[REVIEW]: robnptests -- An R package for robust two-sample location and variability tests

[editorialbot]

Submitting author: @s-abbas (Sermad Abbas)
Repository: https://github.com/s-abbas/robnptests
Branch with paper.md (empty if default branch): develop
Version: v1.1.0
Editor: @jbytecode
Reviewers: @mingzehuang, @msalibian
Archive: 10.5281/zenodo.7641636

Status

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Markdown: [![status](https://joss.theoj.org/papers/99e34c86845719986f57cc82dbdd09f8/status.svg)](https://joss.theoj.org/papers/99e34c86845719986f57cc82dbdd09f8)

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

@mingzehuang & @msalibian, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
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@editorialbot generate my checklist

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✨ 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 @msalibian

📝 Checklist for @mingzehuang

[editorialbot]

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

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.11 s (804.9 files/s, 80645.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               69            653           3611           1842
Markdown                        10            397              0            905
TeX                              2             32              0            295
Rmd                              2            183            545             92
YAML                             2              5              4             36
XML                              1              0              1             16
-------------------------------------------------------------------------------
SUM:                            86           1270           4161           3186
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1506

[editorialbot]

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

[editorialbot]

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

OK DOIs

- 10.1080/00949655.2016.1194839 is OK
- 10.1007/978-3-319-41706-6 is OK
- 10.1080/00949655.2020.1788562 is OK
- 10.1007/978-3-030-25147-5_16 is OK
- 10.1016/j.csda.2011.02.012 is OK
- 10.1007/s10260-011-0164-1 is OK
- 10.1016/j.csda.2006.12.017 is OK
- 10.1214/aoms/1177703732 is OK
- 10.3758/s13428-019-01246-w is OK
- 10.2202/1544-6115.1585 is OK
- 10.1002/9781118165485 is OK
- 10.1016/C2010-0-67044-1 is OK
- 10.1016/B978-0-12-751541-0.X5021-4 is OK
- 10.1214/aoms/1177704172 is OK
- 10.2307/2334550 is OK
- 10.1002/0470010940 is OK

MISSING DOIs

- 10.1080/03610919208813011 may be a valid DOI for title: Some robust two-sample test statistics based on M-estimators of location

INVALID DOIs

- None

[jbytecode]

Dear @mingzehuang and @msalibian

This is the review thread. Firstly, type

@editorialbot generate my checklist

to generate your own checklist. In that checklist, there are nearly 23 check items. Whenever you complete the corresponding task, you can check off them.

Please write your comments as separate posts and do not modify your checklist descriptions.

The review process is interactive so you can always interact with the authors, reviewers, and the editor. You can also create issues and pull requests in the target repo. Please do mention this thread's URL in the issues so we can keep tracking what is going on out of our world.

Please do not hesitate to ask me about anything, anytime.

Thank you in advance!

cc: @s-abbas

[msalibian]

Review checklist for @msalibian

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/s-abbas/robnptests?
• 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 (@s-abbas) 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?

[jbytecode]

@mingzehuang - It seems you haven't created your checklist. Could you please generate it and update your review status and inform us? Thank you in advance.

[mingzehuang]

Review checklist for @mingzehuang

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/s-abbas/robnptests?
• 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 (@s-abbas) 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?

[mingzehuang]

@jbytecode Sorry about that!

[msalibian]

I have finished my revision. This is a nice contribution, and my suggestions are rather minor, some of them perhaps just due to my not understanding the requirements on the checklist.

Regarding the checklist:

• The LICENSE file is missing.
• I did not find Community guidelines (for reporting issues or contributing to the project) in the documentation (they are there on the GitHub repo). This is not typically present in R packages stored on CRAN, so I'm inclined to not require it here.
• Automated tests to verify functionality, I'm happy with the "seeded" examples in one vignette, even if these are not proper unit tests, they do provide a way to check the behaviour of the software.
• Quality of writing: the paper is well written, my suggestions here are fairly minor and mostly about disambiguation (see below).

