[REVIEW]: rigr: Regression, Inference, and General Data Analysis Tools in R

[editorialbot]

Submitting author: @yiqunchen (Yiqun Chen)
Repository: https://github.com/statdivlab/rigr
Branch with paper.md (empty if default branch): joss_submission
Version: v.1.0.5
Editor: @osorensen
Reviewers: @stefanocoretta, @tomsing1
Archive: 10.5281/zenodo.7456326

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/32b5abe359230799e6ed1f5e3fdee4b8"><img src="https://joss.theoj.org/papers/32b5abe359230799e6ed1f5e3fdee4b8/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/32b5abe359230799e6ed1f5e3fdee4b8/status.svg)](https://joss.theoj.org/papers/32b5abe359230799e6ed1f5e3fdee4b8)

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

@stefanocoretta & @tomsing1, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

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

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @stefanocoretta

📝 Checklist for @tomsing1

[editorialbot]

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.17 s (540.2 files/s, 196906.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               35           1028           2621           9180
HTML                            35           1349            112           7050
JavaScript                       4           2099           1928           7019
Markdown                         3             64              0            223
YAML                             6             29              9            164
TeX                              1             12              0            114
XML                              1              0              0            108
Rmd                              4            143            218             48
SVG                              1              0              1             11
CSS                              1              0              0              1
JSON                             1              0              0              1
-------------------------------------------------------------------------------
SUM:                            92           4724           4889          23919
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1598

[editorialbot]

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

[editorialbot]

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

OK DOIs

- 10.18637/jss.v095.i01 is OK

MISSING DOIs

- 10.1016/j.neurobiolaging.2006.06.010 may be a valid DOI for title: White matter grade and ventricular volume on brain MRI as markers of longevity in the cardiovascular health study
- 10.1038/nrg1916 may be a valid DOI for title: A tutorial on statistical methods for population association studies
- 10.1534/genetics.118.301394 may be a valid DOI for title: Joint Analysis of Multiple Interaction Parameters in Genetic Association Studies
- 10.1093/pan/mpu015 may be a valid DOI for title: How robust standard errors expose methodological problems they do not fix, and what to do about it
- 10.1093/ije/dyaa260 may be a valid DOI for title: Reflection on modern methods: demystifying robust standard errors for epidemiologists

INVALID DOIs

- None

[stefanocoretta]

Review checklist for @stefanocoretta

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 https://github.com/statdivlab/rigr?
• 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 (@yiqunchen) 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
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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, who the target audience is, and its relation to other work?
• 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?

[yiqunchen]

@osorensen, @stefanocoretta, @tomsing1: thank you so much for agreeing to review our manuscript!! Just wanna check in to see if there's anything I could assist with your review process :)

[tomsing1]

Review checklist for @tomsing1

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 https://github.com/statdivlab/rigr?
• 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 (@yiqunchen) 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
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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, who the target audience is, and its relation to other work?
• 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?

[tomsing1]

Great R package, @yiqunchen et al - and congratulations to getting it released on CRAN!
@osorensen : looks great to me, I didn't spot any issues. My review is complete.

[osorensen]

Thanks for your review @tomsing1!

[osorensen]

👋 @stefanocoretta, could you please update us on how its going with your review?

[stefanocoretta]

Hi @osorensen, Sorry for the delay. It's peak teaching term here in Edinburgh and I am overwhelmed with work. I should be able to do my review by Nov 20th rather than Nov 17th, would that work anyway?

[osorensen]

Thanks @stefanocoretta, that would work very well

[stefanocoretta]

Hi! Sorry, I will need more time. I am taking part of industrial action for the pension cuts on higher education employees in the UK.

[osorensen]

That's fine @stefanocoretta. Thanks for getting back to us

[yiqunchen]

Dear Reviewers, hope your Dec is starting strong!! We would love to know if we expect to have the reviews of our manuscript submission (submitted on 10/12) by end of the year so we can prioritize our holiday schedule accordingly :) Thank you so much!! @stefanocoretta @osorensen

[stefanocoretta]

@osorensen Just to say that I have completed my review and I think the paper can be accepted as is. Thanks a lot to the authors for such a very useful package!

