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

OK DOIs

- 10.1080/00224065.2020.1848366 is OK
- 10.1080/10691898.2020.1730734 is OK
- 10.1080/10691898.2020.1804497 is OK
- 10.1080/10986065.2021.1922856 is OK
- 10.1080/26939169.2021.1920866 is OK
- 10.1089/cell.2020.0078 is OK
- 10.1002/etc.4978 is OK
- 10.1016/j.bbrc.2021.03.129 is OK
- 10.21105/joss.01686 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon · 2021-08-25T19:45:40Z

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.22 s (889.8 files/s, 221223.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                            45           2293            608          13001
SVG                             77              0              2           9619
R                               41           1417           2196           7472
CSS                              6           1054             74           6358
Rmd                              6            721           1062            888
Markdown                         7            221              0            775
XML                              2              0              2            579
JavaScript                       5             64             39            272
YAML                             6             35              5            238
TeX                              2             14              0            125
JSON                             1              1              0             94
-------------------------------------------------------------------------------
SUM:                           198           5820           3988          39421
-------------------------------------------------------------------------------


Statistical information for the repository 'f21b5bc0c30588b95b25c50e' was
gathered on 2021/08/25.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Chester Ismay                    2            34             28            4.63
Simon P. Couch                   2           220              6           16.88
andrewpbray                      1            54              0            4.03
ismayc                           8           536            461           74.46

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Simon P. Couch              220          100.0         10.1               11.82
ismayc                      203           37.9         35.8               10.34

whedon · 2021-08-25T19:45:56Z

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

csoneson · 2021-08-25T19:48:03Z

👋🏼 @simonpcouch, @prdm0, @kellieotto - this is the review thread for the submission. All of our communications will happen here from now on.

Both reviewers have checklists at the top of this thread. As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues directly in the software repository. If you do so, please mention this thread so that a link is created (and I can keep an eye on what is happening). Please also feel free to comment and ask questions in this thread. It is often easier to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

Please feel free to ping me (@csoneson) if you have any questions or concerns. Thanks!

kellieotto · 2021-09-06T21:11:41Z

@csoneson @simonpcouch: I've gone through the review checklist and just left two issues pertaining to functionality documentation, tidymodels/infer#415 and tidymodels/infer#416. I'll take another look when those are resolved.

csoneson · 2021-09-07T06:47:20Z

Thank you @kellieotto!

simonpcouch · 2021-09-07T17:14:30Z

Thank you @kellieotto! These are really helpful. Getting started on your feedback this morning.

simonpcouch · 2021-09-07T22:51:10Z

Okay, addressed in tidymodels/infer#418 and tidymodels/infer#417, respectively. Thanks again!

kellieotto · 2021-09-07T23:03:47Z

Looks great! I recommend this package be accepted.

prdm0 · 2021-09-08T13:44:06Z

Dear @csoneson and @simonpcouch, at issue #420 I leave my review for the paper. Beforehand I accept the paper, but I would be happy to see at least a prototype of my suggestion implemented. Best regards.

simonpcouch · 2021-09-09T14:07:21Z

Just left a reply to your issue, @prdm0! Thank you for your review.

prdm0 · 2021-09-09T18:03:07Z

Dear @simonpcouch , thanks for your reply. I've added a counterargument that is actually a hint of a glimpse of future improvement. Finally, @csoneson , I recommend this package be accepted.

csoneson · 2021-09-11T13:52:55Z

Thanks @prdm0 for your thoughtful review!

@simonpcouch - as the reviewers both recommend accepting the submission, I will take a quick look as well and get back to you shortly with the next steps.

csoneson · 2021-09-11T13:57:12Z

@whedon generate pdf

whedon · 2021-09-11T13:57:39Z

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

csoneson · 2021-09-11T14:11:30Z

@whedon check references

whedon · 2021-09-11T14:11:44Z

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

OK DOIs

- 10.1080/00224065.2020.1848366 is OK
- 10.1080/10691898.2020.1730734 is OK
- 10.1080/10691898.2020.1804497 is OK
- 10.1080/10986065.2021.1922856 is OK
- 10.1080/26939169.2021.1920866 is OK
- 10.1089/cell.2020.0078 is OK
- 10.1002/etc.4978 is OK
- 10.1016/j.bbrc.2021.03.129 is OK
- 10.21105/joss.01686 is OK

MISSING DOIs

- None

INVALID DOIs

- None

csoneson · 2021-09-11T14:52:29Z

👋🏻 @simonpcouch - I went through the submission and it looks good to me! Only a couple of things related to the references:

There's a missing space between Modern and Dive in Ismay & Kim (2019)
Could you provide more info/a link for Downey (2016)?
I'd recommend adding references for the packages mentioned in the "Comparison to other packages" section

Could you fix these and ask whedon to generate a new proof (with @whedon generate pdf)?

The next steps would then be to:

Make a tagged release of the software, and list the version tag of the archived version here.
Archive the reviewed software in Zenodo or a similar service
Check that the archival deposit (e.g., in Zenodo) has the correct metadata. In particular, the title and author list should be identical to those of the paper. You can also add the authors' ORCID.
Please list the DOI of the archived version here.