Specific suggestions for the text of the paper:

• Title: "location and variability tests", I suggest using "location and dispersion tests". Variability may be perceived as implying the existence of second moments. In the same spirit as the authors use "location", I'd suggest using "dispersion" instead of variability.
• Summary: "high efficiency", efficiency is a concept usually associated with point estimators, not tests. Can this be rephrased in terms of power of the tests instead?
• Line 26: the CDFs need to be "centered" around zero, it is not immediately clear what this means (presumably the CDFs need not be symmetric around zero, although perhaps this is the case?). I suggest that this assumption be defined explicitly.
• Line 36: I believe when the authors write "distribution independence" they mean "distribution-free", but "independence" is a loaded word in this context. If the authors do not want to repeat "distribution-free", I would suggest using a few more words but avoid saying that the tests are "distribution independent".
• Line 39: "for somewhat larger computational costs", this phrase sounds a bit awkward, I'd use "at the cost of a larger computational cost", or something along those lines.
• Line 57: "the denominator is a robust estimator for the within-sample variability", I believe this is not accurate, the denominator is an estimator of the squared root of the asymptotic variance of the difference of the estimators (or the estimator of the difference in location parameters), which in this case is a multiple of the within-sample dispersion, but this is just an artifact of using these particular estimators. Also note that I would avoid using words derived from "variance", and rely on "dispersion" instead.
• Lines 69 and 73: efficiency vs power, these terms seem to be used exchangeably here, but although more efficient estimators may result in more powerful tests, the concepts are different. I'd suggest referring to the power of the tests throughout the paper.
• Lines 80/1: same comment as above regarding the reference to the "within-sample variance".
• Lines 108/9: the packages robustbase and RobStatTM also contain functions for tests for the coefficients of linear regression models
• Line 119: "distribution independence", see my comment above.
• The reference to Maronna et al (2006) should be updated to the 2nd edition of the book (2018): https://www.wiley.com/en-ca/Robust+Statistics:+Theory+and+Methods+(with+R),+2nd+Edition-p-9781119214687

[jbytecode]

@msalibian - thank you for your quick and detailed review.

@s-abbas - could you please check out the corrections and suggestions and update your status? Thank you in advance.

[s-abbas]

@msalibian - Thank you very much for your review.
@jbytecode - I will work on the remarks and hope to come back to you by the end of next week.

[s-abbas]

Hello @msalibian,

Thank you again for your review. We decided to revise the paper, when we receive the suggestions and corrections from the second review. Thus, I only address the first three remarks.

The LICENSE file is missing.

The LICENSE.md file is in our develop branch. Our plan was to merge the develop branch to the main branch after the review process is finished so that we can submit a new, reviewed version of the package to CRAN. Would this be all right or should we merge the branches now?

I did not find Community guidelines (for reporting issues or contributing to the project) in the documentation (they are there on the GitHub repo). This is not typically present in R packages stored on CRAN, so I'm inclined to not require it here.

Does this mean that we do not have to change anything or should we present the Community guidelines at some other place?

Automated tests to verify functionality, I'm happy with the "seeded" examples in one vignette, even if these are not proper unit tests, they do provide a way to check the behaviour of the software.

We implemented several unit tests in the folder "tests". They can be performed, e.g. by calling devtools::test() directly in R from the package folder.

Best regards,
Sermad

[msalibian]

Hi @s-abbas,

• My guess is that as long as the license file eventually is put in the main branch, then it's OK, but of course I'll defer to @jbytecode on this;
• Again, I think @jbytecode will know better than me what is the exact journal policy about where Community Guidelines should appear;
• Thanks for setting up the tests.

I look forward to reading the revised manuscript.

[jbytecode]

@msalibian - Yes, during the review process, a suitable license should be provided. And this is current for the Community Guidelines. Thank you for your comments

[mingzehuang]

Hi, @s-abbas,
I just read your paper and it seems great:) You have clear explanation and comparison with alternative methods:)
I see you have 'Other packages with robust two-sample tests' part at the end of paper. Do you think it might be a part of extension of 'Statement of need'? Probably you may put it right after 'Statement of need'.
Also, do you mind putting a simple small example with code block somewhere in 'Implemented two-sample tests' or 'Applications' to help readers quickly understand the usage of your package since it is a software paper?