[osorensen]

Thanks @stefanocoretta!

[osorensen]

@editorialbot generate pdf

[editorialbot]

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

[osorensen]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.18637/jss.v095.i01 is OK

MISSING DOIs

- Errored finding suggestions for "White matter grade and ventricular volume on brain...", please try later
- Errored finding suggestions for "Modern Epidemiology", please try later
- Errored finding suggestions for "Regression analysis", please try later
- Errored finding suggestions for "An R Companion to Applied Regression", please try later
- Errored finding suggestions for "A Package for Survival Analysis in R", please try later
- 10.1038/nrg1916 may be a valid DOI for title: A tutorial on statistical methods for population association studies
- 10.1534/genetics.118.301394 may be a valid DOI for title: Joint Analysis of Multiple Interaction Parameters in Genetic Association Studies
- Errored finding suggestions for "How robust standard errors expose methodological p...", please try later
- 10.1093/ije/dyaa260 may be a valid DOI for title: Reflection on modern methods: demystifying robust standard errors for epidemiologists

INVALID DOIs

- None

[editorialbot]

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

[editorialbot]

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

OK DOIs

- 10.1016/j.neurobiolaging.2006.06.010 is OK
- 10.1016/S0140-6736(86)92832-1 is OK
- 10.18637/jss.v095.i01 is OK
- 10.1038/nrg1916 is OK
- 10.1534/genetics.118.301394 is OK
- 10.1093/pan/mpu015 is OK
- 10.1093/ije/dyaa260 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[osorensen]

Thanks for addressing my points @yiqunchen.

At this point could you:

• Make a tagged release of your software, and list the version tag of the archived version here.
• 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.

I can then move forward with recommending acceptance of the submission.

[yiqunchen]

Thank you @osorensen for your prompt reviews and actions throughout the review process!! Please see below for the response:

• Make a tagged release of your software, and list the version tag of the archived version here: v.1.0.5 (https://github.com/statdivlab/rigr/releases/tag/v.1.0.5)
• Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository): https://zenodo.org/record/7456326#.Y6Ac7OzMI6A
• 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: On behalf of the authors, I confirm that the metadata is correct and people who are listed as a co-author of this paper has made significant contributions to the software.
• Please list the DOI of the archived version here:

Thank you again for your consideration of our submission to JOSS!

[osorensen]

@editorialbot set v.1.0.5 as version

[editorialbot]

Done! version is now v.1.0.5

[osorensen]

@editorialbot set 10.5281/zenodo.7456326 as archive

[editorialbot]

Done! Archive is now 10.5281/zenodo.7456326

[osorensen]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1016/j.neurobiolaging.2006.06.010 is OK
- 10.1016/S0140-6736(86)92832-1 is OK
- 10.18637/jss.v095.i01 is OK
- 10.1038/nrg1916 is OK
- 10.1534/genetics.118.301394 is OK
- 10.1093/pan/mpu015 is OK
- 10.1093/ije/dyaa260 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3826, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[arfon]

@editorialbot accept

[editorialbot]

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

[editorialbot]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[editorialbot]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

🚨🚨🚨 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.04847 joss-papers#3850
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04847
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]

@stefanocoretta, @tomsing1 – 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 ✨

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

[editorialbot]

🎉🎉🎉 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.04847/status.svg)](https://doi.org/10.21105/joss.04847)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.04847">
  <img src="https://joss.theoj.org/papers/10.21105/joss.04847/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04847/status.svg
   :target: https://doi.org/10.21105/joss.04847

This is how it will look in your documentation:

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The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

• Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://joss.theoj.org/reviewer-signup.html
• Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss

[yiqunchen]

Happy new year and thank you everyone for your prompt, detailed, and helpful feedback!! It's been an amazing submission process at JOSS!