I can then move forward with accepting the submission.

csoneson · 2021-09-14T16:40:23Z

@whedon set v1.0.1 as version

whedon · 2021-09-14T16:40:27Z

OK. v1.0.1 is the version.

csoneson · 2021-09-14T16:41:22Z

@whedon set 10.5281/zenodo.5504495 as archive

whedon · 2021-09-14T16:41:25Z

OK. 10.5281/zenodo.5504495 is the archive.

csoneson · 2021-09-14T16:47:34Z

Great, thanks @simonpcouch! Just one final tiny detail...could you please case protect the final "R" in the title of Pruim et al (so it shows up as 'R' instead of 'r')? Then I'll pass the submission on for the final steps.

simonpcouch · 2021-09-14T17:45:59Z

Thank you, @csoneson! Just made that edit—your attention to detail is much appreciated.

simonpcouch · 2021-09-14T17:46:05Z

@whedon generate pdf

whedon · 2021-09-14T17:46:32Z

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

csoneson · 2021-09-14T21:44:24Z

Perfect - I'm going to hand this over now to the associate EiC on rotation for the final steps.

csoneson · 2021-09-14T21:44:28Z

@whedon recommend-accept

whedon · 2021-09-14T21:44:30Z

Attempting dry run of processing paper acceptance...

whedon · 2021-09-14T21:44:40Z

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

OK DOIs

- 10.1080/00224065.2020.1848366 is OK
- 10.1080/10691898.2020.1730734 is OK
- 10.1080/10691898.2020.1804497 is OK
- 10.1080/10986065.2021.1922856 is OK
- 10.1080/26939169.2021.1920866 is OK
- 10.1089/cell.2020.0078 is OK
- 10.1002/etc.4978 is OK
- 10.1016/j.bbrc.2021.03.129 is OK
- 10.21105/joss.01686 is OK
- 10.21105/joss.03236 is OK
- 10.21105/joss.02445 is OK

MISSING DOIs

- 10.32614/rj-2017-024 may be a valid DOI for title: The mosaic Package: Helping Students to ‘Think with Data’ Using R

INVALID DOIs

- None

whedon · 2021-09-14T21:45:00Z

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#2587

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2587, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

simonpcouch · 2021-09-15T11:51:07Z

Ah, that new flag for the missing mosaic DOI is correct. Just fixed!

simonpcouch · 2021-09-15T11:52:25Z

@whedon check references

whedon · 2021-09-15T11:52:36Z

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

OK DOIs

- 10.1080/00224065.2020.1848366 is OK
- 10.1080/10691898.2020.1730734 is OK
- 10.1080/10691898.2020.1804497 is OK
- 10.1080/10986065.2021.1922856 is OK
- 10.1080/26939169.2021.1920866 is OK
- 10.1089/cell.2020.0078 is OK
- 10.1002/etc.4978 is OK
- 10.1016/j.bbrc.2021.03.129 is OK
- 10.21105/joss.01686 is OK
- 10.32614/RJ-2017-024 is OK
- 10.21105/joss.03236 is OK
- 10.21105/joss.02445 is OK

MISSING DOIs

- None

INVALID DOIs

- None

simonpcouch · 2021-09-15T11:52:55Z

@whedon generate pdf

whedon · 2021-09-15T11:53:27Z

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

Kevin-Mattheus-Moerman · 2021-09-16T21:06:57Z

@whedon accept deposit=true

whedon · 2021-09-16T21:07:00Z

Doing it live! Attempting automated processing of paper acceptance...

whedon · 2021-09-16T21:07:40Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon · 2021-09-16T21:07:40Z

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.03661 joss-papers#2588
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03661
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

Kevin-Mattheus-Moerman · 2021-09-16T21:10:26Z

@simonpcouch congratulations on getting this work published in JOSS

@csoneson, thanks for editing!

@prdm0, @kellieotto thanks a lot for your help reviewing this work!

whedon · 2021-09-16T21:10:29Z

🎉🎉🎉 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.03661/status.svg)](https://doi.org/10.21105/joss.03661)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03661">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03661/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03661/status.svg
   :target: https://doi.org/10.21105/joss.03661

This is how it will look in your documentation:

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simonpcouch · 2021-09-16T21:14:07Z

Thank you, all!🦋

whedon added R review TeX labels Aug 25, 2021

whedon assigned csoneson Aug 25, 2021

whedon mentioned this issue Aug 25, 2021

[PRE REVIEW]: infer: An R package for tidyverse-friendly statistical inference #3637

Closed

whedon assigned kellieotto and prdm0 Aug 27, 2021

This was referenced Sep 6, 2021

[JOSS Review] Don't understand when generate(..., type="draw") is applicable tidymodels/infer#415

Closed

[JOSS Review] Random seeds for reproducibility tidymodels/infer#416

Closed

prdm0 mentioned this issue Sep 8, 2021

[JOSS Review] Review of the paper submitted to JOSS @prdm0 tidymodels/infer#420

Closed

whedon added the recommend-accept Papers recommended for acceptance in JOSS. label Sep 14, 2021

whedon added accepted published Papers published in JOSS labels Sep 16, 2021

Kevin-Mattheus-Moerman closed this as completed Sep 16, 2021

editorialbot mentioned this issue Nov 11, 2024

[PRE REVIEW]: Nemo Gradebook: An R Package for Calculating Course Grades #7445

Closed

[REVIEW]: infer: An R package for tidyverse-friendly statistical inference #3661

[REVIEW]: infer: An R package for tidyverse-friendly statistical inference #3661

Comments

whedon commented Aug 25, 2021 • edited Loading

Status

Reviewer instructions & questions

Review checklist for @prdm0

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @kellieotto

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented Aug 25, 2021

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whedon commented Aug 25, 2021 •

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