[mingzehuang]

Hi, @s-abbas, I raise an issue and put a template of community guildline there which maybe help you add something about how to contribute to this software:)

[s-abbas]

Hi @mingzehuang,

Thank you very much for your review and the template for the community guidelines. :)

@jbytecode, @msalibian, @mingzehuang,

We will work on the comments and suggestions. I hope to be able to provide an updated version of the manuscript by the end of next week.

[jbytecode]

@s-abbas - Thank you for informing us. Please ping me when you've done with them so we can go forward. Thank you in advance.

[s-abbas]

This is just a status update. We are still working on the revision. I cannot give an exact time frame, but I hope that we will have a new version within the next two or three weeks.

[jbytecode]

Dear @s-abbas

After a 21-days period, may I kindly ask you to inform us on how is your work going?

Thank you in advance

[jbytecode]

@s-abbas - Seems there is not an action yet. Do you need help?

[s-abbas]

@jbytecode - I'm sorry, but I couldn't work on the last steps yesterday and today. I plan to finish them this weekend.

[s-abbas]

@editorialbot generate pdf

[editorialbot]

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

[s-abbas]

@editorialbot generate pdf

[editorialbot]

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

[s-abbas]

@editorialbot generate pdf

[editorialbot]

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

[s-abbas]

Hello @jbytecode,

I have now finished the proof reading of the paper and created the tagged release on GitHub and the Zenodo archive.

* [ ]  Please read the paper pdf carefully, one more time, correct any issue if exists. Please perform a full grammar check.

I made some small grammatical changes and corrected a page number in a citation.

* [ ]  Create a tagged release in the software repository. Report the version here. The version should be in form of `vx.y.z`, e.g. `v1.2.3`.

The version of the tagged release is v1.1.0.

* [ ]  Create a Zenodo archive of the repository in https://zenodo.org/

* [ ]  The Zenodo archive (with the same name/title with the JOSS paper) should have the correct metadata, e.g. author names, **ORCID**s, the title of the archive. **Please set the archive title as the paper title.**

* [ ]  Please provide the tagged release id, zenodo archive DOI, and Zenodo archive URL here.

The Zenodo archive DOI for version v1.1.0 is 10.5281/zenodo.7641636 and the archive URL is https://zenodo.org/record/7641636

[jbytecode]

@editorialbot set v1.1.0 as version

[editorialbot]

Done! version is now v1.1.0

[jbytecode]

@editorialbot set 10.5281/zenodo.7641636 as archive

[editorialbot]

Done! Archive is now 10.5281/zenodo.7641636

[jbytecode]

@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

- 10.1080/00949655.2016.1194839 is OK
- 10.1007/978-3-319-41706-6 is OK
- 10.1080/00949655.2020.1788562 is OK
- 10.1007/978-3-030-25147-5_16 is OK
- 10.1016/j.csda.2011.02.012 is OK
- 10.1007/s10260-011-0164-1 is OK
- 10.1016/j.csda.2006.12.017 is OK
- 10.1214/aoms/1177703732 is OK
- 10.3758/s13428-019-01246-w is OK
- 10.2202/1544-6115.1585 is OK
- 10.1002/9781118165485 is OK
- 10.1016/C2010-0-67044-1 is OK
- 10.1016/B978-0-12-751541-0.X5021-4 is OK
- 10.1214/aoms/1177704172 is OK
- 10.2307/2334550 is OK
- 10.1002/9781119214656 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#3970, 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.04947 joss-papers#3971
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04947
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]

@mingzehuang, @msalibian – many thanks for your reviews here and to @jbytecode 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 ✨

@s-abbas – your paper is now accepted and published in JOSS ⚡🚀💥

[editorialbot]

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

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[s-abbas]

Thank you very much for your time and effort you put into editing and reviewing the paper and the code @jbytecode, @msalibian, @mingzehuang, and @arfon!